add gin example

examples/gin/Dataset.py

+# 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 dataset for GIN model.
+"""
+
+import os
+import sys
+import numpy as np
+
+from sklearn.model_selection import StratifiedKFold
+
+import pgl
+from pgl.utils.logger import log
+
+
+def fold10_split(dataset, fold_idx=0, seed=0, shuffle=True):
+    """10 fold splitter"""
+    assert 0 <= fold_idx and fold_idx < 10, print(
+        "fold_idx must be from 0 to 9.")
+
+    skf = StratifiedKFold(n_splits=10, shuffle=shuffle, random_state=seed)
+    labels = []
+    for i in range(len(dataset)):
+        g, c = dataset[i]
+        labels.append(c)
+
+    idx_list = []
+    for idx in skf.split(np.zeros(len(labels)), labels):
+        idx_list.append(idx)
+    train_idx, valid_idx = idx_list[fold_idx]
+
+    log.info("train_set : test_set == %d : %d" %
+             (len(train_idx), len(valid_idx)))
+    return Subset(dataset, train_idx), Subset(dataset, valid_idx)
+
+
+def random_split(dataset, split_ratio=0.7, seed=0, shuffle=True):
+    """random splitter"""
+    np.random.seed(seed)
+    indices = list(range(len(dataset)))
+    np.random.shuffle(indices)
+    split = int(split_ratio * len(dataset))
+    train_idx, valid_idx = indices[:split], indices[split:]
+
+    log.info("train_set : test_set == %d : %d" %
+             (len(train_idx), len(valid_idx)))
+    return Subset(dataset, train_idx), Subset(dataset, valid_idx)
+
+
+class BaseDataset(object):
+    """BaseDataset"""
+
+    def __init__(self):
+        pass
+
+    def __getitem__(self, idx):
+        """getitem"""
+        raise NotImplementedError
+
+    def __len__(self):
+        """len"""
+        raise NotImplementedError
+
+
+class Subset(BaseDataset):
+    """
+    Subset of a dataset at specified indices.
+    """
+
+    def __init__(self, dataset, indices):
+        self.dataset = dataset
+        self.indices = indices
+
+    def __getitem__(self, idx):
+        """getitem"""
+        return self.dataset[self.indices[idx]]
+
+    def __len__(self):
+        """len"""
+        return len(self.indices)
+
+
+class GINDataset(BaseDataset):
+    """Dataset for Graph Isomorphism Network (GIN)
+    Adapted from https://github.com/weihua916/powerful-gnns/blob/master/dataset.zip.
+    """
+
+    def __init__(self,
+                 data_path,
+                 dataset_name,
+                 self_loop,
+                 degree_as_nlabel=False):
+        self.data_path = data_path
+        self.dataset_name = dataset_name
+        self.self_loop = self_loop
+        self.degree_as_nlabel = degree_as_nlabel
+
+        self.graph_list = []
+        self.glabel_list = []
+
+        # relabel
+        self.glabel_dict = {}
+        self.nlabel_dict = {}
+        self.elabel_dict = {}
+        self.ndegree_dict = {}
+
+        # global num
+        self.num_graph = 0  # total graphs number
+        self.n = 0  # total nodes number
+        self.m = 0  # total edges number
+
+        # global num of classes
+        self.gclasses = 0
+        self.nclasses = 0
+        self.eclasses = 0
+        self.dim_nfeats = 0
+
+        # flags
+        self.degree_as_nlabel = degree_as_nlabel
+        self.nattrs_flag = False
+        self.nlabels_flag = False
+
+        self._load_data()
+
+    def __len__(self):
+        """return the number of graphs"""
+        return len(self.graph_list)
+
+    def __getitem__(self, idx):
+        """getitem"""
+        return self.graph_list[idx], self.glabel_list[idx]
+
+    def _load_data(self):
+        """Loads dataset
+        """
+        filename = os.path.join(self.data_path, self.dataset_name,
+                                "%s.txt" % self.dataset_name)
+        log.info("loading data from %s" % filename)
+
+        with open(filename, 'r') as reader:
+            # first line --> N, means total number of graphs
+            self.num_graph = int(reader.readline().strip())
+
+            for i in range(self.num_graph):
+                if (i + 1) % int(self.num_graph / 10) == 0:
+                    log.info("processing graph %s" % (i + 1))
+                graph = dict()
+                # second line --> [num_node, label] 
+                # means [node number of a graph, class label of a graph]
+                grow = reader.readline().strip().split()
+                n_nodes, glabel = [int(w) for w in grow]
+
+                # relabel graphs
+                if glabel not in self.glabel_dict:
+                    mapped = len(self.glabel_dict)
+                    self.glabel_dict[glabel] = mapped
+
+                graph['num_nodes'] = n_nodes
+                self.glabel_list.append(self.glabel_dict[glabel])
+
+                nlabels = []
+                node_features = []
+                num_edges = 0
+                edges = []
+
+                for j in range(graph['num_nodes']):
+                    slots = reader.readline().strip().split()
+
+                    # handle edges and node feature(if has)
+                    tmp = int(slots[
+                        1]) + 2  # tmp == 2 + num_edges of current node
+                    if tmp == len(slots):
+                        # no node feature
+                        nrow = [int(w) for w in slots]
+                        nfeat = None
+                    elif tmp < len(slots):
+                        nrow = [int(w) for w in slots[:tmp]]
+                        nfeat = [float(w) for w in slots[tmp:]]
+                        node_features.append(nfeat)
+                    else:
+                        raise Exception('edge number is not correct!')
+
+                    # relabel nodes if is has labels
+                    # if it doesn't have node labels, then every nrow[0] == 0
+                    if not nrow[0] in self.nlabel_dict:
+                        mapped = len(self.nlabel_dict)
+                        self.nlabel_dict[nrow[0]] = mapped
+
+                    nlabels.append(self.nlabel_dict[nrow[0]])
+                    num_edges += nrow[1]
+                    edges.extend([(j, u) for u in nrow[2:]])
+
+                    if self.self_loop:
+                        num_edges += 1
+                        edges.append((j, j))
+
+                if node_features != []:
+                    node_features = np.stack(node_features)
+                    graph['attr'] = node_features
+                    self.nattrs_flag = True
+                else:
+                    node_features = None
+                    graph['attr'] = node_features
+
+                graph['nlabel'] = np.array(
+                    nlabels, dtype="int64").reshape(-1, 1)
+                if len(self.nlabel_dict) > 1:
+                    self.nlabels_flag = True
+
+                graph['edges'] = edges
+                assert num_edges == len(edges)
+
+                g = pgl.graph.Graph(
+                    num_nodes=graph['num_nodes'],
+                    edges=graph['edges'],
+                    node_feat={
+                        'nlabel': graph['nlabel'],
+                        'attr': graph['attr']
+                    })
+
+                self.graph_list.append(g)
+
+                # update statistics of graphs
+                self.n += graph['num_nodes']
+                self.m += num_edges
+
+        # if no attr
+        if not self.nattrs_flag:
+            log.info('there are no node features in this dataset!')
+            label2idx = {}
+            # generate node attr by node degree
+            if self.degree_as_nlabel:
+                log.info('generate node features by node degree...')
+                nlabel_set = set([])
+                for g in self.graph_list:
+
+                    g.node_feat['nlabel'] = g.indegree()
+                    # extracting unique node labels
+                    nlabel_set = nlabel_set.union(set(g.node_feat['nlabel']))
+                    g.node_feat['nlabel'] = g.node_feat['nlabel'].reshape(-1,
+                                                                          1)
+
+                nlabel_set = list(nlabel_set)
+                # in case the labels/degrees are not continuous number
+                self.ndegree_dict = {
+                    nlabel_set[i]: i
+                    for i in range(len(nlabel_set))
+                }
+                label2idx = self.ndegree_dict
+            # generate node attr by node label
+            else:
+                log.info('generate node features by node label...')
+                label2idx = self.nlabel_dict
+
+            for g in self.graph_list:
+                attr = np.zeros((g.num_nodes, len(label2idx)))
+                idx = [
+                    label2idx[tag]
+                    for tag in g.node_feat['nlabel'].reshape(-1, )
+                ]
+                attr[:, idx] = 1
+                g.node_feat['attr'] = attr.astype("float32")
+
+        # after load, get the #classes and #dim
+        self.gclasses = len(self.glabel_dict)
+        self.nclasses = len(self.nlabel_dict)
+        self.eclasses = len(self.elabel_dict)
+        self.dim_nfeats = len(self.graph_list[0].node_feat['attr'][0])
+
+        message = "finished loading data\n"
+        message += """
+                    num_graph: %d
+                    num_graph_class: %d
+                    total_num_nodes: %d
+                    node Classes: %d
+                    node_features_dim: %d
+                    num_edges: %d
+                    edge_classes: %d
+                    Avg. of #Nodes: %.2f
+                    Avg. of #Edges: %.2f
+                    Graph Relabeled: %s
+                    Node Relabeled: %s
+                    Degree Relabeled(If degree_as_nlabel=True): %s""" % (
+            self.num_graph,
+            self.gclasses,
+            self.n,
+            self.nclasses,
+            self.dim_nfeats,
+            self.m,
+            self.eclasses,
+            self.n / self.num_graph,
+            self.m / self.num_graph,
+            self.glabel_dict,
+            self.nlabel_dict,
+            self.ndegree_dict, )
+        log.info(message)
+
+
+if __name__ == "__main__":
+    gindataset = GINDataset(
+        "./dataset/", "MUTAG", self_loop=True, degree_as_nlabel=False)

examples/gin/README.md

+# Graph Isomorphism Network (GIN)
+
+[Graph Isomorphism Network \(GIN\)](https://arxiv.org/pdf/1810.00826.pdf) is a simple graph neural network that expects to achieve the ability as the Weisfeiler-Lehman graph isomorphism test. Based on PGL, we reproduce the GIN model.
+
+### Datasets
+
+The dataset can be downloaded from [here](https://github.com/weihua916/powerful-gnns/blob/master/dataset.zip)
+
+### Dependencies
+
+- paddlepaddle 1.6
+- pgl 1.0.2
+
+### How to run
+
+For examples, use GPU to train GIN model on MUTAG dataset.
+```
+python main.py --use_cuda --dataset_name MUTAG 
+```
+
+### Hyperparameters
+
+- data\_path: the root path of your dataset 
+- dataset\_name: the name of the dataset
+- fold\_idx: The $fold\_idx^{th}$ fold of dataset splited. Here we use 10 fold cross-validation
+- train\_eps: whether the $\epsilon$ parameter is learnable.
+
+### Experiment results （Accuracy）
+| |MUTAG | COLLAB   | IMDBBINARY | IMDBMULTI |
+|--|-------------|----------|------------|-----------------|
+|PGL result | 90.8           | 78.6 | 76.8     | 50.8          |
+|paper reuslt |90.0           | 80.0 | 75.1     | 52.3          |

examples/gin/dataloader.py

+# 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 graph dataloader.
+"""
+
+from __future__ import absolute_import
+from __future__ import division
+from __future__ import print_function
+from __future__ import unicode_literals
+from __future__ import absolute_import
+
+import os
+import sys
+import time
+import argparse
+import numpy as np
+import collections
+
+import paddle
+import paddle.fluid as fluid
+import paddle.fluid.layers as fl
+import pgl
+from pgl.utils import mp_reader
+from pgl.utils.logger import log
+
+
+def batch_iter(data, batch_size, fid, num_workers):
+    """node_batch_iter
+    """
+    size = len(data)
+    perm = np.arange(size)
+    np.random.shuffle(perm)
+    start = 0
+    cc = 0
+    while start < size:
+        index = perm[start:start + batch_size]
+        start += batch_size
+        cc += 1
+        if cc % num_workers != fid:
+            continue
+        yield data[index]
+
+
+def scan_batch_iter(data, batch_size, fid, num_workers):
+    """scan_batch_iter
+    """
+    batch = []
+    cc = 0
+    for line_example in data.scan():
+        cc += 1
+        if cc % num_workers != fid:
+            continue
+        batch.append(line_example)
+        if len(batch) == batch_size:
+            yield batch
+            batch = []
+
+    if len(batch) > 0:
+        yield batch
+
+
+class GraphDataloader(object):
+    """Graph Dataloader
+    """
+
+    def __init__(
+            self,
+            dataset,
+            batch_size,
+            seed=0,
+            num_workers=1,
+            buf_size=1000,
+            shuffle=True, ):
+
+        self.shuffle = shuffle
+        self.seed = seed
+        self.num_workers = num_workers
+        self.buf_size = buf_size
+        self.batch_size = batch_size
+        self.dataset = dataset
+
+    def batch_fn(self, batch_examples):
+        """ batch_fn batch producer"""
+        graphs = [b[0] for b in batch_examples]
+        labels = [b[1] for b in batch_examples]
+        join_graph = pgl.graph.MultiGraph(graphs)
+        labels = np.array(labels, dtype="int64").reshape(-1, 1)
+        return join_graph, labels
+        #  feed_dict = self.graph_wrapper.to_feed(join_graph)
+
+        #  raise NotImplementedError("No defined Batch Fn")
+
+    def batch_iter(self, fid):
+        """batch_iter"""
+        if self.shuffle:
+            for batch in batch_iter(self, self.batch_size, fid,
+                                    self.num_workers):
+                yield batch
+        else:
+            for batch in scan_batch_iter(self, self.batch_size, fid,
+                                         self.num_workers):
+                yield batch
+
+    def __len__(self):
+        """__len__"""
+        return len(self.dataset)
+
+    def __getitem__(self, idx):
+        """__getitem__"""
+        if isinstance(idx, collections.Iterable):
+            return [self[bidx] for bidx in idx]
+        else:
+            return self.dataset[idx]
+
+    def __iter__(self):
+        """__iter__"""
+
+        def worker(filter_id):
+            def func_run():
+                for batch_examples in self.batch_iter(filter_id):
+                    batch_dict = self.batch_fn(batch_examples)
+                    yield batch_dict
+
+            return func_run
+
+        if self.num_workers == 1:
+            r = paddle.reader.buffered(worker(0), self.buf_size)
+        else:
+            worker_pool = [worker(wid) for wid in range(self.num_workers)]
+            worker = mp_reader.multiprocess_reader(
+                worker_pool, use_pipe=True, queue_size=1000)
+            r = paddle.reader.buffered(worker, self.buf_size)
+
+        for batch in r():
+            yield batch
+
+    def scan(self):
+        """scan"""
+        for example in self.dataset:
+            yield example

examples/gin/main.py

+# 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 GIN model.
+"""
+import os
+import sys
+import time
+import argparse
+import numpy as np
+
+import paddle.fluid as fluid
+import paddle.fluid.layers as fl
+import pgl
+from pgl.utils.logger import log
+
+from Dataset import GINDataset, fold10_split, random_split
+from dataloader import GraphDataloader
+from model import GINModel
+
+
+def main(args):
+    """main function"""
+    dataset = GINDataset(
+        args.data_path,
+        args.dataset_name,
+        self_loop=not args.train_eps,
+        degree_as_nlabel=True)
+    train_dataset, test_dataset = fold10_split(
+        dataset, fold_idx=args.fold_idx, seed=args.seed)
+
+    train_loader = GraphDataloader(train_dataset, batch_size=args.batch_size)
+    test_loader = GraphDataloader(
+        test_dataset, batch_size=args.batch_size, shuffle=False)
+
+    place = fluid.CUDAPlace(0) if args.use_cuda else fluid.CPUPlace()
+    train_program = fluid.Program()
+    startup_program = fluid.Program()
+
+    with fluid.program_guard(train_program, startup_program):
+        gw = pgl.graph_wrapper.GraphWrapper(
+            "gw", place=place, node_feat=dataset[0][0].node_feat_info())
+
+        model = GINModel(args, gw, dataset.gclasses)
+        model.forward()
+
+    infer_program = train_program.clone(for_test=True)
+
+    with fluid.program_guard(train_program, startup_program):
+        epoch_step = int(len(train_dataset) / args.batch_size) + 1
+        boundaries = [
+            i
+            for i in range(50 * epoch_step, args.epochs * epoch_step,
+                           epoch_step * 50)
+        ]
+        values = [args.lr * 0.5**i for i in range(0, len(boundaries) + 1)]
+        lr = fl.piecewise_decay(boundaries=boundaries, values=values)
+        train_op = fluid.optimizer.Adam(lr).minimize(model.loss)
+
+    exe = fluid.Executor(place)
+    exe.run(startup_program)
+
+    # train and evaluate
+    global_step = 0
+    for epoch in range(1, args.epochs + 1):
+        for idx, batch_data in enumerate(train_loader):
+            g, labels = batch_data
+            feed_dict = gw.to_feed(g)
+            feed_dict['labels'] = labels
+            ret_loss, ret_lr, ret_acc = exe.run(
+                train_program,
+                feed=feed_dict,
+                fetch_list=[model.loss, lr, model.acc])
+
+            global_step += 1
+            if global_step % 10 == 0:
+                message = "epoch %d | step %d | " % (epoch, global_step)
+                message += "lr %.6f | loss %.6f | acc %.4f" % (
+                    ret_lr, ret_loss, ret_acc)
+                log.info(message)
+
+        # evaluate
+        result = evaluate(exe, infer_program, model, gw, test_loader)
+
+        message = "evaluating result"
+        for key, value in result.items():
+            message += " | %s %.6f" % (key, value)
+        log.info(message)
+
+
+def evaluate(exe, prog, model, gw, loader):
+    """evaluate"""
+    total_loss = []
+    total_acc = []
+    for idx, batch_data in enumerate(loader):
+        g, labels = batch_data
+        feed_dict = gw.to_feed(g)
+        feed_dict['labels'] = labels
+        ret_loss, ret_acc = exe.run(prog,
+                                    feed=feed_dict,
+                                    fetch_list=[model.loss, model.acc])
+        total_loss.append(ret_loss)
+        total_acc.append(ret_acc)
+
+    total_loss = np.mean(total_loss)
+    total_acc = np.mean(total_acc)
+
+    return {"loss": total_loss, "acc": total_acc}
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--data_path', type=str, default='./dataset')
+    parser.add_argument('--dataset_name', type=str, default='MUTAG')
+    parser.add_argument('--batch_size', type=int, default=32)
+    parser.add_argument('--fold_idx', type=int, default=0)
+    parser.add_argument('--output_path', type=str, default='./outputs/')
+    parser.add_argument('--use_cuda', action='store_true')
+    parser.add_argument('--num_layers', type=int, default=5)
+    parser.add_argument('--num_mlp_layers', type=int, default=2)
+    parser.add_argument('--hidden_size', type=int, default=64)
+    parser.add_argument(
+        '--pool_type',
+        type=str,
+        default="sum",
+        choices=["sum", "average", "max"])
+    parser.add_argument('--train_eps', action='store_true')
+    parser.add_argument('--epochs', type=int, default=350)
+    parser.add_argument('--lr', type=float, default=0.01)
+    parser.add_argument('--dropout_prob', type=float, default=0.5)
+    parser.add_argument('--seed', type=int, default=0)
+    args = parser.parse_args()
+
+    log.info(args)
+    if not os.path.exists(args.output_path):
+        os.makedirs(args.output_path)
+
+    main(args)

examples/gin/model.py

+# Copyright (c) 2020 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 GIN model.
+"""
+
+import numpy as np
+
+import paddle.fluid as fluid
+import paddle.fluid.layers as fl
+import pgl
+from pgl.layers.conv import gin
+
+
+class GINModel(object):
+    """GINModel"""
+
+    def __init__(self, args, gw, num_class):
+        self.args = args
+        self.num_layers = self.args.num_layers
+        self.hidden_size = self.args.hidden_size
+        self.train_eps = self.args.train_eps
+        self.pool_type = self.args.pool_type
+        self.dropout_prob = self.args.dropout_prob
+        self.num_class = num_class
+
+        self.gw = gw
+        self.labels = fl.data(name="labels", shape=[None, 1], dtype="int64")
+
+    def forward(self):
+        """forward"""
+        features_list = [self.gw.node_feat["attr"]]
+
+        for i in range(self.num_layers):
+            h = gin(self.gw,
+                    features_list[i],
+                    hidden_size=self.hidden_size,
+                    activation="relu",
+                    name="gin_%s" % (i),
+                    init_eps=0.0,
+                    train_eps=self.train_eps)
+
+            h = fl.batch_norm(h)
+            h = fl.relu(h)
+
+            features_list.append(h)
+
+        pooled_h = pgl.layers.graph_pooling(self.gw, features_list[0],
+                                            self.pool_type)
+        output = fl.dropout(
+            pooled_h,
+            self.dropout_prob,
+            dropout_implementation="upscale_in_train")
+
+        output = fl.fc(output,
+                       size=self.num_class,
+                       act=None,
+                       param_attr=fluid.ParamAttr(name="final_fc_0"))
+
+        for i, h in enumerate(features_list):
+            if i == 0:
+                continue
+            pooled_h = pgl.layers.graph_pooling(self.gw, h, self.pool_type)
+            drop_h = fl.dropout(
+                pooled_h,
+                self.dropout_prob,
+                dropout_implementation="upscale_in_train")
+            output += fl.fc(drop_h,
+                            size=self.num_class,
+                            act=None,
+                            param_attr=fluid.ParamAttr(name="final_fc_%s" %
+                                                       (i)))
+
+        # calculate loss
+        self.loss = fl.softmax_with_cross_entropy(output, self.labels)
+        self.loss = fl.reduce_mean(self.loss)
+        self.acc = fl.accuracy(fl.softmax(output), self.labels)