diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 041ee06ca3b78d358d73bebabb5eaa05205161e1..625f91ebd5ea5276a4d1740a3f4c6ea1e3df1b63 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -23,7 +23,7 @@ repos: sha: 5bf6c09bfa1297d3692cadd621ef95f1284e33c0 hooks: - id: check-added-large-files - args: [--maxkb=1024] + args: [--maxkb=4096] - id: check-merge-conflict - id: check-symlinks - id: detect-private-key diff --git a/docs/requirements.txt b/docs/requirements.txt index 290d4cfaac5de7970d534d97819b286afaa2934e..4e7960b2517dee1e49324ec1245b1a49595126bc 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -2,7 +2,6 @@ sphinx==2.1.0 mistune sphinx_rtd_theme numpy >= 1.16.4 -networkx==2.3 cython >= 0.25.2 -paddlepaddle==1.5.1 +paddlepaddle pgl diff --git a/docs/source/api/pgl.rst b/docs/source/api/pgl.rst index bf5fc0e29ff53f10f7b1fc1570d178b469e4d3e5..36da0df57a7e8174f813dd4a4c869fff962d8462 100644 --- a/docs/source/api/pgl.rst +++ b/docs/source/api/pgl.rst @@ -8,3 +8,4 @@ API Reference pgl.layers pgl.data_loader pgl.utils.paddle_helper + pgl.utils.mp_reader diff --git a/docs/source/api/pgl.utils.mp_reader.rst b/docs/source/api/pgl.utils.mp_reader.rst new file mode 100644 index 0000000000000000000000000000000000000000..1952a6f3afd0d3309b3de60194b24dae0e33c317 --- /dev/null +++ b/docs/source/api/pgl.utils.mp_reader.rst @@ -0,0 +1,7 @@ +pgl.utils.mp\_reader module: MultiProcessing reader helper function for Paddle. +=============================== + +.. automodule:: pgl.utils.mp_reader + :members: + :undoc-members: + :show-inheritance: diff --git a/docs/source/examples/md/gat_examples.md b/docs/source/examples/md/gat_examples.md index 51534442d9f8e6c631eb2dc4f16da14adb2ecc8e..fd55c0469afc8e68f515377b9265b7569b35acf3 100644 --- a/docs/source/examples/md/gat_examples.md +++ b/docs/source/examples/md/gat_examples.md @@ -32,18 +32,18 @@ The datasets contain three citation networks: CORA, PUBMED, CITESEER. The detail ### Dependencies -- paddlepaddle>=1.4 (The speed can be faster in 1.5.) +- paddlepaddle>=1.6 - pgl ### Performance We train our models for 200 epochs and report the accuracy on the test dataset. -| Dataset | Accuracy | Speed with paddle 1.4
(epoch time) | Speed with paddle 1.5
(epoch time)| -| --- | --- | --- |---| -| Cora | ~83% | 0.0188s | 0.0175s | -| Pubmed | ~78% | 0.0449s | 0.0295s | -| Citeseer | ~70% | 0.0275 | 0.0253s | +| Dataset | Accuracy | +| --- | --- | +| Cora | ~83% | +| Pubmed | ~78% | +| Citeseer | ~70% | ### How to run diff --git a/docs/source/examples/md/gcn_examples.md b/docs/source/examples/md/gcn_examples.md index 37af6683695944ead0ad21b6068537fb995273f1..11d5f4ee88aeb46575da8ee7b26b24bfb837b85a 100644 --- a/docs/source/examples/md/gcn_examples.md +++ b/docs/source/examples/md/gcn_examples.md @@ -27,18 +27,18 @@ The datasets contain three citation networks: CORA, PUBMED, CITESEER. The detail ### Dependencies -- paddlepaddle>=1.4 (The speed can be faster in 1.5.) +- paddlepaddle>=1.6 - pgl ### Performance We train our models for 200 epochs and report the accuracy on the test dataset. -| Dataset | Accuracy | Speed with paddle 1.4
(epoch time) | Speed with paddle 1.5
(epoch time)| -| --- | --- | --- |---| -| Cora | ~81% | 0.0106s | 0.0104s | -| Pubmed | ~79% | 0.0210s | 0.0154s | -| Citeseer | ~71% | 0.0175s | 0.0177s | +| Dataset | Accuracy | +| --- | --- | +| Cora | ~81% | +| Pubmed | ~79% | +| Citeseer | ~71% | ### How to run diff --git a/docs/source/examples/md/graphsage_examples.md b/docs/source/examples/md/graphsage_examples.md index c52c2e04740517e69705f540c7bd23e5789ad536..6ad6901fd464752fb47a81a07604e706d59ee56b 100644 --- a/docs/source/examples/md/graphsage_examples.md +++ b/docs/source/examples/md/graphsage_examples.md @@ -12,7 +12,7 @@ The reddit dataset should be downloaded from the following links and placed in d ### Dependencies -- paddlepaddle>=1.4 (The speed can be faster in 1.5.) +- paddlepaddle>=1.6 - pgl ### How to run @@ -22,6 +22,14 @@ To train a GraphSAGE model on Reddit Dataset, you can just run python train.py --use_cuda --epoch 10 --graphsage_type graphsage_mean --normalize --symmetry ``` +If you want to train a GraphSAGE model with multiple GPUs, you can just run + +``` +CUDA_VISIBLE_DEVICES=0,1 python train_multi.py --use_cuda --epoch 10 --graphsage_type graphsage_mean --normalize --symmetry --num_trainer 2 +``` + + + #### Hyperparameters - epoch: Number of epochs default (10) diff --git a/docs/source/examples/md/node2vec_examples.md b/docs/source/examples/md/node2vec_examples.md index 7324b9ddaf7d4f4b0fc6e2ca30164bc0462cfe3e..981c39f3f0c3e1cdd33137deeb1e40b935773b2d 100644 --- a/docs/source/examples/md/node2vec_examples.md +++ b/docs/source/examples/md/node2vec_examples.md @@ -5,7 +5,7 @@ ## Datasets The datasets contain two networks: [BlogCatalog](http://socialcomputing.asu.edu/datasets/BlogCatalog3) and [Arxiv](http://snap.stanford.edu/data/ca-AstroPh.html). ## Dependencies -- paddlepaddle>=1.4 +- paddlepaddle>=1.6 - pgl ## How to run diff --git a/docs/source/examples/md/static_gat_examples.md b/docs/source/examples/md/static_gat_examples.md index 6be646d3235d050d0383e8d8e74a85ee5b36ffa4..7659be190179e88c4739181f7e6b0dbaa9899900 100644 --- a/docs/source/examples/md/static_gat_examples.md +++ b/docs/source/examples/md/static_gat_examples.md @@ -19,11 +19,11 @@ The datasets contain three citation networks: CORA, PUBMED, CITESEER. The detail We train our models for 200 epochs and report the accuracy on the test dataset. -| Dataset | Accuracy | Speed with paddle 1.4
(epoch time) | Speed with paddle 1.5
(epoch time)| examples/gat | Improvement | -| --- | --- | --- |---| --- | --- | -| Cora | ~83% | 0.0145s | 0.0119s | 0.0175s | 1.47x | -| Pubmed | ~78% | 0.0352s | 0.0193s |0.0295s | 1.53x | -| Citeseer | ~70% | 0.0148s | 0.0124s |0.0253s | 2.04x | +| Dataset | Accuracy | epoch time | examples/gat | Improvement | +| --- | --- | --- | --- | --- | +| Cora | ~83% | 0.0119s | 0.0175s | 1.47x | +| Pubmed | ~78% | 0.0193s |0.0295s | 1.53x | +| Citeseer | ~70% | 0.0124s |0.0253s | 2.04x | ### How to run diff --git a/docs/source/examples/md/static_gcn_examples.md b/docs/source/examples/md/static_gcn_examples.md index d9ad8b3cc31a725eb2c8b48d85794446d12f794a..6b0997dcf587ad398e41c37b720275d1edbeb236 100644 --- a/docs/source/examples/md/static_gcn_examples.md +++ b/docs/source/examples/md/static_gcn_examples.md @@ -10,7 +10,7 @@ The datasets contain three citation networks: CORA, PUBMED, CITESEER. The detail ### Dependencies -- paddlepaddle>=1.4 (The speed can be faster in 1.5.) +- paddlepaddle>=1.6 - pgl ### Performance @@ -18,11 +18,11 @@ The datasets contain three citation networks: CORA, PUBMED, CITESEER. The detail We train our models for 200 epochs and report the accuracy on the test dataset. -| Dataset | Accuracy | Speed with paddle 1.4
(epoch time) | Speed with paddle 1.5
(epoch time)| examples/gcn | Improvement | +| Dataset | Accuracy | epoch time | examples/gcn | Improvement | | --- | --- | --- |---| --- | --- | -| Cora | ~81% | 0.0053s | 0.0047s | 0.0104s | 2.21x | -| Pubmed | ~79% | 0.0105s | 0.0049s |0.0154s | 3.14x | -| Citeseer | ~71% | 0.0051s | 0.0045s |0.0177s | 3.93x | +| Cora | ~81% | 0.0047s | 0.0104s | 2.21x | +| Pubmed | ~79% | 0.0049s |0.0154s | 3.14x | +| Citeseer | ~71% | 0.0045s |0.0177s | 3.93x | diff --git a/docs/source/instruction.rst b/docs/source/instruction.rst index 6a338516e55c97567e801f4cc8c15252f7fb2685..9ece98772ca31b4fe428e916d733da441f82459b 100644 --- a/docs/source/instruction.rst +++ b/docs/source/instruction.rst @@ -8,8 +8,7 @@ To install Paddle Graph Learning, we need the following packages. .. code-block:: sh - paddlepaddle >= 1.4 (Faster performance on 1.5) - networkx + paddlepaddle >= 1.6 cython We can simply install pgl by pip. diff --git a/docs/source/md/introduction.md b/docs/source/md/introduction.md index 6dd06fa1f461d4075b250d7c79b5006f9fe1cd9f..bd42565b410e84661cf18731645dbc131102085f 100644 --- a/docs/source/md/introduction.md +++ b/docs/source/md/introduction.md @@ -35,8 +35,8 @@ Users only need to call the ```sequence_ops``` functions provided by Paddle to e return fluid.layers.sequence_pool(msg, "sum") ``` +Although DGL does some kernel fusion optimization for general sum, max and other aggregate functions with scatter-gather. For **complex user-defined functions** with degree bucketing algorithm, the serial execution for each degree bucket cannot take full advantage of the performance improvement provided by GPU. However, operations on the PGL LodTensor-based message is performed in parallel, which can fully utilize GPU parallel optimization. Even without scatter-gather optimization, PGL still has excellent performance. Of course, we still provide build-in scatter-optimized message aggregation functions. -Although DGL does some kernel fusion optimization for general sum, max and other aggregate functions with scatter-gather. For **complex user-defined functions** with degree bucketing algorithm, the serial execution for each degree bucket cannot take full advantage of the performance improvement provided by GPU. However, operations on the PGL LodTensor-based message is performed in parallel, which can fully utilize GPU parallel optimization. In our experiments, PGL can reach up to 13 times the speed of DGL with complex user-defined functions. Even without scatter-gather optimization, PGL still has excellent performance. Of course, we still provide build-in scatter-optimized message aggregation functions. ## Performance @@ -50,11 +50,3 @@ We test all the GNN algorithms with Tesla V100-SXM2-16G running for 200 epochs t | Pubmed | GAT | 77% |0.0193s|**0.0144s**| | Citeseer | GCN |70.2%| **0.0045** |0.0046s| | Citeseer | GAT |68.8%| **0.0124s** |0.0139s| - -If we use complex user-defined aggregation like [GraphSAGE-LSTM](https://cs.stanford.edu/people/jure/pubs/graphsage-nips17.pdf) that aggregates neighbor features with LSTM ignoring the order of recieved messages, the optimized message-passing in DGL will be forced to degenerate into degree bucketing scheme. The speed performance will be much slower than the one implemented in PGL. Performances may be various with different scale of the graph, in our experiments, PGL can reach up to 13 times the speed of DGL. - -| Dataset | PGL speed (epoch time) | DGL 0.3.0 speed (epoch time) | Speed up| -| -------- | ------------ | ------------------------------------ |----| -| Cora | **0.0186s** | 0.1638s | 8.80x| -| Pubmed | **0.0388s** |0.5275s | 13.59x| -| Citeseer | **0.0150s** | 0.1278s | 8.52x | diff --git a/docs/source/md/quick_start.md b/docs/source/md/quick_start.md index 9356362127e800b53e5dca9258e251eab3868ea6..0a30c39e822cb700b84f4df37df54d7de2e80b1a 100644 --- a/docs/source/md/quick_start.md +++ b/docs/source/md/quick_start.md @@ -95,7 +95,7 @@ After defining the GCN layer, we can construct a deeper GCN model with two GCN l ```python output = gcn_layer(gw, gw.node_feat['feature'], hidden_size=8, name='gcn_layer_1', activation='relu') -output = gcn_layer(gw, output, hidden_size=1, +output = gcn_layer(gw, output, hidden_size=2, name='gcn_layer_2', activation=None) ``` diff --git a/examples/dgi/README.md b/examples/dgi/README.md new file mode 100644 index 0000000000000000000000000000000000000000..3de5252e1ceb5482013cc8de224cc4080a5fab58 --- /dev/null +++ b/examples/dgi/README.md @@ -0,0 +1,36 @@ +# PGL Examples for GCN + +[Deep Graph Infomax \(DGI\)](https://arxiv.org/abs/1809.10341) is a general approach for learning node representations within graph-structured data in an unsupervised manner. DGI relies on maximizing mutual information between patch representations and corresponding high-level summaries of graphs---both derived using established graph convolutional network architectures. + +### Datasets + +The datasets contain three citation networks: CORA, PUBMED, CITESEER. The details for these three datasets can be found in the [paper](https://arxiv.org/abs/1609.02907). + +### Dependencies + +- paddlepaddle>=1.6 +- pgl + +### Performance + +We use DGI to pretrain embeddings for each nodes. Then we fix the embedding to train a node classifier. + +| Dataset | Accuracy | +| --- | --- | +| Cora | ~81% | +| Pubmed | ~77.6% | +| Citeseer | ~71.3% | + + +### How to run + +For examples, use gpu to train gcn on cora dataset. +``` +python dgi.py --dataset cora --use_cuda +python train.py --dataset cora --use_cuda +``` + +#### Hyperparameters + +- dataset: The citation dataset "cora", "citeseer", "pubmed". +- use_cuda: Use gpu if assign use_cuda. diff --git a/examples/dgi/dgi.py b/examples/dgi/dgi.py new file mode 100644 index 0000000000000000000000000000000000000000..2f8706a940ea93367e025fa6beeea3f97271e47f --- /dev/null +++ b/examples/dgi/dgi.py @@ -0,0 +1,160 @@ +# Copyright (c) 2019 PaddlePaddle Authors. All Rights Reserved +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +""" + DGI Pretrain +""" +import os +import pgl +from pgl import data_loader +from pgl.utils.logger import log +import paddle.fluid as fluid +import numpy as np +import time +import argparse + + +def load(name): + """Load dataset""" + if name == 'cora': + dataset = data_loader.CoraDataset() + elif name == "pubmed": + dataset = data_loader.CitationDataset("pubmed", symmetry_edges=False) + elif name == "citeseer": + dataset = data_loader.CitationDataset("citeseer", symmetry_edges=False) + else: + raise ValueError(name + " dataset doesn't exists") + return dataset + + +def save_param(dirname, var_name_list): + """save_param""" + for var_name in var_name_list: + var = fluid.global_scope().find_var(var_name) + var_tensor = var.get_tensor() + np.save(os.path.join(dirname, var_name + '.npy'), np.array(var_tensor)) + + +def main(args): + """main""" + dataset = load(args.dataset) + + # normalize + indegree = dataset.graph.indegree() + norm = np.zeros_like(indegree, dtype="float32") + norm[indegree > 0] = np.power(indegree[indegree > 0], -0.5) + dataset.graph.node_feat["norm"] = np.expand_dims(norm, -1) + + place = fluid.CUDAPlace(0) if args.use_cuda else fluid.CPUPlace() + train_program = fluid.Program() + startup_program = fluid.Program() + hidden_size = 512 + + with fluid.program_guard(train_program, startup_program): + pos_gw = pgl.graph_wrapper.GraphWrapper( + name="pos_graph", + place=place, + node_feat=dataset.graph.node_feat_info()) + + neg_gw = pgl.graph_wrapper.GraphWrapper( + name="neg_graph", + place=place, + node_feat=dataset.graph.node_feat_info()) + + positive_feat = pgl.layers.gcn(pos_gw, + pos_gw.node_feat["words"], + hidden_size, + activation="relu", + norm=pos_gw.node_feat['norm'], + name="gcn_layer_1") + + negative_feat = pgl.layers.gcn(neg_gw, + neg_gw.node_feat["words"], + hidden_size, + activation="relu", + norm=neg_gw.node_feat['norm'], + name="gcn_layer_1") + + summary_feat = fluid.layers.sigmoid( + fluid.layers.reduce_mean( + positive_feat, [0], keep_dim=True)) + + summary_feat = fluid.layers.fc(summary_feat, + hidden_size, + bias_attr=False, + name="discriminator") + pos_logits = fluid.layers.matmul( + positive_feat, summary_feat, transpose_y=True) + neg_logits = fluid.layers.matmul( + negative_feat, summary_feat, transpose_y=True) + pos_loss = fluid.layers.sigmoid_cross_entropy_with_logits( + x=pos_logits, + label=fluid.layers.ones( + shape=[dataset.graph.num_nodes, 1], dtype="float32")) + neg_loss = fluid.layers.sigmoid_cross_entropy_with_logits( + x=neg_logits, + label=fluid.layers.zeros( + shape=[dataset.graph.num_nodes, 1], dtype="float32")) + loss = fluid.layers.reduce_mean(pos_loss) + fluid.layers.reduce_mean( + neg_loss) + + adam = fluid.optimizer.Adam(learning_rate=1e-3) + adam.minimize(loss) + + exe = fluid.Executor(place) + exe.run(startup_program) + + best_loss = 1e9 + dur = [] + + for epoch in range(args.epoch): + feed_dict = pos_gw.to_feed(dataset.graph) + node_feat = dataset.graph.node_feat["words"].copy() + perm = np.arange(0, dataset.graph.num_nodes) + np.random.shuffle(perm) + + dataset.graph.node_feat["words"] = dataset.graph.node_feat["words"][ + perm] + + feed_dict.update(neg_gw.to_feed(dataset.graph)) + dataset.graph.node_feat["words"] = node_feat + if epoch >= 3: + t0 = time.time() + train_loss = exe.run(train_program, + feed=feed_dict, + fetch_list=[loss], + return_numpy=True) + if train_loss[0] < best_loss: + best_loss = train_loss[0] + save_param(args.checkpoint, ["gcn_layer_1", "gcn_layer_1_bias"]) + + if epoch >= 3: + time_per_epoch = 1.0 * (time.time() - t0) + dur.append(time_per_epoch) + + log.info("Epoch %d " % epoch + "(%.5lf sec) " % np.mean(dur) + + "Train Loss: %f " % train_loss[0]) + + +if __name__ == '__main__': + parser = argparse.ArgumentParser(description='DGI pretrain') + parser.add_argument( + "--dataset", type=str, default="cora", help="dataset (cora, pubmed)") + parser.add_argument( + "--checkpoint", type=str, default="best_model", help="checkpoint") + parser.add_argument( + "--epoch", type=int, default=200, help="pretrain epochs") + parser.add_argument("--use_cuda", action='store_true', help="use_cuda") + args = parser.parse_args() + log.info(args) + main(args) diff --git a/examples/dgi/train.py b/examples/dgi/train.py new file mode 100644 index 0000000000000000000000000000000000000000..67742093486e9e391cea0d141d504580c2985df0 --- /dev/null +++ b/examples/dgi/train.py @@ -0,0 +1,165 @@ +# Copyright (c) 2019 PaddlePaddle Authors. All Rights Reserved +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +""" + Train +""" +import os +import pgl +from pgl import data_loader +from pgl.utils.logger import log +import paddle.fluid as fluid +import numpy as np +import time +import argparse + + +def load(name): + """Load""" + if name == 'cora': + dataset = data_loader.CoraDataset() + elif name == "pubmed": + dataset = data_loader.CitationDataset("pubmed", symmetry_edges=False) + elif name == "citeseer": + dataset = data_loader.CitationDataset("citeseer", symmetry_edges=False) + else: + raise ValueError(name + " dataset doesn't exists") + return dataset + + +def load_param(dirname, var_name_list): + """load_param""" + for var_name in var_name_list: + var = fluid.global_scope().find_var(var_name) + var_tensor = var.get_tensor() + var_tmp = np.load(os.path.join(dirname, var_name + '.npy')) + var_tensor.set(var_tmp, fluid.CPUPlace()) + + +def main(args): + """main""" + dataset = load(args.dataset) + + # normalize + indegree = dataset.graph.indegree() + norm = np.zeros_like(indegree, dtype="float32") + norm[indegree > 0] = np.power(indegree[indegree > 0], -0.5) + dataset.graph.node_feat["norm"] = np.expand_dims(norm, -1) + + place = fluid.CUDAPlace(0) if args.use_cuda else fluid.CPUPlace() + train_program = fluid.Program() + startup_program = fluid.Program() + test_program = fluid.Program() + hidden_size = 512 + + with fluid.program_guard(train_program, startup_program): + gw = pgl.graph_wrapper.GraphWrapper( + name="graph", + place=place, + node_feat=dataset.graph.node_feat_info()) + + output = pgl.layers.gcn(gw, + gw.node_feat["words"], + hidden_size, + activation="relu", + norm=gw.node_feat['norm'], + name="gcn_layer_1") + output.stop_gradient = True + output = fluid.layers.fc(output, + dataset.num_classes, + act=None, + name="classifier") + node_index = fluid.layers.data( + "node_index", + shape=[None, 1], + dtype="int64", + append_batch_size=False) + node_label = fluid.layers.data( + "node_label", + shape=[None, 1], + dtype="int64", + append_batch_size=False) + + pred = fluid.layers.gather(output, node_index) + loss, pred = fluid.layers.softmax_with_cross_entropy( + logits=pred, label=node_label, return_softmax=True) + acc = fluid.layers.accuracy(input=pred, label=node_label, k=1) + loss = fluid.layers.mean(loss) + + test_program = train_program.clone(for_test=True) + with fluid.program_guard(train_program, startup_program): + adam = fluid.optimizer.Adam(learning_rate=1e-2) + adam.minimize(loss) + + exe = fluid.Executor(place) + exe.run(startup_program) + + load_param(args.checkpoint, ["gcn_layer_1", "gcn_layer_1_bias"]) + feed_dict = gw.to_feed(dataset.graph) + + train_index = dataset.train_index + train_label = np.expand_dims(dataset.y[train_index], -1) + train_index = np.expand_dims(train_index, -1) + + val_index = dataset.val_index + val_label = np.expand_dims(dataset.y[val_index], -1) + val_index = np.expand_dims(val_index, -1) + + test_index = dataset.test_index + test_label = np.expand_dims(dataset.y[test_index], -1) + test_index = np.expand_dims(test_index, -1) + + dur = [] + for epoch in range(200): + if epoch >= 3: + t0 = time.time() + feed_dict["node_index"] = np.array(train_index, dtype="int64") + feed_dict["node_label"] = np.array(train_label, dtype="int64") + train_loss, train_acc = exe.run(train_program, + feed=feed_dict, + fetch_list=[loss, acc], + return_numpy=True) + + if epoch >= 3: + time_per_epoch = 1.0 * (time.time() - t0) + dur.append(time_per_epoch) + feed_dict["node_index"] = np.array(val_index, dtype="int64") + feed_dict["node_label"] = np.array(val_label, dtype="int64") + val_loss, val_acc = exe.run(test_program, + feed=feed_dict, + fetch_list=[loss, acc], + return_numpy=True) + + log.info("Epoch %d " % epoch + "(%.5lf sec) " % np.mean(dur) + + "Train Loss: %f " % train_loss + "Train Acc: %f " % train_acc + + "Val Loss: %f " % val_loss + "Val Acc: %f " % val_acc) + + feed_dict["node_index"] = np.array(test_index, dtype="int64") + feed_dict["node_label"] = np.array(test_label, dtype="int64") + test_loss, test_acc = exe.run(test_program, + feed=feed_dict, + fetch_list=[loss, acc], + return_numpy=True) + log.info("Accuracy: %f" % test_acc) + + +if __name__ == '__main__': + parser = argparse.ArgumentParser(description='GCN') + parser.add_argument( + "--dataset", type=str, default="cora", help="dataset (cora, pubmed)") + parser.add_argument( + "--checkpoint", type=str, default="best_model", help="checkpoint") + parser.add_argument("--use_cuda", action='store_true', help="use_cuda") + args = parser.parse_args() + log.info(args) + main(args) diff --git a/examples/distribute_deepwalk/README.md b/examples/distribute_deepwalk/README.md new file mode 100644 index 0000000000000000000000000000000000000000..24775aaae8bfbae11c69a68fa6eb49c9863a0ae3 --- /dev/null +++ b/examples/distribute_deepwalk/README.md @@ -0,0 +1,31 @@ +# PGL Examples for distributed deepwalk +[Deepwalk](https://arxiv.org/pdf/1403.6652.pdf) is an algorithmic framework for representational learning on graphs. Given any graph, it can learn continuous feature representations for the nodes, which can then be used for various downstream machine learning tasks. Based on PGL, we reproduce distributed deepwalk algorithms and reach the same level of indicators as the paper. +## Datasets +The datasets contain two networks: [BlogCatalog](http://socialcomputing.asu.edu/datasets/BlogCatalog3). +## Dependencies +- paddlepaddle>=1.6 +- pgl>=1.0 + +## How to run + +For examples, train deepwalk in distributed mode on cora dataset. +```sh +# train deepwalk in distributed mode. +sh cloud_run.sh + +# multiclass task example +python3 multi_class.py --use_cuda --ckpt_path ./model_path/4029 --epoch 1000 + +``` + +## Hyperparameters +- dataset: The citation dataset "BlogCatalog". +- hidden_size: Hidden size of the embedding. +- lr: Learning rate. +- neg_num: Number of negative samples. +- epoch: Number of training epoch. + +### Experiment results +Dataset|model|Task|Metric|PGL Result|Reported Result +--|--|--|--|--|-- +BlogCatalog|distributed deepwalk|multi-label classification|MacroF1|0.233|0.211 diff --git a/examples/distribute_deepwalk/cloud_run.sh b/examples/distribute_deepwalk/cloud_run.sh new file mode 100755 index 0000000000000000000000000000000000000000..4d400849ec10cb51aa0a813f4756b02905246800 --- /dev/null +++ b/examples/distribute_deepwalk/cloud_run.sh @@ -0,0 +1,42 @@ +#!/bin/bash + +set -x +source ./pgl_deepwalk.cfg +source ./local_config + +unset http_proxy https_proxy + +# build train_data +trainer_num=`echo $PADDLE_PORT | awk -F',' '{print NF}'` +rm -rf train_data && mkdir -p train_data +cd train_data +if [[ $build_train_data == True ]];then + seq 0 $((num_nodes-1)) | shuf | split -l $((num_nodes/trainer_num/CPU_NUM+1)) +else + for i in `seq 1 $trainer_num`;do + touch $i + done +fi +cd - + +# mkdir workspace +if [ -d ${BASE} ]; then + rm -rf ${BASE} +fi +mkdir ${BASE} + +# start ps +for((i=0;i<${PADDLE_PSERVERS_NUM};i++)) +do + echo "start ps server: ${i}" + echo $BASE + TRAINING_ROLE="PSERVER" PADDLE_TRAINER_ID=${i} sh job.sh &> $BASE/pserver.$i.log & +done +sleep 5s + +# start trainers +for((j=0;j<${PADDLE_TRAINERS_NUM};j++)) +do + echo "start ps work: ${j}" + TRAINING_ROLE="TRAINER" PADDLE_TRAINER_ID=${j} sh job.sh &> $BASE/worker.$j.log & +done diff --git a/examples/distribute_deepwalk/cluster_train.py b/examples/distribute_deepwalk/cluster_train.py new file mode 100644 index 0000000000000000000000000000000000000000..aa4c9ce122dccff538b5ab5dee3a45b4ae405df2 --- /dev/null +++ b/examples/distribute_deepwalk/cluster_train.py @@ -0,0 +1,348 @@ +# Copyright (c) 2019 PaddlePaddle Authors. All Rights Reserved +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +import argparse +import time +import os +import math +from multiprocessing import Process + +import numpy as np +import paddle.fluid as F +import paddle.fluid.layers as L +from paddle.fluid.incubate.fleet.parameter_server.distribute_transpiler import fleet +from paddle.fluid.transpiler.distribute_transpiler import DistributeTranspilerConfig +import paddle.fluid.incubate.fleet.base.role_maker as role_maker +from pgl.utils.logger import log +from pgl import data_loader + +from reader import DeepwalkReader +from model import DeepwalkModel +from utils import get_file_list +from utils import build_graph +from utils import build_fake_graph +from utils import build_gen_func + + +def init_role(): + # reset the place according to role of parameter server + training_role = os.getenv("TRAINING_ROLE", "TRAINER") + paddle_role = role_maker.Role.WORKER + place = F.CPUPlace() + if training_role == "PSERVER": + paddle_role = role_maker.Role.SERVER + + # set the fleet runtime environment according to configure + ports = os.getenv("PADDLE_PORT", "6174").split(",") + pserver_ips = os.getenv("PADDLE_PSERVERS").split(",") # ip,ip... + eplist = [] + if len(ports) > 1: + # local debug mode, multi port + for port in ports: + eplist.append(':'.join([pserver_ips[0], port])) + else: + # distributed mode, multi ip + for ip in pserver_ips: + eplist.append(':'.join([ip, ports[0]])) + + pserver_endpoints = eplist # ip:port,ip:port... + worker_num = int(os.getenv("PADDLE_TRAINERS_NUM", "0")) + trainer_id = int(os.getenv("PADDLE_TRAINER_ID", "0")) + role = role_maker.UserDefinedRoleMaker( + current_id=trainer_id, + role=paddle_role, + worker_num=worker_num, + server_endpoints=pserver_endpoints) + fleet.init(role) + + +def optimization(base_lr, loss, train_steps, optimizer='sgd'): + decayed_lr = L.learning_rate_scheduler.polynomial_decay( + learning_rate=base_lr, + decay_steps=train_steps, + end_learning_rate=0.0001 * base_lr, + power=1.0, + cycle=False) + if optimizer == 'sgd': + optimizer = F.optimizer.SGD(decayed_lr) + elif optimizer == 'adam': + optimizer = F.optimizer.Adam(decayed_lr, lazy_mode=True) + else: + raise ValueError + + log.info('learning rate:%f' % (base_lr)) + #create the DistributeTranspiler configure + config = DistributeTranspilerConfig() + config.sync_mode = False + #config.runtime_split_send_recv = False + + config.slice_var_up = False + #create the distributed optimizer + optimizer = fleet.distributed_optimizer(optimizer, config) + optimizer.minimize(loss) + + +def build_complied_prog(train_program, model_loss): + num_threads = int(os.getenv("CPU_NUM", 10)) + trainer_id = int(os.getenv("PADDLE_TRAINER_ID", 0)) + exec_strategy = F.ExecutionStrategy() + exec_strategy.num_threads = num_threads + #exec_strategy.use_experimental_executor = True + build_strategy = F.BuildStrategy() + build_strategy.enable_inplace = True + #build_strategy.memory_optimize = True + build_strategy.memory_optimize = False + build_strategy.remove_unnecessary_lock = False + if num_threads > 1: + build_strategy.reduce_strategy = F.BuildStrategy.ReduceStrategy.Reduce + + compiled_prog = F.compiler.CompiledProgram( + train_program).with_data_parallel( + loss_name=model_loss.name, + build_strategy=build_strategy, + exec_strategy=exec_strategy) + return compiled_prog + + +def train_prog(exe, program, loss, node2vec_pyreader, args, train_steps): + trainer_id = int(os.getenv("PADDLE_TRAINER_ID", "0")) + step = 0 + while True: + try: + begin_time = time.time() + loss_val, = exe.run(program, fetch_list=[loss]) + log.info("step %s: loss %.5f speed: %.5f s/step" % + (step, np.mean(loss_val), time.time() - begin_time)) + step += 1 + except F.core.EOFException: + node2vec_pyreader.reset() + + if step % args.steps_per_save == 0 or step == train_steps: + if trainer_id == 0 or args.is_distributed: + model_save_dir = args.save_path + model_path = os.path.join(model_save_dir, str(step)) + if not os.path.exists(model_save_dir): + os.makedirs(model_save_dir) + fleet.save_persistables(exe, model_path) + + if step == train_steps: + break + + +def test(args): + graph = build_graph(args.num_nodes, args.edge_path) + gen_func = build_gen_func(args, graph) + + start = time.time() + num = 10 + for idx, _ in enumerate(gen_func()): + if idx % num == num - 1: + log.info("%s" % (1.0 * (time.time() - start) / num)) + start = time.time() + + +def walk(args): + graph = build_graph(args.num_nodes, args.edge_path) + num_sample_workers = args.num_sample_workers + + if args.train_files is None or args.train_files == "None": + log.info("Walking from graph...") + train_files = [None for _ in range(num_sample_workers)] + else: + log.info("Walking from train_data...") + files = get_file_list(args.train_files) + train_files = [[] for i in range(num_sample_workers)] + for idx, f in enumerate(files): + train_files[idx % num_sample_workers].append(f) + + def walk_to_file(walk_gen, filename, max_num): + with open(filename, "w") as outf: + num = 0 + for walks in walk_gen: + for walk in walks: + outf.write("%s\n" % "\t".join([str(i) for i in walk])) + num += 1 + if num % 1000 == 0: + log.info("Total: %s, %s walkpath is saved. " % + (max_num, num)) + if num == max_num: + return + + m_args = [(DeepwalkReader( + graph, + batch_size=args.batch_size, + walk_len=args.walk_len, + win_size=args.win_size, + neg_num=args.neg_num, + neg_sample_type=args.neg_sample_type, + walkpath_files=None, + train_files=train_files[i]).walk_generator(), + "%s/%s" % (args.walkpath_files, i), + args.epoch * args.num_nodes // args.num_sample_workers) + for i in range(num_sample_workers)] + ps = [] + for i in range(num_sample_workers): + p = Process(target=walk_to_file, args=m_args[i]) + p.start() + ps.append(p) + for i in range(num_sample_workers): + ps[i].join() + + +def train(args): + import logging + log.setLevel(logging.DEBUG) + log.info("start") + + worker_num = int(os.getenv("PADDLE_TRAINERS_NUM", "0")) + num_devices = int(os.getenv("CPU_NUM", 10)) + + model = DeepwalkModel(args.num_nodes, args.hidden_size, args.neg_num, + args.is_sparse, args.is_distributed, 1.) + pyreader = model.pyreader + loss = model.forward() + + # init fleet + init_role() + + train_steps = math.ceil(1. * args.num_nodes * args.epoch / + args.batch_size / num_devices / worker_num) + log.info("Train step: %s" % train_steps) + + if args.optimizer == "sgd": + args.lr *= args.batch_size * args.walk_len * args.win_size + optimization(args.lr, loss, train_steps, args.optimizer) + + # init and run server or worker + if fleet.is_server(): + fleet.init_server(args.warm_start_from_dir) + fleet.run_server() + + if fleet.is_worker(): + log.info("start init worker done") + fleet.init_worker() + #just the worker, load the sample + log.info("init worker done") + + exe = F.Executor(F.CPUPlace()) + exe.run(fleet.startup_program) + log.info("Startup done") + + if args.dataset is not None: + if args.dataset == "BlogCatalog": + graph = data_loader.BlogCatalogDataset().graph + elif args.dataset == "ArXiv": + graph = data_loader.ArXivDataset().graph + else: + raise ValueError(args.dataset + " dataset doesn't exists") + log.info("Load buildin BlogCatalog dataset done.") + elif args.walkpath_files is None or args.walkpath_files == "None": + graph = build_graph(args.num_nodes, args.edge_path) + log.info("Load graph from '%s' done." % args.edge_path) + else: + graph = build_fake_graph(args.num_nodes) + log.info("Load fake graph done.") + + # bind gen + gen_func = build_gen_func(args, graph) + + pyreader.decorate_tensor_provider(gen_func) + pyreader.start() + + compiled_prog = build_complied_prog(fleet.main_program, loss) + train_prog(exe, compiled_prog, loss, pyreader, args, train_steps) + + +if __name__ == '__main__': + + def str2bool(v): + if isinstance(v, bool): + return v + if v.lower() in ('yes', 'true', 't', 'y', '1'): + return True + elif v.lower() in ('no', 'false', 'f', 'n', '0'): + return False + else: + raise argparse.ArgumentTypeError('Boolean value expected.') + + parser = argparse.ArgumentParser(description='Deepwalk') + parser.add_argument( + "--hidden_size", + type=int, + default=64, + help="Hidden size of the embedding.") + parser.add_argument( + "--lr", type=float, default=0.025, help="Learning rate.") + parser.add_argument( + "--neg_num", type=int, default=5, help="Number of negative samples.") + parser.add_argument( + "--epoch", type=int, default=1, help="Number of training epoch.") + parser.add_argument( + "--batch_size", + type=int, + default=128, + help="Numbert of walk paths in a batch.") + parser.add_argument( + "--walk_len", type=int, default=40, help="Length of a walk path.") + parser.add_argument( + "--win_size", type=int, default=5, help="Window size in skip-gram.") + parser.add_argument( + "--save_path", + type=str, + default="model_path", + help="Output path for saving model.") + parser.add_argument( + "--num_sample_workers", + type=int, + default=1, + help="Number of sampling workers.") + parser.add_argument( + "--steps_per_save", + type=int, + default=3000, + help="Steps for model saveing.") + parser.add_argument( + "--num_nodes", + type=int, + default=10000, + help="Number of nodes in graph.") + parser.add_argument("--edge_path", type=str, default="./graph_data") + parser.add_argument("--train_files", type=str, default=None) + parser.add_argument("--walkpath_files", type=str, default=None) + parser.add_argument("--is_distributed", type=str2bool, default=False) + parser.add_argument("--is_sparse", type=str2bool, default=True) + parser.add_argument("--warm_start_from_dir", type=str, default=None) + parser.add_argument("--dataset", type=str, default=None) + parser.add_argument( + "--neg_sample_type", + type=str, + default="average", + choices=["average", "outdegree"]) + parser.add_argument( + "--mode", + type=str, + required=False, + choices=['train', 'walk'], + default="train") + parser.add_argument( + "--optimizer", + type=str, + required=False, + choices=['adam', 'sgd'], + default="sgd") + args = parser.parse_args() + log.info(args) + if args.mode == "train": + train(args) + elif args.mode == "walk": + walk(args) diff --git a/examples/distribute_deepwalk/gpu_train.py b/examples/distribute_deepwalk/gpu_train.py new file mode 100644 index 0000000000000000000000000000000000000000..f6c4d9853c48e0a8f3083e4b813dc7057317e7cc --- /dev/null +++ b/examples/distribute_deepwalk/gpu_train.py @@ -0,0 +1,156 @@ +# Copyright (c) 2019 PaddlePaddle Authors. All Rights Reserved +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +import argparse +import time +import os + +import numpy as np +import paddle.fluid as F +import paddle.fluid.layers as L +from pgl.utils.logger import log + +from model import DeepwalkModel +from utils import build_graph +from utils import build_gen_func + + +def optimization(base_lr, loss, train_steps, optimizer='adam'): + decayed_lr = L.polynomial_decay(base_lr, train_steps, 0.0001) + + if optimizer == 'sgd': + optimizer = F.optimizer.SGD( + decayed_lr, + regularization=F.regularizer.L2DecayRegularizer( + regularization_coeff=0.0025)) + elif optimizer == 'adam': + # dont use gpu's lazy mode + optimizer = F.optimizer.Adam(decayed_lr) + else: + raise ValueError + + log.info('learning rate:%f' % (base_lr)) + optimizer.minimize(loss) + + +def get_parallel_exe(program, loss): + exec_strategy = F.ExecutionStrategy() + exec_strategy.num_threads = 1 #2 for fp32 4 for fp16 + exec_strategy.use_experimental_executor = True + exec_strategy.num_iteration_per_drop_scope = 1 #important shit + + build_strategy = F.BuildStrategy() + build_strategy.enable_inplace = True + build_strategy.memory_optimize = True + build_strategy.remove_unnecessary_lock = True + + #return compiled_prog + train_exe = F.ParallelExecutor( + use_cuda=True, + loss_name=loss.name, + build_strategy=build_strategy, + exec_strategy=exec_strategy, + main_program=program) + return train_exe + + +def train(train_exe, exe, program, loss, node2vec_pyreader, args, train_steps): + trainer_id = int(os.getenv("PADDLE_TRAINER_ID", "0")) + step = 0 + while True: + try: + begin_time = time.time() + loss_val, = train_exe.run(fetch_list=[loss]) + log.info("step %s: loss %.5f speed: %.5f s/step" % + (step, np.mean(loss_val), time.time() - begin_time)) + step += 1 + except F.core.EOFException: + node2vec_pyreader.reset() + + if (step == train_steps or + step % args.steps_per_save == 0) and trainer_id == 0: + + model_save_dir = args.output_path + model_path = os.path.join(model_save_dir, str(step)) + if not os.path.exists(model_save_dir): + os.makedirs(model_save_dir) + F.io.save_params(exe, model_path, program) + if step == train_steps: + break + + +def main(args): + import logging + log.setLevel(logging.DEBUG) + log.info("start") + + num_devices = len(F.cuda_places()) + model = DeepwalkModel(args.num_nodes, args.hidden_size, args.neg_num, + False, False, 1.) + pyreader = model.pyreader + loss = model.forward() + + train_steps = int(args.num_nodes * args.epoch / args.batch_size / + num_devices) + optimization(args.lr * num_devices, loss, train_steps, args.optimizer) + + place = F.CUDAPlace(0) + exe = F.Executor(place) + exe.run(F.default_startup_program()) + + graph = build_graph(args.num_nodes, args.edge_path) + gen_func = build_gen_func(args, graph) + + pyreader.decorate_tensor_provider(gen_func) + pyreader.start() + + train_prog = F.default_main_program() + + if args.warm_start_from_dir is not None: + F.io.load_params(exe, args.warm_start_from_dir, train_prog) + + train_exe = get_parallel_exe(train_prog, loss) + train(train_exe, exe, train_prog, loss, pyreader, args, train_steps) + + +if __name__ == '__main__': + parser = argparse.ArgumentParser(description='Deepwalk') + parser.add_argument("--hidden_size", type=int, default=64) + parser.add_argument("--lr", type=float, default=0.025) + parser.add_argument("--neg_num", type=int, default=5) + parser.add_argument("--epoch", type=int, default=100) + parser.add_argument("--batch_size", type=int, default=128) + parser.add_argument("--walk_len", type=int, default=40) + parser.add_argument("--win_size", type=int, default=5) + parser.add_argument("--output_path", type=str, default="output") + parser.add_argument("--num_sample_workers", type=int, default=1) + parser.add_argument("--steps_per_save", type=int, default=3000) + parser.add_argument("--num_nodes", type=int, default=10000) + parser.add_argument("--edge_path", type=str, default="./graph_data") + parser.add_argument("--walkpath_files", type=str, default=None) + parser.add_argument("--train_files", type=str, default="./train_data") + parser.add_argument("--warm_start_from_dir", type=str, default=None) + parser.add_argument( + "--neg_sample_type", + type=str, + default="average", + choices=["average", "outdegree"]) + parser.add_argument( + "--optimizer", + type=str, + required=False, + choices=['adam', 'sgd'], + default="adam") + args = parser.parse_args() + log.info(args) + main(args) diff --git a/examples/distribute_deepwalk/job.sh b/examples/distribute_deepwalk/job.sh new file mode 100644 index 0000000000000000000000000000000000000000..e0a0ba5d914e778cfd88d4947d3628f181518fc3 --- /dev/null +++ b/examples/distribute_deepwalk/job.sh @@ -0,0 +1,42 @@ +#!/bin/bash + +set -x +source ./pgl_deepwalk.cfg + +export CPU_NUM=$CPU_NUM +export FLAGS_rpc_deadline=3000000 +export FLAGS_communicator_send_queue_size=1 +export FLAGS_communicator_min_send_grad_num_before_recv=0 +export FLAGS_communicator_max_merge_var_num=1 +export FLAGS_communicator_merge_sparse_grad=1 + +if [[ $build_train_data == True ]];then + train_files="./train_data" +else + train_files="None" +fi + +if [[ $pre_walk == True ]]; then + walkpath_files="./walk_path" + if [[ $TRAINING_ROLE == "PSERVER" ]];then + while [[ ! -d train_data ]];do + sleep 60 + echo "Waiting for train_data ..." + done + rm -rf $walkpath_files && mkdir -p $walkpath_files + python -u cluster_train.py --num_sample_workers $num_sample_workers --num_nodes $num_nodes --mode walk --walkpath_files $walkpath_files --epoch $epoch \ + --walk_len $walk_len --batch_size $batch_size --train_files $train_files --dataset "BlogCatalog" + touch build_graph_done + fi + + while [[ ! -f build_graph_done ]];do + sleep 60 + echo "Waiting for walk_path ..." + done +else + walkpath_files="None" +fi + +python -u cluster_train.py --num_sample_workers $num_sample_workers --num_nodes $num_nodes --optimizer $optimizer --walkpath_files $walkpath_files --epoch $epoch \ + --is_distributed $distributed_embedding --lr $learning_rate --neg_num $neg_num --walk_len $walk_len --win_size $win_size --is_sparse $is_sparse --hidden_size $dim \ + --batch_size $batch_size --steps_per_save $steps_per_save --train_files $train_files --dataset "BlogCatalog" diff --git a/examples/distribute_deepwalk/local_config b/examples/distribute_deepwalk/local_config new file mode 100644 index 0000000000000000000000000000000000000000..455a34228c6f1af38e01e149d7963c19a4dde3c7 --- /dev/null +++ b/examples/distribute_deepwalk/local_config @@ -0,0 +1,7 @@ +#!/bin/bash +export PADDLE_TRAINERS_NUM=2 +export PADDLE_PSERVERS_NUM=2 +export PADDLE_PORT=6184,6185 +export PADDLE_PSERVERS="127.0.0.1" +export BASE="./local_dir" + diff --git a/examples/distribute_deepwalk/model.py b/examples/distribute_deepwalk/model.py new file mode 100644 index 0000000000000000000000000000000000000000..3740ff2848b73a2def81f6ec7a8b2f96d029e520 --- /dev/null +++ b/examples/distribute_deepwalk/model.py @@ -0,0 +1,167 @@ +# Copyright (c) 2019 PaddlePaddle Authors. All Rights Reserved +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +""" + Deepwalk model file. +""" +from __future__ import division +from __future__ import absolute_import +from __future__ import print_function +from __future__ import unicode_literals +import math + +import paddle.fluid.layers as L +import paddle.fluid as F + + +def split_embedding(input, + dict_size, + hidden_size, + initializer, + name, + num_part=16, + is_sparse=False, + learning_rate=1.0): + """ split_embedding + """ + _part_size = hidden_size // num_part + if hidden_size % num_part != 0: + _part_size += 1 + output_embedding = [] + p_num = 0 + while hidden_size > 0: + _part_size = min(_part_size, hidden_size) + hidden_size -= _part_size + print("part", p_num, "size=", (dict_size, _part_size)) + part_embedding = L.embedding( + input=input, + size=(dict_size, _part_size), + is_sparse=is_sparse, + is_distributed=False, + param_attr=F.ParamAttr( + name=name + '_part%s' % p_num, + initializer=initializer, + learning_rate=learning_rate)) + p_num += 1 + output_embedding.append(part_embedding) + return L.concat(output_embedding, -1) + + +class DeepwalkModel(object): + def __init__(self, + num_nodes, + hidden_size=16, + neg_num=5, + is_sparse=False, + is_distributed=False, + embedding_lr=1.0): + self.pyreader = L.py_reader( + capacity=70, + shapes=[[-1, 1, 1], [-1, neg_num + 1, 1]], + dtypes=['int64', 'int64'], + lod_levels=[0, 0], + name='train', + use_double_buffer=True) + + self.num_nodes = num_nodes + self.neg_num = neg_num + + self.embed_init = F.initializer.Uniform( + low=-1. / math.sqrt(hidden_size), high=1. / math.sqrt(hidden_size)) + self.is_sparse = is_sparse + self.is_distributed = is_distributed + self.hidden_size = hidden_size + self.loss = None + self.embedding_lr = embedding_lr + max_hidden_size = int(math.pow(2, 31) / 4 / num_nodes) + self.num_part = int(math.ceil(1. * hidden_size / max_hidden_size)) + + def forward(self): + src, dsts = L.read_file(self.pyreader) + + if self.is_sparse: + # sparse mode use 2 dims input. + src = L.reshape(src, [-1, 1]) + dsts = L.reshape(dsts, [-1, 1]) + + if self.num_part is not None and self.num_part != 1 and not self.is_distributed: + src_embed = split_embedding( + src, + self.num_nodes, + self.hidden_size, + self.embed_init, + "weight", + self.num_part, + self.is_sparse, + learning_rate=self.embedding_lr) + + dsts_embed = split_embedding( + dsts, + self.num_nodes, + self.hidden_size, + self.embed_init, + "weight", + self.num_part, + self.is_sparse, + learning_rate=self.embedding_lr) + else: + src_embed = L.embedding( + src, (self.num_nodes, self.hidden_size), + self.is_sparse, + self.is_distributed, + param_attr=F.ParamAttr( + name="weight", + learning_rate=self.embedding_lr, + initializer=self.embed_init)) + + dsts_embed = L.embedding( + dsts, (self.num_nodes, self.hidden_size), + self.is_sparse, + self.is_distributed, + param_attr=F.ParamAttr( + name="weight", + learning_rate=self.embedding_lr, + initializer=self.embed_init)) + + if self.is_sparse: + # reshape back + src_embed = L.reshape(src_embed, [-1, 1, self.hidden_size]) + dsts_embed = L.reshape(dsts_embed, + [-1, self.neg_num + 1, self.hidden_size]) + + logits = L.matmul( + src_embed, dsts_embed, + transpose_y=True) # [batch_size, 1, neg_num+1] + + pos_label = L.fill_constant_batch_size_like(logits, [-1, 1, 1], + "float32", 1) + neg_label = L.fill_constant_batch_size_like( + logits, [-1, 1, self.neg_num], "float32", 0) + label = L.concat([pos_label, neg_label], -1) + + pos_weight = L.fill_constant_batch_size_like(logits, [-1, 1, 1], + "float32", self.neg_num) + neg_weight = L.fill_constant_batch_size_like( + logits, [-1, 1, self.neg_num], "float32", 1) + weight = L.concat([pos_weight, neg_weight], -1) + + weight.stop_gradient = True + label.stop_gradient = True + + loss = L.sigmoid_cross_entropy_with_logits(logits, label) + loss = loss * weight + loss = L.reduce_mean(loss) + loss = loss * ((self.neg_num + 1) / 2 / self.neg_num) + loss.persistable = True + self.loss = loss + return loss diff --git a/examples/distribute_deepwalk/mp_reader.py b/examples/distribute_deepwalk/mp_reader.py new file mode 100644 index 0000000000000000000000000000000000000000..d4df8998cc4ad672627dc7ba9f846c91ccca0bba --- /dev/null +++ b/examples/distribute_deepwalk/mp_reader.py @@ -0,0 +1,145 @@ +# Copyright (c) 2019 PaddlePaddle Authors. All Rights Reserved. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +"""Optimized Multiprocessing Reader for PaddlePaddle +""" +import multiprocessing +import numpy as np +import time + +import paddle.fluid as fluid +import pyarrow + + +def _serialize_serializable(obj): + """Serialize Feed Dict + """ + return {"type": type(obj), "data": obj.__dict__} + + +def _deserialize_serializable(obj): + """Deserialize Feed Dict + """ + + val = obj["type"].__new__(obj["type"]) + val.__dict__.update(obj["data"]) + return val + + +context = pyarrow.default_serialization_context() + +context.register_type( + object, + "object", + custom_serializer=_serialize_serializable, + custom_deserializer=_deserialize_serializable) + + +def serialize_data(data): + """serialize_data""" + return pyarrow.serialize(data, context=context).to_buffer().to_pybytes() + + +def deserialize_data(data): + """deserialize_data""" + return pyarrow.deserialize(data, context=context) + + +def multiprocess_reader(readers, use_pipe=True, queue_size=1000): + """ + multiprocess_reader use python multi process to read data from readers + and then use multiprocess.Queue or multiprocess.Pipe to merge all + data. The process number is equal to the number of input readers, each + process call one reader. + Multiprocess.Queue require the rw access right to /dev/shm, some + platform does not support. + you need to create multiple readers first, these readers should be independent + to each other so that each process can work independently. + An example: + .. code-block:: python + reader0 = reader(["file01", "file02"]) + reader1 = reader(["file11", "file12"]) + reader1 = reader(["file21", "file22"]) + reader = multiprocess_reader([reader0, reader1, reader2], + queue_size=100, use_pipe=False) + """ + + assert type(readers) is list and len(readers) > 0 + + def _read_into_queue(reader, queue): + """read_into_queue""" + for sample in reader(): + if sample is None: + raise ValueError("sample has None") + queue.put(serialize_data(sample)) + queue.put(serialize_data(None)) + + def queue_reader(): + """queue_reader""" + queue = multiprocessing.Queue(queue_size) + for reader in readers: + p = multiprocessing.Process( + target=_read_into_queue, args=(reader, queue)) + p.start() + + reader_num = len(readers) + finish_num = 0 + while finish_num < reader_num: + sample = deserialize_data(queue.get()) + if sample is None: + finish_num += 1 + else: + yield sample + + def _read_into_pipe(reader, conn): + """read_into_pipe""" + for sample in reader(): + if sample is None: + raise ValueError("sample has None!") + conn.send(serialize_data(sample)) + conn.send(serialize_data(None)) + conn.close() + + def pipe_reader(): + """pipe_reader""" + conns = [] + for reader in readers: + parent_conn, child_conn = multiprocessing.Pipe() + conns.append(parent_conn) + p = multiprocessing.Process( + target=_read_into_pipe, args=(reader, child_conn)) + p.start() + + reader_num = len(readers) + finish_num = 0 + conn_to_remove = [] + finish_flag = np.zeros(len(conns), dtype="int32") + while finish_num < reader_num: + for conn_id, conn in enumerate(conns): + if finish_flag[conn_id] > 0: + continue + buff = conn.recv() + now = time.time() + sample = deserialize_data(buff) + out = time.time() - now + if sample is None: + finish_num += 1 + conn.close() + finish_flag[conn_id] = 1 + else: + yield sample + + if use_pipe: + return pipe_reader + else: + return queue_reader diff --git a/examples/distribute_deepwalk/multi_class.py b/examples/distribute_deepwalk/multi_class.py new file mode 100644 index 0000000000000000000000000000000000000000..5ffe69060b7af620ceb5aecdd2f06a33768b8d3d --- /dev/null +++ b/examples/distribute_deepwalk/multi_class.py @@ -0,0 +1,244 @@ +# Copyright (c) 2019 PaddlePaddle Authors. All Rights Reserved +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +import argparse +import time +import math +import os + +import numpy as np +import sklearn.metrics +from sklearn.metrics import f1_score + +import pgl +from pgl import data_loader +from pgl.utils import op +from pgl.utils.logger import log +import paddle.fluid as fluid +import paddle.fluid.layers as l + +np.random.seed(123) + + +def load(name): + if name == 'BlogCatalog': + dataset = data_loader.BlogCatalogDataset() + else: + raise ValueError(name + " dataset doesn't exists") + return dataset + + +def node_classify_model(graph, + num_labels, + hidden_size=16, + name='node_classify_task'): + pyreader = l.py_reader( + capacity=70, + shapes=[[-1, 1], [-1, num_labels]], + dtypes=['int64', 'float32'], + lod_levels=[0, 0], + name=name + '_pyreader', + use_double_buffer=True) + nodes, labels = l.read_file(pyreader) + embed_nodes = l.embedding( + input=nodes, + size=[graph.num_nodes, hidden_size], + param_attr=fluid.ParamAttr(name='weight')) + embed_nodes.stop_gradient = True + logits = l.fc(input=embed_nodes, size=num_labels) + loss = l.sigmoid_cross_entropy_with_logits(logits, labels) + loss = l.reduce_mean(loss) + prob = l.sigmoid(logits) + topk = l.reduce_sum(labels, -1) + return pyreader, loss, prob, labels, topk + + +def node_classify_generator(graph, + all_nodes=None, + batch_size=512, + epoch=1, + shuffle=True): + + if all_nodes is None: + all_nodes = np.arange(graph.num_nodes) + #labels = (np.random.rand(512, 39) > 0.95).astype(np.float32) + + def batch_nodes_generator(shuffle=shuffle): + perm = np.arange(len(all_nodes), dtype=np.int64) + if shuffle: + np.random.shuffle(perm) + start = 0 + while start < len(all_nodes): + yield all_nodes[perm[start:start + batch_size]] + start += batch_size + + def wrapper(): + for _ in range(epoch): + for batch_nodes in batch_nodes_generator(): + batch_nodes_expanded = np.expand_dims(batch_nodes, + -1).astype(np.int64) + batch_labels = graph.node_feat['group_id'][batch_nodes].astype( + np.float32) + yield [batch_nodes_expanded, batch_labels] + + return wrapper + + +def topk_f1_score(labels, + probs, + topk_list=None, + average="macro", + threshold=None): + assert topk_list is not None or threshold is not None, "one of topklist and threshold should not be None" + if threshold is not None: + preds = probs > threshold + else: + preds = np.zeros_like(labels, dtype=np.int64) + for idx, (prob, topk) in enumerate(zip(np.argsort(probs), topk_list)): + preds[idx][prob[-int(topk):]] = 1 + return f1_score(labels, preds, average=average) + + +def main(args): + hidden_size = args.hidden_size + epoch = args.epoch + ckpt_path = args.ckpt_path + threshold = args.threshold + + dataset = load(args.dataset) + + if args.batch_size is None: + batch_size = len(dataset.train_index) + else: + batch_size = args.batch_size + + train_steps = (len(dataset.train_index) // batch_size) * epoch + + place = fluid.CUDAPlace(0) if args.use_cuda else fluid.CPUPlace() + train_prog = fluid.Program() + test_prog = fluid.Program() + startup_prog = fluid.Program() + + with fluid.program_guard(train_prog, startup_prog): + with fluid.unique_name.guard(): + train_pyreader, train_loss, train_probs, train_labels, train_topk = node_classify_model( + dataset.graph, + dataset.num_groups, + hidden_size=hidden_size, + name='train') + lr = l.polynomial_decay(0.025, train_steps, 0.0001) + adam = fluid.optimizer.Adam(lr) + adam.minimize(train_loss) + + with fluid.program_guard(test_prog, startup_prog): + with fluid.unique_name.guard(): + test_pyreader, test_loss, test_probs, test_labels, test_topk = node_classify_model( + dataset.graph, + dataset.num_groups, + hidden_size=hidden_size, + name='test') + test_prog = test_prog.clone(for_test=True) + + exe = fluid.Executor(place) + exe.run(startup_prog) + + train_pyreader.decorate_tensor_provider( + node_classify_generator( + dataset.graph, + dataset.train_index, + batch_size=batch_size, + epoch=epoch)) + test_pyreader.decorate_tensor_provider( + node_classify_generator( + dataset.graph, dataset.test_index, batch_size=batch_size, epoch=1)) + + def existed_params(var): + if not isinstance(var, fluid.framework.Parameter): + return False + return os.path.exists(os.path.join(ckpt_path, var.name)) + + fluid.io.load_vars( + exe, ckpt_path, main_program=train_prog, predicate=existed_params) + step = 0 + prev_time = time.time() + train_pyreader.start() + + while 1: + try: + train_loss_val, train_probs_val, train_labels_val, train_topk_val = exe.run( + train_prog, + fetch_list=[ + train_loss, train_probs, train_labels, train_topk + ], + return_numpy=True) + train_macro_f1 = topk_f1_score(train_labels_val, train_probs_val, + train_topk_val, "macro", threshold) + train_micro_f1 = topk_f1_score(train_labels_val, train_probs_val, + train_topk_val, "micro", threshold) + step += 1 + log.info("Step %d " % step + "Train Loss: %f " % train_loss_val + + "Train Macro F1: %f " % train_macro_f1 + + "Train Micro F1: %f " % train_micro_f1) + except fluid.core.EOFException: + train_pyreader.reset() + break + + test_pyreader.start() + test_probs_vals, test_labels_vals, test_topk_vals = [], [], [] + while 1: + try: + test_loss_val, test_probs_val, test_labels_val, test_topk_val = exe.run( + test_prog, + fetch_list=[ + test_loss, test_probs, test_labels, test_topk + ], + return_numpy=True) + test_probs_vals.append( + test_probs_val), test_labels_vals.append(test_labels_val) + test_topk_vals.append(test_topk_val) + except fluid.core.EOFException: + test_pyreader.reset() + test_probs_array = np.concatenate(test_probs_vals) + test_labels_array = np.concatenate(test_labels_vals) + test_topk_array = np.concatenate(test_topk_vals) + test_macro_f1 = topk_f1_score( + test_labels_array, test_probs_array, test_topk_array, + "macro", threshold) + test_micro_f1 = topk_f1_score( + test_labels_array, test_probs_array, test_topk_array, + "micro", threshold) + log.info("\t\tStep %d " % step + "Test Loss: %f " % + test_loss_val + "Test Macro F1: %f " % test_macro_f1 + + "Test Micro F1: %f " % test_micro_f1) + break + + +if __name__ == '__main__': + parser = argparse.ArgumentParser(description='node2vec') + parser.add_argument( + "--dataset", + type=str, + default="BlogCatalog", + help="dataset (BlogCatalog)") + parser.add_argument("--use_cuda", action='store_true', help="use_cuda") + parser.add_argument("--hidden_size", type=int, default=128) + parser.add_argument("--epoch", type=int, default=400) + parser.add_argument("--batch_size", type=int, default=None) + parser.add_argument("--threshold", type=float, default=0.3) + parser.add_argument( + "--ckpt_path", + type=str, + default="./tmp/baseline_node2vec/paddle_model") + args = parser.parse_args() + log.info(args) + main(args) diff --git a/examples/distribute_deepwalk/pgl_deepwalk.cfg b/examples/distribute_deepwalk/pgl_deepwalk.cfg new file mode 100644 index 0000000000000000000000000000000000000000..8c06b3174378829d5c9b7334c92e60041857bda4 --- /dev/null +++ b/examples/distribute_deepwalk/pgl_deepwalk.cfg @@ -0,0 +1,22 @@ + +# deepwalk config +num_nodes=10312 # max node_id + 1 +num_sample_workers=2 +epoch=100 + +optimizer=sgd # sgd or adam +learning_rate=0.5 + +neg_num=5 +walk_len=40 +win_size=5 +dim=128 +batch_size=8 +steps_per_save=5000 + +is_sparse=False +distributed_embedding=False # only use when num_nodes > 100,000,000, slower than noraml embedding +build_train_data=True +pre_walk=False + +CPU_NUM=16 diff --git a/examples/distribute_deepwalk/reader.py b/examples/distribute_deepwalk/reader.py new file mode 100644 index 0000000000000000000000000000000000000000..f797c18ed4ac91c63d9a57b8a8741782c6151b23 --- /dev/null +++ b/examples/distribute_deepwalk/reader.py @@ -0,0 +1,146 @@ +# Copyright (c) 2019 PaddlePaddle Authors. All Rights Reserved +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +""" + Reader file. +""" +from __future__ import division +from __future__ import absolute_import +from __future__ import print_function +import time +import io +import os + +import numpy as np +import paddle +from pgl.utils.logger import log +from pgl.sample import node2vec_sample +from pgl.sample import deepwalk_sample +from pgl.sample import alias_sample +from pgl.graph_kernel import skip_gram_gen_pair +from pgl.graph_kernel import alias_sample_build_table +from pgl.utils import mp_reader + + +class DeepwalkReader(object): + def __init__(self, + graph, + batch_size=512, + walk_len=40, + win_size=5, + neg_num=5, + train_files=None, + walkpath_files=None, + neg_sample_type="average"): + """ + Args: + walkpath_files: if is not None, read walk path from walkpath_files + """ + self.graph = graph + self.batch_size = batch_size + self.walk_len = walk_len + self.win_size = win_size + self.neg_num = neg_num + self.train_files = train_files + self.walkpath_files = walkpath_files + self.neg_sample_type = neg_sample_type + + def walk_from_files(self): + bucket = [] + while True: + for filename in self.walkpath_files: + with io.open(filename) as inf: + for line in inf: + #walk = [hash_map[x] for x in line.strip('\n\t').split('\t')] + walk = [int(x) for x in line.strip('\n\t').split('\t')] + bucket.append(walk) + if len(bucket) == self.batch_size: + yield bucket + bucket = [] + if len(bucket): + yield bucket + + def walk_from_graph(self): + def node_generator(): + if self.train_files is None: + while True: + for nodes in self.graph.node_batch_iter(self.batch_size): + yield nodes + else: + nodes = [] + while True: + for filename in self.train_files: + with io.open(filename) as inf: + for line in inf: + node = int(line.strip('\n\t')) + nodes.append(node) + if len(nodes) == self.batch_size: + yield nodes + nodes = [] + if len(nodes): + yield nodes + + if "alias" in self.graph.node_feat and "events" in self.graph.node_feat: + log.info("Deepwalk using alias sample") + for nodes in node_generator(): + if "alias" in self.graph.node_feat and "events" in self.graph.node_feat: + walks = deepwalk_sample(self.graph, nodes, self.walk_len, + "alias", "events") + else: + walks = deepwalk_sample(self.graph, nodes, self.walk_len) + yield walks + + def walk_generator(self): + if self.walkpath_files is not None: + for i in self.walk_from_files(): + yield i + else: + for i in self.walk_from_graph(): + yield i + + def __call__(self): + np.random.seed(os.getpid()) + if self.neg_sample_type == "outdegree": + outdegree = self.graph.outdegree() + distribution = 1. * outdegree / outdegree.sum() + alias, events = alias_sample_build_table(distribution) + max_len = int(self.batch_size * self.walk_len * ( + (1 + self.win_size) - 0.3)) + for walks in self.walk_generator(): + try: + src_list, pos_list = [], [] + for walk in walks: + s, p = skip_gram_gen_pair(walk, self.win_size) + src_list.append(s[:max_len]), pos_list.append(p[:max_len]) + src = [s for x in src_list for s in x] + pos = [s for x in pos_list for s in x] + src = np.array(src, dtype=np.int64), + pos = np.array(pos, dtype=np.int64) + src, pos = np.reshape(src, [-1, 1, 1]), np.reshape(pos, + [-1, 1, 1]) + + neg_sample_size = [len(pos), self.neg_num, 1] + if src.shape[0] == 0: + continue + if self.neg_sample_type == "average": + negs = np.random.randint( + low=0, high=self.graph.num_nodes, size=neg_sample_size) + elif self.neg_sample_type == "outdegree": + negs = alias_sample(neg_sample_size, alias, events) + elif self.neg_sample_type == "inbatch": + pass + dst = np.concatenate([pos, negs], 1) + # [batch_size, 1, 1] [batch_size, neg_num+1, 1] + yield src[:max_len], dst[:max_len] + except Exception as e: + log.exception(e) diff --git a/examples/distribute_deepwalk/utils.py b/examples/distribute_deepwalk/utils.py new file mode 100644 index 0000000000000000000000000000000000000000..0958d63d6d4cdc9a661192914bfd29a8a09280cd --- /dev/null +++ b/examples/distribute_deepwalk/utils.py @@ -0,0 +1,144 @@ +# Copyright (c) 2019 PaddlePaddle Authors. All Rights Reserved +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +""" + Utils file. +""" +from __future__ import division +from __future__ import absolute_import +from __future__ import print_function +from __future__ import unicode_literals + +import os +import time + +import numpy as np +from pgl.utils.logger import log +from pgl.graph import Graph +from pgl.sample import graph_alias_sample_table + +from reader import DeepwalkReader +import mp_reader + + +def get_file_list(path): + filelist = [] + if os.path.isfile(path): + filelist = [path] + elif os.path.isdir(path): + filelist = [ + os.path.join(dp, f) + for dp, dn, filenames in os.walk(path) for f in filenames + ] + else: + raise ValueError(path + " not supported") + return filelist + + +def build_graph(num_nodes, edge_path): + filelist = [] + if os.path.isfile(edge_path): + filelist = [edge_path] + elif os.path.isdir(edge_path): + filelist = [ + os.path.join(dp, f) + for dp, dn, filenames in os.walk(edge_path) for f in filenames + ] + else: + raise ValueError(edge_path + " not supported") + edges, edge_weight = [], [] + for name in filelist: + with open(name) as inf: + for line in inf: + slots = line.strip("\n").split() + edges.append([slots[0], slots[1]]) + edges.append([slots[1], slots[0]]) + if len(slots) > 2: + edge_weight.extend([float(slots[2]), float(slots[2])]) + edges = np.array(edges, dtype="int64") + assert num_nodes > edges.max( + ), "Node id in any edges should be smaller then num_nodes!" + + edge_feat = dict() + if len(edge_weight) == len(edges): + edge_feat["weight"] = np.array(edge_weight) + + graph = Graph(num_nodes, edges, edge_feat=edge_feat) + log.info("Build graph done") + + graph.outdegree() + + del edges, edge_feat + + log.info("Build graph index done") + if "weight" in graph.edge_feat: + graph.node_feat["alias"], graph.node_feat[ + "events"] = graph_alias_sample_table(graph, "weight") + log.info("Build graph alias sample table done") + return graph + + +def build_fake_graph(num_nodes): + class FakeGraph(): + pass + + graph = FakeGraph() + graph.num_nodes = num_nodes + return graph + + +def build_gen_func(args, graph): + num_sample_workers = args.num_sample_workers + + if args.walkpath_files is None or args.walkpath_files == "None": + walkpath_files = [None for _ in range(num_sample_workers)] + else: + files = get_file_list(args.walkpath_files) + walkpath_files = [[] for i in range(num_sample_workers)] + for idx, f in enumerate(files): + walkpath_files[idx % num_sample_workers].append(f) + + if args.train_files is None or args.train_files == "None": + train_files = [None for _ in range(num_sample_workers)] + else: + files = get_file_list(args.train_files) + train_files = [[] for i in range(num_sample_workers)] + for idx, f in enumerate(files): + train_files[idx % num_sample_workers].append(f) + + gen_func_pool = [ + DeepwalkReader( + graph, + batch_size=args.batch_size, + walk_len=args.walk_len, + win_size=args.win_size, + neg_num=args.neg_num, + neg_sample_type=args.neg_sample_type, + walkpath_files=walkpath_files[i], + train_files=train_files[i]) for i in range(num_sample_workers) + ] + if num_sample_workers == 1: + gen_func = gen_func_pool[0] + else: + gen_func = mp_reader.multiprocess_reader( + gen_func_pool, use_pipe=True, queue_size=100) + return gen_func + + +def test_gen_speed(gen_func): + cur_time = time.time() + for idx, _ in enumerate(gen_func()): + log.info("iter %s: %s s" % (idx, time.time() - cur_time)) + cur_time = time.time() + if idx == 100: + break diff --git a/examples/distribute_graphsage/README.md b/examples/distribute_graphsage/README.md new file mode 100644 index 0000000000000000000000000000000000000000..7e424d4668955476eecf459ade84603b71e26ebe --- /dev/null +++ b/examples/distribute_graphsage/README.md @@ -0,0 +1,57 @@ +# Distribute GraphSAGE in PGL + +[GraphSAGE](https://cs.stanford.edu/people/jure/pubs/graphsage-nips17.pdf) is a general inductive framework that leverages node feature +information (e.g., text attributes) to efficiently generate node embeddings for previously unseen data. Instead of training individual embeddings for each node, GraphSAGE learns a function that generates embeddings by sampling and aggregating features from a node’s local neighborhood. Based on PGL, we reproduce GraphSAGE algorithm and reach the same level of indicators as the paper in Reddit Dataset. Besides, this is an example of subgraph sampling and training in PGL. + +For purpose of high scalability, we use redis as distribute graph storage solution and training graphsage against redis server. + +### Datasets(Quickstart) +The reddit dataset should be downloaded from [reddit_adj.npz](https://drive.google.com/open?id=174vb0Ws7Vxk_QTUtxqTgDHSQ4El4qDHt) and [reddit.npz](https://drive.google.com/open?id=19SphVl_Oe8SJ1r87Hr5a6znx3nJu1F2Jthe). The details for Reddit Dataset can be found [here](https://cs.stanford.edu/people/jure/pubs/graphsage-nips17.pdf). + +Alternatively, reddit dataset has been preprocessed and packed into docker image, which can be instantly pulled using following commands. + +```sh +docker pull githubutilities/reddit_redis_demo:v0.1 +``` + +### Dependencies + +```txt +- paddlepaddle>=1.6 +- pgl +- scipy +- redis==2.10.6 +- redis-py-cluster==1.3.6 +``` + +### How to run + +#### 1. Start reddit data service + +```sh +docker run \ + --net=host \ + -d --rm \ + --name reddit_demo \ + -it githubutilities/reddit_redis_demo:v0.1 \ + /bin/bash -c "/bin/bash ./before_hook.sh && /bin/bash" +docker logs -f `docker ps -aqf "name=reddit_demo"` +``` + +#### 2. training GraphSAGE model + +```sh +python train.py --use_cuda --epoch 10 --graphsage_type graphsage_mean --sample_workers 10 +``` + +#### Hyperparameters + +- epoch: Number of epochs default (10) +- use_cuda: Use gpu if assign use_cuda. +- graphsage_type: We support 4 aggregator types including "graphsage_mean", "graphsage_maxpool", "graphsage_meanpool" and "graphsage_lstm". +- sample_workers: The number of workers for multiprocessing subgraph sample. +- lr: Learning rate. +- batch_size: Batch size. +- samples_1: The max neighbors for the first hop neighbor sampling. (default: 25) +- samples_2: The max neighbors for the second hop neighbor sampling. (default: 10) +- hidden_size: The hidden size of the GraphSAGE models. diff --git a/examples/distribute_graphsage/data/reddit_index_label.npz b/examples/distribute_graphsage/data/reddit_index_label.npz new file mode 100644 index 0000000000000000000000000000000000000000..69c2ae1ced956dd5b40221ea0e8e11d2b470230a Binary files /dev/null and b/examples/distribute_graphsage/data/reddit_index_label.npz differ diff --git a/examples/distribute_graphsage/model.py b/examples/distribute_graphsage/model.py new file mode 100644 index 0000000000000000000000000000000000000000..145a979e86951dc4b5a2522154a0dc0373eea065 --- /dev/null +++ b/examples/distribute_graphsage/model.py @@ -0,0 +1,130 @@ +# Copyright (c) 2019 PaddlePaddle Authors. All Rights Reserved +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +import paddle +import paddle.fluid as fluid + + +def copy_send(src_feat, dst_feat, edge_feat): + return src_feat["h"] + + +def mean_recv(feat): + return fluid.layers.sequence_pool(feat, pool_type="average") + + +def sum_recv(feat): + return fluid.layers.sequence_pool(feat, pool_type="sum") + + +def max_recv(feat): + return fluid.layers.sequence_pool(feat, pool_type="max") + + +def lstm_recv(feat): + hidden_dim = 128 + forward, _ = fluid.layers.dynamic_lstm( + input=feat, size=hidden_dim * 4, use_peepholes=False) + output = fluid.layers.sequence_last_step(forward) + return output + + +def graphsage_mean(gw, feature, hidden_size, act, name): + msg = gw.send(copy_send, nfeat_list=[("h", feature)]) + neigh_feature = gw.recv(msg, mean_recv) + self_feature = feature + self_feature = fluid.layers.fc(self_feature, + hidden_size, + act=act, + name=name + '_l') + neigh_feature = fluid.layers.fc(neigh_feature, + hidden_size, + act=act, + name=name + '_r') + output = fluid.layers.concat([self_feature, neigh_feature], axis=1) + output = fluid.layers.l2_normalize(output, axis=1) + return output + + +def graphsage_meanpool(gw, + feature, + hidden_size, + act, + name, + inner_hidden_size=512): + neigh_feature = fluid.layers.fc(feature, inner_hidden_size, act="relu") + msg = gw.send(copy_send, nfeat_list=[("h", neigh_feature)]) + neigh_feature = gw.recv(msg, mean_recv) + neigh_feature = fluid.layers.fc(neigh_feature, + hidden_size, + act=act, + name=name + '_r') + + self_feature = feature + self_feature = fluid.layers.fc(self_feature, + hidden_size, + act=act, + name=name + '_l') + output = fluid.layers.concat([self_feature, neigh_feature], axis=1) + output = fluid.layers.l2_normalize(output, axis=1) + return output + + +def graphsage_maxpool(gw, + feature, + hidden_size, + act, + name, + inner_hidden_size=512): + neigh_feature = fluid.layers.fc(feature, inner_hidden_size, act="relu") + msg = gw.send(copy_send, nfeat_list=[("h", neigh_feature)]) + neigh_feature = gw.recv(msg, max_recv) + neigh_feature = fluid.layers.fc(neigh_feature, + hidden_size, + act=act, + name=name + '_r') + + self_feature = feature + self_feature = fluid.layers.fc(self_feature, + hidden_size, + act=act, + name=name + '_l') + output = fluid.layers.concat([self_feature, neigh_feature], axis=1) + output = fluid.layers.l2_normalize(output, axis=1) + return output + + +def graphsage_lstm(gw, feature, hidden_size, act, name): + inner_hidden_size = 128 + neigh_feature = fluid.layers.fc(feature, inner_hidden_size, act="relu") + + hidden_dim = 128 + forward_proj = fluid.layers.fc(input=neigh_feature, + size=hidden_dim * 4, + bias_attr=False, + name="lstm_proj") + msg = gw.send(copy_send, nfeat_list=[("h", forward_proj)]) + neigh_feature = gw.recv(msg, lstm_recv) + neigh_feature = fluid.layers.fc(neigh_feature, + hidden_size, + act=act, + name=name + '_r') + + self_feature = feature + self_feature = fluid.layers.fc(self_feature, + hidden_size, + act=act, + name=name + '_l') + output = fluid.layers.concat([self_feature, neigh_feature], axis=1) + output = fluid.layers.l2_normalize(output, axis=1) + return output diff --git a/examples/distribute_graphsage/reader.py b/examples/distribute_graphsage/reader.py new file mode 100644 index 0000000000000000000000000000000000000000..9c230cce3c40161881163a0446ab51977ecc9700 --- /dev/null +++ b/examples/distribute_graphsage/reader.py @@ -0,0 +1,148 @@ +# Copyright (c) 2019 PaddlePaddle Authors. All Rights Reserved +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +import numpy as np +import pickle as pkl +import paddle +import paddle.fluid as fluid +import socket +import pgl +import time + +from pgl.utils import mp_reader +from pgl.utils.logger import log +from pgl import redis_graph + + +def node_batch_iter(nodes, node_label, batch_size): + """node_batch_iter + """ + perm = np.arange(len(nodes)) + np.random.shuffle(perm) + start = 0 + while start < len(nodes): + index = perm[start:start + batch_size] + start += batch_size + yield nodes[index], node_label[index] + + +def traverse(item): + """traverse + """ + if isinstance(item, list) or isinstance(item, np.ndarray): + for i in iter(item): + for j in traverse(i): + yield j + else: + yield item + + +def flat_node_and_edge(nodes, eids): + """flat_node_and_edge + """ + nodes = list(set(traverse(nodes))) + eids = list(set(traverse(eids))) + return nodes, eids + + +def worker(batch_info, graph_wrapper, samples): + """Worker + """ + + def work(): + """work + """ + redis_configs = [{ + "host": socket.gethostbyname(socket.gethostname()), + "port": 7430 + }, ] + graph = redis_graph.RedisGraph("sub_graph", redis_configs, 64) + first = True + for batch_train_samples, batch_train_labels in batch_info: + start_nodes = batch_train_samples + nodes = start_nodes + eids = [] + eid2edges = {} + for max_deg in samples: + pred, pred_eid = graph.sample_predecessor( + start_nodes, max_degree=max_deg, return_eids=True) + for _dst, _srcs, _eids in zip(start_nodes, pred, pred_eid): + for _src, _eid in zip(_srcs, _eids): + eid2edges[_eid] = (_src, _dst) + + last_nodes = nodes + nodes = [nodes, pred] + eids = [eids, pred_eid] + nodes, eids = flat_node_and_edge(nodes, eids) + # Find new nodes + start_nodes = list(set(nodes) - set(last_nodes)) + if len(start_nodes) == 0: + break + + subgraph = graph.subgraph( + nodes=nodes, eid=eids, edges=[eid2edges[e] for e in eids]) + sub_node_index = subgraph.reindex_from_parrent_nodes( + batch_train_samples) + feed_dict = graph_wrapper.to_feed(subgraph) + feed_dict["node_label"] = np.expand_dims( + np.array( + batch_train_labels, dtype="int64"), -1) + feed_dict["node_index"] = sub_node_index + yield feed_dict + + return work + + +def multiprocess_graph_reader(graph_wrapper, + samples, + node_index, + batch_size, + node_label, + num_workers=4): + """multiprocess_graph_reader + """ + + def parse_to_subgraph(rd): + """parse_to_subgraph + """ + + def work(): + """work + """ + last = time.time() + for data in rd(): + this = time.time() + feed_dict = data + now = time.time() + last = now + yield feed_dict + + return work + + def reader(): + """reader""" + batch_info = list( + node_batch_iter( + node_index, node_label, batch_size=batch_size)) + block_size = int(len(batch_info) / num_workers + 1) + reader_pool = [] + for i in range(num_workers): + reader_pool.append( + worker(batch_info[block_size * i:block_size * (i + 1)], + graph_wrapper, samples)) + multi_process_sample = mp_reader.multiprocess_reader( + reader_pool, use_pipe=True, queue_size=1000) + r = parse_to_subgraph(multi_process_sample) + return paddle.reader.buffered(r, 1000) + + return reader() diff --git a/examples/distribute_graphsage/requirements.txt b/examples/distribute_graphsage/requirements.txt new file mode 100644 index 0000000000000000000000000000000000000000..bfc094c11eb1cebe90f8acbc4c399eb688d9c7cb --- /dev/null +++ b/examples/distribute_graphsage/requirements.txt @@ -0,0 +1,3 @@ +scipy +redis==2.10.6 +redis-py-cluster==1.3.6 diff --git a/examples/distribute_graphsage/train.py b/examples/distribute_graphsage/train.py new file mode 100644 index 0000000000000000000000000000000000000000..cb62acf8c20b1e63126c6ff20687d6e59f597d7f --- /dev/null +++ b/examples/distribute_graphsage/train.py @@ -0,0 +1,265 @@ +# Copyright (c) 2019 PaddlePaddle Authors. All Rights Reserved +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +import os +import argparse +import time + +import numpy as np +import scipy.sparse as sp +from sklearn.preprocessing import StandardScaler + +import pgl +from pgl.utils.logger import log +from pgl.utils import paddle_helper +import paddle +import paddle.fluid as fluid +import reader +from model import graphsage_mean, graphsage_meanpool,\ + graphsage_maxpool, graphsage_lstm + + +def load_data(): + """ + data from https://github.com/matenure/FastGCN/issues/8 + reddit.npz: https://drive.google.com/open?id=19SphVl_Oe8SJ1r87Hr5a6znx3nJu1F2J + reddit_index_label is preprocess from reddit.npz without feats key. + """ + data_dir = os.path.dirname(os.path.abspath(__file__)) + data = np.load(os.path.join(data_dir, "data/reddit_index_label.npz")) + + num_class = 41 + + train_label = data['y_train'] + val_label = data['y_val'] + test_label = data['y_test'] + + train_index = data['train_index'] + val_index = data['val_index'] + test_index = data['test_index'] + + return { + "train_index": train_index, + "train_label": train_label, + "val_label": val_label, + "val_index": val_index, + "test_index": test_index, + "test_label": test_label, + "num_class": 41 + } + + +def build_graph_model(graph_wrapper, num_class, k_hop, graphsage_type, + hidden_size): + node_index = fluid.layers.data( + "node_index", shape=[None], dtype="int64", append_batch_size=False) + + node_label = fluid.layers.data( + "node_label", shape=[None, 1], dtype="int64", append_batch_size=False) + + #feature = fluid.layers.gather(feature, graph_wrapper.node_feat['feats']) + feature = graph_wrapper.node_feat['feats'] + feature.stop_gradient = True + + for i in range(k_hop): + if graphsage_type == 'graphsage_mean': + feature = graphsage_mean( + graph_wrapper, + feature, + hidden_size, + act="relu", + name="graphsage_mean_%s" % i) + elif graphsage_type == 'graphsage_meanpool': + feature = graphsage_meanpool( + graph_wrapper, + feature, + hidden_size, + act="relu", + name="graphsage_meanpool_%s" % i) + elif graphsage_type == 'graphsage_maxpool': + feature = graphsage_maxpool( + graph_wrapper, + feature, + hidden_size, + act="relu", + name="graphsage_maxpool_%s" % i) + elif graphsage_type == 'graphsage_lstm': + feature = graphsage_lstm( + graph_wrapper, + feature, + hidden_size, + act="relu", + name="graphsage_maxpool_%s" % i) + else: + raise ValueError("graphsage type %s is not" + " implemented" % graphsage_type) + + feature = fluid.layers.gather(feature, node_index) + logits = fluid.layers.fc(feature, + num_class, + act=None, + name='classification_layer') + proba = fluid.layers.softmax(logits) + + loss = fluid.layers.softmax_with_cross_entropy( + logits=logits, label=node_label) + loss = fluid.layers.mean(loss) + acc = fluid.layers.accuracy(input=proba, label=node_label, k=1) + return loss, acc + + +def run_epoch(batch_iter, + exe, + program, + prefix, + model_loss, + model_acc, + epoch, + log_per_step=100): + batch = 0 + total_loss = 0. + total_acc = 0. + total_sample = 0 + start = time.time() + for batch_feed_dict in batch_iter(): + batch += 1 + batch_loss, batch_acc = exe.run(program, + fetch_list=[model_loss, model_acc], + feed=batch_feed_dict) + + if batch % log_per_step == 0: + log.info("Batch %s %s-Loss %s %s-Acc %s" % + (batch, prefix, batch_loss, prefix, batch_acc)) + + num_samples = len(batch_feed_dict["node_index"]) + total_loss += batch_loss * num_samples + total_acc += batch_acc * num_samples + total_sample += num_samples + end = time.time() + + log.info("%s Epoch %s Loss %.5lf Acc %.5lf Speed(per batch) %.5lf sec" % + (prefix, epoch, total_loss / total_sample, + total_acc / total_sample, (end - start) / batch)) + + +def main(args): + data = load_data() + log.info("preprocess finish") + log.info("Train Examples: %s" % len(data["train_index"])) + log.info("Val Examples: %s" % len(data["val_index"])) + log.info("Test Examples: %s" % len(data["test_index"])) + + place = fluid.CUDAPlace(0) if args.use_cuda else fluid.CPUPlace() + train_program = fluid.Program() + startup_program = fluid.Program() + samples = [] + if args.samples_1 > 0: + samples.append(args.samples_1) + if args.samples_2 > 0: + samples.append(args.samples_2) + + with fluid.program_guard(train_program, startup_program): + graph_wrapper = pgl.graph_wrapper.GraphWrapper( + "sub_graph", + fluid.CPUPlace(), + node_feat=[('feats', [None, 602], np.dtype('float32'))]) + model_loss, model_acc = build_graph_model( + graph_wrapper, + num_class=data["num_class"], + hidden_size=args.hidden_size, + graphsage_type=args.graphsage_type, + k_hop=len(samples)) + + test_program = train_program.clone(for_test=True) + + with fluid.program_guard(train_program, startup_program): + adam = fluid.optimizer.Adam(learning_rate=args.lr) + adam.minimize(model_loss) + + exe = fluid.Executor(place) + exe.run(startup_program) + + train_iter = reader.multiprocess_graph_reader( + graph_wrapper, + samples=samples, + num_workers=args.sample_workers, + batch_size=args.batch_size, + node_index=data['train_index'], + node_label=data["train_label"]) + + val_iter = reader.multiprocess_graph_reader( + graph_wrapper, + samples=samples, + num_workers=args.sample_workers, + batch_size=args.batch_size, + node_index=data['val_index'], + node_label=data["val_label"]) + + test_iter = reader.multiprocess_graph_reader( + graph_wrapper, + samples=samples, + num_workers=args.sample_workers, + batch_size=args.batch_size, + node_index=data['test_index'], + node_label=data["test_label"]) + + for epoch in range(args.epoch): + run_epoch( + train_iter, + program=train_program, + exe=exe, + prefix="train", + model_loss=model_loss, + model_acc=model_acc, + log_per_step=1, + epoch=epoch) + + run_epoch( + val_iter, + program=test_program, + exe=exe, + prefix="val", + model_loss=model_loss, + model_acc=model_acc, + log_per_step=10000, + epoch=epoch) + + run_epoch( + test_iter, + program=test_program, + prefix="test", + exe=exe, + model_loss=model_loss, + model_acc=model_acc, + log_per_step=10000, + epoch=epoch) + + +if __name__ == "__main__": + parser = argparse.ArgumentParser(description='graphsage') + parser.add_argument("--use_cuda", action='store_true', help="use_cuda") + parser.add_argument( + "--normalize", action='store_true', help="normalize features") + parser.add_argument( + "--symmetry", action='store_true', help="undirect graph") + parser.add_argument("--graphsage_type", type=str, default="graphsage_mean") + parser.add_argument("--sample_workers", type=int, default=10) + parser.add_argument("--epoch", type=int, default=10) + parser.add_argument("--hidden_size", type=int, default=128) + parser.add_argument("--batch_size", type=int, default=128) + parser.add_argument("--lr", type=float, default=0.01) + parser.add_argument("--samples_1", type=int, default=25) + parser.add_argument("--samples_2", type=int, default=10) + args = parser.parse_args() + log.info(args) + main(args) diff --git a/examples/gat/README.md b/examples/gat/README.md index 6b18dcc8d33d14c9b7818a5ab216ad83e48e3ee9..573316ea729a03441d47f7a54fe83163142cf96c 100644 --- a/examples/gat/README.md +++ b/examples/gat/README.md @@ -26,24 +26,25 @@ def gat_layer(graph_wrapper, node_feature, hidden_size): return output ``` + ### Datasets The datasets contain three citation networks: CORA, PUBMED, CITESEER. The details for these three datasets can be found in the [paper](https://arxiv.org/abs/1609.02907). ### Dependencies -- paddlepaddle>=1.4 (The speed can be faster in 1.5.) +- paddlepaddle>=1.6 - pgl ### Performance We train our models for 200 epochs and report the accuracy on the test dataset. -| Dataset | Accuracy | Speed with paddle 1.4
(epoch time) | Speed with paddle 1.5
(epoch time)| -| --- | --- | --- |---| -| Cora | ~83% | 0.0188s | 0.0175s | -| Pubmed | ~78% | 0.0449s | 0.0295s | -| Citeseer | ~70% | 0.0275 | 0.0253s | +| Dataset | Accuracy | +| --- | --- | +| Cora | ~83% | +| Pubmed | ~78% | +| Citeseer | ~70% | ### How to run diff --git a/examples/gat/train.py b/examples/gat/train.py index 0446f0262defbb85a39e235223183eb85706778f..344948803539f260bbe7288a4ee16a423c5c5f8a 100644 --- a/examples/gat/train.py +++ b/examples/gat/train.py @@ -68,7 +68,7 @@ def main(args): node_index = fluid.layers.data( "node_index", shape=[None, 1], - dtype="int32", + dtype="int64", append_batch_size=False) node_label = fluid.layers.data( "node_label", @@ -111,7 +111,7 @@ def main(args): for epoch in range(200): if epoch >= 3: t0 = time.time() - feed_dict["node_index"] = np.array(train_index, dtype="int32") + feed_dict["node_index"] = np.array(train_index, dtype="int64") feed_dict["node_label"] = np.array(train_label, dtype="int64") train_loss, train_acc = exe.run(train_program, feed=feed_dict, @@ -121,7 +121,7 @@ def main(args): time_per_epoch = 1.0 * (time.time() - t0) dur.append(time_per_epoch) - feed_dict["node_index"] = np.array(val_index, dtype="int32") + feed_dict["node_index"] = np.array(val_index, dtype="int64") feed_dict["node_label"] = np.array(val_label, dtype="int64") val_loss, val_acc = exe.run(test_program, feed=feed_dict, @@ -132,7 +132,7 @@ def main(args): "Train Loss: %f " % train_loss + "Train Acc: %f " % train_acc + "Val Loss: %f " % val_loss + "Val Acc: %f " % val_acc) - feed_dict["node_index"] = np.array(test_index, dtype="int32") + feed_dict["node_index"] = np.array(test_index, dtype="int64") feed_dict["node_label"] = np.array(test_label, dtype="int64") test_loss, test_acc = exe.run(test_program, feed=feed_dict, diff --git a/examples/gcn/README.md b/examples/gcn/README.md index c56c604e0f89eef2c714dac49a1f10c3fbbe48d3..1a1cf4fc54b3c7232b8c3b1cb0516b34de05240d 100644 --- a/examples/gcn/README.md +++ b/examples/gcn/README.md @@ -26,18 +26,18 @@ The datasets contain three citation networks: CORA, PUBMED, CITESEER. The detail ### Dependencies -- paddlepaddle>=1.4 (The speed can be faster in 1.5.) +- paddlepaddle>=1.6 - pgl ### Performance We train our models for 200 epochs and report the accuracy on the test dataset. -| Dataset | Accuracy | Speed with paddle 1.4
(epoch time) | Speed with paddle 1.5
(epoch time)| -| --- | --- | --- |---| -| Cora | ~81% | 0.0106s | 0.0104s | -| Pubmed | ~79% | 0.0210s | 0.0154s | -| Citeseer | ~71% | 0.0175s | 0.0177s | +| Dataset | Accuracy | +| --- | --- | +| Cora | ~81% | +| Pubmed | ~79% | +| Citeseer | ~71% | ### How to run diff --git a/examples/gcn/train.py b/examples/gcn/train.py index 6dfef67965a9179710a25ff9c2529da6108b40ce..7a1aaf3ab36d3abdfdafe4451572f4104284b9a1 100644 --- a/examples/gcn/train.py +++ b/examples/gcn/train.py @@ -70,7 +70,7 @@ def main(args): node_index = fluid.layers.data( "node_index", shape=[None, 1], - dtype="int32", + dtype="int64", append_batch_size=False) node_label = fluid.layers.data( "node_label", @@ -113,7 +113,7 @@ def main(args): for epoch in range(200): if epoch >= 3: t0 = time.time() - feed_dict["node_index"] = np.array(train_index, dtype="int32") + feed_dict["node_index"] = np.array(train_index, dtype="int64") feed_dict["node_label"] = np.array(train_label, dtype="int64") train_loss, train_acc = exe.run(train_program, feed=feed_dict, @@ -123,7 +123,7 @@ def main(args): if epoch >= 3: time_per_epoch = 1.0 * (time.time() - t0) dur.append(time_per_epoch) - feed_dict["node_index"] = np.array(val_index, dtype="int32") + feed_dict["node_index"] = np.array(val_index, dtype="int64") feed_dict["node_label"] = np.array(val_label, dtype="int64") val_loss, val_acc = exe.run(test_program, feed=feed_dict, @@ -134,7 +134,7 @@ def main(args): "Train Loss: %f " % train_loss + "Train Acc: %f " % train_acc + "Val Loss: %f " % val_loss + "Val Acc: %f " % val_acc) - feed_dict["node_index"] = np.array(test_index, dtype="int32") + feed_dict["node_index"] = np.array(test_index, dtype="int64") feed_dict["node_label"] = np.array(test_label, dtype="int64") test_loss, test_acc = exe.run(test_program, feed=feed_dict, diff --git a/examples/ges/README.md b/examples/ges/README.md new file mode 100644 index 0000000000000000000000000000000000000000..5636cb13c2eec606141b469f3b1a13e347ae8bda --- /dev/null +++ b/examples/ges/README.md @@ -0,0 +1,22 @@ +# PGL Examples for GES +[Graph Embedding with Side Information](https://arxiv.org/pdf/1803.02349.pdf) is an algorithmic framework for representational learning on graphs. Given any graph, it can learn continuous feature representations for the nodes, which can then be used for various downstream machine learning tasks. Based on PGL, we reproduce ges algorithms. +## Datasets +The datasets contain two networks: [BlogCatalog](http://socialcomputing.asu.edu/datasets/BlogCatalog3). +## Dependencies +- paddlepaddle>=1.6 +- pgl>=1.0.0 + +## How to run + +For examples, train ges on cora dataset. +```sh +# train deepwalk in distributed mode. +sh gpu_run.sh +``` + +## Hyperparameters +- dataset: The citation dataset "BlogCatalog". +- hidden_size: Hidden size of the embedding. +- lr: Learning rate. +- neg_num: Number of negative samples. +- epoch: Number of training epoch. diff --git a/examples/ges/gpu_run.sh b/examples/ges/gpu_run.sh new file mode 100755 index 0000000000000000000000000000000000000000..2eca3a6a140b84bc6be9ea49c5bff1203e920a55 --- /dev/null +++ b/examples/ges/gpu_run.sh @@ -0,0 +1,22 @@ +#!/bin/bash + +export FLAGS_sync_nccl_allreduce=1 +export FLAGS_eager_delete_tensor_gb=0 +export FLAGS_fraction_of_gpu_memory_to_use=1 +export NCCL_DEBUG=INFO +export NCCL_IB_GID_INDEX=3 +export GLOG_v=1 +export GLOG_logtostderr=1 + +num_nodes=10312 +num_embedding=10351 +num_sample_workers=20 + +# build train_data +rm -rf train_data && mkdir -p train_data +cd train_data +seq 0 $((num_nodes-1)) | shuf | split -l $((num_nodes/num_sample_workers+1)) +cd - + +python3 gpu_train.py --output_path ./output --epoch 100 --walk_len 40 --win_size 5 --neg_num 5 --batch_size 128 --hidden_size 128 \ + --num_nodes $num_nodes --num_embedding $num_embedding --num_sample_workers $num_sample_workers --steps_per_save 2000 --dataset "BlogCatalog" diff --git a/examples/ges/gpu_train.py b/examples/ges/gpu_train.py new file mode 100644 index 0000000000000000000000000000000000000000..62fcf3588e3be8a332258c1c6e44d59d6259fcba --- /dev/null +++ b/examples/ges/gpu_train.py @@ -0,0 +1,314 @@ +# Copyright (c) 2019 PaddlePaddle Authors. All Rights Reserved +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +""" gpu_train +""" +import argparse +import time +import os +import glob + +import numpy as np +import paddle.fluid as F +import paddle.fluid.layers as L +from pgl.utils.logger import log +from pgl.graph import Graph +from pgl.sample import graph_alias_sample_table +from pgl import data_loader + +import mp_reader +from reader import GESReader +from model import GESModel + + +def get_file_list(path): + """get_file_list + """ + filelist = [] + if os.path.isfile(path): + filelist = [path] + elif os.path.isdir(path): + filelist = [ + os.path.join(dp, f) + for dp, dn, filenames in os.walk(path) for f in filenames + ] + else: + raise ValueError(path + " not supported") + return filelist + + +def build_graph(num_nodes, edge_path, output_path, undigraph=True): + """ build_graph + """ + edge_file = os.path.join(output_path, "edge.npy") + edge_weight_file = os.path.join(output_path, "edge_weight.npy") + alias_file = os.path.join(output_path, "alias.npy") + events_file = os.path.join(output_path, "events.npy") + if os.path.isfile(edge_file): + edges = np.load(edge_file) + edge_feat = dict() + if os.path.isfile(edge_weight_file): + log.info("Loading weight from cache") + edge_feat["weight"] = np.load(edge_weight_file, allow_pickle=True) + node_feat = dict() + if os.path.isfile(alias_file): + log.info("Loading alias from cache") + node_feat["alias"] = np.load(alias_file, allow_pickle=True) + if os.path.isfile(events_file): + log.info("Loading events from cache") + node_feat["events"] = np.load(events_file, allow_pickle=True) + else: + filelist = get_file_list(edge_path) + edges, edge_weight = [], [] + log.info("Reading edge files") + for name in filelist: + with open(name) as inf: + for line in inf: + slots = line.strip("\n").split() + edges.append([slots[0], slots[1]]) + if len(slots) > 2: + edge_weight.append(slots[2]) + edges = np.array(edges, dtype="int64") + assert num_nodes > edges.max( + ), "Node id in any edges should be smaller then num_nodes!" + + log.info("Read edge files done.") + edge_feat = dict() + node_feat = dict() + if len(edge_weight) == len(edges): + edge_feat["weight"] = np.array(edge_weight, dtype="float32") + + if undigraph is True: + edges = np.concatenate([edges, edges[:, [1, 0]]], 0) + if "weight" in edge_feat: + edge_feat["weight"] = np.concatenate( + [edge_feat["weight"], edge_feat["weight"]], + 0).astype("float64") + + graph = Graph(num_nodes, edges, node_feat, edge_feat=edge_feat) + log.info("Build graph done") + graph.outdegree() + log.info("Build graph index done") + if "weight" in graph.edge_feat and "alias" not in graph.node_feat and "events" not in graph.node_feat: + graph.node_feat["alias"], graph.node_feat[ + "events"] = graph_alias_sample_table(graph, "weight") + log.info( + "Build graph alias sample table done, and saving alias & evnets cache" + ) + np.save(alias_file, graph.node_feat["alias"]) + np.save(events_file, graph.node_feat["events"]) + return graph + + +def optimization(base_lr, loss, train_steps, optimizer='adam'): + """ optimization + """ + decayed_lr = L.polynomial_decay(base_lr, train_steps, 0.0001) + + if optimizer == 'sgd': + optimizer = F.optimizer.SGD( + decayed_lr, + regularization=F.regularizer.L2DecayRegularizer( + regularization_coeff=0.0025)) + elif optimizer == 'adam': + # dont use gpu's lazy mode + optimizer = F.optimizer.Adam(decayed_lr) + else: + raise ValueError + + log.info('learning rate:%f' % (base_lr)) + optimizer.minimize(loss) + + +def build_gen_func(args, graph, node_feat): + """ build_gen_func + """ + num_sample_workers = args.num_sample_workers + + if args.walkpath_files is None: + walkpath_files = [None for _ in range(num_sample_workers)] + else: + files = get_file_list(args.walkpath_files) + walkpath_files = [[] for i in range(num_sample_workers)] + for idx, f in enumerate(files): + walkpath_files[idx % num_sample_workers].append(f) + + if args.train_files is None: + train_files = [None for _ in range(num_sample_workers)] + else: + files = get_file_list(args.train_files) + train_files = [[] for i in range(num_sample_workers)] + for idx, f in enumerate(files): + train_files[idx % num_sample_workers].append(f) + + gen_func_pool = [ + GESReader( + graph, + node_feat, + batch_size=args.batch_size, + walk_len=args.walk_len, + win_size=args.win_size, + neg_num=args.neg_num, + neg_sample_type=args.neg_sample_type, + walkpath_files=walkpath_files[i], + train_files=train_files[i]) for i in range(num_sample_workers) + ] + if num_sample_workers == 1: + gen_func = gen_func_pool[0] + else: + gen_func = mp_reader.multiprocess_reader( + gen_func_pool, use_pipe=True, queue_size=100) + return gen_func + + +def get_parallel_exe(program, loss): + """ get_parallel_exe + """ + exec_strategy = F.ExecutionStrategy() + exec_strategy.num_threads = 1 #2 for fp32 4 for fp16 + exec_strategy.use_experimental_executor = True + exec_strategy.num_iteration_per_drop_scope = 10 #important shit + + build_strategy = F.BuildStrategy() + build_strategy.enable_inplace = True + build_strategy.memory_optimize = True + build_strategy.remove_unnecessary_lock = True + + #return compiled_prog + train_exe = F.ParallelExecutor( + use_cuda=True, + loss_name=loss.name, + build_strategy=build_strategy, + exec_strategy=exec_strategy, + main_program=program) + return train_exe + + +def train(train_exe, exe, program, loss, node2vec_pyreader, args, train_steps): + """ train + """ + trainer_id = int(os.getenv("PADDLE_TRAINER_ID", "0")) + step = 0 + while True: + try: + begin_time = time.time() + loss_val, = train_exe.run(fetch_list=[loss]) + log.info("step %s: loss %.5f speed: %.5f s/step" % + (step, np.mean(loss_val), time.time() - begin_time)) + step += 1 + except F.core.EOFException: + node2vec_pyreader.reset() + + if (step % args.steps_per_save == 0 or + step == train_steps) and trainer_id == 0: + + model_save_dir = args.output_path + model_path = os.path.join(model_save_dir, str(step)) + if not os.path.exists(model_save_dir): + os.makedirs(model_save_dir) + F.io.save_params(exe, model_path, program) + + if step == train_steps: + break + + +def test_gen_speed(gen_func): + """ test_gen_speed + """ + cur_time = time.time() + for idx, _ in enumerate(gen_func()): + log.info("iter %s: %s s" % (idx, time.time() - cur_time)) + cur_time = time.time() + if idx == 100: + break + + +def main(args): + """ main + """ + import logging + log.setLevel(logging.DEBUG) + log.info("start") + + if args.dataset is not None: + if args.dataset == "BlogCatalog": + graph = data_loader.BlogCatalogDataset().graph + else: + raise ValueError(args.dataset + " dataset doesn't exists") + log.info("Load buildin BlogCatalog dataset done.") + node_feat = np.expand_dims(graph.node_feat["group_id"].argmax(-1), + -1) + graph.num_nodes + args.num_nodes = graph.num_nodes + args.num_embedding = graph.num_nodes + graph.node_feat[ + "group_id"].shape[-1] + else: + graph = build_graph(args.num_nodes, args.edge_path, args.output_path) + node_feat = np.load(args.node_feat_npy) + + model = GESModel(args.num_embedding, node_feat.shape[1] + 1, + args.hidden_size, args.neg_num, False, 2) + pyreader = model.pyreader + loss = model.forward() + num_devices = len(F.cuda_places()) + + train_steps = int(args.num_nodes * args.epoch / args.batch_size / + num_devices) + log.info("Train steps: %s" % train_steps) + optimization(args.lr * num_devices, loss, train_steps, args.optimizer) + + place = F.CUDAPlace(0) + exe = F.Executor(place) + exe.run(F.default_startup_program()) + + gen_func = build_gen_func(args, graph, node_feat) + + pyreader.decorate_tensor_provider(gen_func) + pyreader.start() + train_prog = F.default_main_program() + train_exe = get_parallel_exe(train_prog, loss) + train(train_exe, exe, train_prog, loss, pyreader, args, train_steps) + + +if __name__ == '__main__': + parser = argparse.ArgumentParser(description='Deepwalk') + parser.add_argument("--hidden_size", type=int, default=64) + parser.add_argument("--lr", type=float, default=0.025) + parser.add_argument("--neg_num", type=int, default=5) + parser.add_argument("--epoch", type=int, default=100) + parser.add_argument("--batch_size", type=int, default=128) + parser.add_argument("--walk_len", type=int, default=40) + parser.add_argument("--win_size", type=int, default=5) + parser.add_argument("--output_path", type=str, default="output") + parser.add_argument("--num_sample_workers", type=int, default=1) + parser.add_argument("--steps_per_save", type=int, default=3000) + parser.add_argument("--num_nodes", type=int, default=10000) + parser.add_argument("--num_embedding", type=int, default=10000) + parser.add_argument("--edge_path", type=str, default="./graph_data") + parser.add_argument("--walkpath_files", type=str, default=None) + parser.add_argument("--train_files", type=str, default="./train_data") + parser.add_argument("--node_feat_npy", type=str, default="./feat.npy") + parser.add_argument("--dataset", type=str, default=None) + parser.add_argument( + "--neg_sample_type", + type=str, + default="average", + choices=["average", "outdegree"]) + parser.add_argument( + "--optimizer", + type=str, + required=False, + choices=['adam', 'sgd'], + default="adam") + args = parser.parse_args() + log.info(args) + main(args) diff --git a/examples/ges/model.py b/examples/ges/model.py new file mode 100644 index 0000000000000000000000000000000000000000..1fce05e79843495f1e4f2abc3984d6311761d3f0 --- /dev/null +++ b/examples/ges/model.py @@ -0,0 +1,222 @@ +# Copyright (c) 2019 PaddlePaddle Authors. All Rights Reserved +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +""" + GES model file. +""" +from __future__ import division +from __future__ import absolute_import +from __future__ import print_function +from __future__ import unicode_literals +import math + +import paddle.fluid.layers as L +import paddle.fluid as F + + +def split_embedding(input, + dict_size, + hidden_size, + initializer, + name, + num_part=16, + is_sparse=False, + learning_rate=1.0): + """ split_embedding + """ + _part_size = hidden_size // num_part + if hidden_size % num_part != 0: + _part_size += 1 + output_embedding = [] + p_num = 0 + while hidden_size > 0: + _part_size = min(_part_size, hidden_size) + hidden_size -= _part_size + print("part", p_num, "size=", (dict_size, _part_size)) + part_embedding = L.embedding( + input=input, + size=(dict_size, _part_size), + is_sparse=is_sparse, + is_distributed=False, + param_attr=F.ParamAttr( + name=name + '_part%s' % p_num, + initializer=initializer, + learning_rate=learning_rate)) + p_num += 1 + output_embedding.append(part_embedding) + return L.concat(output_embedding, -1) + + +class GESModel(object): + """ GESModel + """ + + def __init__(self, + num_nodes, + num_featuers, + hidden_size=16, + neg_num=5, + is_sparse=False, + num_part=1): + self.pyreader = L.py_reader( + capacity=70, + shapes=[[-1, 1, num_featuers, 1], + [-1, neg_num + 1, num_featuers, 1]], + dtypes=['int64', 'int64'], + lod_levels=[0, 0], + name='train', + use_double_buffer=True) + + self.num_nodes = num_nodes + self.num_featuers = num_featuers + self.neg_num = neg_num + self.embed_init = F.initializer.TruncatedNormal(scale=1.0 / + math.sqrt(hidden_size)) + self.is_sparse = is_sparse + self.num_part = num_part + self.hidden_size = hidden_size + self.loss = None + + def forward(self): + """ forward + """ + src, dst = L.read_file(self.pyreader) + + if self.is_sparse: + # sparse mode use 2 dims input. + src = L.reshape(src, [-1, 1]) + dst = L.reshape(dst, [-1, 1]) + + src_embed = split_embedding(src, self.num_nodes, self.hidden_size, + self.embed_init, "weight", self.num_part, + self.is_sparse) + + dst_embed = split_embedding(dst, self.num_nodes, self.hidden_size, + self.embed_init, "weight", self.num_part, + self.is_sparse) + + if self.is_sparse: + src_embed = L.reshape( + src_embed, [-1, 1, self.num_featuers, self.hidden_size]) + dst_embed = L.reshape( + dst_embed, + [-1, self.neg_num + 1, self.num_featuers, self.hidden_size]) + + src_embed = L.reduce_mean(src_embed, 2) + dst_embed = L.reduce_mean(dst_embed, 2) + + logits = L.matmul( + src_embed, dst_embed, + transpose_y=True) # [batch_size, 1, neg_num+1] + + pos_label = L.fill_constant_batch_size_like(logits, [-1, 1, 1], + "float32", 1) + neg_label = L.fill_constant_batch_size_like( + logits, [-1, 1, self.neg_num], "float32", 0) + label = L.concat([pos_label, neg_label], -1) + + pos_weight = L.fill_constant_batch_size_like(logits, [-1, 1, 1], + "float32", self.neg_num) + neg_weight = L.fill_constant_batch_size_like( + logits, [-1, 1, self.neg_num], "float32", 1) + weight = L.concat([pos_weight, neg_weight], -1) + + weight.stop_gradient = True + label.stop_gradient = True + + loss = L.sigmoid_cross_entropy_with_logits(logits, label) + loss = loss * weight + loss = L.reduce_mean(loss) + loss = loss * ((self.neg_num + 1) / 2 / self.neg_num) + loss.persistable = True + self.loss = loss + return loss + + +class EGESModel(GESModel): + """ EGESModel + """ + + def forward(self): + """ forward + """ + src, dst = L.read_file(self.pyreader) + + src_id = L.slice(src, [0, 1, 2, 3], [0, 0, 0, 0], + [int(math.pow(2, 30)) - 1, 1, 1, 1]) + dst_id = L.slice(dst, [0, 1, 2, 3], [0, 0, 0, 0], + [int(math.pow(2, 30)) - 1, self.neg_num + 1, 1, 1]) + + if self.is_sparse: + # sparse mode use 2 dims input. + src = L.reshape(src, [-1, 1]) + dst = L.reshape(dst, [-1, 1]) + + # [b, 1, f, h] + src_embed = split_embedding(src, self.num_nodes, self.hidden_size, + self.embed_init, "weight", self.num_part, + self.is_sparse) + + # [b, n+1, f, h] + dst_embed = split_embedding(dst, self.num_nodes, self.hidden_size, + self.embed_init, "weight", self.num_part, + self.is_sparse) + + if self.is_sparse: + src_embed = L.reshape( + src_embed, [-1, 1, self.num_featuers, self.hidden_size]) + dst_embed = L.reshape( + dst_embed, + [-1, self.neg_num + 1, self.num_featuers, self.hidden_size]) + + # [b, 1, 1, f] + src_weight = L.softmax( + L.embedding( + src_id, [self.num_nodes, self.num_featuers], + param_attr=F.ParamAttr(name="alpha"))) + # [b, n+1, 1, f] + dst_weight = L.softmax( + L.embedding( + dst_id, [self.num_nodes, self.num_featuers], + param_attr=F.ParamAttr(name="alpha"))) + + # [b, 1, h] + src_sum = L.squeeze(L.matmul(src_weight, src_embed), axes=[2]) + # [b, n+1, h] + dst_sum = L.squeeze(L.matmul(dst_weight, dst_embed), axes=[2]) + + logits = L.matmul( + src_sum, dst_sum, transpose_y=True) # [batch_size, 1, neg_num+1] + + pos_label = L.fill_constant_batch_size_like(logits, [-1, 1, 1], + "float32", 1) + neg_label = L.fill_constant_batch_size_like( + logits, [-1, 1, self.neg_num], "float32", 0) + label = L.concat([pos_label, neg_label], -1) + + pos_weight = L.fill_constant_batch_size_like(logits, [-1, 1, 1], + "float32", self.neg_num) + neg_weight = L.fill_constant_batch_size_like( + logits, [-1, 1, self.neg_num], "float32", 1) + weight = L.concat([pos_weight, neg_weight], -1) + + weight.stop_gradient = True + label.stop_gradient = True + + loss = L.sigmoid_cross_entropy_with_logits(logits, label) + loss = loss * weight + loss = L.reduce_mean(loss) + loss = loss * ((self.neg_num + 1) / 2 / self.neg_num) + loss.persistable = True + self.loss = loss + return loss diff --git a/examples/ges/mp_reader.py b/examples/ges/mp_reader.py new file mode 100644 index 0000000000000000000000000000000000000000..d4df8998cc4ad672627dc7ba9f846c91ccca0bba --- /dev/null +++ b/examples/ges/mp_reader.py @@ -0,0 +1,145 @@ +# Copyright (c) 2019 PaddlePaddle Authors. All Rights Reserved. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +"""Optimized Multiprocessing Reader for PaddlePaddle +""" +import multiprocessing +import numpy as np +import time + +import paddle.fluid as fluid +import pyarrow + + +def _serialize_serializable(obj): + """Serialize Feed Dict + """ + return {"type": type(obj), "data": obj.__dict__} + + +def _deserialize_serializable(obj): + """Deserialize Feed Dict + """ + + val = obj["type"].__new__(obj["type"]) + val.__dict__.update(obj["data"]) + return val + + +context = pyarrow.default_serialization_context() + +context.register_type( + object, + "object", + custom_serializer=_serialize_serializable, + custom_deserializer=_deserialize_serializable) + + +def serialize_data(data): + """serialize_data""" + return pyarrow.serialize(data, context=context).to_buffer().to_pybytes() + + +def deserialize_data(data): + """deserialize_data""" + return pyarrow.deserialize(data, context=context) + + +def multiprocess_reader(readers, use_pipe=True, queue_size=1000): + """ + multiprocess_reader use python multi process to read data from readers + and then use multiprocess.Queue or multiprocess.Pipe to merge all + data. The process number is equal to the number of input readers, each + process call one reader. + Multiprocess.Queue require the rw access right to /dev/shm, some + platform does not support. + you need to create multiple readers first, these readers should be independent + to each other so that each process can work independently. + An example: + .. code-block:: python + reader0 = reader(["file01", "file02"]) + reader1 = reader(["file11", "file12"]) + reader1 = reader(["file21", "file22"]) + reader = multiprocess_reader([reader0, reader1, reader2], + queue_size=100, use_pipe=False) + """ + + assert type(readers) is list and len(readers) > 0 + + def _read_into_queue(reader, queue): + """read_into_queue""" + for sample in reader(): + if sample is None: + raise ValueError("sample has None") + queue.put(serialize_data(sample)) + queue.put(serialize_data(None)) + + def queue_reader(): + """queue_reader""" + queue = multiprocessing.Queue(queue_size) + for reader in readers: + p = multiprocessing.Process( + target=_read_into_queue, args=(reader, queue)) + p.start() + + reader_num = len(readers) + finish_num = 0 + while finish_num < reader_num: + sample = deserialize_data(queue.get()) + if sample is None: + finish_num += 1 + else: + yield sample + + def _read_into_pipe(reader, conn): + """read_into_pipe""" + for sample in reader(): + if sample is None: + raise ValueError("sample has None!") + conn.send(serialize_data(sample)) + conn.send(serialize_data(None)) + conn.close() + + def pipe_reader(): + """pipe_reader""" + conns = [] + for reader in readers: + parent_conn, child_conn = multiprocessing.Pipe() + conns.append(parent_conn) + p = multiprocessing.Process( + target=_read_into_pipe, args=(reader, child_conn)) + p.start() + + reader_num = len(readers) + finish_num = 0 + conn_to_remove = [] + finish_flag = np.zeros(len(conns), dtype="int32") + while finish_num < reader_num: + for conn_id, conn in enumerate(conns): + if finish_flag[conn_id] > 0: + continue + buff = conn.recv() + now = time.time() + sample = deserialize_data(buff) + out = time.time() - now + if sample is None: + finish_num += 1 + conn.close() + finish_flag[conn_id] = 1 + else: + yield sample + + if use_pipe: + return pipe_reader + else: + return queue_reader diff --git a/examples/ges/reader.py b/examples/ges/reader.py new file mode 100644 index 0000000000000000000000000000000000000000..cd2d9d21cc47cf64e83859094379d29696b2598f --- /dev/null +++ b/examples/ges/reader.py @@ -0,0 +1,153 @@ +# Copyright (c) 2019 PaddlePaddle Authors. All Rights Reserved +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +""" + Reader file. +""" +from __future__ import division +from __future__ import absolute_import +from __future__ import print_function +import time +import io +import os + +import numpy as np +import paddle +from pgl.utils.logger import log +from pgl.sample import node2vec_sample +from pgl.sample import deepwalk_sample +from pgl.sample import alias_sample +from pgl.graph_kernel import skip_gram_gen_pair +from pgl.graph_kernel import alias_sample_build_table + + +class GESReader(object): + """ GESReader + """ + + def __init__(self, + graph, + node_feat, + batch_size=512, + walk_len=40, + win_size=5, + neg_num=5, + train_files=None, + walkpath_files=None, + neg_sample_type="average"): + """ + Args: + walkpath_files: if is not None, read walk path from walkpath_files + """ + self.graph = graph + self.node_feat = node_feat + self.batch_size = batch_size + self.walk_len = walk_len + self.win_size = win_size + self.neg_num = neg_num + self.train_files = train_files + self.walkpath_files = walkpath_files + self.neg_sample_type = neg_sample_type + + def walk_from_files(self): + """ walk_from_files + """ + bucket = [] + while True: + for filename in self.walkpath_files: + with io.open(filename) as inf: + for line in inf: + walk = [int(x) for x in line.strip('\n\t').split('\t')] + bucket.append(walk) + if len(bucket) == self.batch_size: + yield bucket + bucket = [] + if len(bucket): + yield bucket + + def walk_from_graph(self): + """ walk_from_graph + """ + + def node_generator(): + """ node_generator + """ + if self.train_files is None: + while True: + for nodes in self.graph.node_batch_iter(self.batch_size): + yield nodes + else: + nodes = [] + while True: + for filename in self.train_files: + with io.open(filename) as inf: + for line in inf: + node = int(line.strip('\n\t')) + nodes.append(node) + if len(nodes) == self.batch_size: + yield nodes + nodes = [] + if len(nodes): + yield nodes + + if "alias" in self.graph.node_feat and "events" in self.graph.node_feat: + log.info("Deepwalk using alias sample") + for nodes in node_generator(): + if "alias" in self.graph.node_feat and "events" in self.graph.node_feat: + walks = deepwalk_sample(self.graph, nodes, self.walk_len, + "alias", "events") + else: + walks = deepwalk_sample(self.graph, nodes, self.walk_len) + yield walks + + def walk_generator(self): + """ walk_generator + """ + if self.walkpath_files is not None: + for i in self.walk_from_files(): + yield i + else: + for i in self.walk_from_graph(): + yield i + + def __call__(self): + np.random.seed(os.getpid()) + if self.neg_sample_type == "outdegree": + outdegree = self.graph.outdegree() + distribution = 1. * outdegree / outdegree.sum() + alias, events = alias_sample_build_table(distribution) + max_len = int(self.batch_size * self.walk_len * ( + (1 + self.win_size) - 0.3)) + for walks in self.walk_generator(): + src, pos = [], [] + for walk in walks: + s, p = skip_gram_gen_pair(walk, self.win_size) + src.extend(s), pos.extend(p) + src = np.array(src, dtype=np.int64), + pos = np.array(pos, dtype=np.int64) + src, pos = np.reshape(src, [-1, 1, 1]), np.reshape(pos, [-1, 1, 1]) + + if src.shape[0] == 0: + continue + neg_sample_size = [len(pos), self.neg_num, 1] + if self.neg_sample_type == "average": + negs = self.graph.sample_nodes(neg_sample_size) + elif self.neg_sample_type == "outdegree": + negs = alias_sample(neg_sample_size, alias, events) + # [batch_size, 1, 1] [batch_size, neg_num+1, 1] + dst = np.concatenate([pos, negs], 1) + src_feat = np.concatenate([src, self.node_feat[src[:, :, 0]]], -1) + dst_feat = np.concatenate([dst, self.node_feat[dst[:, :, 0]]], -1) + src_feat, dst_feat = np.expand_dims(src_feat, -1), np.expand_dims( + dst_feat, -1) + yield src_feat[:max_len], dst_feat[:max_len] diff --git a/examples/graphsage/README.md b/examples/graphsage/README.md index 6eb17f6cfec52194cf499d6a1273dc0e9b89d555..449aaf8c72112eb979ec916f104a0c29b06f1064 100644 --- a/examples/graphsage/README.md +++ b/examples/graphsage/README.md @@ -12,17 +12,23 @@ The reddit dataset should be downloaded from the following links and placed in d ### Dependencies -- sklearn -- paddlepaddle>=1.4 (The speed can be faster in 1.5.) +- paddlepaddle>=1.6 - pgl ### How to run To train a GraphSAGE model on Reddit Dataset, you can just run + ``` python train.py --use_cuda --epoch 10 --graphsage_type graphsage_mean --normalize --symmetry ``` +If you want to train a GraphSAGE model with multiple GPUs, you can just run + +``` +CUDA_VISIBLE_DEVICES=0,1 python train_multi.py --use_cuda --epoch 10 --graphsage_type graphsage_mean --normalize --symmetry --num_trainer 2 +``` + #### Hyperparameters - epoch: Number of epochs default (10) diff --git a/examples/graphsage/reader.py b/examples/graphsage/reader.py index f05bfaba2837840e991000d14f18671d3fff6bcb..abc3fe8cbe8bdd380261ffde8933871b1a6094c9 100644 --- a/examples/graphsage/reader.py +++ b/examples/graphsage/reader.py @@ -17,12 +17,15 @@ import paddle import paddle.fluid as fluid import pgl import time +from pgl.utils import mp_reader from pgl.utils.logger import log import train import time def node_batch_iter(nodes, node_label, batch_size): + """node_batch_iter + """ perm = np.arange(len(nodes)) np.random.shuffle(perm) start = 0 @@ -33,6 +36,8 @@ def node_batch_iter(nodes, node_label, batch_size): def traverse(item): + """traverse + """ if isinstance(item, list) or isinstance(item, np.ndarray): for i in iter(item): for j in traverse(i): @@ -42,13 +47,21 @@ def traverse(item): def flat_node_and_edge(nodes, eids): + """flat_node_and_edge + """ nodes = list(set(traverse(nodes))) eids = list(set(traverse(eids))) return nodes, eids -def worker(batch_info, graph, samples): +def worker(batch_info, graph, graph_wrapper, samples): + """Worker + """ + def work(): + """work + """ + first = True for batch_train_samples, batch_train_labels in batch_info: start_nodes = batch_train_samples nodes = start_nodes @@ -65,11 +78,14 @@ def worker(batch_info, graph, samples): if len(start_nodes) == 0: break - feed_dict = {} - feed_dict["nodes"] = [int(n) for n in nodes] - feed_dict["eids"] = [int(e) for e in eids] - feed_dict["node_label"] = [int(n) for n in batch_train_labels] - feed_dict["node_index"] = [int(n) for n in batch_train_samples] + subgraph = graph.subgraph(nodes=nodes, eid=eids) + sub_node_index = subgraph.reindex_from_parrent_nodes( + batch_train_samples) + feed_dict = graph_wrapper.to_feed(subgraph) + feed_dict["node_label"] = np.expand_dims( + np.array( + batch_train_labels, dtype="int64"), -1) + feed_dict["node_index"] = sub_node_index yield feed_dict return work @@ -82,26 +98,28 @@ def multiprocess_graph_reader(graph, batch_size, node_label, num_workers=4): + """multiprocess_graph_reader + """ + def parse_to_subgraph(rd): + """parse_to_subgraph + """ + def work(): + """work + """ + last = time.time() for data in rd(): - nodes = data["nodes"] - eids = data["eids"] - batch_train_labels = data["node_label"] - batch_train_samples = data["node_index"] - subgraph = graph.subgraph(nodes=nodes, eid=eids) - sub_node_index = subgraph.reindex_from_parrent_nodes( - batch_train_samples) - feed_dict = graph_wrapper.to_feed(subgraph) - feed_dict["node_label"] = np.expand_dims( - np.array( - batch_train_labels, dtype="int64"), -1) - feed_dict["node_index"] = sub_node_index + this = time.time() + feed_dict = data + now = time.time() + last = now yield feed_dict return work def reader(): + """reader""" batch_info = list( node_batch_iter( node_index, node_label, batch_size=batch_size)) @@ -110,9 +128,9 @@ def multiprocess_graph_reader(graph, for i in range(num_workers): reader_pool.append( worker(batch_info[block_size * i:block_size * (i + 1)], graph, - samples)) - multi_process_sample = paddle.reader.multiprocess_reader( - reader_pool, use_pipe=False) + graph_wrapper, samples)) + multi_process_sample = mp_reader.multiprocess_reader( + reader_pool, use_pipe=True, queue_size=1000) r = parse_to_subgraph(multi_process_sample) return paddle.reader.buffered(r, 1000) @@ -121,7 +139,10 @@ def multiprocess_graph_reader(graph, def graph_reader(graph, graph_wrapper, samples, node_index, batch_size, node_label): + """graph_reader""" + def reader(): + """reader""" for batch_train_samples, batch_train_labels in node_batch_iter( node_index, node_label, batch_size=batch_size): start_nodes = batch_train_samples diff --git a/examples/graphsage/train.py b/examples/graphsage/train.py index 5d5bca2728aa23fa8589c53ba3704a4f386a1019..fa19463a5222a306b72686ee47d3d18772808a93 100644 --- a/examples/graphsage/train.py +++ b/examples/graphsage/train.py @@ -11,6 +11,7 @@ # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. # See the License for the specific language governing permissions and # limitations under the License. +import os import argparse import time @@ -34,8 +35,9 @@ def load_data(normalize=True, symmetry=True): reddit_adj.npz: https://drive.google.com/open?id=174vb0Ws7Vxk_QTUtxqTgDHSQ4El4qDHt reddit.npz: https://drive.google.com/open?id=19SphVl_Oe8SJ1r87Hr5a6znx3nJu1F2J """ - data = np.load("data/reddit.npz") - adj = sp.load_npz("data/reddit_adj.npz") + data_dir = os.path.dirname(os.path.abspath(__file__)) + data = np.load(os.path.join(data_dir, "data/reddit.npz")) + adj = sp.load_npz(os.path.join(data_dir, "data/reddit_adj.npz")) if symmetry: adj = adj + adj.T adj = adj.tocoo() @@ -64,7 +66,7 @@ def load_data(normalize=True, symmetry=True): num_nodes=feature.shape[0], edges=list(zip(src, dst)), node_feat={"index": np.arange( - 0, len(feature), dtype="int32")}) + 0, len(feature), dtype="int64")}) return { "graph": graph, @@ -82,7 +84,7 @@ def load_data(normalize=True, symmetry=True): def build_graph_model(graph_wrapper, num_class, k_hop, graphsage_type, hidden_size, feature): node_index = fluid.layers.data( - "node_index", shape=[None], dtype="int32", append_batch_size=False) + "node_index", shape=[None], dtype="int64", append_batch_size=False) node_label = fluid.layers.data( "node_label", shape=[None, 1], dtype="int64", append_batch_size=False) @@ -198,7 +200,9 @@ def main(args): hide_batch_size=False) graph_wrapper = pgl.graph_wrapper.GraphWrapper( - "sub_graph", place, node_feat=data['graph'].node_feat_info()) + "sub_graph", + fluid.CPUPlace(), + node_feat=data['graph'].node_feat_info()) model_loss, model_acc = build_graph_model( graph_wrapper, num_class=data["num_class"], diff --git a/examples/graphsage/train_multi.py b/examples/graphsage/train_multi.py new file mode 100644 index 0000000000000000000000000000000000000000..8a1e799312e25ff2314de326ea3880ca0970b708 --- /dev/null +++ b/examples/graphsage/train_multi.py @@ -0,0 +1,369 @@ +# Copyright (c) 2019 PaddlePaddle Authors. All Rights Reserved +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +import os +import argparse +import time + +import sys +import traceback +import numpy as np +import scipy.sparse as sp +from sklearn.preprocessing import StandardScaler + +import pgl +from pgl.utils.logger import log +from pgl.utils import paddle_helper +import paddle +import paddle.fluid as fluid +import reader +from model import graphsage_mean, graphsage_meanpool,\ + graphsage_maxpool, graphsage_lstm + + +def load_data(normalize=True, symmetry=True): + """ + data from https://github.com/matenure/FastGCN/issues/8 + reddit_adj.npz: https://drive.google.com/open?id=174vb0Ws7Vxk_QTUtxqTgDHSQ4El4qDHt + reddit.npz: https://drive.google.com/open?id=19SphVl_Oe8SJ1r87Hr5a6znx3nJu1F2J + """ + data_dir = os.path.dirname(os.path.abspath(__file__)) + data = np.load(os.path.join(data_dir, "data/reddit.npz")) + adj = sp.load_npz(os.path.join(data_dir, "data/reddit_adj.npz")) + if symmetry: + adj = adj + adj.T + adj = adj.tocoo() + src = adj.row + dst = adj.col + + num_class = 41 + + train_label = data['y_train'] + val_label = data['y_val'] + test_label = data['y_test'] + + train_index = data['train_index'] + val_index = data['val_index'] + test_index = data['test_index'] + + feature = data["feats"].astype("float32") + + if normalize: + scaler = StandardScaler() + scaler.fit(feature[train_index]) + feature = scaler.transform(feature) + + log.info("Feature shape %s" % (repr(feature.shape))) + graph = pgl.graph.Graph( + num_nodes=feature.shape[0], + edges=list(zip(src, dst)), + node_feat={"feat": feature.astype("float32")}) + + return { + "graph": graph, + "train_index": train_index, + "train_label": train_label, + "val_label": val_label, + "val_index": val_index, + "test_index": test_index, + "test_label": test_label, + "num_class": 41 + } + + +def build_graph_model(graph_wrapper, num_class, k_hop, graphsage_type, + hidden_size): + """build_graph_model""" + node_index = fluid.layers.data( + "node_index", shape=[None], dtype="int64", append_batch_size=False) + + node_label = fluid.layers.data( + "node_label", shape=[None, 1], dtype="int64", append_batch_size=False) + + feature = graph_wrapper.node_feat["feat"] + + for i in range(k_hop): + if graphsage_type == 'graphsage_mean': + feature = graphsage_mean( + graph_wrapper, + feature, + hidden_size, + act="relu", + name="graphsage_mean_%s" % i) + elif graphsage_type == 'graphsage_meanpool': + feature = graphsage_meanpool( + graph_wrapper, + feature, + hidden_size, + act="relu", + name="graphsage_meanpool_%s" % i) + elif graphsage_type == 'graphsage_maxpool': + feature = graphsage_maxpool( + graph_wrapper, + feature, + hidden_size, + act="relu", + name="graphsage_maxpool_%s" % i) + elif graphsage_type == 'graphsage_lstm': + feature = graphsage_lstm( + graph_wrapper, + feature, + hidden_size, + act="relu", + name="graphsage_maxpool_%s" % i) + else: + raise ValueError("graphsage type %s is not" + " implemented" % graphsage_type) + + feature = fluid.layers.gather(feature, node_index) + logits = fluid.layers.fc(feature, + num_class, + act=None, + name='classification_layer') + proba = fluid.layers.softmax(logits) + + loss = fluid.layers.softmax_with_cross_entropy( + logits=logits, label=node_label) + loss = fluid.layers.mean(loss) + acc = fluid.layers.accuracy(input=proba, label=node_label, k=1) + return loss, acc + + +def to_multidevice(batch_iter, num_trainer): + """to_multidevice""" + batch_dict = [] + for batch in batch_iter(): + batch_dict.append(batch) + if len(batch_dict) == num_trainer: + yield batch_dict + batch_dict = [] + + if len(batch_dict) > 0: + log.warning("The batch (%s) can't fill all device (%s)" + "which will be discarded." % + (len(batch_dict), num_trainer)) + + +def run_epoch(batch_iter, + exe, + program, + prefix, + model_loss, + model_acc, + epoch, + log_per_step=100, + num_trainer=1): + """run_epoch""" + batch = 0 + total_loss = 0. + total_acc = 0. + total_sample = 0 + start = time.time() + if num_trainer > 1: + batch_iter = to_multidevice(batch_iter, num_trainer) + else: + batch_iter = batch_iter() + + for batch_feed_dict in batch_iter: + batch += 1 + if num_trainer > 1: + batch_loss, batch_acc = exe.run( + fetch_list=[model_loss.name, model_acc.name], + feed=batch_feed_dict) + + batch_loss = np.mean(batch_loss) + batch_acc = np.mean(batch_acc) + else: + batch_loss, batch_acc = exe.run( + program, + fetch_list=[model_loss.name, model_acc.name], + feed=batch_feed_dict) + + if batch % log_per_step == 0: + log.info("Batch %s %s-Loss %s %s-Acc %s" % + (batch, prefix, batch_loss, prefix, batch_acc)) + + if num_trainer > 1: + num_samples = sum( + [len(batch["node_index"]) for batch in batch_feed_dict]) + else: + num_samples = len(batch_feed_dict["node_index"]) + total_loss += batch_loss * num_samples + total_acc += batch_acc * num_samples + total_sample += num_samples + end = time.time() + + log.info("%s Epoch %s Loss %.5lf Acc %.5lf Speed(per batch) %.5lf sec" % + (prefix, epoch, total_loss / total_sample, + total_acc / total_sample, (end - start) / batch)) + + +def main(args): + """main""" + data = load_data(args.normalize, args.symmetry) + log.info("preprocess finish") + log.info("Train Examples: %s" % len(data["train_index"])) + log.info("Val Examples: %s" % len(data["val_index"])) + log.info("Test Examples: %s" % len(data["test_index"])) + log.info("Num nodes %s" % data["graph"].num_nodes) + log.info("Num edges %s" % data["graph"].num_edges) + log.info("Average Degree %s" % np.mean(data["graph"].indegree())) + + place = fluid.CUDAPlace(0) if args.use_cuda else fluid.CPUPlace() + train_program = fluid.Program() + startup_program = fluid.Program() + samples = [] + if args.samples_1 > 0: + samples.append(args.samples_1) + if args.samples_2 > 0: + samples.append(args.samples_2) + + with fluid.program_guard(train_program, startup_program): + graph_wrapper = pgl.graph_wrapper.GraphWrapper( + "sub_graph", + fluid.CPUPlace(), + node_feat=data['graph'].node_feat_info()) + + model_loss, model_acc = build_graph_model( + graph_wrapper, + num_class=data["num_class"], + hidden_size=args.hidden_size, + graphsage_type=args.graphsage_type, + k_hop=len(samples)) + + test_program = train_program.clone(for_test=True) + + with fluid.program_guard(train_program, startup_program): + adam = fluid.optimizer.Adam(learning_rate=args.lr) + adam.minimize(model_loss) + + exe = fluid.Executor(place) + exe.run(startup_program) + if args.num_trainer > 1: + build_strategy = fluid.BuildStrategy() + build_strategy.remove_unnecessary_lock = False + build_strategy.enable_sequential_execution = True + + train_exe = fluid.ParallelExecutor( + use_cuda=args.use_cuda, + main_program=train_program, + build_strategy=build_strategy, + loss_name=model_loss.name) + else: + train_exe = exe + + if args.sample_workers > 1: + train_iter = reader.multiprocess_graph_reader( + data['graph'], + graph_wrapper, + samples=samples, + num_workers=args.sample_workers, + batch_size=args.batch_size, + node_index=data['train_index'], + node_label=data["train_label"]) + else: + train_iter = reader.graph_reader( + data['graph'], + graph_wrapper, + samples=samples, + batch_size=args.batch_size, + node_index=data['train_index'], + node_label=data["train_label"]) + + if args.sample_workers > 1: + val_iter = reader.multiprocess_graph_reader( + data['graph'], + graph_wrapper, + samples=samples, + num_workers=args.sample_workers, + batch_size=args.batch_size, + node_index=data['val_index'], + node_label=data["val_label"]) + else: + val_iter = reader.graph_reader( + data['graph'], + graph_wrapper, + samples=samples, + batch_size=args.batch_size, + node_index=data['val_index'], + node_label=data["val_label"]) + + if args.sample_workers > 1: + test_iter = reader.multiprocess_graph_reader( + data['graph'], + graph_wrapper, + samples=samples, + num_workers=args.sample_workers, + batch_size=args.batch_size, + node_index=data['test_index'], + node_label=data["test_label"]) + else: + test_iter = reader.graph_reader( + data['graph'], + graph_wrapper, + samples=samples, + batch_size=args.batch_size, + node_index=data['test_index'], + node_label=data["test_label"]) + + for epoch in range(args.epoch): + run_epoch( + train_iter, + program=train_program, + exe=train_exe, + prefix="train", + model_loss=model_loss, + model_acc=model_acc, + num_trainer=args.num_trainer, + epoch=epoch) + + run_epoch( + val_iter, + program=test_program, + exe=exe, + prefix="val", + model_loss=model_loss, + model_acc=model_acc, + log_per_step=10000, + epoch=epoch) + + run_epoch( + test_iter, + program=test_program, + prefix="test", + exe=exe, + model_loss=model_loss, + model_acc=model_acc, + log_per_step=10000, + epoch=epoch) + + +if __name__ == "__main__": + parser = argparse.ArgumentParser(description='graphsage') + parser.add_argument("--use_cuda", action='store_true', help="use_cuda") + parser.add_argument( + "--normalize", action='store_true', help="normalize features") + parser.add_argument( + "--symmetry", action='store_true', help="undirect graph") + parser.add_argument("--graphsage_type", type=str, default="graphsage_mean") + parser.add_argument("--sample_workers", type=int, default=5) + parser.add_argument("--epoch", type=int, default=10) + parser.add_argument("--hidden_size", type=int, default=128) + parser.add_argument("--batch_size", type=int, default=128) + parser.add_argument("--num_trainer", type=int, default=1) + parser.add_argument("--lr", type=float, default=0.01) + parser.add_argument("--samples_1", type=int, default=25) + parser.add_argument("--samples_2", type=int, default=10) + args = parser.parse_args() + log.info(args) + main(args) diff --git a/examples/graphsage/train_scale.py b/examples/graphsage/train_scale.py new file mode 100644 index 0000000000000000000000000000000000000000..31a615ff5515d54af7589389ebf7bf5a925fa6cb --- /dev/null +++ b/examples/graphsage/train_scale.py @@ -0,0 +1,357 @@ +# Copyright (c) 2019 PaddlePaddle Authors. All Rights Reserved. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +""" +Multi-GPU settings +""" +import argparse +import time + +import numpy as np +import scipy.sparse as sp +from sklearn.preprocessing import StandardScaler + +import pgl +from pgl.utils.logger import log +from pgl.utils import paddle_helper +import paddle +import paddle.fluid as fluid +import reader +from model import graphsage_mean, graphsage_meanpool,\ + graphsage_maxpool, graphsage_lstm + + +def fixed_offset(data, num_nodes, scale): + """Test + """ + len_data = len(data) + len_per_part = int(len_data / scale) + offset = np.arange(0, scale, dtype="int64") + offset = offset * num_nodes + offset = np.repeat(offset, len_per_part) + if len(data.shape) > 1: + data += offset.reshape([-1, 1]) + else: + data += offset + + +def load_data(normalize=True, symmetry=True, scale=1): + """ + data from https://github.com/matenure/FastGCN/issues/8 + reddit_adj.npz: https://drive.google.com/open?id=174vb0Ws7Vxk_QTUtxqTgDHSQ4El4qDHt + reddit.npz: https://drive.google.com/open?id=19SphVl_Oe8SJ1r87Hr5a6znx3nJu1F2J + """ + data = np.load("data/reddit.npz") + adj = sp.load_npz("data/reddit_adj.npz") + if symmetry: + adj = adj + adj.T + adj = adj.tocoo() + src = adj.row.reshape([-1, 1]) + dst = adj.col.reshape([-1, 1]) + edges = np.hstack([src, dst]) + + num_class = 41 + + train_label = data['y_train'] + val_label = data['y_val'] + test_label = data['y_test'] + + train_index = data['train_index'] + val_index = data['val_index'] + test_index = data['test_index'] + + feature = data["feats"].astype("float32") + + if normalize: + scaler = StandardScaler() + scaler.fit(feature[train_index]) + feature = scaler.transform(feature) + + if scale > 1: + num_nodes = feature.shape[0] + feature = np.tile(feature, [scale, 1]) + train_label = np.tile(train_label, [scale]) + val_label = np.tile(val_label, [scale]) + test_label = np.tile(test_label, [scale]) + edges = np.tile(edges, [scale, 1]) + fixed_offset(edges, num_nodes, scale) + train_index = np.tile(train_index, [scale]) + fixed_offset(train_index, num_nodes, scale) + val_index = np.tile(val_index, [scale]) + fixed_offset(val_index, num_nodes, scale) + test_index = np.tile(test_index, [scale]) + fixed_offset(test_index, num_nodes, scale) + + log.info("Feature shape %s" % (repr(feature.shape))) + + graph = pgl.graph.Graph( + num_nodes=feature.shape[0], + edges=edges, + node_feat={ + "index": np.arange( + 0, len(feature), dtype="int64"), + "feature": feature + }) + + return { + "graph": graph, + "train_index": train_index, + "train_label": train_label, + "val_label": val_label, + "val_index": val_index, + "test_index": test_index, + "test_label": test_label, + "feature": feature, + "num_class": 41 + } + + +def build_graph_model(graph_wrapper, num_class, k_hop, graphsage_type, + hidden_size, feature): + """Test""" + node_index = fluid.layers.data( + "node_index", shape=[None], dtype="int64", append_batch_size=False) + + node_label = fluid.layers.data( + "node_label", shape=[None, 1], dtype="int64", append_batch_size=False) + + for i in range(k_hop): + if graphsage_type == 'graphsage_mean': + feature = graphsage_mean( + graph_wrapper, + feature, + hidden_size, + act="relu", + name="graphsage_mean_%s % i") + elif graphsage_type == 'graphsage_meanpool': + feature = graphsage_meanpool( + graph_wrapper, + feature, + hidden_size, + act="relu", + name="graphsage_meanpool_%s % i") + elif graphsage_type == 'graphsage_maxpool': + feature = graphsage_maxpool( + graph_wrapper, + feature, + hidden_size, + act="relu", + name="graphsage_maxpool_%s % i") + elif graphsage_type == 'graphsage_lstm': + feature = graphsage_lstm( + graph_wrapper, + feature, + hidden_size, + act="relu", + name="graphsage_maxpool_%s % i") + else: + raise ValueError("graphsage type %s is not" + " implemented" % graphsage_type) + + feature = fluid.layers.gather(feature, node_index) + logits = fluid.layers.fc(feature, + num_class, + act=None, + name='classification_layer') + proba = fluid.layers.softmax(logits) + + loss = fluid.layers.softmax_with_cross_entropy( + logits=logits, label=node_label) + loss = fluid.layers.mean(loss) + acc = fluid.layers.accuracy(input=proba, label=node_label, k=1) + return loss, acc + + +def run_epoch(batch_iter, + exe, + program, + prefix, + model_loss, + model_acc, + epoch, + log_per_step=100): + """Test""" + batch = 0 + total_loss = 0. + total_acc = 0. + total_sample = 0 + start = time.time() + for batch_feed_dict in batch_iter(): + batch += 1 + batch_loss, batch_acc = exe.run(program, + fetch_list=[model_loss, model_acc], + feed=batch_feed_dict) + + if batch % log_per_step == 0: + log.info("Batch %s %s-Loss %s %s-Acc %s" % + (batch, prefix, batch_loss, prefix, batch_acc)) + + num_samples = len(batch_feed_dict["node_index"]) + total_loss += batch_loss * num_samples + total_acc += batch_acc * num_samples + total_sample += num_samples + end = time.time() + + log.info("%s Epoch %s Loss %.5lf Acc %.5lf Speed(per batch) %.5lf sec" % + (prefix, epoch, total_loss / total_sample, + total_acc / total_sample, (end - start) / batch)) + + +def main(args): + """Test """ + data = load_data(args.normalize, args.symmetry, args.scale) + log.info("preprocess finish") + log.info("Train Examples: %s" % len(data["train_index"])) + log.info("Val Examples: %s" % len(data["val_index"])) + log.info("Test Examples: %s" % len(data["test_index"])) + log.info("Num nodes %s" % data["graph"].num_nodes) + log.info("Num edges %s" % data["graph"].num_edges) + log.info("Average Degree %s" % np.mean(data["graph"].indegree())) + + place = fluid.CUDAPlace(0) if args.use_cuda else fluid.CPUPlace() + train_program = fluid.Program() + startup_program = fluid.Program() + + samples = [] + if args.samples_1 > 0: + samples.append(args.samples_1) + if args.samples_2 > 0: + samples.append(args.samples_2) + + with fluid.program_guard(train_program, startup_program): + graph_wrapper = pgl.graph_wrapper.GraphWrapper( + "sub_graph", + fluid.CPUPlace(), + node_feat=data['graph'].node_feat_info()) + + model_loss, model_acc = build_graph_model( + graph_wrapper, + num_class=data["num_class"], + feature=graph_wrapper.node_feat["feature"], + hidden_size=args.hidden_size, + graphsage_type=args.graphsage_type, + k_hop=len(samples)) + + test_program = train_program.clone(for_test=True) + + if args.sample_workers > 1: + train_iter = reader.multiprocess_graph_reader( + data['graph'], + graph_wrapper, + samples=samples, + num_workers=args.sample_workers, + batch_size=args.batch_size, + node_index=data['train_index'], + node_label=data["train_label"]) + else: + train_iter = reader.graph_reader( + data['graph'], + graph_wrapper, + samples=samples, + batch_size=args.batch_size, + node_index=data['train_index'], + node_label=data["train_label"]) + + if args.sample_workers > 1: + val_iter = reader.multiprocess_graph_reader( + data['graph'], + graph_wrapper, + samples=samples, + num_workers=args.sample_workers, + batch_size=args.batch_size, + node_index=data['val_index'], + node_label=data["val_label"]) + else: + val_iter = reader.graph_reader( + data['graph'], + graph_wrapper, + samples=samples, + batch_size=args.batch_size, + node_index=data['val_index'], + node_label=data["val_label"]) + + if args.sample_workers > 1: + test_iter = reader.multiprocess_graph_reader( + data['graph'], + graph_wrapper, + samples=samples, + num_workers=args.sample_workers, + batch_size=args.batch_size, + node_index=data['test_index'], + node_label=data["test_label"]) + else: + test_iter = reader.graph_reader( + data['graph'], + graph_wrapper, + samples=samples, + batch_size=args.batch_size, + node_index=data['test_index'], + node_label=data["test_label"]) + + with fluid.program_guard(train_program, startup_program): + adam = fluid.optimizer.Adam(learning_rate=args.lr) + adam.minimize(model_loss) + + exe = fluid.Executor(place) + exe.run(startup_program) + + for epoch in range(args.epoch): + run_epoch( + train_iter, + program=train_program, + exe=exe, + prefix="train", + model_loss=model_loss, + model_acc=model_acc, + epoch=epoch) + + run_epoch( + val_iter, + program=test_program, + exe=exe, + prefix="val", + model_loss=model_loss, + model_acc=model_acc, + log_per_step=10000, + epoch=epoch) + + run_epoch( + test_iter, + program=test_program, + prefix="test", + exe=exe, + model_loss=model_loss, + model_acc=model_acc, + log_per_step=10000, + epoch=epoch) + + +if __name__ == "__main__": + parser = argparse.ArgumentParser(description='graphsage') + parser.add_argument("--use_cuda", action='store_true', help="use_cuda") + parser.add_argument( + "--normalize", action='store_true', help="normalize features") + parser.add_argument( + "--symmetry", action='store_true', help="undirect graph") + parser.add_argument("--graphsage_type", type=str, default="graphsage_mean") + parser.add_argument("--sample_workers", type=int, default=5) + parser.add_argument("--epoch", type=int, default=10) + parser.add_argument("--hidden_size", type=int, default=128) + parser.add_argument("--batch_size", type=int, default=128) + parser.add_argument("--lr", type=float, default=0.01) + parser.add_argument("--samples_1", type=int, default=25) + parser.add_argument("--samples_2", type=int, default=10) + parser.add_argument("--scale", type=int, default=1) + args = parser.parse_args() + log.info(args) + main(args) diff --git a/examples/line/README.md b/examples/line/README.md new file mode 100644 index 0000000000000000000000000000000000000000..abbe0d4e28e6ae47e72e6aeec6a7b70f04ae988d --- /dev/null +++ b/examples/line/README.md @@ -0,0 +1,55 @@ +# PGL Examples for LINE +[LINE](http://www.www2015.it/documents/proceedings/proceedings/p1067.pdf) is an algorithmic framework for embedding very large-scale information networks. It is suitable to a variety of networks including directed, undirected, binary or weighted edges. Based on PGL, we reproduce LINE algorithms and reach the same level of indicators as the paper. + +## Datasets +[Flickr network](http://socialnetworks.mpi-sws.org/data-imc2007.html) is a social network, which contains 1715256 nodes and 22613981 edges. + +You can dowload data from [here](http://socialnetworks.mpi-sws.org/data-imc2007.html). + +Flickr network contains four files: +* flickr-groupmemberships.txt.gz +* flickr-groups.txt.gz +* flickr-links.txt.gz +* flickr-users.txt.gz + +After downloading the data，uncompress them, let's say, in **./data/flickr/** . Note that the current directory is the root directory of LINE model. + +Then you can run the below command to preprocess the data. +```sh +python data_process.py +``` + +Then it will produce three files in **./data/flickr/** directory: +* nodes.txt +* edges.txt +* nodes_label.txt + + +## Dependencies +- paddlepaddle>=1.6 +- pgl + +## How to run + +For examples, use gpu to train LINE on Flickr dataset. +```sh +# multiclass task example +python line.py --use_cuda --order first_order --data_path ./data/flickr/ --save_dir ./checkpoints/model/ + +python multi_class.py --ckpt_path ./checkpoints/model/model_eopch_20 --percent 0.5 + +``` + +## Hyperparameters + +- -use_cuda: Use gpu if assign use_cuda. +- -order: LINE with First_order Proximity or Second_order Proximity +- -percent: The percentage of data as training data + +### Experiment results +Dataset|model|Task|Metric|PGL Result|Reported Result +--|--|--|--|--|-- +Flickr|LINE with first_order|multi-label classification|MacroF1|0.626|0.627 +Flickr|LINE with first_order|multi-label classification|MicroF1|0.637|0.639 +Flickr|LINE with second_order|multi-label classification|MacroF1|0.615|0.621 +Flickr|LINE with second_order|multi-label classification|MicroF1|0.630|0.635 diff --git a/examples/line/data_loader.py b/examples/line/data_loader.py new file mode 100644 index 0000000000000000000000000000000000000000..58a118aa6a5d0839480fc84538b9b760a4fccc82 --- /dev/null +++ b/examples/line/data_loader.py @@ -0,0 +1,233 @@ +# Copyright (c) 2019 PaddlePaddle Authors. All Rights Reserved +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +""" +This file provides the Dataset for LINE model. +""" +import os +import io +import sys +import numpy as np + +from pgl import graph +from pgl.utils.logger import log + + +class FlickrDataset(object): + """Flickr dataset implementation + + Args: + name: The name of the dataset. + + symmetry_edges: Whether to create symmetry edges. + + self_loop: Whether to contain self loop edges. + + train_percentage: The percentage of nodes to be trained in multi class task. + + Attributes: + graph: The :code:`Graph` data object. + + num_groups: Number of classes. + + train_index: The index for nodes in training set. + + test_index: The index for nodes in validation set. + """ + + def __init__(self, + data_path, + symmetry_edges=False, + self_loop=False, + train_percentage=0.5): + self.path = data_path + # self.name = name + self.num_groups = 5 + self.symmetry_edges = symmetry_edges + self.self_loop = self_loop + self.train_percentage = train_percentage + self._load_data() + + def _load_data(self): + edge_path = os.path.join(self.path, 'edges.txt') + node_path = os.path.join(self.path, 'nodes.txt') + nodes_label_path = os.path.join(self.path, 'nodes_label.txt') + + all_edges = [] + edges_weight = [] + + with io.open(node_path) as inf: + num_nodes = len(inf.readlines()) + + node_feature = np.zeros((num_nodes, self.num_groups)) + + with io.open(nodes_label_path) as inf: + for line in inf: + # group_id means the label of the node + node_id, group_id = line.strip('\n').split(',') + node_id = int(node_id) - 1 + labels = group_id.split(' ') + for i in labels: + node_feature[node_id][int(i) - 1] = 1 + + node_degree_list = [1 for _ in range(num_nodes)] + + with io.open(edge_path) as inf: + for line in inf: + items = line.strip().split('\t') + if len(items) == 2: + u, v = int(items[0]), int(items[1]) + weight = 1 # binary weight, default set to 1 + else: + u, v, weight = int(items[0]), int(items[1]), float(items[ + 2]), + u, v = u - 1, v - 1 + all_edges.append((u, v)) + edges_weight.append(weight) + + if self.symmetry_edges: + all_edges.append((v, u)) + edges_weight.append(weight) + + # sum the weights of the same node as the outdegree + node_degree_list[u] += weight + + if self.self_loop: + for i in range(num_nodes): + all_edges.append((i, i)) + edges_weight.append(1.) + + all_edges = list(set(all_edges)) + self.graph = graph.Graph( + num_nodes=num_nodes, + edges=all_edges, + node_feat={"group_id": node_feature}) + + perm = np.arange(0, num_nodes) + np.random.shuffle(perm) + train_num = int(num_nodes * self.train_percentage) + self.train_index = perm[:train_num] + self.test_index = perm[train_num:] + + edge_distribution = np.array(edges_weight, dtype=np.float32) + self.edge_distribution = edge_distribution / np.sum(edge_distribution) + self.edge_sampling = AliasSampling(prob=edge_distribution) + + node_dist = np.array(node_degree_list, dtype=np.float32) + node_negative_distribution = np.power(node_dist, 0.75) + self.node_negative_distribution = node_negative_distribution / np.sum( + node_negative_distribution) + self.node_sampling = AliasSampling(prob=node_negative_distribution) + + self.node_index = {} + self.node_index_reversed = {} + for index, e in enumerate(self.graph.edges): + self.node_index[e[0]] = index + self.node_index_reversed[index] = e[0] + + def fetch_batch(self, + batch_size=16, + K=10, + edge_sampling='alias', + node_sampling='alias'): + """Fetch batch data from dataset. + """ + if edge_sampling == 'numpy': + edge_batch_index = np.random.choice( + self.graph.num_edges, + size=batch_size, + p=self.edge_distribution) + elif edge_sampling == 'alias': + edge_batch_index = self.edge_sampling.sampling(batch_size) + elif edge_sampling == 'uniform': + edge_batch_index = np.random.randint( + 0, self.graph.num_edges, size=batch_size) + u_i = [] + u_j = [] + label = [] + for edge_index in edge_batch_index: + edge = self.graph.edges[edge_index] + u_i.append(edge[0]) + u_j.append(edge[1]) + label.append(1) + for i in range(K): + while True: + if node_sampling == 'numpy': + negative_node = np.random.choice( + self.graph.num_nodes, + p=self.node_negative_distribution) + elif node_sampling == 'alias': + negative_node = self.node_sampling.sampling() + elif node_sampling == 'uniform': + negative_node = np.random.randint(0, + self.graph.num_nodes) + + # make sure the sampled node has no edge with the source node + if not self.graph.has_edges_between( + np.array( + [self.node_index_reversed[negative_node]]), + np.array([self.node_index_reversed[edge[0]]])): + break + u_i.append(edge[0]) + u_j.append(negative_node) + label.append(-1) + u_i = np.array([u_i], dtype=np.int64).T + u_j = np.array([u_j], dtype=np.int64).T + label = np.array(label, dtype=np.float32) + return u_i, u_j, label + + +class AliasSampling: + """Implemention of Alias-Method + + This is an implementation of Alias-Method for sampling efficiently from + a discrete probability distribution. + + Reference: https://en.wikipedia.org/wiki/Alias_method + + Args: + prob: The discrete probability distribution. + + """ + + def __init__(self, prob): + self.n = len(prob) + self.U = np.array(prob) * self.n + self.K = [i for i in range(len(prob))] + overfull, underfull = [], [] + for i, U_i in enumerate(self.U): + if U_i > 1: + overfull.append(i) + elif U_i < 1: + underfull.append(i) + while len(overfull) and len(underfull): + i, j = overfull.pop(), underfull.pop() + self.K[j] = i + self.U[i] = self.U[i] - (1 - self.U[j]) + if self.U[i] > 1: + overfull.append(i) + elif self.U[i] < 1: + underfull.append(i) + + def sampling(self, n=1): + """Sampling. + """ + x = np.random.rand(n) + i = np.floor(self.n * x) + y = self.n * x - i + i = i.astype(np.int64) + res = [i[k] if y[k] < self.U[i[k]] else self.K[i[k]] for k in range(n)] + if n == 1: + return res[0] + else: + return res diff --git a/examples/line/data_process.py b/examples/line/data_process.py new file mode 100644 index 0000000000000000000000000000000000000000..d81a5c7e2678e75c8562f840ac857321794fe003 --- /dev/null +++ b/examples/line/data_process.py @@ -0,0 +1,137 @@ +# Copyright (c) 2019 PaddlePaddle Authors. All Rights Reserved +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +""" +This file preprocess the FlickrDataset for LINE model. +""" +import argparse +import operator +import os + + +def process_data(groupsMemberships_file, flickr_links_file, users_label_file, + edges_file, users_file): + """Preprocess flickr network dataset. + + Args: + groupsMemberships_file: flickr-groupmemberships.txt file, + each line is a pair (user, group), which indicates a user belongs to a group. + + flickr_links_file: flickr-links.txt file, + each line is a pair (user, user), which indicates + the two users have a relationship. + + users_label_file: each line is a pair (user, list of group), + each user may belong to multiple groups. + + edges_file: each line is a pair (user, user), which indicates + the two users have a relationship. It filters some unused edges. + + users_file: each line is a int number, which indicates the ID of a user. + """ + group2users = {} + with open(groupsMemberships_file, 'r') as f: + for line in f: + user, group = line.strip().split() + try: + group2users[int(group)].append(user) + except: + group2users[int(group)] = [user] + + # counting how many users belong to every group + group2usersNum = {} + for key, item in group2users.items(): + group2usersNum[key] = len(item) + + groups_sorted_by_usersNum = sorted( + group2usersNum.items(), key=operator.itemgetter(1), reverse=True) + + # the paper only need the 5 groups with the largest number of users + label = 1 # remapping the 5 groups from 1 to 5 + users_label = {} + for i in range(5): + users_list = group2users[groups_sorted_by_usersNum[i][0]] + for user in users_list: + # one user may have multi-labels + try: + users_label[user].append(label) + except: + users_label[user] = [label] + label += 1 + + # remapping the users IDs to make the IDs from 0 to N + userID2nodeID = {} + count = 1 + for key in sorted(users_label.keys()): + userID2nodeID[key] = count + count += 1 + + with open(users_label_file, 'w') as writer: + for key in sorted(users_label.keys()): + line = ' '.join([str(i) for i in users_label[key]]) + writer.write(str(userID2nodeID[key]) + ',' + line + '\n') + + # produce edges file + with open(flickr_links_file, 'r') as reader, open(edges_file, + 'w') as writer: + for line in reader: + src, dst = line.strip().split('\t') + # filter unused user IDs + if src in users_label and dst in users_label: + # remapping the users IDs + src = userID2nodeID[src] + dst = userID2nodeID[dst] + + writer.write(str(src) + '\t' + str(dst) + '\n') + + # produce nodes file + with open(users_file, 'w') as writer: + for i in range(1, 1 + len(userID2nodeID)): + writer.write(str(i) + '\n') + + +if __name__ == "__main__": + parser = argparse.ArgumentParser(description='LINE') + parser.add_argument( + '--groupmemberships', + type=str, + default='./data/flickr/flickr-groupmemberships.txt', + help='groupmemberships of flickr dataset') + + parser.add_argument( + '--flickr_links', + type=str, + default='./data/flickr/flickr-links.txt', + help='the flickr-links.txt file for training') + + parser.add_argument( + '--nodes_label', + type=str, + default='./data/flickr/nodes_label.txt', + help='nodes (users) label file for training') + + parser.add_argument( + '--edges', + type=str, + default='./data/flickr/edges.txt', + help='the result edges (links) file for training') + + parser.add_argument( + '--nodes', + type=str, + default='./data/flickr/nodes.txt', + help='the nodes (users) file for training') + + args = parser.parse_args() + process_data(args.groupmemberships, args.flickr_links, args.nodes_label, + args.edges, args.nodes) diff --git a/examples/line/line.py b/examples/line/line.py new file mode 100644 index 0000000000000000000000000000000000000000..a6e17f6d20122f806cdc27e88abdfb1585fc99a2 --- /dev/null +++ b/examples/line/line.py @@ -0,0 +1,197 @@ +# Copyright (c) 2019 PaddlePaddle Authors. All Rights Reserved +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +""" +This file implement the training process of LINE model. +""" + +import time +import argparse +import random +import os +import numpy as np + +import pgl +import paddle.fluid as fluid +import paddle.fluid.layers as fl +from pgl.utils.logger import log + +from data_loader import FlickrDataset + + +def make_dir(path): + """Create directory if path is not existed. + + Args: + path: The directory that wants to create. + """ + try: + os.makedirs(path) + except: + if not os.path.isdir(path): + raise + + +def set_seed(seed): + """Set global random seed. + """ + random.seed(seed) + np.random.seed(seed) + + +def build_model(args, graph): + """Build LINE model. + + Args: + args: The hyperparameters for configure. + + graph: The :code:`Graph` data object. + + """ + u_i = fl.data( + name='u_i', shape=[None, 1], dtype='int64', append_batch_size=False) + u_j = fl.data( + name='u_j', shape=[None, 1], dtype='int64', append_batch_size=False) + + label = fl.data( + name='label', shape=[None], dtype='float32', append_batch_size=False) + + lr = fl.data( + name='learning_rate', + shape=[1], + dtype='float32', + append_batch_size=False) + + u_i_embed = fl.embedding( + input=u_i, + size=[graph.num_nodes, args.embed_dim], + param_attr='shared_w') + + if args.order == 'first_order': + u_j_embed = fl.embedding( + input=u_j, + size=[graph.num_nodes, args.embed_dim], + param_attr='shared_w') + elif args.order == 'second_order': + u_j_embed = fl.embedding( + input=u_j, + size=[graph.num_nodes, args.embed_dim], + param_attr='context_w') + else: + raise ValueError("order should be first_order or second_order, not %s" + % (args.order)) + + inner_product = fl.reduce_sum(u_i_embed * u_j_embed, dim=1) + + loss = -1 * fl.reduce_mean(fl.logsigmoid(label * inner_product)) + optimizer = fluid.optimizer.RMSPropOptimizer(learning_rate=lr) + train_op = optimizer.minimize(loss) + + return loss, optimizer + + +def main(args): + """The main funciton for training LINE model. + """ + make_dir(args.save_dir) + set_seed(args.seed) + + dataset = FlickrDataset(args.data_path) + + log.info('num nodes in graph: %d' % dataset.graph.num_nodes) + log.info('num edges in graph: %d' % dataset.graph.num_edges) + + place = fluid.CUDAPlace(0) if args.use_cuda else fluid.CPUPlace() + + main_program = fluid.default_main_program() + startup_program = fluid.default_startup_program() + + # build model here + with fluid.program_guard(main_program, startup_program): + loss, opt = build_model(args, dataset.graph) + + exe = fluid.Executor(place) + exe.run(startup_program) #initialize the parameters of the network + + batchrange = int(dataset.graph.num_edges / args.batch_size) + T = batchrange * args.epochs + for epoch in range(args.epochs): + for b in range(batchrange): + lr = max(args.lr * (1 - (batchrange * epoch + b) / T), 0.0001) + + u_i, u_j, label = dataset.fetch_batch( + batch_size=args.batch_size, + K=args.neg_sample_size, + edge_sampling=args.sample_method, + node_sampling=args.sample_method) + + feed_dict = { + 'u_i': u_i, + 'u_j': u_j, + 'label': label, + 'learning_rate': lr + } + + ret_loss = exe.run(main_program, + feed=feed_dict, + fetch_list=[loss], + return_numpy=True) + + if b % 500 == 0: + log.info("Epoch %d | Step %d | Loss %f | lr: %f" % + (epoch, b, ret_loss[0], lr)) + + # save parameters in every epoch + log.info("saving persistables parameters...") + fluid.io.save_persistables(exe, + os.path.join(args.save_dir, "model_epoch_%d" + % (epoch + 1)), main_program) + + +if __name__ == '__main__': + parser = argparse.ArgumentParser(description='LINE') + parser.add_argument( + '--data_path', + type=str, + default='./data/flickr/', + help='dataset for training') + parser.add_argument("--use_cuda", action='store_true', help="use_cuda") + parser.add_argument("--epochs", type=int, default=20, help='total epochs') + parser.add_argument("--seed", type=int, default=1667, help='random seed') + parser.add_argument("--lr", type=float, default=0.01, help='learning rate') + parser.add_argument( + "--neg_sample_size", + type=int, + default=5, + help='negative samplle number') + parser.add_argument("--save_dir", type=str, default="./checkpoints/model") + parser.add_argument("--batch_size", type=int, default=32) + parser.add_argument( + "--embed_dim", + type=int, + default=128, + help='the dimension of node embedding') + parser.add_argument( + "--sample_method", + type=str, + default="alias", + help='negative sample method (uniform, numpy, alias)') + parser.add_argument( + "--order", + type=str, + default="first_order", + help='the order of neighbors (first_order, second_order)') + + args = parser.parse_args() + + main(args) diff --git a/examples/line/multi_class.py b/examples/line/multi_class.py new file mode 100644 index 0000000000000000000000000000000000000000..3f191f23504359995c3a9f279c9948ff5402b15c --- /dev/null +++ b/examples/line/multi_class.py @@ -0,0 +1,286 @@ +# Copyright (c) 2019 PaddlePaddle Authors. All Rights Reserved +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +""" +This file provides the multi class task for testing the embedding +learned by LINE model. +""" +import argparse +import time +import math +import os +import random + +import numpy as np +import sklearn.metrics +from sklearn.metrics import f1_score + +import pgl +from pgl.utils import op +import paddle.fluid as fluid +import paddle.fluid.layers as l +from pgl.utils.logger import log +from data_loader import FlickrDataset + + +def set_seed(seed): + """Set global random seed. + """ + random.seed(seed) + np.random.seed(seed) + + +def node_classify_model(graph, + num_labels, + embed_dim=16, + name='node_classify_task'): + """Build node classify model. + + Args: + graph: The :code:`Graph` data object. + + num_labels: The number of labels. + + embed_dim: The dimension of embedding. + + name: The name of the model. + """ + pyreader = l.py_reader( + capacity=70, + shapes=[[-1, 1], [-1, num_labels]], + dtypes=['int64', 'float32'], + lod_levels=[0, 0], + name=name + '_pyreader', + use_double_buffer=True) + nodes, labels = l.read_file(pyreader) + embed_nodes = l.embedding( + input=nodes, size=[graph.num_nodes, embed_dim], param_attr='shared_w') + embed_nodes.stop_gradient = True + logits = l.fc(input=embed_nodes, size=num_labels) + loss = l.sigmoid_cross_entropy_with_logits(logits, labels) + loss = l.reduce_mean(loss) + prob = l.sigmoid(logits) + topk = l.reduce_sum(labels, -1) + return { + 'pyreader': pyreader, + 'loss': loss, + 'prob': prob, + 'labels': labels, + 'topk': topk + } + # return pyreader, loss, prob, labels, topk + + +def node_classify_generator(graph, + all_nodes=None, + batch_size=512, + epoch=1, + shuffle=True): + """Data generator for node classify. + + Args: + graph: The :code:`Graph` data object. + + all_nodes: the total number of nodes. + + batch_size: batch size for training. + + epoch: The number of epochs. + + shuffle: Random shuffle of data. + """ + + if all_nodes is None: + all_nodes = np.arange(graph.num_nodes) + + def batch_nodes_generator(shuffle=shuffle): + """Batch nodes generator. + """ + perm = np.arange(len(all_nodes), dtype=np.int64) + if shuffle: + np.random.shuffle(perm) + start = 0 + while start < len(all_nodes): + yield all_nodes[perm[start:start + batch_size]] + start += batch_size + + def wrapper(): + """Wrapper function. + """ + for _ in range(epoch): + for batch_nodes in batch_nodes_generator(): + batch_nodes_expanded = np.expand_dims(batch_nodes, + -1).astype(np.int64) + batch_labels = graph.node_feat['group_id'][batch_nodes].astype( + np.float32) + yield [batch_nodes_expanded, batch_labels] + + return wrapper + + +def topk_f1_score(labels, + probs, + topk_list=None, + average="macro", + threshold=None): + """Calculate top K F1 score. + """ + assert topk_list is not None or threshold is not None, "one of topklist and threshold should not be None" + if threshold is not None: + preds = probs > threshold + else: + preds = np.zeros_like(labels, dtype=np.int64) + for idx, (prob, topk) in enumerate(zip(np.argsort(probs), topk_list)): + preds[idx][prob[-int(topk):]] = 1 + return f1_score(labels, preds, average=average) + + +def main(args): + """The main funciton for nodes classify task. + """ + set_seed(args.seed) + log.info(args) + dataset = FlickrDataset(args.data_path, train_percentage=args.percent) + + train_steps = (len(dataset.train_index) // args.batch_size) * args.epochs + place = fluid.CUDAPlace(0) if args.use_cuda else fluid.CPUPlace() + train_prog = fluid.Program() + test_prog = fluid.Program() + startup_prog = fluid.Program() + + with fluid.program_guard(train_prog, startup_prog): + with fluid.unique_name.guard(): + train_model = node_classify_model( + dataset.graph, + dataset.num_groups, + embed_dim=args.embed_dim, + name='train') + + lr = l.polynomial_decay(args.lr, train_steps, 0.0001) + adam = fluid.optimizer.Adam(lr) + adam.minimize(train_model['loss']) + with fluid.program_guard(test_prog, startup_prog): + with fluid.unique_name.guard(): + test_model = node_classify_model( + dataset.graph, + dataset.num_groups, + embed_dim=args.embed_dim, + name='test') + test_prog = test_prog.clone(for_test=True) + exe = fluid.Executor(place) + exe.run(startup_prog) + + train_model['pyreader'].decorate_tensor_provider( + node_classify_generator( + dataset.graph, + dataset.train_index, + batch_size=args.batch_size, + epoch=args.epochs)) + test_model['pyreader'].decorate_tensor_provider( + node_classify_generator( + dataset.graph, + dataset.test_index, + batch_size=args.batch_size, + epoch=1)) + + def existed_params(var): + """existed_params + """ + if not isinstance(var, fluid.framework.Parameter): + return False + return os.path.exists(os.path.join(args.ckpt_path, var.name)) + + fluid.io.load_vars( + exe, args.ckpt_path, main_program=train_prog, predicate=existed_params) + step = 0 + prev_time = time.time() + train_model['pyreader'].start() + + while 1: + try: + train_loss_val, train_probs_val, train_labels_val, train_topk_val = exe.run( + train_prog, + fetch_list=[ + train_model['loss'], train_model['prob'], + train_model['labels'], train_model['topk'] + ], + return_numpy=True) + train_macro_f1 = topk_f1_score(train_labels_val, train_probs_val, + train_topk_val, "macro", + args.threshold) + train_micro_f1 = topk_f1_score(train_labels_val, train_probs_val, + train_topk_val, "micro", + args.threshold) + step += 1 + log.info("Step %d " % step + "Train Loss: %f " % train_loss_val + + "Train Macro F1: %f " % train_macro_f1 + + "Train Micro F1: %f " % train_micro_f1) + except fluid.core.EOFException: + train_model['pyreader'].reset() + break + + test_model['pyreader'].start() + test_probs_vals, test_labels_vals, test_topk_vals = [], [], [] + while 1: + try: + test_loss_val, test_probs_val, test_labels_val, test_topk_val = exe.run( + test_prog, + fetch_list=[ + test_model['loss'], test_model['prob'], + test_model['labels'], test_model['topk'] + ], + return_numpy=True) + test_probs_vals.append( + test_probs_val), test_labels_vals.append(test_labels_val) + test_topk_vals.append(test_topk_val) + except fluid.core.EOFException: + test_model['pyreader'].reset() + test_probs_array = np.concatenate(test_probs_vals) + test_labels_array = np.concatenate(test_labels_vals) + test_topk_array = np.concatenate(test_topk_vals) + test_macro_f1 = topk_f1_score( + test_labels_array, test_probs_array, test_topk_array, + "macro", args.threshold) + test_micro_f1 = topk_f1_score( + test_labels_array, test_probs_array, test_topk_array, + "micro", args.threshold) + log.info("\t\tStep %d " % step + "Test Loss: %f " % + test_loss_val + "Test Macro F1: %f " % test_macro_f1 + + "Test Micro F1: %f " % test_micro_f1) + break + + +if __name__ == '__main__': + parser = argparse.ArgumentParser(description='LINE') + parser.add_argument( + '--data_path', + type=str, + default='./data/flickr/', + help='dataset for training') + parser.add_argument("--use_cuda", action='store_true', help="use_cuda") + parser.add_argument("--epochs", type=int, default=10) + parser.add_argument("--seed", type=int, default=1667) + parser.add_argument( + "--lr", type=float, default=0.025, help='learning rate') + parser.add_argument("--embed_dim", type=int, default=128) + parser.add_argument("--batch_size", type=int, default=256) + parser.add_argument("--threshold", type=float, default=None) + parser.add_argument( + "--percent", + type=float, + default=0.5, + help="the percentage of data as training data") + parser.add_argument( + "--ckpt_path", type=str, default="./checkpoints/model/model_epoch_0/") + args = parser.parse_args() + main(args) diff --git a/examples/sgc/README.md b/examples/sgc/README.md new file mode 100644 index 0000000000000000000000000000000000000000..92fc546d51a9b07a45ff3d44fc000fa44a36b6b0 --- /dev/null +++ b/examples/sgc/README.md @@ -0,0 +1,35 @@ +# PGL Examples for SGC + +[Simplifying Graph Convolutional Networks \(SGC\)](https://arxiv.org/pdf/1902.07153.pdf) is a powerful neural network designed for machine learning on graphs. Based on PGL, we reproduce SGC algorithms and reach the same level of indicators as the paper in citation network benchmarks. + +### Datasets + +The datasets contain three citation networks: CORA, PUBMED, CITESEER. The details for these three datasets can be found in the [paper](https://arxiv.org/abs/1609.02907). + +### Dependencies + +- paddlepaddle 1.5 +- pgl + +### Performance + +We train our models for 200 epochs and report the accuracy on the test dataset. + +| Dataset | Accuracy | Speed with paddle 1.5
(epoch time)| +| --- | --- | ---| +| Cora | 0.818 (paper: 0.810) | 0.0015s | +| Pubmed | 0.788 (paper: 0.789) | 0.0015s | +| Citeseer | 0.719 (paper: 0.719) | 0.0015s | + + +### How to run + +For examples, use gpu to train SGC on cora dataset. +``` +python sgc.py --dataset cora --use_cuda +``` + +#### Hyperparameters + +- dataset: The citation dataset "cora", "citeseer", "pubmed". +- use_cuda: Use gpu if assign use_cuda. diff --git a/examples/sgc/sgc.py b/examples/sgc/sgc.py new file mode 100644 index 0000000000000000000000000000000000000000..85ec6855f7696fb65898361a24bbd6c61871d0ba --- /dev/null +++ b/examples/sgc/sgc.py @@ -0,0 +1,271 @@ +# Copyright (c) 2019 PaddlePaddle Authors. All Rights Reserved +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +""" +This file implement the training process of SGC model with StaticGraphWrapper. +""" + +import os +import argparse +import numpy as np +import random +import time + +import pgl +from pgl import data_loader +from pgl.utils.logger import log +from pgl.utils import paddle_helper +import paddle.fluid as fluid + + +def load(name): + """Load dataset.""" + if name == 'cora': + dataset = data_loader.CoraDataset() + elif name == "pubmed": + dataset = data_loader.CitationDataset("pubmed", symmetry_edges=False) + elif name == "citeseer": + dataset = data_loader.CitationDataset("citeseer", symmetry_edges=False) + else: + raise ValueError(name + " dataset doesn't exists") + return dataset + + +def expand_data_dim(dataset): + """Expand the dimension of data.""" + train_index = dataset.train_index + train_label = np.expand_dims(dataset.y[train_index], -1) + train_index = np.expand_dims(train_index, -1) + + val_index = dataset.val_index + val_label = np.expand_dims(dataset.y[val_index], -1) + val_index = np.expand_dims(val_index, -1) + + test_index = dataset.test_index + test_label = np.expand_dims(dataset.y[test_index], -1) + test_index = np.expand_dims(test_index, -1) + + return { + 'train_index': train_index, + 'train_label': train_label, + 'val_index': val_index, + 'val_label': val_label, + 'test_index': test_index, + 'test_label': test_label, + } + + +def MessagePassing(gw, feature, num_layers, norm=None): + """Precomputing message passing. + """ + + def send_src_copy(src_feat, dst_feat, edge_feat): + """send_src_copy + """ + return src_feat["h"] + + for _ in range(num_layers): + if norm is not None: + feature = feature * norm + + msg = gw.send(send_src_copy, nfeat_list=[("h", feature)]) + + feature = gw.recv(msg, "sum") + + if norm is not None: + feature = feature * norm + + return feature + + +def pre_gather(features, name_prefix, node_index_val): + """Get features with respect to node index. + """ + node_index, init = paddle_helper.constant( + "%s_node_index" % (name_prefix), dtype='int32', value=node_index_val) + logits = fluid.layers.gather(features, node_index) + + return logits, init + + +def calculate_loss(name, np_cached_h, node_label_val, num_classes, args): + """Calculate loss function. + """ + initializer = [] + const_cached_h, init = paddle_helper.constant( + "const_%s_cached_h" % name, dtype='float32', value=np_cached_h) + initializer.append(init) + + node_label, init = paddle_helper.constant( + "%s_node_label" % (name), dtype='int64', value=node_label_val) + initializer.append(init) + + output = fluid.layers.fc(const_cached_h, + size=num_classes, + bias_attr=args.bias, + name='fc') + + loss, probs = fluid.layers.softmax_with_cross_entropy( + logits=output, label=node_label, return_softmax=True) + loss = fluid.layers.mean(loss) + + acc = None + if name != 'train': + acc = fluid.layers.accuracy(input=probs, label=node_label, k=1) + + return { + 'loss': loss, + 'acc': acc, + 'probs': probs, + 'initializer': initializer + } + + +def main(args): + """"Main function.""" + dataset = load(args.dataset) + + # normalize + indegree = dataset.graph.indegree() + norm = np.zeros_like(indegree, dtype="float32") + norm[indegree > 0] = np.power(indegree[indegree > 0], -0.5) + dataset.graph.node_feat["norm"] = np.expand_dims(norm, -1) + + data = expand_data_dim(dataset) + + place = fluid.CUDAPlace(0) if args.use_cuda else fluid.CPUPlace() + precompute_program = fluid.Program() + startup_program = fluid.Program() + train_program = fluid.Program() + val_program = train_program.clone(for_test=True) + test_program = train_program.clone(for_test=True) + + # precompute message passing and gather + initializer = [] + with fluid.program_guard(precompute_program, startup_program): + gw = pgl.graph_wrapper.StaticGraphWrapper( + name="graph", place=place, graph=dataset.graph) + + cached_h = MessagePassing( + gw, + gw.node_feat["words"], + num_layers=args.num_layers, + norm=gw.node_feat['norm']) + + train_cached_h, init = pre_gather(cached_h, 'train', + data['train_index']) + initializer.append(init) + val_cached_h, init = pre_gather(cached_h, 'val', data['val_index']) + initializer.append(init) + test_cached_h, init = pre_gather(cached_h, 'test', data['test_index']) + initializer.append(init) + + exe = fluid.Executor(place) + gw.initialize(place) + for init in initializer: + init(place) + + # get train features, val features and test features + np_train_cached_h, np_val_cached_h, np_test_cached_h = exe.run( + precompute_program, + feed={}, + fetch_list=[train_cached_h, val_cached_h, test_cached_h], + return_numpy=True) + + initializer = [] + with fluid.program_guard(train_program, startup_program): + with fluid.unique_name.guard(): + train_handle = calculate_loss('train', np_train_cached_h, + data['train_label'], + dataset.num_classes, args) + initializer += train_handle['initializer'] + adam = fluid.optimizer.Adam( + learning_rate=args.lr, + regularization=fluid.regularizer.L2DecayRegularizer( + regularization_coeff=args.weight_decay)) + adam.minimize(train_handle['loss']) + + with fluid.program_guard(val_program, startup_program): + with fluid.unique_name.guard(): + val_handle = calculate_loss('val', np_val_cached_h, + data['val_label'], dataset.num_classes, + args) + initializer += val_handle['initializer'] + + with fluid.program_guard(test_program, startup_program): + with fluid.unique_name.guard(): + test_handle = calculate_loss('test', np_test_cached_h, + data['test_label'], + dataset.num_classes, args) + initializer += test_handle['initializer'] + + exe.run(startup_program) + for init in initializer: + init(place) + + dur = [] + for epoch in range(args.epochs): + if epoch >= 3: + t0 = time.time() + train_loss_t = exe.run(train_program, + feed={}, + fetch_list=[train_handle['loss']], + return_numpy=True)[0] + + if epoch >= 3: + time_per_epoch = 1.0 * (time.time() - t0) + dur.append(time_per_epoch) + + val_loss_t, val_acc_t = exe.run( + val_program, + feed={}, + fetch_list=[val_handle['loss'], val_handle['acc']], + return_numpy=True) + + log.info("Epoch %d " % epoch + "(%.5lf sec) " % np.mean( + dur) + "Train Loss: %f " % train_loss_t + "Val Loss: %f " % + val_loss_t + "Val Acc: %f " % val_acc_t) + + test_loss_t, test_acc_t = exe.run( + test_program, + feed={}, + fetch_list=[test_handle['loss'], test_handle['acc']], + return_numpy=True) + log.info("Test Accuracy: %f" % test_acc_t) + + +if __name__ == '__main__': + parser = argparse.ArgumentParser(description='SGC') + parser.add_argument( + "--dataset", + type=str, + default="cora", + help="dataset (cora, pubmed, citeseer)") + parser.add_argument("--use_cuda", action='store_true', help="use_cuda") + parser.add_argument( + "--seed", type=int, default=1667, help="global random seed") + parser.add_argument("--lr", type=float, default=0.2, help="learning rate") + parser.add_argument( + "--weight_decay", + type=float, + default=0.000005, + help="Weight for L2 loss") + parser.add_argument( + "--bias", action='store_true', default=False, help="flag to use bias") + parser.add_argument( + "--epochs", type=int, default=200, help="number of training epochs") + parser.add_argument( + "--num_layers", type=int, default=2, help="number of SGC layers") + args = parser.parse_args() + log.info(args) + main(args) diff --git a/examples/static_gat/README.md b/examples/static_gat/README.md index bab075f815dd5a5a235363f4942cdbf239f6fd4b..1071e27e48c2c76d13a11c5db22e8947e966da11 100644 --- a/examples/static_gat/README.md +++ b/examples/static_gat/README.md @@ -11,7 +11,7 @@ The datasets contain three citation networks: CORA, PUBMED, CITESEER. The detail ### Dependencies -- paddlepaddle>=1.4 (The speed can be faster in 1.5.) +- paddlepaddle>=1.6 - pgl ### Performance @@ -19,11 +19,11 @@ The datasets contain three citation networks: CORA, PUBMED, CITESEER. The detail We train our models for 200 epochs and report the accuracy on the test dataset. -| Dataset | Accuracy | Speed with paddle 1.4
(epoch time) | Speed with paddle 1.5
(epoch time)| examples/gat | Improvement | -| --- | --- | --- |---| --- | --- | -| Cora | ~83% | 0.0145s | 0.0119s | 0.0175s | 1.47x | -| Pubmed | ~78% | 0.0352s | 0.0193s |0.0295s | 1.53x | -| Citeseer | ~70% | 0.0148s | 0.0124s |0.0253s | 2.04x | +| Dataset | Accuracy | epoch time | examples/gat | Improvement | +| --- | --- | --- | --- | --- | +| Cora | ~83% | 0.0119s | 0.0175s | 1.47x | +| Pubmed | ~78% | 0.0193s |0.0295s | 1.53x | +| Citeseer | ~70% | 0.0124s |0.0253s | 2.04x | ### How to run diff --git a/examples/static_gat/train.py b/examples/static_gat/train.py index 42c2da80195927f5642ec751dc3538591218fd2b..3fa38a19b7db601da501302883a74ff138361cb0 100644 --- a/examples/static_gat/train.py +++ b/examples/static_gat/train.py @@ -84,7 +84,7 @@ def main(args): initializer = [] with fluid.program_guard(train_program, startup_program): train_node_index, init = paddle_helper.constant( - "train_node_index", dtype="int32", value=train_index) + "train_node_index", dtype="int64", value=train_index) initializer.append(init) train_node_label, init = paddle_helper.constant( @@ -103,7 +103,7 @@ def main(args): with fluid.program_guard(val_program, startup_program): val_node_index, init = paddle_helper.constant( - "val_node_index", dtype="int32", value=val_index) + "val_node_index", dtype="int64", value=val_index) initializer.append(init) val_node_label, init = paddle_helper.constant( @@ -119,7 +119,7 @@ def main(args): with fluid.program_guard(test_program, startup_program): test_node_index, init = paddle_helper.constant( - "test_node_index", dtype="int32", value=test_index) + "test_node_index", dtype="int64", value=test_index) initializer.append(init) test_node_label, init = paddle_helper.constant( diff --git a/examples/static_gcn/README.md b/examples/static_gcn/README.md index 9e87d51d94fad5774dd62cb7cfa33e49200cc033..cabd9cf3be06779b77e44ddfa471937c05ae95d6 100644 --- a/examples/static_gcn/README.md +++ b/examples/static_gcn/README.md @@ -10,7 +10,7 @@ The datasets contain three citation networks: CORA, PUBMED, CITESEER. The detail ### Dependencies -- paddlepaddle>=1.4 (The speed can be faster in 1.5.) +- paddlepaddle>=1.6 - pgl ### Performance @@ -18,12 +18,11 @@ The datasets contain three citation networks: CORA, PUBMED, CITESEER. The detail We train our models for 200 epochs and report the accuracy on the test dataset. -| Dataset | Accuracy | Speed with paddle 1.4
(epoch time) | Speed with paddle 1.5
(epoch time)| examples/gcn | Improvement | -| --- | --- | --- |---| --- | --- | -| Cora | ~81% | 0.0053s | 0.0047s | 0.0104s | 2.21x | -| Pubmed | ~79% | 0.0105s | 0.0049s |0.0154s | 3.14x | -| Citeseer | ~71% | 0.0051s | 0.0045s |0.0177s | 3.93x | - +| Dataset | Accuracy | epoch time | examples/gcn | Improvement | +| --- | --- | --- | --- | --- | +| Cora | ~81% | 0.0047s | 0.0104s | 2.21x | +| Pubmed | ~79% | 0.0049s |0.0154s | 3.14x | +| Citeseer | ~71% | 0.0045s |0.0177s | 3.93x | ### How to run diff --git a/examples/static_gcn/train.py b/examples/static_gcn/train.py index f01435d4b93e35247ee664c83409f17b0e11e482..4c9724e0cec79c3aab291f03727279ac46a1452f 100644 --- a/examples/static_gcn/train.py +++ b/examples/static_gcn/train.py @@ -85,7 +85,7 @@ def main(args): initializer = [] with fluid.program_guard(train_program, startup_program): train_node_index, init = paddle_helper.constant( - "train_node_index", dtype="int32", value=train_index) + "train_node_index", dtype="int64", value=train_index) initializer.append(init) train_node_label, init = paddle_helper.constant( @@ -104,7 +104,7 @@ def main(args): with fluid.program_guard(val_program, startup_program): val_node_index, init = paddle_helper.constant( - "val_node_index", dtype="int32", value=val_index) + "val_node_index", dtype="int64", value=val_index) initializer.append(init) val_node_label, init = paddle_helper.constant( @@ -120,7 +120,7 @@ def main(args): with fluid.program_guard(test_program, startup_program): test_node_index, init = paddle_helper.constant( - "test_node_index", dtype="int32", value=test_index) + "test_node_index", dtype="int64", value=test_index) initializer.append(init) test_node_label, init = paddle_helper.constant( diff --git a/examples/strucvec/README.md b/examples/strucvec/README.md new file mode 100644 index 0000000000000000000000000000000000000000..b23c10a297014f6822e0ce1e4c7b3b1ac4559cd9 --- /dev/null +++ b/examples/strucvec/README.md @@ -0,0 +1,44 @@ +## PGL Examples For Struc2Vec +[Struc2vec](https://arxiv.org/abs/1704.03165) is is a concept of symmetry in which network nodes are identified according to the network structure and their relationship to other nodes. A novel and flexible framework for learning latent representations is proposed in the paper of struc2vec. We reproduce Struc2vec algorithm in the PGL. +## DataSet +The paper of use air-traffic network to valid algorithm of Struc2vec. +The each edge in the dataset indicate that having one flight between the airports. Using the the connection between the airports to predict the level of activity. The following dataset will be used to valid the algorithm accuracy.Data collected from the Bureau of Transportation Statistics2 from January to October, 2016. The network has 1,190 nodes, 13,599 edges (diameter is 8). [Link](https://www.transtats.bts.gov/) + +- usa-airports.edgelist +- labels-usa-airports.txt + +## Dependencies +If use want to use the struc2vec model in pgl, please install the gensim, pathos, fastdtw additional. +- paddlepaddle>=1.6 +- pgl +- gensim +- pathos +- fastdtw + +## How to use +For examples, we want to train and valid the Struc2vec model on American airpot dataset +> python struc2vec.py --edge_file data/usa-airports.edgelist --label_file data/labels-usa-airports.txt --train True --valid True --opt2 True + +## Hyperparameters +| Args| Meaning| +| ------------- | ------------- | +| edge_file | input file name for edges| +| label_file | input file name for node label| +| emb_file | input file name for node label| +| walk_depth| The step3 for random walk| +| opt1| The flag to open optimization 1 to reduce time cost| +| opt2| The flag to open optimization 2 to reduce time cost| +| w2v_emb_size| The dims of output the word2vec embedding| +| w2v_window_size| The context length of word2vec| +| w2v_epoch| The num of epoch to train the model.| +| train| The flag to run the struc2vec algorithm to get the w2v embedding| +| valid| The flag to use the w2v embedding to valid the classification result| +| num_class| The num of class in classification model to be trained| + +## Experiment results +| Dataset | Model | Metric | PGL Result | Paper repo Result | +| ------------- | ------------- |------------- |------------- |------------- | +| American airport dataset | Struc2vec without time cost optimization| ACC |0.6483|0.6340| +| American airport dataset | Struc2vec with optimization 1| ACC |0.6466|0.6242| +| American airport dataset | Struc2vec with optimization 2| ACC |0.6252|0.6241| +| American airport dataset | Struc2vec with optimization1&2| ACC |0.6226|0.6083| diff --git a/examples/strucvec/classify.py b/examples/strucvec/classify.py new file mode 100644 index 0000000000000000000000000000000000000000..daaa87eb8dee6e117ae1c523c089ddcc51af206f --- /dev/null +++ b/examples/strucvec/classify.py @@ -0,0 +1,110 @@ +# Copyright (c) 2019 PaddlePaddle Authors. All Rights Reserved. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + +import numpy as np +import paddle +import paddle.fluid as fluid + + +def build_lr_model(args): + """ + Build the LR model to train. + """ + emb_x = fluid.layers.data( + name="emb_x", dtype='float32', shape=[args.w2v_emb_size]) + label = fluid.layers.data(name="label_y", dtype='int64', shape=[1]) + logits = fluid.layers.fc(input=emb_x, + size=args.num_class, + act=None, + name='classification_layer') + proba = fluid.layers.softmax(logits) + loss = fluid.layers.softmax_with_cross_entropy(logits, label) + loss = fluid.layers.mean(loss) + acc = fluid.layers.accuracy(input=proba, label=label, k=1) + return loss, acc + + +def construct_feed_data(data): + """ + Construct the data to feed model. + """ + datas = [] + labels = [] + for sample in data: + if len(datas) < 16: + labels.append([sample[-1]]) + datas.append(sample[1:-1]) + else: + yield np.array(datas).astype(np.float32), np.array(labels).astype( + np.int64) + datas = [] + labels = [] + if len(datas) != 0: + yield np.array(datas).astype(np.float32), np.array(labels).astype( + np.int64) + + +def run_epoch(exe, data, program, stage, epoch, loss, acc): + """ + The epoch funtcion to run each epoch. + """ + print('start {} epoch of {}'.format(stage, epoch)) + all_loss = 0.0 + all_acc = 0.0 + all_samples = 0.0 + count = 0 + for datas, labels in construct_feed_data(data): + batch_loss, batch_acc = exe.run( + program, + fetch_list=[loss, acc], + feed={"emb_x": datas, + "label_y": labels}) + len_samples = len(datas) + all_loss = batch_loss * len_samples + all_acc = batch_acc * len_samples + all_samples += len_samples + count += 1 + print("pass:{}, epoch:{}, loss:{}, acc:{}".format(stage, epoch, batch_loss, + all_acc / (len_samples))) + + +def train_lr_model(args, data): + """ + The main function to run the lr model. + """ + data_nums = len(data) + train_data_nums = int(0.8 * data_nums) + train_data = data[:train_data_nums] + test_data = data[train_data_nums:] + + place = fluid.CPUPlace() + + train_program = fluid.Program() + startup_program = fluid.Program() + + with fluid.program_guard(train_program, startup_program): + loss, acc = build_lr_model(args) + test_program = train_program.clone(for_test=True) + + with fluid.program_guard(train_program, startup_program): + adam = fluid.optimizer.Adam(learning_rate=args.lr) + adam.minimize(loss) + + exe = fluid.Executor(place) + exe.run(startup_program) + + for epoch in range(0, args.epoch): + run_epoch(exe, train_data, train_program, "train", epoch, loss, acc) + print('-------------------') + run_epoch(exe, test_data, test_program, "valid", epoch, loss, acc) diff --git a/examples/strucvec/data_loader.py b/examples/strucvec/data_loader.py new file mode 100644 index 0000000000000000000000000000000000000000..98cb932a8b873e1df506640527b4a797e771a5ef --- /dev/null +++ b/examples/strucvec/data_loader.py @@ -0,0 +1,55 @@ +# Copyright (c) 2019 PaddlePaddle Authors. All Rights Reserved. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +""" +data_loader.py +""" +from pgl import graph +import numpy as np + + +class EdgeDataset(): + """ + The data load just read the edge file, at the same time reindex the source and destination. + """ + + def __init__(self, undirected=True, data_dir=""): + self._undirected = undirected + self._data_dir = data_dir + self._load_edge_data() + + def _load_edge_data(self): + node_sets = set() + edges = [] + with open(self._data_dir, "r") as f: + node_dict = dict() + for line in f: + src, dist = [ + int(data) for data in line.strip("\n\r").split(" ") + ] + if src not in node_dict: + node_dict[src] = len(node_dict) + 1 + src = node_dict[src] + if dist not in node_dict: + node_dict[dist] = len(node_dict) + 1 + dist = node_dict[dist] + node_sets.add(src) + node_sets.add(dist) + edges.append((src, dist)) + if self._undirected: + edges.append((dist, src)) + + num_nodes = len(node_sets) + self.graph = graph.Graph(num_nodes=num_nodes + 1, edges=edges) + self.nodes = np.array(list(node_sets)) + self.node_dict = node_dict diff --git a/examples/strucvec/requirements.txt b/examples/strucvec/requirements.txt new file mode 100644 index 0000000000000000000000000000000000000000..a3e7c50d255fe9a8dba5ba7054f9637f9a8665f8 --- /dev/null +++ b/examples/strucvec/requirements.txt @@ -0,0 +1,3 @@ +gensim +pathos +fastdtw diff --git a/examples/strucvec/sklearn_classify.py b/examples/strucvec/sklearn_classify.py new file mode 100644 index 0000000000000000000000000000000000000000..b2dde24b9af2f5d9e8455a4efb114ea7e51b3d14 --- /dev/null +++ b/examples/strucvec/sklearn_classify.py @@ -0,0 +1,54 @@ +# Copyright (c) 2019 PaddlePaddle Authors. All Rights Reserved. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +import numpy as np +import sklearn +from sklearn.linear_model import LogisticRegression +from sklearn.model_selection import train_test_split +from sklearn.metrics import accuracy_score + +random_seed = 67 + + +def train_lr_l2_model(args, data): + """ + The main function to train lr model with l2 regularization. + """ + acc_list = [] + data = np.array(data) + data = data[data[:, 0].argsort()] + x_data = data[:, 1:-1] + y_data = data[:, -1] + for random_num in range(0, 10): + X_train, X_test, y_train, y_test = train_test_split( + x_data, + y_data, + test_size=0.2, + random_state=random_num + random_seed) + + # use the one vs rest to train the lr model with l2 + pred_test = [] + for i in range(0, args.num_class): + y_train_relabel = np.where(y_train == i, 1, 0) + y_test_relabel = np.where(y_test == i, 1, 0) + lr = LogisticRegression(C=10.0, random_state=0, max_iter=100) + lr.fit(X_train, y_train_relabel) + pred = lr.predict_proba(X_test) + pred_test.append(pred[:, -1].tolist()) + pred_test = np.array(pred_test) + pred_test = np.transpose(pred_test) + c_index = np.argmax(pred_test, axis=1) + acc = accuracy_score(y_test.flatten(), c_index) + acc_list.append(acc) + print("pass:{}-acc:{}".format(random_num, acc)) + print("the avg acc is {}".format(np.mean(acc_list))) diff --git a/examples/strucvec/struc2vec.py b/examples/strucvec/struc2vec.py new file mode 100644 index 0000000000000000000000000000000000000000..11c87073d972436ec1223a3ddaa13793a62ff717 --- /dev/null +++ b/examples/strucvec/struc2vec.py @@ -0,0 +1,545 @@ +# Copyright (c) 2019 PaddlePaddle Authors. All Rights Reserved. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +""" +struc2vec.py +""" +import argparse +import math +import random +import numpy as np +import pgl +from pgl import graph +from pgl.graph_kernel import alias_sample_build_table +from pgl.sample import alias_sample +from data_loader import EdgeDataset +from classify import train_lr_model +from sklearn_classify import train_lr_l2_model + + +def selectDegrees(degree_root, index_left, index_right, degree_left, + degree_right): + """ + Select the which degree to be next step. + """ + + if index_left == -1: + degree_now = degree_right + elif index_right == -1: + degree_now = degree_left + elif (abs(degree_left - degree_root) < abs(degree_right - degree_root)): + degree_now = degree_left + else: + degree_now = degree_right + + return degree_now + + +class StrucVecGraph(): + """ + The class wrapper the PGL graph, the class involve the funtions to implement struc2vec algorithm. + """ + + def __init__(self, graph, nodes, opt1, opt2, opt3, depth, num_walks, + walk_depth): + self.graph = graph + self.nodes = nodes + self.opt1 = opt1 + self.opt2 = opt2 + self.opt3 = opt3 + self.num_walks = num_walks + self.walk_depth = walk_depth + self.tag = args.tag + self.degree_list = dict() + self.degree2nodes = dict() + self.node2degree = dict() + self.distance = dict() + self.degrees_sorted = None + self.layer_distance = dict() + self.layer_message = dict() + self.layer_norm_distance = dict() + self.sample_alias = dict() + self.sample_events = dict() + self.layer_node_weight_count = dict() + if opt3 == True: + self.depth = depth + else: + self.depth = 1000 + + def distance_func(self, a, b): + """ + The basic function to calculate the distance between two list with different length. + """ + ep = 0.5 + m = max(a, b) + ep + mi = min(a, b) + ep + return ((m / mi) - 1) + + def distance_opt1_func(self, a, b): + """ + The optimization function to calculate the distance between two list with list count. + """ + ep = 0.5 + m = max(a[0], b[0]) + ep + mi = min(a[0], b[0]) + ep + return ((m / mi) - 1) * max(a[1], b[1]) + + def add_degree_todict(self, node_id, degree, depth, opt1): + """ + output the degree of each node to a dict + """ + if node_id not in self.degree_list: + self.degree_list[node_id] = dict() + if depth not in self.degree_list[node_id]: + self.degree_list[node_id][depth] = None + if opt1: + degree = np.array(np.unique(degree, return_counts=True)).T + self.degree_list[node_id][depth] = degree + + def output_degree_with_depth(self, depth, opt1): + """ + according to the BFS to get the degree of each layer + """ + degree_dict = dict() + + for node in self.nodes: + start_node = node + cur_node = node + cur_dep = 0 + flag_visit = set() + while cur_node is not None and cur_dep < depth: + if not isinstance(cur_node, list): + cur_node = [cur_node] + filter_node = [] + for node in cur_node: + if node not in flag_visit: + flag_visit.add(node) + filter_node.append(node) + cur_node = filter_node + if len(cur_node) == 0: + break + outdegree = self.graph.outdegree(cur_node) + mask = (outdegree != 0) + if np.any(mask): + outdegree = np.sort(outdegree[mask]) + else: + break + # save the layer degree message to dict + self.add_degree_todict(start_node, outdegree[mask], cur_dep, + opt1) + succes = self.graph.successor(cur_node) + cur_node = [] + for succ in succes: + if isinstance(succ, np.ndarray): + cur_node.extend(succ.flatten().tolist()) + elif isinstance(succ, int): + cur_node.append(succ) + cur_node = list(set(cur_node)) + cur_dep += 1 + + def get_sim_neighbours(self, node, selected_num): + """ + Select the neighours by using the degree similiarity. + """ + degree = self.node2degree[node] + select_count = 0 + node_nbh_list = list() + for node_nbh in self.degree2nodes[degree]: + if node != node_nbh: + node_nbh_list.append(node_nbh) + select_count += 1 + if select_count > selected_num: + return node_nbh_list + degree_vec_len = len(self.degrees_sorted) + index_degree = self.degrees_sorted.index(degree) + + index_left = -1 + index_right = -1 + degree_left = -1 + degree_right = -1 + + if index_degree != -1 and index_degree >= 1: + index_left = index_degree - 1 + if index_degree != -1 and index_degree <= degree_vec_len - 2: + index_right = index_degree + 1 + if index_left == -1 and index_right == -1: + return node_nbh_list + if index_left != -1: + degree_left = self.degrees_sorted[index_left] + if index_right != -1: + degree_right = self.degrees_sorted[index_right] + select_degree = selectDegrees(degree, index_left, index_right, + degree_left, degree_right) + while True: + for node_nbh in self.degree2nodes[select_degree]: + if node_nbh != node: + node_nbh_list.append(node_nbh) + select_count += 1 + if select_count > selected_num: + return node_nbh_list + + if select_degree == degree_left: + if index_left >= 1: + index_left = index_left - 1 + else: + index_left = -1 + + else: + if index_right <= degree_vec_len - 2: + index_right += 1 + else: + index_right = -1 + + if index_left == -1 and index_right == -1: + return node_nbh_list + + if index_left != -1: + degree_left = self.degrees_sorted[index_left] + if index_right != -1: + degree_right = self.degrees_sorted[index_right] + select_degree = selectDegrees(degree, index_left, index_right, + degree_left, degree_right) + return node_nbh_list + + def calc_node_with_neighbor_dtw_opt2(self, src): + """ + Use the optimization algorithm to reduce the next steps range. + """ + from fastdtw import fastdtw + node_nbh_list = self.get_sim_neighbours(src, self.selected_nbh_nums) + distance = {} + for dist in node_nbh_list: + calc_layer_len = min(len(self.degree_list[src]), \ + len(self.degree_list[dist])) + distance_iteration = 0.0 + distance[src, dist] = {} + for layer in range(0, calc_layer_len): + src_layer = self.degree_list[src][layer] + dist_layer = self.degree_list[dist][layer] + weight, path = fastdtw( + src_layer, + dist_layer, + radius=1, + dist=self.distance_calc_func) + distance_iteration += weight + distance[src, dist][layer] = distance_iteration + return distance + + def calc_node_with_neighbor_dtw(self, src_index): + """ + No optimization algorithm to reduce the next steps range, just calculate distance of all path. + """ + from fastdtw import fastdtw + distance = {} + for dist_index in range(src_index + 1, self.graph.num_nodes - 1): + src = self.nodes[src_index] + dist = self.nodes[dist_index] + calc_layer_len = min(len(self.degree_list[src]), \ + len(self.degree_list[dist])) + distance_iteration = 0.0 + distance[src, dist] = {} + for layer in range(0, calc_layer_len): + src_layer = self.degree_list[src][layer] + dist_layer = self.degree_list[dist][layer] + weight, path = fastdtw( + src_layer, + dist_layer, + radius=1, + dist=self.distance_calc_func) + distance_iteration += weight + distance[src, dist][layer] = distance_iteration + return distance + + def calc_distances_between_nodes(self): + """ + Use the dtw algorithm to calculate the distance between nodes. + """ + from fastdtw import fastdtw + from pathos.multiprocessing import Pool + # decide use which algo to use + if self.opt1 == True: + self.distance_calc_func = self.distance_opt1_func + else: + self.distance_calc_func = self.distance_func + + dtws = [] + if self.opt2: + depth = 0 + for node in self.nodes: + if node in self.degree_list: + if depth in self.degree_list[node]: + degree = self.degree_list[node][depth] + if args.opt1: + degree = degree[0][0] + else: + degree = degree[0] + if degree not in self.degree2nodes: + self.degree2nodes[degree] = [] + if node not in self.node2degree: + self.node2degree[node] = degree + self.degree2nodes[degree].append(node) + # select the log(n) node to select data + degree_keys = self.degree2nodes.keys() + degree_keys = np.array(list(degree_keys), dtype='int') + self.degrees_sorted = list(np.sort(degree_keys)) + selected_nbh_nums = 2 * math.log(self.graph.num_nodes - 1, 2) + self.selected_nbh_nums = selected_nbh_nums + + pool = Pool(10) + dtws = pool.map(self.calc_node_with_neighbor_dtw_opt2, self.nodes) + pool.close() + pool.join() + else: + src_indices = range(0, self.graph.num_nodes - 2) + + pool = Pool(10) + dtws = pool.map(self.calc_node_with_neighbor_dtw, src_indices) + pool.close() + pool.join() + print('calc the dtw done.') + for dtw in dtws: + self.distance.update(dtw) + + def normlization_layer_weight(self): + """ + Normlation the distance between nodes, weight[1, 2, ....N] = distance[1, 2, ......N] / sum(distance) + """ + for sd_keys, layer_weight in self.distance.items(): + src, dist = sd_keys + layers, weights = layer_weight.keys(), layer_weight.values() + for layer, weight in zip(layers, weights): + if layer not in self.layer_distance: + self.layer_distance[layer] = {} + if layer not in self.layer_message: + self.layer_message[layer] = {} + self.layer_distance[layer][src, dist] = weight + + if src not in self.layer_message[layer]: + self.layer_message[layer][src] = [] + if dist not in self.layer_message[layer]: + self.layer_message[layer][dist] = [] + self.layer_message[layer][src].append(dist) + self.layer_message[layer][dist].append(src) + + # normalization the layer weight + for i in range(0, self.depth): + layer_weight = 0.0 + layer_count = 0 + if i not in self.layer_norm_distance: + self.layer_norm_distance[i] = {} + if i not in self.sample_alias: + self.sample_alias[i] = {} + if i not in self.sample_events: + self.sample_events[i] = {} + if i not in self.layer_message: + continue + for node in self.nodes: + if node not in self.layer_message[i]: + continue + nbhs = self.layer_message[i][node] + weights = [] + sum_weight = 0.0 + for dist in nbhs: + if (node, dist) in self.layer_distance[i]: + weight = self.layer_distance[i][node, dist] + else: + weight = self.layer_distance[i][dist, node] + weight = np.exp(-float(weight)) + weights.append(weight) + # norm the weight + sum_weight = sum(weights) + if sum_weight == 0.0: + sum_weight = 1.0 + weight_list = [weight / sum_weight for weight in weights] + self.layer_norm_distance[i][node] = weight_list + alias, events = alias_sample_build_table(np.array(weight_list)) + self.sample_alias[i][node] = alias + self.sample_events[i][node] = events + layer_weight += 1.0 + #layer_weight += sum(weight_list) + layer_count += len(weights) + layer_avg_weight = layer_weight / (1.0 * layer_count) + + self.layer_node_weight_count[i] = dict() + for node in self.nodes: + if node not in self.layer_norm_distance[i]: + continue + weight_list = self.layer_norm_distance[i][node] + node_cnt = 0 + for weight in weight_list: + if weight > layer_avg_weight: + node_cnt += 1 + self.layer_node_weight_count[i][node] = node_cnt + + def choose_neighbor_alias_method(self, node, layer): + """ + Choose the neighhor with strategy of random + """ + weight_list = self.layer_norm_distance[layer][node] + neighbors = self.layer_message[layer][node] + select_idx = alias_sample(1, self.sample_alias[layer][node], + self.sample_events[layer][node]) + return neighbors[select_idx[0]] + + def choose_layer_to_walk(self, node, layer): + """ + Choose the layer to random walk + """ + random_value = random.random() + higher_neigbours_nums = self.layer_node_weight_count[layer][node] + prob = math.log(higher_neigbours_nums + math.e) + prob = prob / (1.0 + prob) + if random_value > prob: + if layer > 0: + layer = layer - 1 + else: + if layer + 1 in self.layer_message and \ + node in self.layer_message[layer + 1]: + layer = layer + 1 + return layer + + def executor_random_walk(self, walk_process_id): + """ + The main function to execute the structual random walk + """ + nodes = self.nodes + random.shuffle(nodes) + walk_path_all_nodes = [] + for node in nodes: + walk_path = [] + walk_path.append(node) + layer = 0 + while len(walk_path) < self.walk_depth: + prop = random.random() + if prop < 0.3: + node = self.choose_neighbor_alias_method(node, layer) + walk_path.append(node) + else: + layer = self.choose_layer_to_walk(node, layer) + walk_path_all_nodes.append(walk_path) + return walk_path_all_nodes + + def random_walk_structual_sim(self): + """ + According to struct distance to walk the path + """ + from pathos.multiprocessing import Pool + print('start process struc2vec random walk.') + walks_process_ids = [i for i in range(0, self.num_walks)] + pool = Pool(10) + walks = pool.map(self.executor_random_walk, walks_process_ids) + pool.close() + pool.join() + + #save the final walk result + file_result = open(args.tag + "_walk_path", "w") + for walk in walks: + for walk_node in walk: + walk_node_str = " ".join([str(node) for node in walk_node]) + file_result.write(walk_node_str + "\n") + file_result.close() + print('process struc2vec random walk done.') + + +def learning_embedding_from_struc2vec(args): + """ + Learning the word2vec from the random path + """ + from gensim.models import Word2Vec + from gensim.models.word2vec import LineSentence + struc_walks = LineSentence(args.tag + "_walk_path") + model = Word2Vec(struc_walks, size=args.w2v_emb_size, window=args.w2v_window_size, iter=args.w2v_epoch, \ + min_count=0, hs=1, sg=1, workers=5) + model.wv.save_word2vec_format(args.emb_file) + + +def main(args): + """ + The main fucntion to run the algorithm struc2vec + """ + if args.train: + dataset = EdgeDataset( + undirected=args.undirected, data_dir=args.edge_file) + graph = StrucVecGraph(dataset.graph, dataset.nodes, args.opt1, args.opt2, args.opt3, args.depth,\ + args.num_walks, args.walk_depth) + graph.output_degree_with_depth(args.depth, args.opt1) + graph.calc_distances_between_nodes() + graph.normlization_layer_weight() + graph.random_walk_structual_sim() + learning_embedding_from_struc2vec(args) + file_label = open(args.label_file) + file_label_reindex = open(args.label_file + "_reindex", "w") + for line in file_label: + items = line.strip("\n\r").split(" ") + try: + items = [int(item) for item in items] + except: + continue + if items[0] not in dataset.node_dict: + continue + reindex = dataset.node_dict[items[0]] + file_label_reindex.write(str(reindex) + " " + str(items[1]) + "\n") + file_label_reindex.close() + + if args.valid: + emb_file = open(args.emb_file) + file_label_reindex = open(args.label_file + "_reindex") + label_dict = dict() + for line in file_label_reindex: + items = line.strip("\n\r").split(" ") + try: + label_dict[int(items[0])] = int(items[1]) + except: + continue + + data_for_train_valid = [] + for line in emb_file: + items = line.strip("\n\r").split(" ") + if len(items) <= 2: + continue + index = int(items[0]) + label = int(label_dict[index]) + sample = [] + sample.append(index) + feature_emb = items[1:] + feature_emb = [float(feature) for feature in feature_emb] + sample.extend(feature_emb) + sample.append(label) + data_for_train_valid.append(sample) + train_lr_l2_model(args, data_for_train_valid) + + +if __name__ == "__main__": + parser = argparse.ArgumentParser(description='struc2vec') + parser.add_argument("--edge_file", type=str, default="") + parser.add_argument("--label_file", type=str, default="") + parser.add_argument("--emb_file", type=str, default="w2v_emb") + parser.add_argument("--undirected", type=bool, default=True) + parser.add_argument("--depth", type=int, default=8) + parser.add_argument("--num_walks", type=int, default=10) + parser.add_argument("--walk_depth", type=int, default=80) + parser.add_argument("--opt1", type=bool, default=False) + parser.add_argument("--opt2", type=bool, default=False) + parser.add_argument("--opt3", type=bool, default=False) + parser.add_argument("--w2v_emb_size", type=int, default=128) + parser.add_argument("--w2v_window_size", type=int, default=10) + parser.add_argument("--w2v_epoch", type=int, default=5) + parser.add_argument("--train", type=bool, default=False) + parser.add_argument("--valid", type=bool, default=False) + parser.add_argument("--lr", type=float, default=0.0001) + parser.add_argument("--num_class", type=int, default=4) + parser.add_argument("--epoch", type=int, default=2000) + parser.add_argument("--tag", type=str, default="") + + args = parser.parse_args() + main(args) diff --git a/examples/unsup_graphsage/model.py b/examples/unsup_graphsage/model.py new file mode 100644 index 0000000000000000000000000000000000000000..dea1f13d9c29a70a883fc44cd94ed434f5de6583 --- /dev/null +++ b/examples/unsup_graphsage/model.py @@ -0,0 +1,140 @@ +# Copyright (c) 2019 PaddlePaddle Authors. All Rights Reserved +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +"""model.py""" +import paddle +import paddle.fluid as fluid + + +def copy_send(src_feat, dst_feat, edge_feat): + """copy_send""" + return src_feat["h"] + + +def mean_recv(feat): + """mean_recv""" + return fluid.layers.sequence_pool(feat, pool_type="average") + + +def sum_recv(feat): + """sum_recv""" + return fluid.layers.sequence_pool(feat, pool_type="sum") + + +def max_recv(feat): + """max_recv""" + return fluid.layers.sequence_pool(feat, pool_type="max") + + +def lstm_recv(feat): + """lstm_recv""" + hidden_dim = 128 + forward, _ = fluid.layers.dynamic_lstm( + input=feat, size=hidden_dim * 4, use_peepholes=False) + output = fluid.layers.sequence_last_step(forward) + return output + + +def graphsage_mean(gw, feature, hidden_size, act, name): + """graphsage_mean""" + msg = gw.send(copy_send, nfeat_list=[("h", feature)]) + neigh_feature = gw.recv(msg, mean_recv) + self_feature = feature + self_feature = fluid.layers.fc(self_feature, + hidden_size, + act=act, + name=name + '_l') + neigh_feature = fluid.layers.fc(neigh_feature, + hidden_size, + act=act, + name=name + '_r') + output = fluid.layers.concat([self_feature, neigh_feature], axis=1) + output = fluid.layers.l2_normalize(output, axis=1) + return output + + +def graphsage_meanpool(gw, + feature, + hidden_size, + act, + name, + inner_hidden_size=512): + """graphsage_meanpool""" + neigh_feature = fluid.layers.fc(feature, inner_hidden_size, act="relu") + msg = gw.send(copy_send, nfeat_list=[("h", neigh_feature)]) + neigh_feature = gw.recv(msg, mean_recv) + neigh_feature = fluid.layers.fc(neigh_feature, + hidden_size, + act=act, + name=name + '_r') + + self_feature = feature + self_feature = fluid.layers.fc(self_feature, + hidden_size, + act=act, + name=name + '_l') + output = fluid.layers.concat([self_feature, neigh_feature], axis=1) + output = fluid.layers.l2_normalize(output, axis=1) + return output + + +def graphsage_maxpool(gw, + feature, + hidden_size, + act, + name, + inner_hidden_size=512): + """graphsage_maxpool""" + neigh_feature = fluid.layers.fc(feature, inner_hidden_size, act="relu") + msg = gw.send(copy_send, nfeat_list=[("h", neigh_feature)]) + neigh_feature = gw.recv(msg, max_recv) + neigh_feature = fluid.layers.fc(neigh_feature, + hidden_size, + act=act, + name=name + '_r') + + self_feature = feature + self_feature = fluid.layers.fc(self_feature, + hidden_size, + act=act, + name=name + '_l') + output = fluid.layers.concat([self_feature, neigh_feature], axis=1) + output = fluid.layers.l2_normalize(output, axis=1) + return output + + +def graphsage_lstm(gw, feature, hidden_size, act, name): + """graphsage_lstm""" + inner_hidden_size = 128 + neigh_feature = fluid.layers.fc(feature, inner_hidden_size, act="relu") + + hidden_dim = 128 + forward_proj = fluid.layers.fc(input=neigh_feature, + size=hidden_dim * 4, + bias_attr=False, + name="lstm_proj") + msg = gw.send(copy_send, nfeat_list=[("h", forward_proj)]) + neigh_feature = gw.recv(msg, lstm_recv) + neigh_feature = fluid.layers.fc(neigh_feature, + hidden_size, + act=act, + name=name + '_r') + + self_feature = feature + self_feature = fluid.layers.fc(self_feature, + hidden_size, + act=act, + name=name + '_l') + output = fluid.layers.concat([self_feature, neigh_feature], axis=1) + output = fluid.layers.l2_normalize(output, axis=1) + return output diff --git a/examples/unsup_graphsage/reader.py b/examples/unsup_graphsage/reader.py new file mode 100644 index 0000000000000000000000000000000000000000..a0c8e4a17026ab1315b8dd0ea63e5c7f59d1deb5 --- /dev/null +++ b/examples/unsup_graphsage/reader.py @@ -0,0 +1,214 @@ +# Copyright (c) 2019 PaddlePaddle Authors. All Rights Reserved +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +"""reader.py""" +import os +import numpy as np +import pickle as pkl +import paddle +import paddle.fluid as fluid +import pgl +import time +from pgl.utils.logger import log +from pgl.utils import mp_reader + + +def batch_iter(data, batch_size): + """batch_iter""" + src, dst, eid = data + perm = np.arange(len(eid)) + np.random.shuffle(perm) + start = 0 + while start < len(src): + index = perm[start:start + batch_size] + start += batch_size + yield src[index], dst[index], eid[index] + + +def traverse(item): + """traverse""" + if isinstance(item, list) or isinstance(item, np.ndarray): + for i in iter(item): + for j in traverse(i): + yield j + else: + yield item + + +def flat_node_and_edge(nodes, eids): + """flat_node_and_edge""" + nodes = list(set(traverse(nodes))) + eids = list(set(traverse(eids))) + return nodes, eids + + +def graph_reader(num_layers, + graph_wrappers, + data, + batch_size, + samples, + num_workers, + feed_name_list, + use_pyreader=False, + graph=None, + predict=False): + """graph_reader + """ + assert num_layers == len(samples), "Must be unified number of layers!" + if num_workers > 1: + return multiprocess_graph_reader( + num_layers, + graph_wrappers, + data, + batch_size, + samples, + num_workers, + feed_name_list, + use_pyreader, + graph=graph, + predict=predict) + + batch_info = list(batch_iter(data, batch_size=batch_size)) + work = worker( + num_layers, + batch_info, + graph_wrappers, + samples, + feed_name_list, + use_pyreader, + graph=graph, + predict=predict) + + def reader(): + """reader""" + for batch in work(): + yield batch + + return reader + #return paddle.reader.buffered(reader, 100) + + +def worker(num_layers, batch_info, graph_wrappers, samples, feed_name_list, + use_pyreader, graph, predict): + """worker + """ + pid = os.getppid() + np.random.seed((int(time.time() * 10000) + pid) % 65535) + + graphs = [graph, graph] + + def work(): + """work + """ + feed_dict = {} + ind = 0 + perm = np.arange(0, len(batch_info)) + np.random.shuffle(perm) + for p in perm: + batch_src, batch_dst, batch_eid = batch_info[p] + ind += 1 + ind_start = time.time() + try: + nodes = start_nodes = np.concatenate([batch_src, batch_dst], 0) + eids = [] + layer_nodes, layer_eids = [], [] + for layer_idx in reversed(range(num_layers)): + if len(start_nodes) == 0: + layer_nodes = [nodes] + layer_nodes + layer_eids = [eids] + layer_eids + continue + pred_nodes, pred_eids = graphs[ + layer_idx].sample_predecessor( + start_nodes, samples[layer_idx], return_eids=True) + last_nodes = nodes + nodes, eids = flat_node_and_edge([nodes, pred_nodes], + [eids, pred_eids]) + layer_nodes = [nodes] + layer_nodes + layer_eids = [eids] + layer_eids + # Find new nodes + start_nodes = list(set(nodes) - set(last_nodes)) + if predict is False: + eids = (batch_eid * 2 + 1).tolist() + (batch_eid * 2 + ).tolist() + layer_eids[0] = list(set(layer_eids[0]) - set(eids)) + + # layer_nodes[0]: use first layer nodes as all subgraphs' nodes + subgraph = graphs[0].subgraph( + nodes=layer_nodes[0], eid=layer_eids[0]) + node_feat = np.array(layer_nodes[0], dtype="int64") + subgraph.node_feat["index"] = node_feat + + except Exception as e: + print(e) + if len(feed_dict) > 0: + yield feed_dict + continue + feed_dict = graph_wrappers[0].to_feed(subgraph) + + # only reindex from first subgraph + sub_src_idx = subgraph.reindex_from_parrent_nodes(batch_src) + sub_dst_idx = subgraph.reindex_from_parrent_nodes(batch_dst) + + feed_dict["src_index"] = sub_src_idx.astype("int64") + feed_dict["dst_index"] = sub_dst_idx.astype("int64") + if predict: + feed_dict["node_id"] = batch_src.astype("int64") + + if use_pyreader: + yield [feed_dict[name] for name in feed_name_list] + else: + yield feed_dict + + return work + + +def multiprocess_graph_reader(num_layers, graph_wrappers, data, batch_size, + samples, num_workers, feed_name_list, + use_pyreader, graph, predict): + """ multiprocess_graph_reader + """ + + def parse_to_subgraph(rd): + """ parse_to_subgraph + """ + + def work(): + """ work + """ + for data in rd(): + yield data + + return work + + def reader(): + """ reader + """ + batch_info = list(batch_iter(data, batch_size=batch_size)) + log.info("The size of batch:%d" % (len(batch_info))) + block_size = int(len(batch_info) / num_workers + 1) + reader_pool = [] + for i in range(num_workers): + reader_pool.append( + worker(num_layers, batch_info[block_size * i:block_size * ( + i + 1)], graph_wrappers, samples, feed_name_list, + use_pyreader, graph, predict)) + use_pipe = True + multi_process_sample = mp_reader.multiprocess_reader( + reader_pool, use_pipe=use_pipe) + r = parse_to_subgraph(multi_process_sample) + if use_pipe: + return paddle.reader.buffered(r, 5 * num_workers) + else: + return r + + return reader() diff --git a/examples/unsup_graphsage/sample.txt b/examples/unsup_graphsage/sample.txt new file mode 100644 index 0000000000000000000000000000000000000000..731d556477db19ca19a0c3a7b18f584ed1a2dc90 --- /dev/null +++ b/examples/unsup_graphsage/sample.txt @@ -0,0 +1,2000 @@ +265 1599 +979 1790 +650 1488 +638 1310 +962 1916 +239 1958 +103 1763 +918 1874 +599 1924 +47 1691 +272 1978 +550 1583 +163 1142 +561 1458 +211 1447 +188 1529 +983 1039 +68 1923 +715 1900 +657 1555 +338 1937 +379 1409 +19 1978 +224 1420 +755 1499 +618 1172 +766 1294 +401 1188 +89 1257 +149 1048 +835 1526 +358 1858 +218 1187 +227 1022 +530 1643 +197 1255 +529 1672 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+874 1658 +455 1770 +790 1487 +651 1249 +855 1143 +386 1439 +298 1007 +2 1028 +217 1428 +318 1191 +968 1588 +5 1329 +625 1475 +140 1718 +401 1543 +936 1260 +311 1625 +711 1886 +832 1395 +114 1259 +782 1156 +434 1891 +539 1855 +448 1748 +199 1518 +735 1380 +908 1798 +301 1759 +876 1155 +63 1637 +739 1461 +558 1305 +533 1177 +801 1914 +97 1422 +423 1377 +920 1775 +215 1512 +691 1628 +905 1824 +540 1573 +567 1285 +573 1665 diff --git a/examples/unsup_graphsage/train.py b/examples/unsup_graphsage/train.py new file mode 100644 index 0000000000000000000000000000000000000000..b5655d61ea32b60f4a8abfa5f283595c8a236ac6 --- /dev/null +++ b/examples/unsup_graphsage/train.py @@ -0,0 +1,389 @@ +# Copyright (c) 2019 PaddlePaddle Authors. All Rights Reserved +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +"""train.py +""" +import argparse +import time +import glob +import os + +import numpy as np + +import pgl +from pgl.utils.logger import log +from pgl.utils import paddle_helper +import paddle +import paddle.fluid as fluid +import tqdm + +import reader +import model + + +def get_layer(layer_type, gw, feature, hidden_size, act, name, is_test=False): + """get_layer""" + return getattr(model, layer_type)(gw, feature, hidden_size, act, name) + + +def load_pos_neg(data_path): + """load_pos_neg""" + train_eid = [] + train_src = [] + train_dst = [] + with open(data_path) as f: + eid = 0 + for idx, line in tqdm.tqdm(enumerate(f)): + src, dst = line.strip().split('\t') + train_src.append(int(src)) + train_dst.append(int(dst)) + train_eid.append(int(eid)) + eid += 1 + # concate the the pos data and neg data + train_eid = np.array(train_eid, dtype="int64") + train_src = np.array(train_src, dtype="int64") + train_dst = np.array(train_dst, dtype="int64") + + returns = {"train_data": (train_src, train_dst, train_eid), } + return returns + + +def binary_op(u_embed, v_embed, binary_op_type): + """binary_op""" + if binary_op_type == "Average": + edge_embed = (u_embed + v_embed) / 2 + elif binary_op_type == "Hadamard": + edge_embed = u_embed * v_embed + elif binary_op_type == "Weighted-L1": + edge_embed = fluid.layers.abs(u_embed - v_embed) + elif binary_op_type == "Weighted-L2": + edge_embed = (u_embed - v_embed) * (u_embed - v_embed) + else: + raise ValueError(binary_op_type + " binary_op_type doesn't exists") + return edge_embed + + +class RetDict(object): + """RetDict""" + pass + + +def build_graph_model(args): + """build_graph_model""" + node_feature_info = [('index', [None], np.dtype('int64'))] + + place = fluid.CUDAPlace(0) if args.use_cuda else fluid.CPUPlace() + graph_wrappers = [] + feed_list = [] + + graph_wrappers.append( + pgl.graph_wrapper.GraphWrapper( + "layer_0", fluid.CPUPlace(), node_feat=node_feature_info)) + #edge_feat=[("f", [None, 1], "float32")])) + + num_embed = args.num_nodes + + num_layers = args.num_layers + + src_index = fluid.layers.data( + "src_index", shape=[None], dtype="int64", append_batch_size=False) + + dst_index = fluid.layers.data( + "dst_index", shape=[None], dtype="int64", append_batch_size=False) + + feature = fluid.layers.embedding( + input=fluid.layers.reshape(graph_wrappers[0].node_feat['index'], + [-1, 1]), + size=(num_embed + 1, args.hidden_size), + is_sparse=args.is_sparse, + is_distributed=args.is_distributed) + + features = [feature] + ret_dict = RetDict() + ret_dict.graph_wrappers = graph_wrappers + edge_data = [src_index, dst_index] + feed_list.extend(edge_data) + ret_dict.feed_list = feed_list + + for i in range(num_layers): + if i == num_layers - 1: + act = None + else: + act = "leaky_relu" + feature = get_layer( + args.layer_type, + graph_wrappers[0], + feature, + args.hidden_size, + act, + name="%s_%s" % (args.layer_type, i)) + features.append(feature) + + src_feat = fluid.layers.gather(features[-1], src_index) + src_feat = fluid.layers.fc(src_feat, + args.hidden_size, + bias_attr=None, + param_attr=fluid.ParamAttr(name="feat")) + dst_feat = fluid.layers.gather(features[-1], dst_index) + dst_feat = fluid.layers.fc(dst_feat, + args.hidden_size, + bias_attr=None, + param_attr=fluid.ParamAttr(name="feat")) + if args.phase == "predict": + node_id = fluid.layers.data( + "node_id", shape=[None, 1], dtype="int64", append_batch_size=False) + ret_dict.src_feat = src_feat + ret_dict.dst_feat = dst_feat + ret_dict.id = node_id + return ret_dict + + batch_size = args.batch_size + batch_negative_label = fluid.layers.reshape( + fluid.layers.range(0, batch_size, 1, "int64"), [-1, 1]) + batch_negative_label = fluid.layers.one_hot(batch_negative_label, + batch_size) + batch_loss_weight = (batch_negative_label * + (batch_size - 2) + 1.0) / (batch_size - 1) + batch_loss_weight.stop_gradient = True + batch_negative_label = batch_negative_label + batch_negative_label = fluid.layers.cast( + batch_negative_label, dtype="float32") + batch_negative_label.stop_gradient = True + + cos_theta = fluid.layers.matmul(src_feat, dst_feat, transpose_y=True) + + # Calc Loss + loss = fluid.layers.sigmoid_cross_entropy_with_logits( + x=cos_theta, label=batch_negative_label) + loss = loss * batch_loss_weight + #loss = fluid.layers.reduce_sum(loss, -1) + loss = fluid.layers.mean(loss) + + # Calc AUC + proba = fluid.layers.sigmoid(cos_theta) + proba = fluid.layers.reshape(proba, [-1, 1]) + proba = fluid.layers.concat([proba * -1 + 1, proba], axis=1) + gold_label = fluid.layers.reshape(batch_negative_label, [-1, 1]) + gold_label = fluid.layers.cast(gold_label, "int64") + auc, batch_auc_out, [batch_stat_pos, batch_stat_neg, stat_pos, stat_neg] = \ + fluid.layers.auc(input=proba, label=gold_label, curve='ROC', ) + + ret_dict.loss = loss + ret_dict.auc = batch_auc_out + return ret_dict + + +def run_epoch( + py_reader, + exe, + program, + prefix, + model_dict, + epoch, + batch_size, + log_per_step=100, + save_per_step=10000, ): + """run_epoch""" + batch = 0 + start = time.time() + + batch_end = time.time() + + for batch_feed_dict in py_reader(): + if prefix == "train": + if batch_feed_dict["src_index"].shape[0] != batch_size: + log.warning( + 'batch_feed_dict["src_index"].shape[0] != 1024, continue') + continue + batch_start = time.time() + batch += 1 + batch_loss, batch_auc = exe.run( + program, + feed=batch_feed_dict, + fetch_list=[model_dict.loss.name, model_dict.auc.name]) + + batch_end = time.time() + if batch % log_per_step == 0: + log.info( + "Batch %s %s-Loss %s \t %s-Auc %s \t Speed(per batch) %.5lf sec" + % (batch, prefix, np.mean(batch_loss), prefix, + np.mean(batch_auc), batch_end - batch_start)) + if batch != 0 and batch % save_per_step == 0: + fluid.io.save_params( + exe, dirname='checkpoint', main_program=program) + fluid.io.save_params(exe, dirname='checkpoint', main_program=program) + + +def run_predict_epoch(py_reader, + exe, + program, + prefix, + model_dict, + num_nodes, + hidden_size, + log_per_step=100): + """run_predict_epoch""" + batch = 0 + start = time.time() + #use the parallel executor to speed up + batch_end = time.time() + all_feat = np.zeros((num_nodes, hidden_size), dtype="float32") + + for batch_feed_dict in tqdm.tqdm(py_reader()): + batch_start = time.time() + batch += 1 + batch_src_feat, batch_id = exe.run( + program, + feed=batch_feed_dict, + fetch_list=[model_dict.src_feat.name, model_dict.id.name]) + + for ind, id in enumerate(batch_id): + all_feat[id] = batch_src_feat[ind] + np.save("emb.npy", all_feat) + + +def main(args): + """main""" + place = fluid.CUDAPlace(0) if args.use_cuda else fluid.CPUPlace() + exe = fluid.Executor(place) + + train_program = fluid.Program() + startup_program = fluid.Program() + + with fluid.program_guard(train_program, startup_program): + ret_dict = build_graph_model(args=args) + + val_program = train_program.clone(for_test=True) + if args.phase == "train": + with fluid.program_guard(train_program, startup_program): + adam = fluid.optimizer.Adam(learning_rate=args.lr) + adam.minimize(ret_dict.loss) + # reset the place according to role of parameter server + exe.run(startup_program) + + with open(args.data_path) as f: + log.info("Begin Load Graph") + src = [] + dst = [] + for idx, line in tqdm.tqdm(enumerate(f)): + s, d = line.strip().split() + src.append(s) + dst.append(d) + dst.append(s) + src.append(d) + src = np.array(src, dtype="int64").reshape(-1, 1) + dst = np.array(dst, dtype="int64").reshape(-1, 1) + edges = np.hstack([src, dst]) + + log.info("Begin Build Index") + ret_dict.graph = pgl.graph.Graph(num_nodes=args.num_nodes, edges=edges) + ret_dict.graph.indegree() + log.info("End Build Index") + + if args.phase == "train": + #just the worker, load the sample + data = load_pos_neg(args.data_path) + + feed_name_list = [var.name for var in ret_dict.feed_list] + train_iter = reader.graph_reader( + args.num_layers, + ret_dict.graph_wrappers, + batch_size=args.batch_size, + data=data['train_data'], + samples=args.samples, + num_workers=args.sample_workers, + feed_name_list=feed_name_list, + use_pyreader=args.use_pyreader, + graph=ret_dict.graph) + + # get PyReader + for epoch in range(args.epoch): + epoch_start = time.time() + try: + run_epoch( + train_iter, + program=train_program, + exe=exe, + prefix="train", + model_dict=ret_dict, + epoch=epoch, + batch_size=args.batch_size, + log_per_step=10) + epoch_end = time.time() + print("Epoch: {0}, Train total expend: {1} ".format( + epoch, epoch_end - epoch_start)) + except Exception as e: + log.info("Run Epoch Error %s" % e) + fluid.io.save_params( + exe, + dirname=args.checkpoint + '_%s' % epoch, + main_program=train_program) + + log.info("EPOCH END") + + log.info("RUN FINISH") + elif args.phase == "predict": + fluid.io.load_params( + exe, + dirname=args.checkpoint + '_%s' % args.epoch, + main_program=val_program) + test_src = np.arange(0, args.num_nodes, dtype="int64") + feed_name_list = [var.name for var in ret_dict.feed_list] + predict_iter = reader.graph_reader( + args.num_layers, + ret_dict.graph_wrappers, + batch_size=args.batch_size, + data=(test_src, test_src, test_src, test_src), + samples=args.samples, + num_workers=args.sample_workers, + feed_name_list=feed_name_list, + use_pyreader=args.use_pyreader, + graph=ret_dict.graph, + predict=True) + run_predict_epoch( + predict_iter, + program=val_program, + exe=exe, + prefix="predict", + hidden_size=args.hidden_size, + model_dict=ret_dict, + num_nodes=args.num_nodes, + log_per_step=100) + log.info("EPOCH END") + + +if __name__ == "__main__": + parser = argparse.ArgumentParser(description='graphsage') + parser.add_argument( + "--use_cuda", action='store_true', help="use_cuda", default=False) + parser.add_argument("--layer_type", type=str, default="graphsage_mean") + parser.add_argument("--epoch", type=int, default=1) + parser.add_argument("--hidden_size", type=int, default=128) + parser.add_argument("--batch_size", type=int, default=1024) + parser.add_argument("--lr", type=float, default=0.001) + parser.add_argument("--num_layers", type=int, default=2) + parser.add_argument("--data_path", type=str, required=True) + parser.add_argument("--checkpoint", type=str, default="model_ckpt") + parser.add_argument("--cache_path", type=str, default="./tmp") + parser.add_argument("--phase", type=str, default="train") + parser.add_argument("--digraph", action='store_true', default=False) + parser.add_argument('--samples', nargs='+', type=int, default=[10, 10]) + parser.add_argument("--sample_workers", type=int, default=10) + parser.add_argument("--num_nodes", type=int, required=True) + parser.add_argument("--is_sparse", action='store_true', default=False) + parser.add_argument("--is_distributed", action='store_true', default=False) + parser.add_argument("--real_graph", action='store_true', default=True) + parser.add_argument("--use_pyreader", action='store_true', default=False) + args = parser.parse_args() + log.info(args) + main(args) diff --git a/pgl/__init__.py b/pgl/__init__.py index ea39debf0ee35f7e73097352b760682495a5c3a3..15c23cc633540a53b2b445a3012f2669319ba5d4 100644 --- a/pgl/__init__.py +++ b/pgl/__init__.py @@ -13,8 +13,9 @@ # limitations under the License. """Generate pgl apis """ -__version__ = "0.1.0.beta" +__version__ = "1.0.0" from pgl import layers from pgl import graph_wrapper from pgl import graph from pgl import data_loader +from pgl import contrib diff --git a/pgl/contrib/__init__.py b/pgl/contrib/__init__.py new file mode 100644 index 0000000000000000000000000000000000000000..5dcd918aebbc3ce1cc9ce77e3e742985d223c39f --- /dev/null +++ b/pgl/contrib/__init__.py @@ -0,0 +1,18 @@ +# Copyright (c) 2019 PaddlePaddle Authors. All Rights Reserved +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +"""Generate Contrib api +""" + +from pgl.contrib import heter_graph +from pgl.contrib import heter_graph_wrapper diff --git a/pgl/contrib/heter_graph.py b/pgl/contrib/heter_graph.py new file mode 100644 index 0000000000000000000000000000000000000000..b82bf46b729ad6f0df56b25db4053b09bf9ef361 --- /dev/null +++ b/pgl/contrib/heter_graph.py @@ -0,0 +1,203 @@ +# Copyright (c) 2019 PaddlePaddle Authors. All Rights Reserved +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +""" + This package implement Heterogeneous Graph structure for handling Heterogeneous graph data. +""" +import numpy as np +import pickle as pkl +import time +import pgl.graph_kernel as graph_kernel +from pgl import graph + +__all__ = ['HeterGraph'] + + +def _hide_num_nodes(shape): + """Set the first dimension as unknown + """ + shape = list(shape) + shape[0] = None + return shape + + +class HeterGraph(object): + """Implementation of graph structure in pgl + + This is a simple implementation of heterogeneous graph structure in pgl + + Args: + num_nodes_every_type: dict, number of nodes for every node type + + edges_every_type: dict, every element is a list of (u, v) tuples. + + node_feat_every_type: features for every node type. + + Examples: + .. code-block:: python + + import numpy as np + num_nodes_every_type = {'type1':3,'type2':4, 'type3':2} + edges_every_type = { + ('type1','type2', 'edges_type1'): [(0,1), (1,2)], + ('type1', 'type3', 'edges_type2'): [(1,2), (3,1)], + } + node_feat_every_type = { + 'type1': {'features1': np.random.randn(3, 4), + 'features2': np.random.randn(3, 4)}, + 'type2': {'features3': np.random.randn(4, 4)}, + 'type3': {'features1': np.random.randn(2, 4), + 'features2': np.random.randn(2, 4)} + } + edges_feat_every_type = { + ('type1','type2','edges_type1'): {'h': np.random.randn(2, 4)}, + ('type1', 'type3', 'edges_type2'): {'h':np.random.randn(2, 4)}, + } + + g = heter_graph.HeterGraph( + num_nodes_every_type=num_nodes_every_type, + edges_every_type=edges_every_type, + node_feat_every_type=node_feat_every_type, + edge_feat_every_type=edges_feat_every_type) + + """ + + def __init__(self, + num_nodes_every_type, + edges_every_type, + node_feat_every_type=None, + edge_feat_every_type=None): + + self._num_nodes_dict = num_nodes_every_type + self._edges_dict = edges_every_type + if node_feat_every_type is not None: + self._node_feat = node_feat_every_type + else: + self._node_feat = {} + + if edge_feat_every_type is not None: + self._edge_feat = edge_feat_every_type + else: + self._edge_feat = {} + + self._multi_graph = {} + for key, value in self._edges_dict.items(): + if not self._node_feat: + node_feat = None + else: + node_feat = self._node_feat[key[0]] + + if not self._edge_feat: + edge_feat = None + else: + edge_feat = self._edge_feat[key] + + self._multi_graph[key] = graph.Graph( + num_nodes=self._num_nodes_dict[key[1]], + edges=value, + node_feat=node_feat, + edge_feat=edge_feat) + + def __getitem__(self, edge_type): + """__getitem__ + """ + return self._multi_graph[edge_type] + + def meta_path_random_walk(self, start_node, edge_types, meta_path, + max_depth): + """Meta path random walk sampling. + + Args: + start_nodes: int, node to begin random walk. + edge_types: list, the edge types to be sampled. + meta_path: 'user-item-user' + max_depth: the max length of every walk. + """ + edges_type_list = [] + node_type_list = meta_path.split('-') + for i in range(1, len(node_type_list)): + edges_type_list.append( + (node_type_list[i - 1], node_type_list[i], edge_types[i - 1])) + + no_neighbors_flag = False + walk = [start_node] + for i in range(max_depth): + for e_type in edges_type_list: + cur_node = [walk[-1]] + nxt_node = self._multi_graph[e_type].sample_successor( + cur_node, max_degree=1) # list of np.array + nxt_node = nxt_node[0] + if len(nxt_node) == 0: + no_neighbors_flag = True + break + else: + walk.append(nxt_node.tolist()[0]) + + if no_neighbors_flag: + break + + return walk + + def node_feat_info(self): + """Return the information of node feature for HeterGraphWrapper. + + This function return the information of node features of all node types. And this + function is used to help constructing HeterGraphWrapper + + Return: + A dict of list of tuple (name, shape, dtype) for all given node feature. + + """ + node_feat_info = {} + for node_type_name, feat_dict in self._node_feat.items(): + tmp_node_feat_info = [] + for feat_name, feat in feat_dict.items(): + full_name = feat_name + tmp_node_feat_info.append( + (full_name, _hide_num_nodes(feat.shape), feat.dtype)) + node_feat_info[node_type_name] = tmp_node_feat_info + + return node_feat_info + + def edge_feat_info(self): + """Return the information of edge feature for HeterGraphWrapper. + + This function return the information of edge features of all edge types. And this + function is used to help constructing HeterGraphWrapper + + Return: + A dict of list of tuple (name, shape, dtype) for all given edge feature. + + """ + edge_feat_info = {} + for edge_type_name, feat_dict in self._edge_feat.items(): + tmp_edge_feat_info = [] + for feat_name, feat in feat_dict.items(): + full_name = feat_name + tmp_edge_feat_info.append( + (full_name, _hide_num_nodes(feat.shape), feat.dtype)) + edge_feat_info[edge_type_name] = tmp_edge_feat_info + return edge_feat_info + + def edge_types_info(self): + """Return the information of all edge types. + + Return: + A list of tuple ('srctype','dsttype', 'edges_type') for all edge types. + + """ + edge_types_info = [] + for key, _ in self._edges_dict.items(): + edge_types_info.append(key) + + return edge_types_info diff --git a/pgl/contrib/heter_graph_wrapper.py b/pgl/contrib/heter_graph_wrapper.py new file mode 100644 index 0000000000000000000000000000000000000000..27937c11c2f1610ff49d670bf24a76e1aa2cb54d --- /dev/null +++ b/pgl/contrib/heter_graph_wrapper.py @@ -0,0 +1,234 @@ +# Copyright (c) 2019 PaddlePaddle Authors. All Rights Reserved +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +""" +This package provides interface to help building static computational graph +for PaddlePaddle. +""" + +import warnings +import numpy as np +import paddle.fluid as fluid + +from pgl.utils import op +from pgl.utils import paddle_helper +from pgl.utils.logger import log +from pgl.graph_wrapper import GraphWrapper + +ALL = "__ALL__" + + +def is_all(arg): + """is_all + """ + return isinstance(arg, str) and arg == ALL + + +class BipartiteGraphWrapper(GraphWrapper): + """Implement a bipartite graph wrapper that creates a graph data holders. + """ + + def __init__(self, name, place, node_feat=[], edge_feat=[]): + super(BipartiteGraphWrapper, self).__init__(name, place, node_feat, + edge_feat) + + def send(self, + message_func, + src_nfeat_list=None, + dst_nfeat_list=None, + efeat_list=None): + """Send message from all src nodes to dst nodes. + + The UDF message function should has the following format. + + .. code-block:: python + + def message_func(src_feat, dst_feat, edge_feat): + ''' + Args: + src_feat: the node feat dict attached to the src nodes. + dst_feat: the node feat dict attached to the dst nodes. + edge_feat: the edge feat dict attached to the + corresponding (src, dst) edges. + + Return: + It should return a tensor or a dictionary of tensor. And each tensor + should have a shape of (num_edges, dims). + ''' + pass + + Args: + message_func: UDF function. + src_nfeat_list: a list of tuple (name, tensor) for src nodes + dst_nfeat_list: a list of tuple (name, tensor) for dst nodes + efeat_list: a list of names or tuple (name, tensor) + + Return: + A dictionary of tensor representing the message. Each of the values + in the dictionary has a shape (num_edges, dim) which should be collected + by :code:`recv` function. + """ + if efeat_list is None: + efeat_list = {} + if src_nfeat_list is None: + src_nfeat_list = {} + if dst_nfeat_list is None: + dst_nfeat_list = {} + + src, dst = self.edges + src_feat = {} + for feat in src_nfeat_list: + if isinstance(feat, str): + src_feat[feat] = self.node_feat[feat] + else: + name, tensor = feat + src_feat[name] = tensor + + dst_feat = {} + for feat in dst_nfeat_list: + if isinstance(feat, str): + dst_feat[feat] = self.node_feat[feat] + else: + name, tensor = feat + dst_feat[name] = tensor + + efeat = {} + for feat in efeat_list: + if isinstance(feat, str): + efeat[feat] = self.edge_feat[feat] + else: + name, tensor = feat + efeat[name] = tensor + + src_feat = op.read_rows(src_feat, src) + dst_feat = op.read_rows(dst_feat, dst) + msg = message_func(src_feat, dst_feat, efeat) + + return msg + + +class HeterGraphWrapper(object): + """Implement a heterogeneous graph wrapper that creates a graph data holders + that attributes and features in the heterogeneous graph. + And we provide interface :code:`to_feed` to help converting :code:`Graph` + data into :code:`feed_dict`. + + Args: + name: The heterogeneous graph data prefix + + place: fluid.CPUPlace or fluid.GPUPlace(n) indicating the + device to hold the graph data. + + node_feat: A dict of list of tuples that decribe the details of node + feature tenosr. Each tuple mush be (name, shape, dtype) + and the first dimension of the shape must be set unknown + (-1 or None) or we can easily use :code:`HeterGraph.node_feat_info()` + to get the node_feat settings. + + edge_feat: A dict of list of tuples that decribe the details of edge + feature tenosr. Each tuple mush be (name, shape, dtype) + and the first dimension of the shape must be set unknown + (-1 or None) or we can easily use :code:`HeterGraph.edge_feat_info()` + to get the edge_feat settings. + + Examples: + .. code-block:: python + + import paddle.fluid as fluid + import numpy as np + num_nodes_every_type = {'type1':3,'type2':4, 'type3':2} + edges_every_type = { + ('type1','type2', 'edges_type1'): [(0,1), (1,2)], + ('type1', 'type3', 'edges_type2'): [(1,2), (3,1)], + } + node_feat_every_type = { + 'type1': {'features1': np.random.randn(3, 4), + 'features2': np.random.randn(3, 4)}, + 'type2': {'features3': np.random.randn(4, 4)}, + 'type3': {'features1': np.random.randn(2, 4), + 'features2': np.random.randn(2, 4)} + } + edges_feat_every_type = { + ('type1','type2','edges_type1'): {'h': np.random.randn(2, 4)}, + ('type1', 'type3', 'edges_type2'): {'h':np.random.randn(2, 4)}, + } + + g = heter_graph.HeterGraph( + num_nodes_every_type=num_nodes_every_type, + edges_every_type=edges_every_type, + node_feat_every_type=node_feat_every_type, + edge_feat_every_type=edges_feat_every_type) + + + place = fluid.CPUPlace() + + gw = pgl.heter_graph_wrapper.HeterGraphWrapper( + name='heter_graph', + place = place, + edge_types = g.edge_types_info(), + node_feat=g.node_feat_info(), + edge_feat=g.edge_feat_info()) + """ + + def __init__(self, name, place, edge_types, node_feat={}, edge_feat={}): + self.__data_name_prefix = name + self._place = place + self._edge_types = edge_types + self._multi_gw = {} + for edge_type in self._edge_types: + type_name = self.__data_name_prefix + '/' + edge_type[ + 0] + '_' + edge_type[1] + if node_feat: + n_feat = node_feat[edge_type[0]] + else: + n_feat = {} + + if edge_feat: + e_feat = edge_feat[edge_type] + else: + e_feat = {} + + self._multi_gw[edge_type] = BipartiteGraphWrapper( + name=type_name, + place=self._place, + node_feat=n_feat, + edge_feat=e_feat) + + def to_feed(self, heterGraph, edge_types_list=ALL): + """Convert the graph into feed_dict. + + This function helps to convert graph data into feed dict + for :code:`fluid.Excecutor` to run the model. + + Args: + heterGraph: the :code:`HeterGraph` data object + edge_types_list: the edge types list to be fed + + Return: + A dictinary contains data holder names and its coresponding data. + """ + multi_graphs = heterGraph._multi_graph + if is_all(edge_types_list): + edge_types_list = self._edge_types + + feed_dict = {} + for edge_type in edge_types_list: + feed_d = self._multi_gw[edge_type].to_feed(multi_graphs[edge_type]) + feed_dict.update(feed_d) + + return feed_dict + + def __getitem__(self, edge_type): + """__getitem__ + """ + return self._multi_gw[edge_type] diff --git a/pgl/data_loader.py b/pgl/data_loader.py index 93d89e5e70fef27fd07306636df761dd0716b135..fb0e107203efc91a9cd8de313b1c15f9dc756366 100644 --- a/pgl/data_loader.py +++ b/pgl/data_loader.py @@ -20,7 +20,6 @@ import io import sys import numpy as np import pickle as pkl -import networkx as nx from pgl import graph from pgl.utils.logger import log @@ -91,6 +90,7 @@ class CitationDataset(object): def _load_data(self): """Load data """ + import networkx as nx objnames = ['x', 'y', 'tx', 'ty', 'allx', 'ally', 'graph'] objects = [] for i in range(len(objnames)): @@ -98,7 +98,7 @@ class CitationDataset(object): 'rb') as f: objects.append(_pickle_load(f)) - x, y, tx, ty, allx, ally, _graph = tuple(objects) + x, y, tx, ty, allx, ally, _graph = objects test_idx_reorder = _parse_index_file("{}/ind.{}.test.index".format( self.path, self.name)) test_idx_range = np.sort(test_idx_reorder) diff --git a/pgl/graph.py b/pgl/graph.py index f341363ef751db012ae49f118a06a96e2450ef16..8af2038f6378bef688f3530757bef3bd2a11b0c2 100644 --- a/pgl/graph.py +++ b/pgl/graph.py @@ -114,25 +114,41 @@ class Graph(object): self._edge_feat = {} if isinstance(edges, np.ndarray): - if edges.dtype != "int32": - edges = edges.astype("int32") + if edges.dtype != "int64": + edges = edges.astype("int64") else: - edges = np.array(edges, dtype="int32") + edges = np.array(edges, dtype="int64") self._edges = edges self._num_nodes = num_nodes if len(edges) == 0: - # check emtpy edges - src, dst = np.array([], dtype="int32"), np.array([], dtype="int32") - else: - src = edges[:, 0] - dst = edges[:, 1] + raise ValueError("The Graph have no edges.") + + self._adj_src_index = None + self._adj_dst_index = None + + @property + def adj_src_index(self): + """Return an EdgeIndex object for src. + """ + if self._adj_src_index is None: + self._adj_src_index = EdgeIndex( + u=self._edges[:, 0], + v=self._edges[:, 1], + num_nodes=self._num_nodes) + return self._adj_src_index - self._adj_src_index = EdgeIndex( - u=src, v=dst, num_nodes=self._num_nodes) - self._adj_dst_index = EdgeIndex( - u=dst, v=src, num_nodes=self._num_nodes) + @property + def adj_dst_index(self): + """Return an EdgeIndex object for dst. + """ + if self._adj_dst_index is None: + self._adj_dst_index = EdgeIndex( + u=self._edges[:, 1], + v=self._edges[:, 0], + num_nodes=self._num_nodes) + return self._adj_dst_index @property def edge_feat(self): @@ -180,16 +196,16 @@ class Graph(object): if sort_by not in ["src", "dst"]: raise ValueError("sort_by should be in 'src' or 'dst'.") if sort_by == 'src': - src, dst, eid = self._adj_src_index.triples() + src, dst, eid = self.adj_src_index.triples() else: - dst, src, eid = self._adj_dst_index.triples() + dst, src, eid = self.adj_dst_index.triples() return src, dst, eid @property def nodes(self): """Return all nodes id from 0 to :code:`num_nodes - 1` """ - return np.arange(self._num_nodes, dtype="int32") + return np.arange(self._num_nodes, dtype="int64") def indegree(self, nodes=None): """Return the indegree of the given nodes @@ -204,9 +220,9 @@ class Graph(object): A numpy.ndarray as the given nodes' indegree. """ if nodes is None: - return self._adj_dst_index.degree + return self.adj_dst_index.degree else: - return self._adj_dst_index.degree[nodes] + return self.adj_dst_index.degree[nodes] def outdegree(self, nodes=None): """Return the outdegree of the given nodes. @@ -221,9 +237,9 @@ class Graph(object): A numpy.array as the given nodes' outdegree. """ if nodes is None: - return self._adj_src_index.degree + return self.adj_src_index.degree else: - return self._adj_src_index.degree[nodes] + return self.adj_src_index.degree[nodes] def successor(self, nodes=None, return_eids=False): """Find successor of given nodes. @@ -273,17 +289,21 @@ class Graph(object): """ if nodes is None: if return_eids: - return self._adj_src_index.v, self._adj_src_index.eid + return self.adj_src_index.v, self.adj_src_index.eid else: - return self._adj_src_index.v + return self.adj_src_index.v else: if return_eids: - return self._adj_src_index.v[nodes], self._adj_src_index.eid[ + return self.adj_src_index.v[nodes], self.adj_src_index.eid[ nodes] else: - return self._adj_src_index.v[nodes] + return self.adj_src_index.v[nodes] - def sample_successor(self, nodes, max_degree, return_eids=False): + def sample_successor(self, + nodes, + max_degree, + return_eids=False, + shuffle=False): """Sample successors of given nodes. Args: @@ -304,26 +324,20 @@ class Graph(object): node_succ = self.successor(nodes, return_eids=return_eids) if return_eids: node_succ, node_succ_eid = node_succ + if nodes is None: nodes = self.nodes - sample_succ, sample_succ_eid = [], [] - for i in range(len(nodes)): - max_size = min(max_degree, len(node_succ[i])) - if max_size == 0: - sample_succ.append([]) - if return_eids: - sample_succ_eid.append([]) - else: - ind = np.random.choice( - len(node_succ[i]), max_size, replace=False) - sample_succ.append(node_succ[i][ind]) - if return_eids: - sample_succ_eid.append(node_succ_eid[i][ind]) + node_succ = node_succ.tolist() + if return_eids: - return sample_succ, sample_succ_eid + node_succ_eid = node_succ_eid.tolist() + + if return_eids: + return graph_kernel.sample_subset_with_eid( + node_succ, node_succ_eid, max_degree, shuffle) else: - return sample_succ + return graph_kernel.sample_subset(node_succ, max_degree, shuffle) def predecessor(self, nodes=None, return_eids=False): """Find predecessor of given nodes. @@ -373,17 +387,21 @@ class Graph(object): """ if nodes is None: if return_eids: - return self._adj_dst_index.v, self._adj_dst_index.eid + return self.adj_dst_index.v, self.adj_dst_index.eid else: - return self._adj_dst_index.v + return self.adj_dst_index.v else: if return_eids: - return self._adj_dst_index.v[nodes], self._adj_dst_index.eid[ + return self.adj_dst_index.v[nodes], self.adj_dst_index.eid[ nodes] else: - return self._adj_dst_index.v[nodes] + return self.adj_dst_index.v[nodes] - def sample_predecessor(self, nodes, max_degree, return_eids=False): + def sample_predecessor(self, + nodes, + max_degree, + return_eids=False, + shuffle=False): """Sample predecessor of given nodes. Args: @@ -407,24 +425,16 @@ class Graph(object): if nodes is None: nodes = self.nodes - sample_pred, sample_pred_eid = [], [] - for i in range(len(nodes)): - max_size = min(max_degree, len(node_pred[i])) - if max_size == 0: - sample_pred.append([]) - if return_eids: - sample_pred_eid.append([]) - else: - ind = np.random.choice( - len(node_pred[i]), max_size, replace=False) - sample_pred.append(node_pred[i][ind]) - if return_eids: - sample_pred_eid.append(node_pred_eid[i][ind]) + node_pred = node_pred.tolist() + + if return_eids: + node_pred_eid = node_pred_eid.tolist() if return_eids: - return sample_pred, sample_pred_eid + return graph_kernel.sample_subset_with_eid( + node_pred, node_pred_eid, max_degree, shuffle) else: - return sample_pred + return graph_kernel.sample_subset(node_pred, max_degree, shuffle) def node_feat_info(self): """Return the information of node feature for GraphWrapper. @@ -500,19 +510,21 @@ class Graph(object): (key, _hide_num_nodes(value.shape), value.dtype)) return edge_feat_info - def subgraph(self, nodes, eid): + def subgraph(self, nodes, eid=None, edges=None): """Generate subgraph with nodes and edge ids. This function will generate a :code:`pgl.graph.Subgraph` object and copy all corresponding node and edge features. Nodes and edges will - be reindex from 0. + be reindex from 0. Eid and edges can't both be None. WARNING: ALL NODES IN EID MUST BE INCLUDED BY NODES Args: nodes: Node ids which will be included in the subgraph. - eid: Edge ids which will be included in the subgraph. + eid (optional): Edge ids which will be included in the subgraph. + + edges (optional): Edge(src, dst) list which will be included in the subgraph. Return: A :code:`pgl.graph.Subgraph` object. @@ -522,11 +534,22 @@ class Graph(object): for ind, node in enumerate(nodes): reindex[node] = ind - eid = np.array(eid, dtype="int32") - sub_edges = graph_kernel.map_edges(eid, self._edges, reindex) + if eid is None and edges is None: + raise ValueError("Eid and edges can't be None at the same time.") + + if edges is None: + edges = self._edges[eid] + else: + edges = np.array(edges, dtype="int64") + + sub_edges = graph_kernel.map_edges( + np.arange( + len(edges), dtype="int64"), edges, reindex) sub_edge_feat = {} for key, value in self._edge_feat.items(): + if eid is None: + raise ValueError("Eid can not be None with edge features.") sub_edge_feat[key] = value[eid] sub_node_feat = {} @@ -554,7 +577,7 @@ class Graph(object): Return: Batch iterator """ - perm = np.arange(self._num_nodes, dtype="int32") + perm = np.arange(self._num_nodes, dtype="int64") if shuffle: np.random.shuffle(perm) start = 0 @@ -644,7 +667,7 @@ class Graph(object): break succ = self.successor(cur_nodes) sample_index = np.floor( - np.random.rand(outdegree.shape[0]) * outdegree).astype("int32") + np.random.rand(outdegree.shape[0]) * outdegree).astype("int64") nxt_cur_nodes = [] for s, ind, walk_id in zip(succ, sample_index, cur_walk_ids): @@ -677,8 +700,8 @@ class Graph(object): cur_walk_ids = np.arange(0, len(nodes)) cur_nodes = np.array(nodes) - prev_nodes = np.array([-1] * len(nodes), dtype="int32") - prev_succs = np.array([[]] * len(nodes), dtype="int32") + prev_nodes = np.array([-1] * len(nodes), dtype="int64") + prev_succs = np.array([[]] * len(nodes), dtype="int64") for l in range(max_depth): # select the walks not end outdegree = self.outdegree(cur_nodes) @@ -693,7 +716,7 @@ class Graph(object): break cur_succs = self.successor(cur_nodes) num_nodes = cur_nodes.shape[0] - nxt_nodes = np.zeros(num_nodes, dtype="int32") + nxt_nodes = np.zeros(num_nodes, dtype="int64") for idx, (succ, prev_succ, walk_id, prev_node) in enumerate( zip(cur_succs, prev_succs, cur_walk_ids, prev_nodes)): diff --git a/pgl/graph_kernel.pyx b/pgl/graph_kernel.pyx index 58095c3031bd77cd630152c5a5430f40f3ae0d2c..a911debe6bf3828838f33ea45b2efb90df98a070 100644 --- a/pgl/graph_kernel.pyx +++ b/pgl/graph_kernel.pyx @@ -26,20 +26,20 @@ from libc.stdlib cimport rand, RAND_MAX @cython.boundscheck(False) @cython.wraparound(False) -def build_index(np.ndarray[np.int32_t, ndim=1] u, - np.ndarray[np.int32_t, ndim=1] v, - int num_nodes): +def build_index(np.ndarray[np.int64_t, ndim=1] u, + np.ndarray[np.int64_t, ndim=1] v, + long long num_nodes): """Building Edge Index """ - cdef int i - cdef int h=len(u) - cdef int n_size = num_nodes - cdef np.ndarray[np.int32_t, ndim=1] degree = np.zeros([n_size], dtype=np.int32) - cdef np.ndarray[np.int32_t, ndim=1] count = np.zeros([n_size], dtype=np.int32) - cdef np.ndarray[np.int32_t, ndim=1] _tmp_v = np.zeros([h], dtype=np.int32) - cdef np.ndarray[np.int32_t, ndim=1] _tmp_u = np.zeros([h], dtype=np.int32) - cdef np.ndarray[np.int32_t, ndim=1] _tmp_eid = np.zeros([h], dtype=np.int32) - cdef np.ndarray[np.int32_t, ndim=1] indptr = np.zeros([n_size + 1], dtype=np.int32) + cdef long long i + cdef long long h=len(u) + cdef long long n_size = num_nodes + cdef np.ndarray[np.int64_t, ndim=1] degree = np.zeros([n_size], dtype=np.int64) + cdef np.ndarray[np.int64_t, ndim=1] count = np.zeros([n_size], dtype=np.int64) + cdef np.ndarray[np.int64_t, ndim=1] _tmp_v = np.zeros([h], dtype=np.int64) + cdef np.ndarray[np.int64_t, ndim=1] _tmp_u = np.zeros([h], dtype=np.int64) + cdef np.ndarray[np.int64_t, ndim=1] _tmp_eid = np.zeros([h], dtype=np.int64) + cdef np.ndarray[np.int64_t, ndim=1] indptr = np.zeros([n_size + 1], dtype=np.int64) with nogil: for i in xrange(h): @@ -64,16 +64,16 @@ def build_index(np.ndarray[np.int32_t, ndim=1] u, @cython.boundscheck(False) @cython.wraparound(False) -def map_edges(np.ndarray[np.int32_t, ndim=1] eid, - np.ndarray[np.int32_t, ndim=2] edges, +def map_edges(np.ndarray[np.int64_t, ndim=1] eid, + np.ndarray[np.int64_t, ndim=2] edges, reindex): """Mapping edges by given dictionary """ - cdef unordered_map[int, int] m = reindex - cdef int i = 0 - cdef int h = len(eid) - cdef np.ndarray[np.int32_t, ndim=2] r_edges = np.zeros([h, 2], dtype=np.int32) - cdef int j + cdef unordered_map[long long, long long] m = reindex + cdef long long i = 0 + cdef long long h = len(eid) + cdef np.ndarray[np.int64_t, ndim=2] r_edges = np.zeros([h, 2], dtype=np.int64) + cdef long long j with nogil: for i in xrange(h): j = eid[i] @@ -86,31 +86,33 @@ def map_edges(np.ndarray[np.int32_t, ndim=1] eid, def map_nodes(nodes, reindex): """Mapping nodes by given dictionary """ - cdef unordered_map[int, int] m = reindex - cdef int i = 0 - cdef int h = len(nodes) - cdef np.ndarray[np.int32_t, ndim=1] new_nodes = np.zeros([h], dtype=np.int32) - cdef int j - for i in xrange(h): - j = nodes[i] - new_nodes[i] = m[j] + cdef np.ndarray[np.int64_t, ndim=1] t_nodes = np.array(nodes, dtype=np.int64) + cdef unordered_map[long long, long long] m = reindex + cdef long long i = 0 + cdef long long h = len(nodes) + cdef np.ndarray[np.int64_t, ndim=1] new_nodes = np.zeros([h], dtype=np.int64) + cdef long long j + with nogil: + for i in xrange(h): + j = t_nodes[i] + new_nodes[i] = m[j] return new_nodes @cython.boundscheck(False) @cython.wraparound(False) -def node2vec_sample(np.ndarray[np.int32_t, ndim=1] succ, - np.ndarray[np.int32_t, ndim=1] prev_succ, int prev_node, +def node2vec_sample(np.ndarray[np.int64_t, ndim=1] succ, + np.ndarray[np.int64_t, ndim=1] prev_succ, long long prev_node, float p, float q): """Fast implement of node2vec sampling """ - cdef int i + cdef long long i cdef succ_len = len(succ) cdef prev_succ_len = len(prev_succ) cdef vector[float] probs cdef float prob_sum = 0 - cdef unordered_set[int] prev_succ_set + cdef unordered_set[long long] prev_succ_set for i in xrange(prev_succ_len): prev_succ_set.insert(prev_succ[i]) @@ -127,9 +129,177 @@ def node2vec_sample(np.ndarray[np.int32_t, ndim=1] succ, cdef float rand_num = float(rand())/RAND_MAX * prob_sum - cdef int sample_succ = 0 + cdef long long sample_succ = 0 for i in xrange(succ_len): rand_num -= probs[i] if rand_num <= 0: sample_succ = succ[i] return sample_succ + +@cython.boundscheck(False) +@cython.wraparound(False) +def subset_choose_index(long long s_size, + np.ndarray[ndim=1, dtype=np.int64_t] nid, + np.ndarray[ndim=1, dtype=np.int64_t] rnd, + np.ndarray[ndim=1, dtype=np.int64_t] buff_nid, + long long offset): + cdef long long n_size = len(nid) + cdef long long i + cdef long long j + cdef unordered_map[long long, long long] m + with nogil: + for i in xrange(s_size): + j = rnd[offset + i] % n_size + if j >= i: + buff_nid[offset + i] = nid[j] if m.find(j) == m.end() else nid[m[j]] + m[j] = i if m.find(i) == m.end() else m[i] + else: + buff_nid[offset + i] = buff_nid[offset + j] + buff_nid[offset + j] = nid[i] if m.find(i) == m.end() else nid[m[i]] + + +@cython.boundscheck(False) +@cython.wraparound(False) +def subset_choose_index_eid(long long s_size, + np.ndarray[ndim=1, dtype=np.int64_t] nid, + np.ndarray[ndim=1, dtype=np.int64_t] eid, + np.ndarray[ndim=1, dtype=np.int64_t] rnd, + np.ndarray[ndim=1, dtype=np.int64_t] buff_nid, + np.ndarray[ndim=1, dtype=np.int64_t] buff_eid, + long long offset): + cdef long long n_size = len(nid) + cdef long long i + cdef long long j + cdef unordered_map[long long, long long] m + with nogil: + for i in xrange(s_size): + j = rnd[offset + i] % n_size + if j >= i: + if m.find(j) == m.end(): + buff_nid[offset + i], buff_eid[offset + i] = nid[j], eid[j] + else: + buff_nid[offset + i], buff_eid[offset + i] = nid[m[j]], eid[m[j]] + m[j] = i if m.find(i) == m.end() else m[i] + else: + buff_nid[offset + i], buff_eid[offset + i] = buff_nid[offset + j], buff_eid[offset + j] + if m.find(i) == m.end(): + buff_nid[offset + j], buff_eid[offset + j] = nid[i], eid[i] + else: + buff_nid[offset + j], buff_eid[offset + j] = nid[m[i]], eid[m[i]] + +@cython.boundscheck(False) +@cython.wraparound(False) +def sample_subset(list nids, long long maxdegree, shuffle=False): + cdef np.ndarray[ndim=1, dtype=np.int64_t] buff_index + cdef long long buff_size, sample_size + cdef long long total_buff_size = 0 + cdef long long inc = 0 + cdef list output = [] + for inc in xrange(len(nids)): + buff_size = len(nids[inc]) + if buff_size > maxdegree: + total_buff_size += maxdegree + elif shuffle: + total_buff_size += buff_size + cdef np.ndarray[ndim=1, dtype=np.int64_t] buff_nid = np.zeros([total_buff_size], dtype=np.int64) + cdef np.ndarray[np.int64_t, ndim=1] rnd = np.random.randint(0, np.iinfo(np.int64).max, + dtype=np.int64, size=total_buff_size) + + cdef long long offset = 0 + for inc in xrange(len(nids)): + buff_size = len(nids[inc]) + if not shuffle and buff_size <= maxdegree: + output.append(nids[inc]) + else: + sample_size = buff_size if buff_size <= maxdegree else maxdegree + subset_choose_index(sample_size, nids[inc], rnd, buff_nid, offset) + output.append(buff_nid[offset:offset+sample_size]) + offset += sample_size + return output + +@cython.boundscheck(False) +@cython.wraparound(False) +def sample_subset_with_eid(list nids, list eids, long long maxdegree, shuffle=False): + cdef np.ndarray[ndim=1, dtype=np.int64_t] buff_index + cdef long long buff_size, sample_size + cdef long long total_buff_size = 0 + cdef long long inc = 0 + cdef list output = [] + cdef list output_eid = [] + for inc in xrange(len(nids)): + buff_size = len(nids[inc]) + if buff_size > maxdegree: + total_buff_size += maxdegree + elif shuffle: + total_buff_size += buff_size + cdef np.ndarray[ndim=1, dtype=np.int64_t] buff_nid = np.zeros([total_buff_size], dtype=np.int64) + cdef np.ndarray[ndim=1, dtype=np.int64_t] buff_eid = np.zeros([total_buff_size], dtype=np.int64) + cdef np.ndarray[np.int64_t, ndim=1] rnd = np.random.randint(0, np.iinfo(np.int64).max, + dtype=np.int64, size=total_buff_size) + + cdef long long offset = 0 + for inc in xrange(len(nids)): + buff_size = len(nids[inc]) + if not shuffle and buff_size <= maxdegree: + output.append(nids[inc]) + output_eid.append(eids[inc]) + else: + sample_size = buff_size if buff_size <= maxdegree else maxdegree + subset_choose_index_eid(sample_size, nids[inc], eids[inc], rnd, buff_nid, buff_eid, offset) + output.append(buff_nid[offset:offset+sample_size]) + output_eid.append(buff_eid[offset:offset+sample_size]) + offset += sample_size + return output, output_eid + +@cython.boundscheck(False) +@cython.wraparound(False) +def skip_gram_gen_pair(vector[long long] walk, long win_size=5): + cdef vector[long long] src + cdef vector[long long] dst + cdef long long l = len(walk) + cdef long long real_win_size, left, right, i + cdef np.ndarray[np.int64_t, ndim=1] rnd = np.random.randint(1, win_size+1, + dtype=np.int64, size=l) + with nogil: + for i in xrange(l): + real_win_size = rnd[i] + left = i - real_win_size + if left < 0: + left = 0 + right = i + real_win_size + if right >= l: + right = l - 1 + for j in xrange(left, right+1): + if walk[i] == walk[j]: + continue + src.push_back(walk[i]) + dst.push_back(walk[j]) + return src, dst + +@cython.boundscheck(False) +@cython.wraparound(False) +def alias_sample_build_table(np.ndarray[np.float64_t, ndim=1] probs): + cdef long long l = len(probs) + cdef np.ndarray[np.float64_t, ndim=1] alias = probs * l + cdef np.ndarray[np.int64_t, ndim=1] events = np.zeros(l, dtype=np.int64) + + cdef vector[long long] larger_num, smaller_num + cdef long long i, s_i, l_i + with nogil: + for i in xrange(l): + if alias[i] > 1: + larger_num.push_back(i) + elif alias[i] < 1: + smaller_num.push_back(i) + + while smaller_num.size() > 0 and larger_num.size() > 0: + s_i = smaller_num.back() + l_i = larger_num.back() + smaller_num.pop_back() + events[s_i] = l_i + alias[l_i] -= (1 - alias[s_i]) + if alias[l_i] <= 1: + larger_num.pop_back() + if alias[l_i] < 1: + smaller_num.push_back(l_i) + return alias, events diff --git a/pgl/graph_wrapper.py b/pgl/graph_wrapper.py index 42cc6c2ec8082a188d288e79468a1a82b07d72f1..d41d09c5fcf62bfc8661f5999a720392c295a186 100644 --- a/pgl/graph_wrapper.py +++ b/pgl/graph_wrapper.py @@ -97,7 +97,6 @@ class BaseGraphWrapper(object): self._indegree = None self._edge_uniq_dst = None self._edge_uniq_dst_count = None - self._bucketing_index = None self._node_ids = None def send(self, message_func, nfeat_list=None, efeat_list=None): @@ -188,7 +187,7 @@ class BaseGraphWrapper(object): output = recv( dst=self._edges_dst, uniq_dst=self._edge_uniq_dst, - bucketing_index=self._bucketing_index, + bucketing_index=self._edge_uniq_dst_count, msg=msg, reduce_function=reduce_function, node_ids=self._node_ids) @@ -200,7 +199,7 @@ class BaseGraphWrapper(object): Return: A tuple of Tensor (src, dst). Src and dst are both - tensor with shape (num_edges, ) and dtype int32. + tensor with shape (num_edges, ) and dtype int64. """ return self._edges_src, self._edges_dst @@ -209,7 +208,7 @@ class BaseGraphWrapper(object): """Return a variable of number of nodes Return: - A variable with shape (1,) as the number of nodes in int32. + A variable with shape (1,) as the number of nodes in int64. """ return self._num_nodes @@ -237,7 +236,7 @@ class BaseGraphWrapper(object): """Return the indegree tensor for all nodes. Return: - A tensor of shape (num_nodes, ) in int32. + A tensor of shape (num_nodes, ) in int64. """ return self._indegree @@ -312,6 +311,8 @@ class StaticGraphWrapper(BaseGraphWrapper): nodes = graph.nodes uniq_dst = nodes[indegree > 0] uniq_dst_count = indegree[indegree > 0] + uniq_dst_count = np.cumsum(uniq_dst_count, dtype='int32') + uniq_dst_count = np.insert(uniq_dst_count, 0, 0) edge_feat = {} @@ -323,56 +324,46 @@ class StaticGraphWrapper(BaseGraphWrapper): self.__create_graph_edge_feat(edge_feat, self._initializers) self._edges_src, init = paddle_helper.constant( - dtype="int32", + dtype="int64", value=src, - name=self.__data_name_prefix + '_edges_src') + name=self.__data_name_prefix + '/edges_src') self._initializers.append(init) self._edges_dst, init = paddle_helper.constant( - dtype="int32", + dtype="int64", value=dst, - name=self.__data_name_prefix + '_edges_dst') + name=self.__data_name_prefix + '/edges_dst') self._initializers.append(init) self._num_nodes, init = paddle_helper.constant( - dtype="int32", + dtype="int64", hide_batch_size=False, value=np.array([graph.num_nodes]), - name=self.__data_name_prefix + '_num_nodes') + name=self.__data_name_prefix + '/num_nodes') self._initializers.append(init) self._edge_uniq_dst, init = paddle_helper.constant( - name=self.__data_name_prefix + "_uniq_dst", - dtype="int32", + name=self.__data_name_prefix + "/uniq_dst", + dtype="int64", value=uniq_dst) self._initializers.append(init) self._edge_uniq_dst_count, init = paddle_helper.constant( - name=self.__data_name_prefix + "_uniq_dst_count", + name=self.__data_name_prefix + "/uniq_dst_count", dtype="int32", value=uniq_dst_count) self._initializers.append(init) - bucket_value = np.expand_dims( - np.arange( - 0, len(dst), dtype="int32"), -1) - self._bucketing_index, init = paddle_helper.lod_constant( - name=self.__data_name_prefix + "_bucketing_index", - dtype="int32", - lod=list(uniq_dst_count), - value=bucket_value) - self._initializers.append(init) - - node_ids_value = np.arange(0, graph.num_nodes, dtype="int32") + node_ids_value = np.arange(0, graph.num_nodes, dtype="int64") self._node_ids, init = paddle_helper.constant( - name=self.__data_name_prefix + "_node_ids", - dtype="int32", + name=self.__data_name_prefix + "/node_ids", + dtype="int64", value=node_ids_value) self._initializers.append(init) self._indegree, init = paddle_helper.constant( - name=self.__data_name_prefix + "_indegree", - dtype="int32", + name=self.__data_name_prefix + "/indegree", + dtype="int64", value=indegree) self._initializers.append(init) @@ -384,7 +375,8 @@ class StaticGraphWrapper(BaseGraphWrapper): node_feat_dtype = node_feat_value.dtype self._node_feat_tensor_dict[ node_feat_name], init = paddle_helper.constant( - name=self.__data_name_prefix + '_' + node_feat_name, + name=self.__data_name_prefix + '/node_feat/' + + node_feat_name, dtype=node_feat_dtype, value=node_feat_value) collector.append(init) @@ -397,7 +389,8 @@ class StaticGraphWrapper(BaseGraphWrapper): edge_feat_dtype = edge_feat_value.dtype self._edge_feat_tensor_dict[ edge_feat_name], init = paddle_helper.constant( - name=self.__data_name_prefix + '_' + edge_feat_name, + name=self.__data_name_prefix + '/edge_feat/' + + edge_feat_name, dtype=edge_feat_dtype, value=edge_feat_value) collector.append(init) @@ -483,6 +476,8 @@ class GraphWrapper(BaseGraphWrapper): def __init__(self, name, place, node_feat=[], edge_feat=[]): super(GraphWrapper, self).__init__() + # collect holders for PyReader + self._holder_list = [] self.__data_name_prefix = name self._place = place self.__create_graph_attr_holders() @@ -498,78 +493,78 @@ class GraphWrapper(BaseGraphWrapper): """Create data holders for graph attributes. """ self._edges_src = fluid.layers.data( - self.__data_name_prefix + '_edges_src', + self.__data_name_prefix + '/edges_src', shape=[None], append_batch_size=False, - dtype="int32", + dtype="int64", stop_gradient=True) self._edges_dst = fluid.layers.data( - self.__data_name_prefix + '_edges_dst', + self.__data_name_prefix + '/edges_dst', shape=[None], append_batch_size=False, - dtype="int32", + dtype="int64", stop_gradient=True) self._num_nodes = fluid.layers.data( - self.__data_name_prefix + '_num_nodes', + self.__data_name_prefix + '/num_nodes', shape=[1], append_batch_size=False, - dtype='int32', + dtype='int64', stop_gradient=True) self._edge_uniq_dst = fluid.layers.data( - self.__data_name_prefix + "_uniq_dst", + self.__data_name_prefix + "/uniq_dst", shape=[None], append_batch_size=False, - dtype="int32", + dtype="int64", stop_gradient=True) self._edge_uniq_dst_count = fluid.layers.data( - self.__data_name_prefix + "_uniq_dst_count", + self.__data_name_prefix + "/uniq_dst_count", shape=[None], append_batch_size=False, dtype="int32", stop_gradient=True) - self._bucketing_index = fluid.layers.data( - self.__data_name_prefix + "_bucketing_index", - shape=[None, 1], - append_batch_size=False, - dtype="int32", - lod_level=1, - stop_gradient=True) self._node_ids = fluid.layers.data( - self.__data_name_prefix + "_node_ids", + self.__data_name_prefix + "/node_ids", shape=[None], append_batch_size=False, - dtype="int32", + dtype="int64", stop_gradient=True) self._indegree = fluid.layers.data( - self.__data_name_prefix + "_indegree", + self.__data_name_prefix + "/indegree", shape=[None], append_batch_size=False, - dtype="int32", + dtype="int64", stop_gradient=True) + self._holder_list.extend([ + self._edges_src, self._edges_dst, self._num_nodes, + self._edge_uniq_dst, self._edge_uniq_dst_count, self._node_ids, + self._indegree + ]) def __create_graph_node_feat_holders(self, node_feat_name, node_feat_shape, node_feat_dtype): """Create data holders for node features. """ feat_holder = fluid.layers.data( - self.__data_name_prefix + '_' + node_feat_name, + self.__data_name_prefix + '/node_feat/' + node_feat_name, shape=node_feat_shape, append_batch_size=False, dtype=node_feat_dtype, stop_gradient=True) self._node_feat_tensor_dict[node_feat_name] = feat_holder + self._holder_list.append(feat_holder) def __create_graph_edge_feat_holders(self, edge_feat_name, edge_feat_shape, edge_feat_dtype): """Create edge holders for edge features. """ feat_holder = fluid.layers.data( - self.__data_name_prefix + '_' + edge_feat_name, + self.__data_name_prefix + '/edge_feat/' + edge_feat_name, shape=edge_feat_shape, append_batch_size=False, dtype=edge_feat_dtype, stop_gradient=True) self._edge_feat_tensor_dict[edge_feat_name] = feat_holder + self._holder_list.append(feat_holder) def to_feed(self, graph): """Convert the graph into feed_dict. @@ -590,6 +585,8 @@ class GraphWrapper(BaseGraphWrapper): nodes = graph.nodes uniq_dst = nodes[indegree > 0] uniq_dst_count = indegree[indegree > 0] + uniq_dst_count = np.cumsum(uniq_dst_count, dtype='int32') + uniq_dst_count = np.insert(uniq_dst_count, 0, 0) edge_feat = {} @@ -597,21 +594,27 @@ class GraphWrapper(BaseGraphWrapper): edge_feat[key] = value[eid] node_feat = graph.node_feat - feed_dict[self.__data_name_prefix + '_edges_src'] = src - feed_dict[self.__data_name_prefix + '_edges_dst'] = dst - feed_dict[self.__data_name_prefix + '_num_nodes'] = graph.num_nodes - feed_dict[self.__data_name_prefix + '_uniq_dst'] = uniq_dst - feed_dict[self.__data_name_prefix + '_uniq_dst_count'] = uniq_dst_count - feed_dict[self.__data_name_prefix + '_node_ids'] = graph.nodes - feed_dict[self.__data_name_prefix + '_indegree'] = indegree - feed_dict[self.__data_name_prefix + '_bucketing_index'] = \ - fluid.create_lod_tensor(np.expand_dims(np.arange(0, len(dst), dtype="int32"), -1), - [list(uniq_dst_count)], self._place) + feed_dict[self.__data_name_prefix + '/edges_src'] = src + feed_dict[self.__data_name_prefix + '/edges_dst'] = dst + feed_dict[self.__data_name_prefix + '/num_nodes'] = np.array( + graph.num_nodes) + feed_dict[self.__data_name_prefix + '/uniq_dst'] = uniq_dst + feed_dict[self.__data_name_prefix + '/uniq_dst_count'] = uniq_dst_count + feed_dict[self.__data_name_prefix + '/node_ids'] = graph.nodes + feed_dict[self.__data_name_prefix + '/indegree'] = indegree for key in self._node_feat_tensor_dict: - feed_dict[self.__data_name_prefix + '_' + key] = node_feat[key] + feed_dict[self.__data_name_prefix + '/node_feat/' + + key] = node_feat[key] for key in self._edge_feat_tensor_dict: - feed_dict[self.__data_name_prefix + '_' + key] = edge_feat[key] + feed_dict[self.__data_name_prefix + '/edge_feat/' + + key] = edge_feat[key] return feed_dict + + @property + def holder_list(self): + """Return the holder list. + """ + return self._holder_list diff --git a/pgl/layers/conv.py b/pgl/layers/conv.py index a1dabdde55697638d07f83446ffab034f6eebe9c..804534a06b0602b1f6ab3698efe2cfc997cb4d13 100644 --- a/pgl/layers/conv.py +++ b/pgl/layers/conv.py @@ -53,7 +53,7 @@ def gcn(gw, feature, hidden_size, activation, name, norm=None): feature = fluid.layers.fc(feature, size=hidden_size, bias_attr=False, - name=name) + param_attr=fluid.ParamAttr(name=name)) if norm is not None: feature = feature * norm @@ -67,7 +67,7 @@ def gcn(gw, feature, hidden_size, activation, name, norm=None): output = fluid.layers.fc(output, size=hidden_size, bias_attr=False, - name=name) + param_attr=fluid.ParamAttr(name=name)) if norm is not None: output = output * norm @@ -152,7 +152,7 @@ def gat(gw, ft = fluid.layers.fc(feature, hidden_size * num_heads, bias_attr=False, - name=name + '_weight') + param_attr=fluid.ParamAttr(name=name + '_weight')) left_a = fluid.layers.create_parameter( shape=[num_heads, hidden_size], dtype='float32', diff --git a/pgl/layers/set2set.py b/pgl/layers/set2set.py new file mode 100644 index 0000000000000000000000000000000000000000..18d65fae97009a770900130ccf14d248df06ebed --- /dev/null +++ b/pgl/layers/set2set.py @@ -0,0 +1,93 @@ +# Copyright (c) 2019 PaddlePaddle Authors. All Rights Reserved +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +"""This package implements common layers to help building pooling operators. +""" +from __future__ import division +from __future__ import absolute_import +from __future__ import print_function +from __future__ import unicode_literals + +import paddle.fluid as F +import paddle.fluid.layers as L + +import pgl + + +class Set2Set(object): + """Implementation of set2set pooling operator. + + This is an implementation of the paper ORDER MATTERS: SEQUENCE TO SEQUENCE + FOR SETS (https://arxiv.org/pdf/1511.06391.pdf). + """ + + def __init__(self, input_dim, n_iters, n_layers): + """ + Args: + input_dim: hidden size of input data. + n_iters: number of set2set iterations. + n_layers: number of lstm layers. + """ + self.input_dim = input_dim + self.output_dim = 2 * input_dim + self.n_iters = n_iters + + # this's set2set n_layers, lstm n_layers = 1 + self.n_layers = n_layers + + def forward(self, feat): + """ + Args: + feat: input feature with shape [batch, n_edges, dim]. + + Return: + output_feat: output feature of set2set pooling with shape [batch, 2*dim]. + """ + + seqlen = 1 + h = L.fill_constant_batch_size_like( + feat, [1, self.n_layers, self.input_dim], "float32", 0) + h = L.transpose(h, [1, 0, 2]) + c = h + + # [seqlen, batch, dim] + q_star = L.fill_constant_batch_size_like( + feat, [1, seqlen, self.output_dim], "float32", 0) + q_star = L.transpose(q_star, [1, 0, 2]) + + for _ in range(self.n_iters): + + # q [seqlen, batch, dim] + # h [layer, batch, dim] + q, h, c = L.lstm( + q_star, + h, + c, + seqlen, + self.input_dim, + self.n_layers, + is_bidirec=False) + + # e [batch, seqlen, n_edges] + e = L.matmul(L.transpose(q, [1, 0, 2]), feat, transpose_y=True) + # alpha [batch, seqlen, n_edges] + alpha = L.softmax(e) + + # readout [batch, seqlen, dim] + readout = L.matmul(alpha, feat) + readout = L.transpose(readout, [1, 0, 2]) + + # q_star [seqlen, batch, dim + dim] + q_star = L.concat([q, readout], -1) + + return L.squeeze(q_star, [0]) diff --git a/pgl/redis_graph.py b/pgl/redis_graph.py new file mode 100644 index 0000000000000000000000000000000000000000..ae6ae1a8b1cd19a9a3eddfab34cd1c5e525f9f47 --- /dev/null +++ b/pgl/redis_graph.py @@ -0,0 +1,478 @@ +# Copyright (c) 2019 PaddlePaddle Authors. All Rights Reserved. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +"""redis_graph""" + +import pgl +import redis +from redis import BlockingConnectionPool, StrictRedis +from redis._compat import b, unicode, bytes, long, basestring +from rediscluster.nodemanager import NodeManager +from rediscluster.crc import crc16 +from collections import OrderedDict +import threading +import numpy as np +import time +import json +import pgl.graph as pgraph +import pickle as pkl +from pgl.utils.logger import log +import pgl.graph_kernel as graph_kernel + + +def encode(value): + """ + Return a bytestring representation of the value. + This method is copied from Redis' connection.py:Connection.encode + """ + if isinstance(value, bytes): + return value + elif isinstance(value, (int, long)): + value = b(str(value)) + elif isinstance(value, float): + value = b(repr(value)) + elif not isinstance(value, basestring): + value = unicode(value) + if isinstance(value, unicode): + value = value.encode('utf-8') + return value + + +def crc16_hash(data): + """crc16_hash""" + return crc16(encode(data)) + + +LUA_SCRIPT = """ +math.randomseed(tonumber(ARGV[1])) + +local function permute(tab, count, bucket_size) + local n = #tab / bucket_size + local o_ret = {} + local o_dict = {} + for i = 1, count do + local j = math.random(i, n) + o_ret[i] = string.sub(tab, (i - 1) * bucket_size + 1, i * bucket_size) + if j > count then + if o_dict[j] ~= nil then + o_ret[i], o_dict[j] = o_dict[j], o_ret[i] + else + o_dict[j], o_ret[i] = o_ret[i], string.sub(tab, (j - 1) * bucket_size + 1, j * bucket_size) + end + end + end + return table.concat(o_ret) +end + +local bucket_size = 16 +local ret = {} +local sample_size = tonumber(ARGV[2]) +for i=1, #ARGV - 2 do + local tab = redis.call("HGET", KEYS[1], ARGV[i + 2]) + if tab then + if #tab / bucket_size <= sample_size then + ret[i] = tab + else + ret[i] = permute(tab, sample_size, bucket_size) + end + else + ret[i] = tab + end +end +return ret +""" + + +class RedisCluster(object): + """RedisCluster""" + + def __init__(self, startup_nodes): + self.nodemanager = NodeManager(startup_nodes=startup_nodes) + self.nodemanager.initialize() + self.redis_worker = {} + for node, config in self.nodemanager.nodes.items(): + rdp = BlockingConnectionPool( + host=config["host"], port=config["port"]) + self.redis_worker[node] = { + "worker": StrictRedis( + connection_pool=rdp, decode_responses=False), + "type": config["server_type"] + } + + def get(self, key): + """get""" + slot = self.nodemanager.keyslot(key) + node = np.random.choice(self.nodemanager.slots[slot]) + worker = self.redis_worker[node['name']] + if worker["type"] == "slave": + worker["worker"].execute_command("READONLY") + return worker["worker"].get(key) + + def hmget(self, key, fields): + """hmget""" + while True: + retry = 0 + try: + slot = self.nodemanager.keyslot(key) + node = np.random.choice(self.nodemanager.slots[slot]) + worker = self.redis_worker[node['name']] + if worker["type"] == "slave": + worker["worker"].execute_command("READONLY") + ret = worker["worker"].hmget(key, fields) + break + except Exception as e: + retry += 1 + if retry > 5: + raise e + print("RETRY hmget after 1 sec. Retry Time %s" % retry) + time.sleep(1) + return ret + + def hmget_sample(self, key, fields, sample): + """hmget_sample""" + while True: + retry = 0 + try: + slot = self.nodemanager.keyslot(key) + node = np.random.choice(self.nodemanager.slots[slot]) + worker = self.redis_worker[node['name']] + if worker["type"] == "slave": + worker["worker"].execute_command("READONLY") + func = worker["worker"].register_script(LUA_SCRIPT) + ret = func( + keys=[key], + args=[np.random.randint(4294967295), sample] + fields) + break + except Exception as e: + retry += 1 + if retry > 5: + raise e + print("RETRY hmget_sample after 1 sec. Retry Time %s" % retry) + time.sleep(1) + return ret + + +def hmget_sample_helper(rs, query, num_parts, sample_size): + """hmget_sample_helper""" + buff = [b""] * len(query) + part_dict = {} + part_ind_dict = {} + for ind, q in enumerate(query): + part = crc16_hash(q) % num_parts + part = "part-%s" % part + if part not in part_dict: + part_dict[part] = [] + part_ind_dict[part] = [] + part_dict[part].append(q) + part_ind_dict[part].append(ind) + + def worker(_key, _value, _buff, _rs, _part_ind_dict, _sample_size): + """worker""" + response = _rs.hmget_sample(_key, _value, _sample_size) + for res, ind in zip(response, _part_ind_dict[_key]): + buff[ind] = res + + def hmget(_part_dict, _rs, _buff, _part_ind_dict, _sample_size): + """hmget""" + key_value = list(_part_dict.items()) + np.random.shuffle(key_value) + for key, value in key_value: + worker(key, value, _buff, _rs, _part_ind_dict, _sample_size) + + hmget(part_dict, rs, buff, part_ind_dict, sample_size) + return buff + + +def hmget_helper(rs, query, num_parts): + """hmget_helper""" + buff = [b""] * len(query) + part_dict = {} + part_ind_dict = {} + for ind, q in enumerate(query): + part = crc16_hash(q) % num_parts + part = "part-%s" % part + if part not in part_dict: + part_dict[part] = [] + part_ind_dict[part] = [] + part_dict[part].append(q) + part_ind_dict[part].append(ind) + + def worker(_key, _value, _buff, _rs, _part_ind_dict): + """worker""" + response = _rs.hmget(_key, _value) + for res, ind in zip(response, _part_ind_dict[_key]): + buff[ind] = res + + def hmget(_part_dict, _rs, _buff, _part_ind_dict): + """hmget""" + key_value = list(_part_dict.items()) + np.random.shuffle(key_value) + for key, value in key_value: + worker(key, value, _buff, _rs, _part_ind_dict) + + hmget(part_dict, rs, buff, part_ind_dict) + return buff + + +class RedisGraph(pgraph.Graph): + """RedisGraph""" + + def __init__(self, name, redis_config, num_parts): + self._rs = RedisCluster(startup_nodes=redis_config) + self.num_parts = num_parts + self._name = name + self._num_nodes = None + self._num_edges = None + self._node_feat_info = None + self._edge_feat_info = None + self._node_feat_dtype = None + self._edge_feat_dtype = None + self._node_feat_shape = None + self._edge_feat_shape = None + + @property + def num_nodes(self): + """num_nodes""" + if self._num_nodes is None: + self._num_nodes = int(self._rs.get("num_nodes")) + return self._num_nodes + + @property + def num_edges(self): + """num_edges""" + if self._num_edges is None: + self._num_edges = int(self._rs.get("num_edges")) + return self._num_edges + + def node_feat_info(self): + """node_feat_info""" + if self._node_feat_info is None: + buff = self._rs.get("nf:infos") + self._node_feat_info = json.loads(buff.decode()) + return self._node_feat_info + + def node_feat_dtype(self, key): + """node_feat_dtype""" + if self._node_feat_dtype is None: + self._node_feat_dtype = {} + for key, _, dtype in self.node_feat_info(): + self._node_feat_dtype[key] = dtype + return self._node_feat_dtype[key] + + def node_feat_shape(self, key): + """node_feat_shape""" + if self._node_feat_shape is None: + self._node_feat_shape = {} + for key, shape, _ in self.node_feat_info(): + self._node_feat_shape[key] = shape + return self._node_feat_shape[key] + + def edge_feat_shape(self, key): + """edge_feat_shape""" + if self._edge_feat_shape is None: + self._edge_feat_shape = {} + for key, shape, _ in self.edge_feat_info(): + self._edge_feat_shape[key] = shape + return self._edge_feat_shape[key] + + def edge_feat_dtype(self, key): + """edge_feat_dtype""" + if self._edge_feat_dtype is None: + self._edge_feat_dtype = {} + for key, _, dtype in self.edge_feat_info(): + self._edge_feat_dtype[key] = dtype + return self._edge_feat_dtype[key] + + def edge_feat_info(self): + """edge_feat_info""" + if self._edge_feat_info is None: + buff = self._rs.get("ef:infos") + self._edge_feat_info = json.loads(buff.decode()) + return self._edge_feat_info + + def sample_predecessor(self, nodes, max_degree, return_eids=False): + """sample_predecessor""" + query = ["d:%s" % n for n in nodes] + rets = hmget_sample_helper(self._rs, query, self.num_parts, max_degree) + v = [] + eid = [] + for buff in rets: + if buff is None: + v.append(np.array([], dtype="int64")) + eid.append(np.array([], dtype="int64")) + else: + npret = np.frombuffer( + buff, dtype="int64").reshape([-1, 2]).astype("int64") + v.append(npret[:, 0]) + eid.append(npret[:, 1]) + if return_eids: + return np.array(v), np.array(eid) + else: + return np.array(v) + + def sample_successor(self, nodes, max_degree, return_eids=False): + """sample_successor""" + query = ["s:%s" % n for n in nodes] + rets = hmget_sample_helper(self._rs, query, self.num_parts, max_degree) + v = [] + eid = [] + for buff in rets: + if buff is None: + v.append(np.array([], dtype="int64")) + eid.append(np.array([], dtype="int64")) + else: + npret = np.frombuffer( + buff, dtype="int64").reshape([-1, 2]).astype("int64") + v.append(npret[:, 0]) + eid.append(npret[:, 1]) + if return_eids: + return np.array(v), np.array(eid) + else: + return np.array(v) + + def predecessor(self, nodes, return_eids=False): + """predecessor""" + query = ["d:%s" % n for n in nodes] + ret = hmget_helper(self._rs, query, self.num_parts) + v = [] + eid = [] + for buff in ret: + if buff is not None: + npret = np.frombuffer( + buff, dtype="int64").reshape([-1, 2]).astype("int64") + v.append(npret[:, 0]) + eid.append(npret[:, 1]) + else: + v.append(np.array([], dtype="int64")) + eid.append(np.array([], dtype="int64")) + if return_eids: + return np.array(v), np.array(eid) + else: + return np.array(v) + + def successor(self, nodes, return_eids=False): + """successor""" + query = ["s:%s" % n for n in nodes] + ret = hmget_helper(self._rs, query, self.num_parts) + v = [] + eid = [] + for buff in ret: + if buff is not None: + npret = np.frombuffer( + buff, dtype="int64").reshape([-1, 2]).astype("int64") + v.append(npret[:, 0]) + eid.append(npret[:, 1]) + else: + v.append(np.array([], dtype="int64")) + eid.append(np.array([], dtype="int64")) + if return_eids: + return np.array(v), np.array(eid) + else: + return np.array(v) + + def get_edges_by_id(self, eids): + """get_edges_by_id""" + queries = ["e:%s" % e for e in eids] + ret = hmget_helper(self._rs, queries, self.num_parts) + o = np.asarray(ret, dtype="int64") + dst = o % self.num_nodes + src = o // self.num_nodes + data = np.hstack( + [src.reshape([-1, 1]), dst.reshape([-1, 1])]).astype("int64") + return data + + def get_node_feat_by_id(self, key, nodes): + """get_node_feat_by_id""" + queries = ["nf:%s:%i" % (key, nid) for nid in nodes] + ret = hmget_helper(self._rs, queries, self.num_parts) + ret = b"".join(ret) + data = np.frombuffer(ret, dtype=self.node_feat_dtype(key)) + data = data.reshape(self.node_feat_shape(key)) + return data + + def get_edge_feat_by_id(self, key, eids): + """get_edge_feat_by_id""" + queries = ["ef:%s:%i" % (key, e) for e in eids] + ret = hmget_helper(self._rs, queries, self.num_parts) + ret = b"".join(ret) + data = np.frombuffer(ret, dtype=self.edge_feat_dtype(key)) + data = data.reshape(self.edge_feat_shape(key)) + return data + + def subgraph(self, nodes, eid, edges=None): + """Generate subgraph with nodes and edge ids. + + This function will generate a :code:`pgl.graph.Subgraph` object and + copy all corresponding node and edge features. Nodes and edges will + be reindex from 0. + + WARNING: ALL NODES IN EID MUST BE INCLUDED BY NODES + + Args: + nodes: Node ids which will be included in the subgraph. + + eid: Edge ids which will be included in the subgraph. + + Return: + A :code:`pgl.graph.Subgraph` object. + """ + reindex = {} + + for ind, node in enumerate(nodes): + reindex[node] = ind + + if edges is None: + edges = self.get_edges_by_id(eid) + else: + edges = np.array(edges, dtype="int64") + + sub_edges = graph_kernel.map_edges( + np.arange( + len(edges), dtype="int64"), edges, reindex) + + sub_edge_feat = {} + for key, _, _ in self.edge_feat_info(): + sub_edge_feat[key] = self.get_edge_feat_by_id(key, eid) + + sub_node_feat = {} + for key, _, _ in self.node_feat_info(): + sub_node_feat[key] = self.get_node_feat_by_id(key, nodes) + + subgraph = pgraph.SubGraph( + num_nodes=len(nodes), + edges=sub_edges, + node_feat=sub_node_feat, + edge_feat=sub_edge_feat, + reindex=reindex) + return subgraph + + def node_batch_iter(self, batch_size, shuffle=True): + """Node batch iterator + + Iterate all node by batch. + + Args: + batch_size: The batch size of each batch of nodes. + + shuffle: Whether shuffle the nodes. + + Return: + Batch iterator + """ + perm = np.arange(self.num_nodes, dtype="int64") + if shuffle: + np.random.shuffle(perm) + start = 0 + while start < self._num_nodes: + yield perm[start:start + batch_size] + start += batch_size diff --git a/pgl/sample.py b/pgl/sample.py new file mode 100644 index 0000000000000000000000000000000000000000..176c32b9c85e7819646de494966120583c2ddb98 --- /dev/null +++ b/pgl/sample.py @@ -0,0 +1,253 @@ +# Copyright (c) 2019 PaddlePaddle Authors. All Rights Reserved +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +""" + This package implement graph sampling algorithm. +""" +import time +import copy + +import numpy as np +import pgl +from pgl.utils.logger import log +from pgl import graph_kernel + +__all__ = ['graphsage_sample', 'node2vec_sample', 'deepwalk_sample'] + + +def edge_hash(src, dst): + """edge_hash + """ + return src * 100000007 + dst + + +def graphsage_sample(graph, nodes, samples, ignore_edges=[]): + """Implement of graphsage sample. + + Reference paper: https://cs.stanford.edu/~jure/pubs/node2vec-kdd16.pdf. + + Args: + graph: A pgl graph instance + nodes: Sample starting from nodes + samples: A list, number of neighbors in each layer + ignore_edges: list of edge(src, dst) will be ignored. + + Return: + A list of subgraphs + """ + start = time.time() + num_layers = len(samples) + start_nodes = nodes + nodes = list(start_nodes) + eids, edges = [], [] + nodes_set = set(nodes) + layer_nodes, layer_eids, layer_edges = [], [], [] + ignore_edge_set = set([edge_hash(src, dst) for src, dst in ignore_edges]) + + for layer_idx in reversed(range(num_layers)): + if len(start_nodes) == 0: + layer_nodes = [nodes] + layer_nodes + layer_eids = [eids] + layer_eids + layer_edges = [edges] + layer_edges + continue + batch_pred_nodes, batch_pred_eids = graph.sample_predecessor( + start_nodes, samples[layer_idx], return_eids=True) + log.debug("sample_predecessor time: %s" % (time.time() - start)) + start = time.time() + last_nodes_set = nodes_set + + nodes, eids = copy.copy(nodes), copy.copy(eids) + edges = copy.copy(edges) + nodes_set, eids_set = set(nodes), set(eids) + for srcs, dst, pred_eids in zip(batch_pred_nodes, start_nodes, + batch_pred_eids): + for src, eid in zip(srcs, pred_eids): + if edge_hash(src, dst) in ignore_edge_set: + continue + if eid not in eids_set: + eids.append(eid) + edges.append([src, dst]) + eids_set.add(eid) + if src not in nodes_set: + nodes.append(src) + nodes_set.add(src) + layer_edges = [edges] + layer_edges + start_nodes = list(nodes_set - last_nodes_set) + layer_nodes = [nodes] + layer_nodes + layer_eids = [eids] + layer_eids + log.debug("flat time: %s" % (time.time() - start)) + start = time.time() + # Find new nodes + + feed_dict = {} + + subgraphs = [] + for i in range(num_layers): + subgraphs.append( + graph.subgraph( + nodes=layer_nodes[0], eid=layer_eids[i], edges=layer_edges[i])) + # only for this task + subgraphs[i].node_feat["index"] = np.array( + layer_nodes[0], dtype="int64") + log.debug("subgraph time: %s" % (time.time() - start)) + + return subgraphs + + +def alias_sample(size, alias, events): + """Implement of alias sample. + Args: + size: Output shape. + alias: The alias table build by `alias_sample_build_table`. + events: The events table build by `alias_sample_build_table`. + + Return: + samples: The generated random samples. + """ + rand_num = np.random.uniform(0.0, len(alias), size) + idx = rand_num.astype("int64") + uni = rand_num - idx + flags = (uni >= alias[idx]) + idx[flags] = events[idx][flags] + return idx + + +def graph_alias_sample_table(graph, edge_weight_name): + """Build alias sample table for weighted deepwalk. + Args: + graph: The input graph + edge_weight_name: The name of edge weight in edge_feat. + + Return: + Alias sample tables for each nodes. + """ + edge_weight = graph.edge_feat[edge_weight_name] + _, eids_array = graph.successor(return_eids=True) + alias_array, events_array = [], [] + for eids in eids_array: + probs = edge_weight[eids] + probs /= np.sum(probs) + alias, events = graph_kernel.alias_sample_build_table(probs) + alias_array.append(alias), events_array.append(events) + alias_array, events_array = np.array(alias_array), np.array(events_array) + return alias_array, events_array + + +def deepwalk_sample(graph, nodes, max_depth, alias_name=None, + events_name=None): + """Implement of random walk. + + This function get random walks path for given nodes and depth. + + Args: + nodes: Walk starting from nodes + max_depth: Max walking depth + + Return: + A list of walks. + """ + walk = [] + # init + for node in nodes: + walk.append([node]) + + cur_walk_ids = np.arange(0, len(nodes)) + cur_nodes = np.array(nodes) + for l in range(max_depth): + # select the walks not end + cur_succs = graph.successor(cur_nodes) + mask = [len(succ) > 0 for succ in cur_succs] + + if np.any(mask): + cur_walk_ids = cur_walk_ids[mask] + cur_nodes = cur_nodes[mask] + cur_succs = cur_succs[mask] + else: + # stop when all nodes have no successor + break + + if alias_name is not None and events_name is not None: + sample_index = [ + alias_sample([1], graph.node_feat[alias_name][node], + graph.node_feat[events_name][node])[0] + for node in cur_nodes + ] + else: + outdegree = [len(cur_succ) for cur_succ in cur_succs] + sample_index = np.floor( + np.random.rand(cur_succs.shape[0]) * outdegree).astype("int64") + + nxt_cur_nodes = [] + for s, ind, walk_id in zip(cur_succs, sample_index, cur_walk_ids): + walk[walk_id].append(s[ind]) + nxt_cur_nodes.append(s[ind]) + cur_nodes = np.array(nxt_cur_nodes) + return walk + + +def node2vec_sample(graph, nodes, max_depth, p=1.0, q=1.0): + """Implement of node2vec random walk. + + Reference paper: https://cs.stanford.edu/~jure/pubs/node2vec-kdd16.pdf. + + Args: + graph: A pgl graph instance + nodes: Walk starting from nodes + max_depth: Max walking depth + p: Return parameter + q: In-out parameter + + Return: + A list of walks. + """ + if p == 1.0 and q == 1.0: + return deepwalk_sample(graph, nodes, max_depth) + + walk = [] + # init + for node in nodes: + walk.append([node]) + + cur_walk_ids = np.arange(0, len(nodes)) + cur_nodes = np.array(nodes) + prev_nodes = np.array([-1] * len(nodes), dtype="int64") + prev_succs = np.array([[]] * len(nodes), dtype="int64") + for l in range(max_depth): + # select the walks not end + cur_succs = graph.successor(cur_nodes) + + mask = [len(succ) > 0 for succ in cur_succs] + if np.any(mask): + cur_walk_ids = cur_walk_ids[mask] + cur_nodes = cur_nodes[mask] + prev_nodes = prev_nodes[mask] + prev_succs = prev_succs[mask] + cur_succs = cur_succs[mask] + else: + # stop when all nodes have no successor + break + num_nodes = cur_nodes.shape[0] + nxt_nodes = np.zeros(num_nodes, dtype="int64") + + for idx, ( + succ, prev_succ, walk_id, prev_node + ) in enumerate(zip(cur_succs, prev_succs, cur_walk_ids, prev_nodes)): + + sampled_succ = graph_kernel.node2vec_sample(succ, prev_succ, + prev_node, p, q) + walk[walk_id].append(sampled_succ) + nxt_nodes[idx] = sampled_succ + + prev_nodes, prev_succs = cur_nodes, cur_succs + cur_nodes = nxt_nodes + return walk diff --git a/pgl/tests/deepwalk/test_alias_sample.py b/pgl/tests/deepwalk/test_alias_sample.py new file mode 100644 index 0000000000000000000000000000000000000000..c14ba5a3c15f6ca3a62531e5cf63c00e3c1bc967 --- /dev/null +++ b/pgl/tests/deepwalk/test_alias_sample.py @@ -0,0 +1,69 @@ +# Copyright (c) 2019 PaddlePaddle Authors. All Rights Reserved. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +"""test_alias_sample""" +import argparse +import time +import unittest +from collections import Counter + +import numpy as np + +from pgl.graph_kernel import alias_sample_build_table +from pgl.sample import alias_sample + + +class AliasSampleTest(unittest.TestCase): + """AliasSampleTest + """ + + def setUp(self): + pass + + def test_speed(self): + """test_speed + """ + + num = 1000 + size = [10240, 1, 5] + probs = np.random.uniform(0.0, 1.0, [num]) + probs /= np.sum(probs) + + start = time.time() + alias, events = alias_sample_build_table(probs) + for i in range(100): + alias_sample(size, alias, events) + alias_sample_time = time.time() - start + + start = time.time() + for i in range(100): + np.random.choice(num, size, p=probs) + np_sample_time = time.time() - start + self.assertTrue(alias_sample_time < np_sample_time) + + def test_resut(self): + """test_result + """ + size = [450000] + num = 10 + probs = np.arange(1, num).astype(np.float64) + probs /= np.sum(probs) + alias, events = alias_sample_build_table(probs) + ret = alias_sample(size, alias, events) + cnt = Counter(ret) + sort_cnt_keys = [x[1] for x in sorted(zip(cnt.values(), cnt.keys()))] + self.assertEqual(sort_cnt_keys, np.arange(0, num - 1).tolist()) + + +if __name__ == '__main__': + unittest.main() diff --git a/pgl/tests/test_redis_graph.py b/pgl/tests/test_redis_graph.py new file mode 100644 index 0000000000000000000000000000000000000000..6d2601de26207b45806052887312bef3fdbd32b8 --- /dev/null +++ b/pgl/tests/test_redis_graph.py @@ -0,0 +1,56 @@ +# Copyright (c) 2019 PaddlePaddle Authors. All Rights Reserved. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +"""test_redis_graph""" +import time +import unittest +import json +import os + +import numpy as np +from pgl.redis_graph import RedisGraph + + +class RedisGraphTest(unittest.TestCase): + """RedisGraphTest + """ + + def setUp(self): + config_path = os.path.join( + os.path.abspath(os.path.dirname(__file__)), + 'test_redis_graph_conf.json') + with open(config_path) as inf: + config = json.load(inf) + redis_configs = [config["redis"], ] + self.graph = RedisGraph( + "reddit-graph", redis_configs, num_parts=config["num_parts"]) + + def test_random_seed(self): + """test_random_seed + """ + np.random.seed(1) + data1 = self.graph.sample_predecessor(range(1000), max_degree=5) + data1 = [nid for nodes in data1 for nid in nodes] + np.random.seed(1) + data2 = self.graph.sample_predecessor(range(1000), max_degree=5) + data2 = [nid for nodes in data2 for nid in nodes] + np.random.seed(3) + data3 = self.graph.sample_predecessor(range(1000), max_degree=5) + data3 = [nid for nodes in data3 for nid in nodes] + + self.assertEqual(data1, data2) + self.assertNotEqual(data2, data3) + + +if __name__ == '__main__': + unittest.main() diff --git a/pgl/tests/test_redis_graph_conf.json b/pgl/tests/test_redis_graph_conf.json new file mode 100644 index 0000000000000000000000000000000000000000..c334656132b75f1bf2a55d802bf4d9a9363239f3 --- /dev/null +++ b/pgl/tests/test_redis_graph_conf.json @@ -0,0 +1,8 @@ +{ + "redis": + { + "host": "10.86.54.13", + "port": "7003" + }, + "num_parts": 64 +} diff --git a/pgl/tests/test_sample.py b/pgl/tests/test_sample.py new file mode 100644 index 0000000000000000000000000000000000000000..6eadb652160b5c7ad917357be52ee1fd8d348aae --- /dev/null +++ b/pgl/tests/test_sample.py @@ -0,0 +1,68 @@ +# Copyright (c) 2019 PaddlePaddle Authors. All Rights Reserved +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +""" + This package implement graph sampling algorithm. +""" +import unittest +import os +import json + +import numpy as np +from pgl.redis_graph import RedisGraph +from pgl.sample import graphsage_sample +from pgl.sample import node2vec_sample + + +class SampleTest(unittest.TestCase): + """SampleTest + """ + + def setUp(self): + config_path = os.path.join( + os.path.abspath(os.path.dirname(__file__)), + 'test_redis_graph_conf.json') + with open(config_path) as inf: + config = json.load(inf) + redis_configs = [config["redis"], ] + self.graph = RedisGraph( + "reddit-graph", redis_configs, num_parts=config["num_parts"]) + + def test_graphsage_sample(self): + """test_graphsage_sample + """ + eids = np.random.choice(self.graph.num_edges, 1000) + edges = self.graph.get_edges_by_id(eids) + nodes = [n for edge in edges for n in edge] + ignore_edges = edges.tolist() + edges[:, [1, 0]].tolist() + + np.random.seed(1) + subgraphs = graphsage_sample(self.graph, nodes, [10, 10], []) + + np.random.seed(1) + subgraphs_ignored = graphsage_sample(self.graph, nodes, [10, 10], + ignore_edges) + + self.assertEqual(subgraphs[0].num_nodes, + subgraphs_ignored[0].num_nodes) + self.assertGreaterEqual(subgraphs[0].num_edges, + subgraphs_ignored[0].num_edges) + + def test_node2vec_sample(self): + """test_node2vec_sample + """ + walks = node2vec_sample(self.graph, range(10), 3) + + +if __name__ == '__main__': + unittest.main() diff --git a/pgl/tests/test_set2set.py b/pgl/tests/test_set2set.py new file mode 100644 index 0000000000000000000000000000000000000000..f0572c1508238602ff21295d6a353d482a7d55f2 --- /dev/null +++ b/pgl/tests/test_set2set.py @@ -0,0 +1,67 @@ +# Copyright (c) 2019 PaddlePaddle Authors. All Rights Reserved +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +""" + Comment. +""" +from __future__ import division +from __future__ import absolute_import +from __future__ import print_function +from __future__ import unicode_literals +import unittest + +import paddle.fluid as F +import paddle.fluid.layers as L + +from pgl.layers.set2set import Set2Set + + +def paddle_easy_run(model_func, data): + prog = F.Program() + startup_prog = F.Program() + with F.program_guard(prog, startup_prog): + ret = model_func() + place = F.CUDAPlace(0) + exe = F.Executor(place) + exe.run(startup_prog) + return exe.run(prog, fetch_list=ret, feed=data) + + +class Set2SetTest(unittest.TestCase): + """Set2SetTest + """ + + def test_graphsage_sample(self): + """test_graphsage_sample + """ + import numpy as np + + def model_func(): + s2s = Set2Set(5, 1, 3) + h0 = L.data( + name='h0', + shape=[2, 10, 5], + dtype='float32', + append_batch_size=False) + h1 = s2s.forward(h0) + return h1, + + data = {"h0": np.random.rand(2, 10, 5).astype("float32")} + h1, = paddle_easy_run(model_func, data) + + self.assertEqual(h1.shape[0], 2) + self.assertEqual(h1.shape[1], 10) + + +if __name__ == "__main__": + unittest.main() diff --git a/pgl/utils/mp_reader.py b/pgl/utils/mp_reader.py new file mode 100644 index 0000000000000000000000000000000000000000..9f26a60ddb38ea7b7044dd211cc629ba679a3616 --- /dev/null +++ b/pgl/utils/mp_reader.py @@ -0,0 +1,152 @@ +# Copyright (c) 2019 PaddlePaddle Authors. All Rights Reserved. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +"""Optimized Multiprocessing Reader for PaddlePaddle +""" +import logging +log = logging.getLogger(__name__) +import multiprocessing +import copy +try: + import ujson as json +except: + log.info("ujson not install, fail back to use json instead") + import json +import numpy as np +import time +import paddle.fluid as fluid + + +def serialize_data(data): + """serialize_data""" + if data is None: + return None + return numpy_serialize_data(data) #, ensure_ascii=False) + + +def numpy_serialize_data(data): + """serialize_data""" + ret_data = {} + for key in data: + if isinstance(data[key], np.ndarray): + ret_data[key] = (data[key].tobytes(), list(data[key].shape), + "%s" % data[key].dtype) + else: + ret_data[key] = data[key] + return ret_data + + +def numpy_deserialize_data(data): + """deserialize_data""" + if data is None: + return None + for key in data: + if isinstance(data[key], tuple): + value = np.frombuffer( + data[key][0], dtype=data[key][2]).reshape(data[key][1]) + data[key] = value + return data + + +def deserialize_data(data): + """deserialize_data""" + return numpy_deserialize_data(data) + + +def multiprocess_reader(readers, use_pipe=True, queue_size=1000, pipe_size=10): + """ + multiprocess_reader use python multi process to read data from readers + and then use multiprocess.Queue or multiprocess.Pipe to merge all + data. The process number is equal to the number of input readers, each + process call one reader. + Multiprocess.Queue require the rw access right to /dev/shm, some + platform does not support. + you need to create multiple readers first, these readers should be independent + to each other so that each process can work independently. + An example: + .. code-block:: python + reader0 = reader(["file01", "file02"]) + reader1 = reader(["file11", "file12"]) + reader1 = reader(["file21", "file22"]) + reader = multiprocess_reader([reader0, reader1, reader2], + queue_size=100, use_pipe=False) + """ + + assert type(readers) is list and len(readers) > 0 + + def _read_into_queue(reader, queue): + """read_into_queue""" + for sample in reader(): + if sample is None: + raise ValueError("sample has None") + queue.put(serialize_data(sample)) + queue.put(serialize_data(None)) + + def queue_reader(): + """queue_reader""" + queue = multiprocessing.Queue(queue_size) + for reader in readers: + p = multiprocessing.Process( + target=_read_into_queue, args=(reader, queue)) + p.start() + + reader_num = len(readers) + finish_num = 0 + while finish_num < reader_num: + sample = deserialize_data(queue.get()) + if sample is None: + finish_num += 1 + else: + yield sample + + def _read_into_pipe(reader, conn, max_pipe_size): + """read_into_pipe""" + for sample in reader(): + if sample is None: + raise ValueError("sample has None!") + conn.send(serialize_data(sample)) + conn.send(serialize_data(None)) + conn.close() + + def pipe_reader(): + """pipe_reader""" + conns = [] + for reader in readers: + parent_conn, child_conn = multiprocessing.Pipe() + conns.append(parent_conn) + p = multiprocessing.Process( + target=_read_into_pipe, args=(reader, child_conn, pipe_size)) + p.start() + + reader_num = len(readers) + finish_num = 0 + conn_to_remove = [] + finish_flag = np.zeros(len(conns), dtype="int32") + while finish_num < reader_num: + for conn_id, conn in enumerate(conns): + if finish_flag[conn_id] > 0: + continue + if conn.poll(0.01): + buff = conn.recv() + sample = deserialize_data(buff) + if sample is None: + finish_num += 1 + conn.close() + finish_flag[conn_id] = 1 + else: + yield sample + + if use_pipe: + return pipe_reader + else: + return queue_reader diff --git a/pgl/utils/mt_reader.py b/pgl/utils/mt_reader.py new file mode 100644 index 0000000000000000000000000000000000000000..3a1aad43243ccbb99b06f1bc8914d2e744c025ad --- /dev/null +++ b/pgl/utils/mt_reader.py @@ -0,0 +1,79 @@ +# Copyright (c) 2019 PaddlePaddle Authors. All Rights Reserved. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +"""Optimized Multithreading Reader for PaddlePaddle +""" +import logging +log = logging.getLogger(__name__) +import threading +import queue +import copy +import numpy as np +import time +import paddle.fluid as fluid + + +def multithreading_reader(readers, queue_size=1000): + """ + multithreading_reader use python multi thread to read data from readers + and then use queue to merge all + data. The process number is equal to the number of input readers, each + process call one reader. + CPU usage rate won't go over 100% with GIL. + you need to create multiple readers first, these readers should be independent + to each other so that each process can work independently. + An example: + .. code-block:: python + reader0 = reader(["file01", "file02"]) + reader1 = reader(["file11", "file12"]) + reader1 = reader(["file21", "file22"]) + reader = multithreading_reader([reader0, reader1, reader2], + queue_size=100) + """ + + assert type(readers) is list and len(readers) > 0 + + def _read_into_queue(reader, queue): + """read_into_queue""" + for sample in reader(): + if sample is None: + raise ValueError("sample has None") + queue.put(sample) + queue.put(None) + + def queue_reader(): + """queue_reader""" + output_queue = queue.Queue(queue_size) + thread_pool = [] + thread_num = 0 + for reader in readers: + p = threading.Thread( + target=_read_into_queue, args=(reader, output_queue)) + p.daemon = True + p.start() + thread_pool.append(p) + thread_num += 1 + + while True: + ret = output_queue.get() + if ret is not None: + yield ret + else: + thread_num -= 1 + if thread_num == 0: + break + + for thread in thread_pool: + thread.join() + + return queue_reader diff --git a/pgl/utils/paddle_helper.py b/pgl/utils/paddle_helper.py index ecea36483967552fc40df61a86397b46e52d09de..f1e53aedcd25389f1994301a5213defabd62ba52 100644 --- a/pgl/utils/paddle_helper.py +++ b/pgl/utils/paddle_helper.py @@ -223,5 +223,25 @@ def scatter_add(input, index, updates): Same type and shape as input. """ - output = fluid.layers.scatter(input, index, updates, overwrite=False) + output = fluid.layers.scatter(input, index, updates, mode='add') + return output + + +def scatter_max(input, index, updates): + """Scatter max updates to input by given index. + + Adds sparse updates to input variables. + + Args: + input: Input tensor to be updated + + index: Slice index + + updates: Must have same type as input. + + Return: + Same type and shape as input. + """ + + output = fluid.layers.scatter(input, index, updates, mode='max') return output diff --git a/requirements.txt b/requirements.txt index b8b9367120ca4e91ddaab29f3dfab8bc6c1e2195..4a13b16b9df0af570752f5dac9857fa7e496d3db 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,2 +1,6 @@ -numpy >= 1.14.5 +numpy >= 1.16.4 cython >= 0.25.2 + +#paddlepaddle + +redis-py-cluster diff --git a/setup.py b/setup.py index 3a720b1a30340a1a9076949c72791ec8b568f107..f0b808afacd550293ecdc47ff221a683c50ae07f 100755 --- a/setup.py +++ b/setup.py @@ -16,10 +16,35 @@ import os import sys import re import codecs -import numpy as np from setuptools import setup, find_packages -from setuptools.extension import Extension -from Cython.Build import cythonize +from setuptools import Extension +from setuptools import dist +from setuptools.command.build_ext import build_ext as _build_ext + +try: + from Cython.Build import cythonize +except ImportError: + + def cythonize(*args, **kwargs): + """cythonize""" + from Cython.Build import cythonize + return cythonize(*args, **kwargs) + + +class CustomBuildExt(_build_ext): + """CustomBuildExt""" + + def finalize_options(self): + _build_ext.finalize_options(self) + # Prevent numpy from thinking it is still in its setup process: + __builtins__.__NUMPY_SETUP__ = False + import numpy + self.include_dirs.append(numpy.get_include()) + + +workdir = os.path.dirname(os.path.abspath(__file__)) +with open(os.path.join(workdir, './requirements.txt')) as f: + requirements = f.read().splitlines() cur_dir = os.path.abspath(os.path.dirname(__file__)) with open(os.path.join(cur_dir, 'README.md'), 'rb') as f: @@ -58,7 +83,6 @@ extensions = [ "pgl.graph_kernel", ["pgl/graph_kernel.pyx"], language="c++", - include_dirs=[np.get_include()], extra_compile_args=compile_extra_args, extra_link_args=link_extra_args, ), ] @@ -66,7 +90,6 @@ extensions = [ def get_package_data(path): files = [] - print(path) for root, dirnames, filenames in os.walk(path): for filename in filenames: files.append(os.path.join(root, filename)) @@ -83,9 +106,16 @@ setup( long_description_content_type='text/markdown', url="https://github.com/PaddlePaddle/PGL", package_data=package_data, + setup_requires=[ + 'setuptools>=18.0', + 'numpy>=1.16.4', + ], + install_requires=requirements, + cmdclass={'build_ext': CustomBuildExt}, packages=find_packages(), include_package_data=True, - ext_modules=cythonize(extensions), + #ext_modules=cythonize(extensions), + ext_modules=extensions, classifiers=[ 'Intended Audience :: Developers', 'License :: OSI Approved :: Apache Software License', diff --git a/tests/scatter_add_test.py b/tests/scatter_add_test.py new file mode 100644 index 0000000000000000000000000000000000000000..04f4ef6639a5c429d7fa76761aa561471fff0171 --- /dev/null +++ b/tests/scatter_add_test.py @@ -0,0 +1,40 @@ +# Copyright (c) 2019 PaddlePaddle Authors. All Rights Reserved. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +"""scatter test cases""" + +import unittest + +import numpy as np +import paddle.fluid as fluid + + +class ScatterAddTest(unittest.TestCase): + """ScatterAddTest""" + + def test_scatter_add(self): + """test_scatter_add""" + with fluid.dygraph.guard(fluid.CPUPlace()): + input = fluid.dygraph.to_variable( + np.array( + [[1, 2], [5, 6]], dtype='float32'), ) + index = fluid.dygraph.to_variable(np.array([1, 1], dtype=np.int32)) + updates = fluid.dygraph.to_variable( + np.array( + [[3, 4], [3, 4]], dtype='float32'), ) + output = fluid.layers.scatter(input, index, updates, mode='add') + assert output.numpy().tolist() == [[1, 2], [11, 14]] + + +if __name__ == '__main__': + unittest.main() diff --git a/tests/unique_with_counts_test.py b/tests/unique_with_counts_test.py new file mode 100644 index 0000000000000000000000000000000000000000..532843c27d4732715f7a325e27bbb66bffa164e6 --- /dev/null +++ b/tests/unique_with_counts_test.py @@ -0,0 +1,74 @@ +# Copyright (c) 2019 PaddlePaddle Authors. All Rights Reserved. +# +# Licensed under the Apache License, Version 2.0 (the "License"); +# you may not use this file except in compliance with the License. +# You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. +"""unique with counts test""" + +import unittest + +import numpy as np +import paddle.fluid as fluid + + +class UniqueWithCountTest(unittest.TestCase): + """UniqueWithCountTest""" + + def _test_unique_with_counts_helper(self, input, output): + place = fluid.CPUPlace() + exe = fluid.Executor(place) + main_program = fluid.Program() + startup_program = fluid.Program() + with fluid.program_guard(main_program, startup_program): + x = fluid.layers.data( + name='input', + dtype='int64', + shape=[-1], + append_batch_size=False) + #x = fluid.assign(np.array([2, 3, 3, 1, 5, 3], dtype='int32')) + out, index, count = fluid.layers.unique_with_counts(x) + + out, index, count = exe.run( + main_program, + feed={'input': np.array( + input, dtype='int64'), }, + fetch_list=[out, index, count], + return_numpy=True, ) + out, index, count = out.tolist(), index.tolist(), count.tolist() + assert [out, index, count] == output + + def test_unique_with_counts(self): + """test_unique_with_counts""" + self._test_unique_with_counts_helper( + input=[1, 1, 2, 4, 4, 4, 7, 8, 8], + output=[ + [1, 2, 4, 7, 8], + [0, 0, 1, 2, 2, 2, 3, 4, 4], + [2, 1, 3, 1, 2], + ], ) + self._test_unique_with_counts_helper( + input=[1], + output=[ + [1], + [0], + [1], + ], ) + self._test_unique_with_counts_helper( + input=[1, 1], + output=[ + [1], + [0, 0], + [2], + ], ) + + +if __name__ == '__main__': + unittest.main()