Merge pull request #25 from Liwb5/develop

develop PGL v1.1

examples/GATNE/Dataset.py

@@ -21,7 +21,7 @@ import tqdm
 import numpy as np
 import logging
 import random
-from pgl.contrib import heter_graph
+from pgl import heter_graph
 import pickle as pkl
 
 

examples/GATNE/model.py

@@ -21,7 +21,7 @@ import logging
 
 import paddle.fluid as fluid
 import paddle.fluid.layers as fl
-from pgl.contrib import heter_graph_wrapper
+from pgl import heter_graph_wrapper
 
 
 class GATNE(object):

examples/graphsage/reader.py

@@ -19,8 +19,8 @@ import pgl
 import time
 from pgl.utils import mp_reader
 from pgl.utils.logger import log
-import train
 import time
+import copy
 
 
 def node_batch_iter(nodes, node_label, batch_size):
@@ -46,12 +46,11 @@ def traverse(item):
         yield item
 
 
-def flat_node_and_edge(nodes, eids):
+def flat_node_and_edge(nodes):
     """flat_node_and_edge
     """
     nodes = list(set(traverse(nodes)))
-    eids = list(set(traverse(eids)))
-    return nodes, eids
+    return nodes
 
 
 def worker(batch_info, graph, graph_wrapper, samples):
@@ -61,31 +60,42 @@ def worker(batch_info, graph, graph_wrapper, samples):
     def work():
         """work
         """
-        first = True
+        _graph_wrapper = copy.copy(graph_wrapper)
+        _graph_wrapper.node_feat_tensor_dict = {}
         for batch_train_samples, batch_train_labels in batch_info:
             start_nodes = batch_train_samples
             nodes = start_nodes
-            eids = []
+            edges = []
             for max_deg in samples:
-                pred, pred_eid = graph.sample_predecessor(
-                    start_nodes, max_degree=max_deg, return_eids=True)
+                pred_nodes = graph.sample_predecessor(
+                    start_nodes, max_degree=max_deg)
+
+                for dst_node, src_nodes in zip(start_nodes, pred_nodes):
+                    for src_node in src_nodes:
+                        edges.append((src_node, dst_node))
+
                 last_nodes = nodes
-                nodes = [nodes, pred]
-                eids = [eids, pred_eid]
-                nodes, eids = flat_node_and_edge(nodes, eids)
+                nodes = [nodes, pred_nodes]
+                nodes = flat_node_and_edge(nodes)
                 # Find new nodes
                 start_nodes = list(set(nodes) - set(last_nodes))
                 if len(start_nodes) == 0:
                     break
 
-            subgraph = graph.subgraph(nodes=nodes, eid=eids)
+            subgraph = graph.subgraph(
+                nodes=nodes,
+                edges=edges,
+                with_node_feat=False,
+                with_edge_feat=False)
+
             sub_node_index = subgraph.reindex_from_parrent_nodes(
                 batch_train_samples)
-            feed_dict = graph_wrapper.to_feed(subgraph)
+            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
+            feed_dict["parent_node_index"] = np.array(nodes, dtype="int64")
             yield feed_dict
 
     return work
@@ -97,23 +107,25 @@ def multiprocess_graph_reader(graph,
                               node_index,
                               batch_size,
                               node_label,
+                              with_parent_node_index=False,
                               num_workers=4):
     """multiprocess_graph_reader
     """
 
-    def parse_to_subgraph(rd):
+    def parse_to_subgraph(rd, prefix, node_feat, _with_parent_node_index):
         """parse_to_subgraph
         """
 
         def work():
             """work
             """
-            last = time.time()
             for data in rd():
-                this = time.time()
                 feed_dict = data
-                now = time.time()
-                last = now
+                for key in node_feat:
+                    feed_dict[prefix + '/node_feat/' + key] = node_feat[key][
+                        feed_dict["parent_node_index"]]
+                if not _with_parent_node_index:
+                    del feed_dict["parent_node_index"]
                 yield feed_dict
 
         return work
@@ -129,46 +141,17 @@ def multiprocess_graph_reader(graph,
             reader_pool.append(
                 worker(batch_info[block_size * i:block_size * (i + 1)], graph,
                        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()
-
-
-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
-            nodes = start_nodes
-            eids = []
-            for max_deg in samples:
-                pred, pred_eid = graph.sample_predecessor(
-                    start_nodes, max_degree=max_deg, return_eids=True)
-                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)
-            feed_dict = graph_wrapper.to_feed(subgraph)
-            sub_node_index = subgraph.reindex_from_parrent_nodes(
-                batch_train_samples)
+        if len(reader_pool) == 1:
+            r = parse_to_subgraph(reader_pool[0],
+                                  repr(graph_wrapper), graph.node_feat,
+                                  with_parent_node_index)
+        else:
+            multi_process_sample = mp_reader.multiprocess_reader(
+                reader_pool, use_pipe=True, queue_size=1000)
+            r = parse_to_subgraph(multi_process_sample,
+                                  repr(graph_wrapper), graph.node_feat,
+                                  with_parent_node_index)
+        return paddle.reader.buffered(r, num_workers)
 
-            feed_dict["node_label"] = np.expand_dims(
-                np.array(
-                    batch_train_labels, dtype="int64"), -1)
-            feed_dict["node_index"] = np.array(sub_node_index, dtype="int32")
-            yield feed_dict
-
-    return paddle.reader.buffered(reader, 1000)
+    return reader()

examples/graphsage/train.py

@@ -63,10 +63,7 @@ def load_data(normalize=True, symmetry=True):
 
     log.info("Feature shape %s" % (repr(feature.shape)))
     graph = pgl.graph.Graph(
-        num_nodes=feature.shape[0],
-        edges=list(zip(src, dst)),
-        node_feat={"index": np.arange(
-            0, len(feature), dtype="int64")})
+        num_nodes=feature.shape[0], edges=list(zip(src, dst)))
 
     return {
         "graph": graph,
@@ -89,7 +86,13 @@ def build_graph_model(graph_wrapper, num_class, k_hop, graphsage_type,
     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['index'])
+    parent_node_index = fluid.layers.data(
+        "parent_node_index",
+        shape=[None],
+        dtype="int64",
+        append_batch_size=False)
+
+    feature = fluid.layers.gather(feature, parent_node_index)
     feature.stop_gradient = True
 
     for i in range(k_hop):
@@ -221,59 +224,35 @@ def main(args):
     exe.run(startup_program)
     feature_init(place)
 
-    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"])
+    train_iter = reader.multiprocess_graph_reader(
+        data['graph'],
+        graph_wrapper,
+        samples=samples,
+        num_workers=args.sample_workers,
+        batch_size=args.batch_size,
+        with_parent_node_index=True,
+        node_index=data['train_index'],
+        node_label=data["train_label"])
+
+    val_iter = reader.multiprocess_graph_reader(
+        data['graph'],
+        graph_wrapper,
+        samples=samples,
+        num_workers=args.sample_workers,
+        batch_size=args.batch_size,
+        with_parent_node_index=True,
+        node_index=data['val_index'],
+        node_label=data["val_label"])
+
+    test_iter = reader.multiprocess_graph_reader(
+        data['graph'],
+        graph_wrapper,
+        samples=samples,
+        num_workers=args.sample_workers,
+        batch_size=args.batch_size,
+        with_parent_node_index=True,
+        node_index=data['test_index'],
+        node_label=data["test_label"])
 
     for epoch in range(args.epoch):
         run_epoch(

examples/graphsage/train_multi.py

@@ -262,59 +262,32 @@ def main(args):
     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"])
+    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"])
+
+    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"])
+
+    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"])
 
     for epoch in range(args.epoch):
         run_epoch(

examples/graphsage/train_scale.py

@@ -97,11 +97,7 @@ def load_data(normalize=True, symmetry=True, scale=1):
     graph = pgl.graph.Graph(
         num_nodes=feature.shape[0],
         edges=edges,
-        node_feat={
-            "index": np.arange(
-                0, len(feature), dtype="int64"),
-            "feature": feature
-        })
+        node_feat={"feature": feature})
 
     return {
         "graph": graph,
@@ -244,59 +240,32 @@ def main(args):
 
     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"])
+    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"])
+
+    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"])
+
+    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"])
 
     with fluid.program_guard(train_program, startup_program):
         adam = fluid.optimizer.Adam(learning_rate=args.lr)

examples/metapath2vec/Dataset.py

@@ -23,7 +23,7 @@ import tqdm
 import time
 import logging
 import random
-from pgl.contrib import heter_graph
+from pgl import heter_graph
 import pickle as pkl
 
 
@@ -71,8 +71,12 @@ class Dataset(object):
                     if len(walk) > 1:
                         self.sentences_count += 1
                         for word in walk:
-                            self.token_count += 1
-                            word_freq[word] = word_freq.get(word, 0) + 1
+                            if int(word) >= self.config[
+                                    'paper_start_index']:  # remove paper
+                                continue
+                            else:
+                                self.token_count += 1
+                                word_freq[word] = word_freq.get(word, 0) + 1
 
         wid = 0
         logging.info('Read %d sentences.' % self.sentences_count)
@@ -126,6 +130,10 @@ class Dataset(object):
             with open(filename) as reader:
                 for line in reader:
                     words = line.strip().split()
+                    words = [
+                        w for w in words
+                        if int(w) < self.config['paper_start_index']
+                    ]
                     if len(words) > 1:
                         word_ids = [
                             self.word2id[w] for w in words if w in self.word2id

examples/metapath2vec/config.yaml

@@ -42,9 +42,10 @@ data_loader:
         walk_path: walks/*
         word2id_file: word2id.pkl
         batch_size: 32
-        win_size: 7  # default: 7
+        win_size: 5  # default: 7
         neg_num: 5
         min_count: 10
+        paper_start_index: 1697414
 
 model:
     type: SkipgramModel

examples/metapath2vec/sample.py

@@ -28,7 +28,7 @@ import tqdm
 import time
 import logging
 import random
-from pgl.contrib import heter_graph
+from pgl import heter_graph
 from pgl.sample import metapath_randomwalk
 from utils import *
 

ogb_examples/linkproppred/main_pgl.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.
+"""test ogb
+"""
+import argparse
+
+import pgl
+import numpy as np
+import paddle.fluid as fluid
+from pgl.contrib.ogb.linkproppred.dataset_pgl import PglLinkPropPredDataset
+from pgl.utils import paddle_helper
+from ogb.linkproppred import Evaluator
+
+
+def send_func(src_feat, dst_feat, edge_feat):
+    """send_func"""
+    return src_feat["h"]
+
+
+def recv_func(feat):
+    """recv_func"""
+    return fluid.layers.sequence_pool(feat, pool_type="sum")
+
+
+class GNNModel(object):
+    """GNNModel"""
+
+    def __init__(self, name, num_nodes, emb_dim, num_layers):
+        self.num_nodes = num_nodes
+        self.emb_dim = emb_dim
+        self.num_layers = num_layers
+        self.name = name
+
+        self.src_nodes = fluid.layers.data(
+            name='src_nodes',
+            shape=[None, 1],
+            dtype='int64', )
+
+        self.dst_nodes = fluid.layers.data(
+            name='dst_nodes',
+            shape=[None, 1],
+            dtype='int64', )
+
+        self.edge_label = fluid.layers.data(
+            name='edge_label',
+            shape=[None, 1],
+            dtype='float32', )
+
+    def forward(self, graph):
+        """forward"""
+        h = fluid.layers.create_parameter(
+            shape=[self.num_nodes, self.emb_dim],
+            dtype="float32",
+            name=self.name + "_embedding")
+        #  edge_attr = fluid.layers.fc(graph.edge_feat["feat"], size=self.emb_dim)
+
+        for layer in range(self.num_layers):
+            msg = graph.send(
+                send_func,
+                nfeat_list=[("h", h)], )
+            h = graph.recv(msg, recv_func)
+            h = fluid.layers.fc(
+                h,
+                size=self.emb_dim,
+                bias_attr=False,
+                param_attr=fluid.ParamAttr(name=self.name + '_%s' % layer))
+            h = h * graph.node_feat["norm"]
+            bias = fluid.layers.create_parameter(
+                shape=[self.emb_dim],
+                dtype='float32',
+                is_bias=True,
+                name=self.name + '_bias_%s' % layer)
+            h = fluid.layers.elementwise_add(h, bias, act="relu")
+
+        src = fluid.layers.gather(h, self.src_nodes)
+        dst = fluid.layers.gather(h, self.dst_nodes)
+        edge_embed = src * dst
+        pred = fluid.layers.fc(input=edge_embed,
+                               size=1,
+                               name=self.name + "_pred_output")
+
+        prob = fluid.layers.sigmoid(pred)
+
+        loss = fluid.layers.sigmoid_cross_entropy_with_logits(pred,
+                                                              self.edge_label)
+        loss = fluid.layers.reduce_mean(loss)
+
+        return pred, prob, loss
+
+
+def main():
+    """main
+    """
+    # Training settings
+    parser = argparse.ArgumentParser(description='Graph Dataset')
+    parser.add_argument(
+        '--epochs',
+        type=int,
+        default=100,
+        help='number of epochs to train (default: 100)')
+    parser.add_argument(
+        '--dataset',
+        type=str,
+        default="ogbl-ppa",
+        help='dataset name (default: protein protein associations)')
+    args = parser.parse_args()
+
+    #place = fluid.CUDAPlace(0)
+    place = fluid.CPUPlace()  # Dataset too big to use GPU
+
+    ### automatic dataloading and splitting
+    print("loadding dataset")
+    dataset = PglLinkPropPredDataset(name=args.dataset)
+    splitted_edge = dataset.get_edge_split()
+    print(splitted_edge['train_edge'].shape)
+    print(splitted_edge['train_edge_label'].shape)
+
+    print("building evaluator")
+    ### automatic evaluator. takes dataset name as input
+    evaluator = Evaluator(args.dataset)
+
+    graph_data = dataset[0]
+    print("num_nodes: %d" % graph_data.num_nodes)
+
+    train_program = fluid.Program()
+    startup_program = fluid.Program()
+    test_program = fluid.Program()
+    # degree normalize
+    indegree = graph_data.indegree()
+    norm = np.zeros_like(indegree, dtype="float32")
+    norm[indegree > 0] = np.power(indegree[indegree > 0], -0.5)
+    graph_data.node_feat["norm"] = np.expand_dims(norm, -1).astype("float32")
+
+    with fluid.program_guard(train_program, startup_program):
+        model = GNNModel(
+            name="gnn",
+            num_nodes=graph_data.num_nodes,
+            emb_dim=64,
+            num_layers=2)
+        gw = pgl.graph_wrapper.GraphWrapper(
+            "graph",
+            place,
+            node_feat=graph_data.node_feat_info(),
+            edge_feat=graph_data.edge_feat_info())
+        pred, prob, loss = model.forward(gw)
+
+    val_program = train_program.clone(for_test=True)
+
+    with fluid.program_guard(train_program, startup_program):
+        adam = fluid.optimizer.Adam(
+            learning_rate=1e-2,
+            regularization=fluid.regularizer.L2DecayRegularizer(
+                regularization_coeff=0.0005))
+        adam.minimize(loss)
+
+    exe = fluid.Executor(place)
+    exe.run(startup_program)
+
+    feed = gw.to_feed(graph_data)
+    for epoch in range(1, args.epochs + 1):
+        feed['src_nodes'] = splitted_edge["train_edge"][:, 0].reshape(-1, 1)
+        feed['dst_nodes'] = splitted_edge["train_edge"][:, 1].reshape(-1, 1)
+        feed['edge_label'] = splitted_edge["train_edge_label"].astype(
+            "float32").reshape(-1, 1)
+        res_loss, y_pred = exe.run(train_program,
+                                   feed=feed,
+                                   fetch_list=[loss, prob])
+        print("Loss %s" % res_loss[0])
+
+        result = {}
+        print("Evaluating...")
+        feed['src_nodes'] = splitted_edge["valid_edge"][:, 0].reshape(-1, 1)
+        feed['dst_nodes'] = splitted_edge["valid_edge"][:, 1].reshape(-1, 1)
+        feed['edge_label'] = splitted_edge["valid_edge_label"].astype(
+            "float32").reshape(-1, 1)
+        y_pred = exe.run(val_program, feed=feed, fetch_list=[prob])[0]
+        input_dict = {
+            "y_true": splitted_edge["valid_edge_label"],
+            "y_pred": y_pred.reshape(-1, ),
+        }
+        result["valid"] = evaluator.eval(input_dict)
+
+        feed['src_nodes'] = splitted_edge["test_edge"][:, 0].reshape(-1, 1)
+        feed['dst_nodes'] = splitted_edge["test_edge"][:, 1].reshape(-1, 1)
+        feed['edge_label'] = splitted_edge["test_edge_label"].astype(
+            "float32").reshape(-1, 1)
+        y_pred = exe.run(val_program, feed=feed, fetch_list=[prob])[0]
+        input_dict = {
+            "y_true": splitted_edge["test_edge_label"],
+            "y_pred": y_pred.reshape(-1, ),
+        }
+        result["test"] = evaluator.eval(input_dict)
+        print(result)
+
+
+if __name__ == "__main__":
+    main()

ogb_examples/nodeproppred/main_pgl.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.
+"""test ogb
+"""
+import argparse
+
+import pgl
+import numpy as np
+import paddle.fluid as fluid
+from pgl.contrib.ogb.nodeproppred.dataset_pgl import PglNodePropPredDataset
+from pgl.utils import paddle_helper
+from ogb.nodeproppred import Evaluator
+
+
+def train():
+    pass
+
+
+def send_func(src_feat, dst_feat, edge_feat):
+    return (src_feat["h"] + edge_feat["h"]) * src_feat["norm"]
+
+
+class GNNModel(object):
+    def __init__(self, name, emb_dim, num_task, num_layers):
+        self.num_task = num_task
+        self.emb_dim = emb_dim
+        self.num_layers = num_layers
+        self.name = name
+
+    def forward(self, graph):
+        h = fluid.layers.embedding(
+            graph.node_feat["x"],
+            size=(2, self.emb_dim))  # name=self.name + "_embedding") 
+        edge_attr = fluid.layers.fc(graph.edge_feat["feat"], size=self.emb_dim)
+        for layer in range(self.num_layers):
+            msg = graph.send(
+                send_func,
+                nfeat_list=[("h", h), ("norm", graph.node_feat["norm"])],
+                efeat_list=[("h", edge_attr)])
+            h = graph.recv(msg, "sum")
+            h = fluid.layers.fc(
+                h,
+                size=self.emb_dim,
+                bias_attr=False,
+                param_attr=fluid.ParamAttr(name=self.name + '_%s' % layer))
+            h = h * graph.node_feat["norm"]
+            bias = fluid.layers.create_parameter(
+                shape=[self.emb_dim],
+                dtype='float32',
+                is_bias=True,
+                name=self.name + '_bias_%s' % layer)
+            h = fluid.layers.elementwise_add(h, bias, act="relu")
+        pred = fluid.layers.fc(h,
+                               self.num_task,
+                               act=None,
+                               name=self.name + "_pred_output")
+        return pred
+
+
+def main():
+    """main
+    """
+    # Training settings
+    parser = argparse.ArgumentParser(description='Graph Dataset')
+    parser.add_argument(
+        '--epochs',
+        type=int,
+        default=100,
+        help='number of epochs to train (default: 100)')
+    parser.add_argument(
+        '--dataset',
+        type=str,
+        default="ogbn-proteins",
+        help='dataset name (default: proteinfunc)')
+    args = parser.parse_args()
+
+    #device = torch.device("cuda:" + str(args.device)) if torch.cuda.is_available() else torch.device("cpu")
+    #place = fluid.CUDAPlace(0)
+    place = fluid.CPUPlace()  # Dataset too big to use GPU
+
+    ### automatic dataloading and splitting
+    dataset = PglNodePropPredDataset(name=args.dataset)
+    splitted_idx = dataset.get_idx_split()
+
+    ### automatic evaluator. takes dataset name as input
+    evaluator = Evaluator(args.dataset)
+
+    graph_data, label = dataset[0]
+
+    train_program = fluid.Program()
+    startup_program = fluid.Program()
+    test_program = fluid.Program()
+    # degree normalize
+    indegree = graph_data.indegree()
+    norm = np.zeros_like(indegree, dtype="float32")
+    norm[indegree > 0] = np.power(indegree[indegree > 0], -0.5)
+    graph_data.node_feat["norm"] = np.expand_dims(norm, -1).astype("float32")
+    graph_data.node_feat["x"] = np.zeros((len(indegree), 1), dtype="int64")
+    graph_data.edge_feat["feat"] = graph_data.edge_feat["feat"].astype(
+        "float32")
+    model = GNNModel(
+        name="gnn", num_task=dataset.num_tasks, emb_dim=64, num_layers=2)
+
+    with fluid.program_guard(train_program, startup_program):
+        gw = pgl.graph_wrapper.StaticGraphWrapper("graph", graph_data, place)
+        pred = model.forward(gw)
+        sigmoid_pred = fluid.layers.sigmoid(pred)
+
+    val_program = train_program.clone(for_test=True)
+
+    initializer = []
+    with fluid.program_guard(train_program, startup_program):
+        train_node_index, init = paddle_helper.constant(
+            "train_node_index", dtype="int64", value=splitted_idx["train"])
+        initializer.append(init)
+
+        train_node_label, init = paddle_helper.constant(
+            "train_node_label",
+            dtype="float32",
+            value=label[splitted_idx["train"]].astype("float32"))
+        initializer.append(init)
+        train_pred_t = fluid.layers.gather(pred, train_node_index)
+        train_loss_t = fluid.layers.sigmoid_cross_entropy_with_logits(
+            x=train_pred_t, label=train_node_label)
+        train_loss_t = fluid.layers.reduce_sum(train_loss_t)
+        train_pred_t = fluid.layers.sigmoid(train_pred_t)
+
+        adam = fluid.optimizer.Adam(
+            learning_rate=1e-2,
+            regularization=fluid.regularizer.L2DecayRegularizer(
+                regularization_coeff=0.0005))
+        adam.minimize(train_loss_t)
+
+    exe = fluid.Executor(place)
+    exe.run(startup_program)
+    gw.initialize(place)
+    for init in initializer:
+        init(place)
+
+    for epoch in range(1, args.epochs + 1):
+        loss = exe.run(train_program, feed={}, fetch_list=[train_loss_t])
+        print("Loss %s" % loss[0])
+        print("Evaluating...")
+        y_pred = exe.run(val_program, feed={}, fetch_list=[sigmoid_pred])[0]
+        result = {}
+        input_dict = {
+            "y_true": label[splitted_idx["train"]],
+            "y_pred": y_pred[splitted_idx["train"]]
+        }
+        result["train"] = evaluator.eval(input_dict)
+        input_dict = {
+            "y_true": label[splitted_idx["valid"]],
+            "y_pred": y_pred[splitted_idx["valid"]]
+        }
+        result["valid"] = evaluator.eval(input_dict)
+        input_dict = {
+            "y_true": label[splitted_idx["test"]],
+            "y_pred": y_pred[splitted_idx["test"]]
+        }
+        result["test"] = evaluator.eval(input_dict)
+        print(result)
+
+
+if __name__ == "__main__":
+    main()

pgl/__init__.py

@@ -18,4 +18,6 @@ from pgl import layers
 from pgl import graph_wrapper
 from pgl import graph
 from pgl import data_loader
+from pgl import heter_graph
+from pgl import heter_graph_wrapper
 from pgl import contrib

pgl/contrib/ogb/__init__.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.

pgl/contrib/ogb/graphproppred/__init__.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.
+"""__init__.py"""

pgl/contrib/ogb/graphproppred/dataset_pgl.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.
+"""PglGraphPropPredDataset
+"""
+import pandas as pd
+import shutil, os
+import os.path as osp
+import numpy as np
+from ogb.utils.url import decide_download, download_url, extract_zip
+from ogb.graphproppred import make_master_file
+from pgl.contrib.ogb.io.read_graph_pgl import read_csv_graph_pgl
+
+
+def to_bool(value):
+    """to_bool"""
+    return np.array([value], dtype="bool")[0]
+
+
+class PglGraphPropPredDataset(object):
+    """PglGraphPropPredDataset"""
+
+    def __init__(self, name, root="dataset"):
+        self.name = name  ## original name, e.g., ogbg-mol-tox21
+        self.dir_name = "_".join(
+            name.split("-")
+        ) + "_pgl"  ## replace hyphen with underline, e.g., ogbg_mol_tox21_dgl
+
+        self.original_root = root
+        self.root = osp.join(root, self.dir_name)
+
+        self.meta_info = make_master_file.df  #pd.read_csv(
+        #os.path.join(os.path.dirname(__file__), "master.csv"), index_col=0)
+        if not self.name in self.meta_info:
+            print(self.name)
+            error_mssg = "Invalid dataset name {}.\n".format(self.name)
+            error_mssg += "Available datasets are as follows:\n"
+            error_mssg += "\n".join(self.meta_info.keys())
+            raise ValueError(error_mssg)
+
+        self.download_name = self.meta_info[self.name][
+            "download_name"]  ## name of downloaded file, e.g., tox21
+
+        self.num_tasks = int(self.meta_info[self.name]["num tasks"])
+        self.task_type = self.meta_info[self.name]["task type"]
+
+        super(PglGraphPropPredDataset, self).__init__()
+
+        self.pre_process()
+
+    def pre_process(self):
+        """Pre-processing"""
+        processed_dir = osp.join(self.root, 'processed')
+        raw_dir = osp.join(self.root, 'raw')
+        pre_processed_file_path = osp.join(processed_dir, 'pgl_data_processed')
+
+        if os.path.exists(pre_processed_file_path):
+            # TODO: Load Preprocessed
+            pass
+        else:
+            ### download
+            url = self.meta_info[self.name]["url"]
+            if decide_download(url):
+                path = download_url(url, self.original_root)
+                extract_zip(path, self.original_root)
+                os.unlink(path)
+                # delete folder if there exists
+                try:
+                    shutil.rmtree(self.root)
+                except:
+                    pass
+                shutil.move(
+                    osp.join(self.original_root, self.download_name),
+                    self.root)
+            else:
+                print("Stop download.")
+                exit(-1)
+
+            ### preprocess
+            add_inverse_edge = to_bool(self.meta_info[self.name][
+                "add_inverse_edge"])
+            self.graphs = read_csv_graph_pgl(
+                raw_dir, add_inverse_edge=add_inverse_edge)
+            self.graphs = np.array(self.graphs)
+            self.labels = np.array(
+                pd.read_csv(
+                    osp.join(raw_dir, "graph-label.csv.gz"),
+                    compression="gzip",
+                    header=None).values)
+
+            # TODO: Load Graph
+            ### load preprocessed files
+
+    def get_idx_split(self):
+        """Train/Valid/Test split"""
+        split_type = self.meta_info[self.name]["split"]
+        path = osp.join(self.root, "split", split_type)
+
+        train_idx = pd.read_csv(
+            osp.join(path, "train.csv.gz"), compression="gzip",
+            header=None).values.T[0]
+        valid_idx = pd.read_csv(
+            osp.join(path, "valid.csv.gz"), compression="gzip",
+            header=None).values.T[0]
+        test_idx = pd.read_csv(
+            osp.join(path, "test.csv.gz"), compression="gzip",
+            header=None).values.T[0]
+
+        return {
+            "train": np.array(
+                train_idx, dtype="int64"),
+            "valid": np.array(
+                valid_idx, dtype="int64"),
+            "test": np.array(
+                test_idx, dtype="int64")
+        }
+
+    def __getitem__(self, idx):
+        """Get datapoint with index"""
+        return self.graphs[idx], self.labels[idx]
+
+    def __len__(self):
+        """Length of the dataset
+        Returns
+        -------
+        int
+            Length of Dataset
+        """
+        return len(self.graphs)
+
+    def __repr__(self):  # pragma: no cover
+        return '{}({})'.format(self.__class__.__name__, len(self))
+
+
+if __name__ == "__main__":
+    pgl_dataset = PglGraphPropPredDataset(name="ogbg-mol-bace")
+    splitted_index = pgl_dataset.get_idx_split()
+    print(pgl_dataset)
+    print(pgl_dataset[3:20])
+    #print(pgl_dataset[splitted_index["train"]])
+    #print(pgl_dataset[splitted_index["valid"]])
+    #print(pgl_dataset[splitted_index["test"]])

pgl/contrib/__init__.py → pgl/contrib/ogb/io/__init__.py

-# Copyright (c) 2019 PaddlePaddle Authors. All Rights Reserved
+# 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.
@@ -11,8 +11,5 @@
 # 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
+"""__init__.py
 """
-
-from pgl.contrib import heter_graph
-from pgl.contrib import heter_graph_wrapper

pgl/contrib/ogb/io/read_graph_pgl.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.
+"""pgl read_csv_graph for ogb
+"""
+
+import pandas as pd
+import os.path as osp
+import numpy as np
+import pgl
+from ogb.io.read_graph_raw import read_csv_graph_raw
+
+
+def read_csv_graph_pgl(raw_dir, add_inverse_edge=False):
+    """Read CSV data and build PGL Graph
+    """
+    graph_list = read_csv_graph_raw(raw_dir, add_inverse_edge)
+    pgl_graph_list = []
+
+    for graph in graph_list:
+        edges = list(zip(graph["edge_index"][0], graph["edge_index"][1]))
+        g = pgl.graph.Graph(num_nodes=graph["num_nodes"], edges=edges)
+
+        if graph["edge_feat"] is not None:
+            g.edge_feat["feat"] = graph["edge_feat"]
+
+        if graph["node_feat"] is not None:
+            g.node_feat["feat"] = graph["node_feat"]
+
+        pgl_graph_list.append(g)
+
+    return pgl_graph_list
+
+
+if __name__ == "__main__":
+    # graph_list = read_csv_graph_dgl('dataset/proteinfunc_v2/raw', add_inverse_edge = True)
+    graph_list = read_csv_graph_pgl(
+        'dataset/ogbn_proteins_pgl/raw', add_inverse_edge=True)
+    print(graph_list)

pgl/contrib/ogb/linkproppred/__init__.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.
+"""__init__.py
+"""

pgl/contrib/ogb/linkproppred/dataset_pgl.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.
+"""LinkPropPredDataset for pgl
+"""
+import pandas as pd
+import shutil, os
+import os.path as osp
+import numpy as np
+from ogb.utils.url import decide_download, download_url, extract_zip
+from ogb.linkproppred import make_master_file
+from pgl.contrib.ogb.io.read_graph_pgl import read_csv_graph_pgl
+
+
+def to_bool(value):
+    """to_bool"""
+    return np.array([value], dtype="bool")[0]
+
+
+class PglLinkPropPredDataset(object):
+    """PglLinkPropPredDataset
+    """
+
+    def __init__(self, name, root="dataset"):
+        self.name = name  ## original name, e.g., ogbl-ppa
+        self.dir_name = "_".join(name.split(
+            "-")) + "_pgl"  ## replace hyphen with underline, e.g., ogbl_ppa_pgl
+
+        self.original_root = root
+        self.root = osp.join(root, self.dir_name)
+
+        self.meta_info = make_master_file.df  #pd.read_csv(os.path.join(os.path.dirname(__file__), "master.csv"), index_col=0)
+        if not self.name in self.meta_info:
+            print(self.name)
+            error_mssg = "Invalid dataset name {}.\n".format(self.name)
+            error_mssg += "Available datasets are as follows:\n"
+            error_mssg += "\n".join(self.meta_info.keys())
+            raise ValueError(error_mssg)
+
+        self.download_name = self.meta_info[self.name][
+            "download_name"]  ## name of downloaded file, e.g., ppassoc
+
+        self.task_type = self.meta_info[self.name]["task type"]
+
+        super(PglLinkPropPredDataset, self).__init__()
+
+        self.pre_process()
+
+    def pre_process(self):
+        """pre_process downlaoding data
+        """
+        processed_dir = osp.join(self.root, 'processed')
+        pre_processed_file_path = osp.join(processed_dir, 'dgl_data_processed')
+
+        if osp.exists(pre_processed_file_path):
+            #TODO: Reload Preprocess files
+            pass
+        else:
+            ### check download
+            if not osp.exists(osp.join(self.root, "raw", "edge.csv.gz")):
+                url = self.meta_info[self.name]["url"]
+                if decide_download(url):
+                    path = download_url(url, self.original_root)
+                    extract_zip(path, self.original_root)
+                    os.unlink(path)
+                    # delete folder if there exists
+                    try:
+                        shutil.rmtree(self.root)
+                    except:
+                        pass
+                    shutil.move(
+                        osp.join(self.original_root, self.download_name),
+                        self.root)
+                else:
+                    print("Stop download.")
+                    exit(-1)
+
+            raw_dir = osp.join(self.root, "raw")
+
+            ### pre-process and save
+            add_inverse_edge = to_bool(self.meta_info[self.name][
+                "add_inverse_edge"])
+            self.graph = read_csv_graph_pgl(
+                raw_dir, add_inverse_edge=add_inverse_edge)
+
+            #TODO: SAVE preprocess graph
+
+    def get_edge_split(self):
+        """Train/Validation/Test split
+        """
+        split_type = self.meta_info[self.name]["split"]
+        path = osp.join(self.root, "split", split_type)
+
+        train_idx = pd.read_csv(
+            osp.join(path, "train.csv.gz"), compression="gzip",
+            header=None).values
+        valid_idx = pd.read_csv(
+            osp.join(path, "valid.csv.gz"), compression="gzip",
+            header=None).values
+        test_idx = pd.read_csv(
+            osp.join(path, "test.csv.gz"), compression="gzip",
+            header=None).values
+
+        if self.task_type == "link prediction":
+            target_type = np.int64
+        else:
+            target_type = np.float32
+
+        return {
+            "train_edge": np.array(
+                train_idx[:, :2], dtype="int64"),
+            "train_edge_label": np.array(
+                train_idx[:, 2], dtype=target_type),
+            "valid_edge": np.array(
+                valid_idx[:, :2], dtype="int64"),
+            "valid_edge_label": np.array(
+                valid_idx[:, 2], dtype=target_type),
+            "test_edge": np.array(
+                test_idx[:, :2], dtype="int64"),
+            "test_edge_label": np.array(
+                test_idx[:, 2], dtype=target_type)
+        }
+
+    def __getitem__(self, idx):
+        assert idx == 0, "This dataset has only one graph"
+        return self.graph[0]
+
+    def __len__(self):
+        return 1
+
+    def __repr__(self):  # pragma: no cover
+        return '{}({})'.format(self.__class__.__name__, len(self))
+
+
+if __name__ == "__main__":
+    pgl_dataset = PglLinkPropPredDataset(name="ogbl-ppa")
+    splitted_edge = pgl_dataset.get_edge_split()
+    print(pgl_dataset[0])
+    print(splitted_edge)

pgl/contrib/ogb/nodeproppred/__init__.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.
+"""__init__.py
+"""

pgl/contrib/ogb/nodeproppred/dataset_pgl.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.
+"""NodePropPredDataset for pgl
+"""
+import pandas as pd
+import shutil, os
+import os.path as osp
+import numpy as np
+from ogb.utils.url import decide_download, download_url, extract_zip
+from ogb.nodeproppred import make_master_file  # create master.csv
+from pgl.contrib.ogb.io.read_graph_pgl import read_csv_graph_pgl
+
+
+def to_bool(value):
+    """to_bool"""
+    return np.array([value], dtype="bool")[0]
+
+
+class PglNodePropPredDataset(object):
+    """PglNodePropPredDataset
+    """
+
+    def __init__(self, name, root="dataset"):
+        self.name = name  ## original name, e.g., ogbn-proteins
+        self.dir_name = "_".join(
+            name.split("-")
+        ) + "_pgl"  ## replace hyphen with underline, e.g., ogbn_proteins_pgl
+
+        self.original_root = root
+        self.root = osp.join(root, self.dir_name)
+
+        self.meta_info = make_master_file.df  #pd.read_csv(
+        #os.path.join(os.path.dirname(__file__), "master.csv"), index_col=0)
+        if not self.name in self.meta_info:
+            error_mssg = "Invalid dataset name {}.\n".format(self.name)
+            error_mssg += "Available datasets are as follows:\n"
+            error_mssg += "\n".join(self.meta_info.keys())
+            raise ValueError(error_mssg)
+
+        self.download_name = self.meta_info[self.name][
+            "download_name"]  ## name of downloaded file, e.g., tox21
+
+        self.num_tasks = int(self.meta_info[self.name]["num tasks"])
+        self.task_type = self.meta_info[self.name]["task type"]
+
+        super(PglNodePropPredDataset, self).__init__()
+
+        self.pre_process()
+
+    def pre_process(self):
+        """pre_process downlaoding data
+        """
+        processed_dir = osp.join(self.root, 'processed')
+        pre_processed_file_path = osp.join(processed_dir, 'pgl_data_processed')
+
+        if osp.exists(pre_processed_file_path):
+            # TODO: Reload Preprocess files 
+            pass
+        else:
+            ### check download
+            if not osp.exists(osp.join(self.root, "raw", "edge.csv.gz")):
+                url = self.meta_info[self.name]["url"]
+                if decide_download(url):
+                    path = download_url(url, self.original_root)
+                    extract_zip(path, self.original_root)
+                    os.unlink(path)
+                    # delete folder if there exists
+                    try:
+                        shutil.rmtree(self.root)
+                    except:
+                        pass
+                    shutil.move(
+                        osp.join(self.original_root, self.download_name),
+                        self.root)
+                else:
+                    print("Stop download.")
+                    exit(-1)
+
+            raw_dir = osp.join(self.root, "raw")
+
+            ### pre-process and save
+            add_inverse_edge = to_bool(self.meta_info[self.name][
+                "add_inverse_edge"])
+            self.graph = read_csv_graph_pgl(
+                raw_dir, add_inverse_edge=add_inverse_edge)
+
+            ### adding prediction target
+            node_label = pd.read_csv(
+                osp.join(raw_dir, 'node-label.csv.gz'),
+                compression="gzip",
+                header=None).values
+            if "classification" in self.task_type:
+                node_label = np.array(node_label, dtype=np.int64)
+            else:
+                node_label = np.array(node_label, dtype=np.float32)
+
+            label_dict = {"labels": node_label}
+
+            # TODO: SAVE preprocess graph
+            self.labels = label_dict['labels']
+
+    def get_idx_split(self):
+        """Train/Validation/Test split
+        """
+        split_type = self.meta_info[self.name]["split"]
+        path = osp.join(self.root, "split", split_type)
+
+        train_idx = pd.read_csv(
+            osp.join(path, "train.csv.gz"), compression="gzip",
+            header=None).values.T[0]
+        valid_idx = pd.read_csv(
+            osp.join(path, "valid.csv.gz"), compression="gzip",
+            header=None).values.T[0]
+        test_idx = pd.read_csv(
+            osp.join(path, "test.csv.gz"), compression="gzip",
+            header=None).values.T[0]
+
+        return {
+            "train": np.array(
+                train_idx, dtype="int64"),
+            "valid": np.array(
+                valid_idx, dtype="int64"),
+            "test": np.array(
+                test_idx, dtype="int64")
+        }
+
+    def __getitem__(self, idx):
+        assert idx == 0, "This dataset has only one graph"
+        return self.graph[idx], self.labels
+
+    def __len__(self):
+        return 1
+
+    def __repr__(self):  # pragma: no cover
+        return '{}({})'.format(self.__class__.__name__, len(self))
+
+
+if __name__ == "__main__":
+    pgl_dataset = PglNodePropPredDataset(name="ogbn-proteins")
+    splitted_index = pgl_dataset.get_idx_split()
+    print(pgl_dataset[0])
+    print(splitted_index)

pgl/graph.py

@@ -15,6 +15,7 @@
     This package implement Graph structure for handling graph data.
 """
 
+import os
 import numpy as np
 import pickle as pkl
 import time
@@ -77,6 +78,15 @@ class EdgeIndex(object):
         """
         return self._sorted_u, self._sorted_v, self._sorted_eid
 
+    def dump(self, path):
+        if not os.path.exists(path):
+            os.makedirs(path)
+        np.save(path + '/degree.npy', self._degree)
+        np.save(path + '/sorted_u.npy', self._sorted_u)
+        np.save(path + '/sorted_v.npy', self._sorted_v)
+        np.save(path + '/sorted_eid.npy', self._sorted_eid)
+        np.save(path + '/indptr.npy', self._indptr)
+
 
 class Graph(object):
     """Implementation of graph structure in pgl.
@@ -136,6 +146,18 @@ class Graph(object):
         self._adj_src_index = None
         self._adj_dst_index = None
 
+    def dump(self, path):
+        if not os.path.exists(path):
+            os.makedirs(path)
+        np.save(path + '/num_nodes.npy', self._num_nodes)
+        np.save(path + '/edges.npy', self._edges)
+
+        if self._adj_src_index:
+            self._adj_src_index.dump(path + '/adj_src')
+
+        if self._adj_dst_index:
+            self._adj_dst_index.dump(path + '/adj_dst')
+
     @property
     def adj_src_index(self):
         """Return an EdgeIndex object for src.
@@ -506,7 +528,13 @@ class Graph(object):
                 (key, _hide_num_nodes(value.shape), value.dtype))
         return edge_feat_info
 
-    def subgraph(self, nodes, eid=None, edges=None):
+    def subgraph(self,
+                 nodes,
+                 eid=None,
+                 edges=None,
+                 edge_feats=None,
+                 with_node_feat=True,
+                 with_edge_feat=True):
         """Generate subgraph with nodes and edge ids.
 
         This function will generate a :code:`pgl.graph.Subgraph` object and
@@ -521,6 +549,10 @@ class Graph(object):
             eid (optional): Edge ids which will be included in the subgraph.
 
             edges (optional): Edge(src, dst) list which will be included in the subgraph.
+    
+            with_node_feat: Whether to inherit node features from parent graph.
+
+            with_edge_feat: Whether to inherit edge features from parent graph.
 
         Return:
             A :code:`pgl.graph.Subgraph` object.
@@ -543,14 +575,20 @@ class Graph(object):
                 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]
+        if edges is None:
+            if with_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]
+        else:
+            sub_edge_feat = edge_feats
 
         sub_node_feat = {}
-        for key, value in self._node_feat.items():
-            sub_node_feat[key] = value[nodes]
+        if with_node_feat:
+            for key, value in self._node_feat.items():
+                sub_node_feat[key] = value[nodes]
 
         subgraph = SubGraph(
             num_nodes=len(nodes),
@@ -779,3 +817,27 @@ class SubGraph(Graph):
             A list of node ids in parent graph.
         """
         return graph_kernel.map_nodes(nodes, self._to_reindex)
+
+
+class MemmapEdgeIndex(EdgeIndex):
+    def __init__(self, path):
+        self._degree = np.load(path + '/degree.npy', mmap_mode="r")
+        self._sorted_u = np.load(path + '/sorted_u.npy', mmap_mode="r")
+        self._sorted_v = np.load(path + '/sorted_v.npy', mmap_mode="r")
+        self._sorted_eid = np.load(path + '/sorted_eid.npy', mmap_mode="r")
+        self._indptr = np.load(path + '/indptr.npy', mmap_mode="r")
+
+
+class MemmapGraph(Graph):
+    def __init__(self, path):
+        self._num_nodes = np.load(path + '/num_nodes.npy')
+        self._edges = np.load(path + '/edges.npy', mmap_mode="r")
+        if os.path.exists(path + '/adj_src'):
+            self._adj_src_index = MemmapEdgeIndex(path + '/adj_src')
+        else:
+            self._adj_src_index = None
+
+        if os.path.exists(path + '/adj_dst'):
+            self._adj_dst_index = MemmapEdgeIndex(path + '/adj_dst')
+        else:
+            self._adj_dst_index = None

pgl/graph_wrapper.py

@@ -89,8 +89,8 @@ class BaseGraphWrapper(object):
     """
 
     def __init__(self):
-        self._node_feat_tensor_dict = {}
-        self._edge_feat_tensor_dict = {}
+        self.node_feat_tensor_dict = {}
+        self.edge_feat_tensor_dict = {}
         self._edges_src = None
         self._edges_dst = None
         self._num_nodes = None
@@ -98,6 +98,10 @@ class BaseGraphWrapper(object):
         self._edge_uniq_dst = None
         self._edge_uniq_dst_count = None
         self._node_ids = None
+        self._data_name_prefix = ""
+
+    def __repr__(self):
+        return self._data_name_prefix
 
     def send(self, message_func, nfeat_list=None, efeat_list=None):
         """Send message from all src nodes to dst nodes.
@@ -220,7 +224,7 @@ class BaseGraphWrapper(object):
             A dictionary whose keys are the feature names and the values
             are feature tensor.
         """
-        return self._edge_feat_tensor_dict
+        return self.edge_feat_tensor_dict
 
     @property
     def node_feat(self):
@@ -230,7 +234,7 @@ class BaseGraphWrapper(object):
             A dictionary whose keys are the feature names and the values
             are feature tensor.
         """
-        return self._node_feat_tensor_dict
+        return self.node_feat_tensor_dict
 
     def indegree(self):
         """Return the indegree tensor for all nodes.
@@ -298,8 +302,8 @@ class StaticGraphWrapper(BaseGraphWrapper):
 
     def __init__(self, name, graph, place):
         super(StaticGraphWrapper, self).__init__()
+        self._data_name_prefix = name
         self._initializers = []
-        self.__data_name_prefix = name
         self.__create_graph_attr(graph)
 
     def __create_graph_attr(self, graph):
@@ -326,43 +330,43 @@ class StaticGraphWrapper(BaseGraphWrapper):
         self._edges_src, init = paddle_helper.constant(
             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="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="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",
+            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)
 
         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",
+            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",
+            name=self._data_name_prefix + "/indegree",
             dtype="int64",
             value=indegree)
         self._initializers.append(init)
@@ -373,9 +377,9 @@ class StaticGraphWrapper(BaseGraphWrapper):
         for node_feat_name, node_feat_value in node_feat.items():
             node_feat_shape = node_feat_value.shape
             node_feat_dtype = node_feat_value.dtype
-            self._node_feat_tensor_dict[
+            self.node_feat_tensor_dict[
                 node_feat_name], init = paddle_helper.constant(
-                    name=self.__data_name_prefix + '/node_feat/' +
+                    name=self._data_name_prefix + '/node_feat/' +
                     node_feat_name,
                     dtype=node_feat_dtype,
                     value=node_feat_value)
@@ -387,9 +391,9 @@ class StaticGraphWrapper(BaseGraphWrapper):
         for edge_feat_name, edge_feat_value in edge_feat.items():
             edge_feat_shape = edge_feat_value.shape
             edge_feat_dtype = edge_feat_value.dtype
-            self._edge_feat_tensor_dict[
+            self.edge_feat_tensor_dict[
                 edge_feat_name], init = paddle_helper.constant(
-                    name=self.__data_name_prefix + '/edge_feat/' +
+                    name=self._data_name_prefix + '/edge_feat/' +
                     edge_feat_name,
                     dtype=edge_feat_dtype,
                     value=edge_feat_value)
@@ -477,8 +481,8 @@ class GraphWrapper(BaseGraphWrapper):
     def __init__(self, name, place, node_feat=[], edge_feat=[]):
         super(GraphWrapper, self).__init__()
         # collect holders for PyReader
+        self._data_name_prefix = name
         self._holder_list = []
-        self.__data_name_prefix = name
         self._place = place
         self.__create_graph_attr_holders()
         for node_feat_name, node_feat_shape, node_feat_dtype in node_feat:
@@ -493,43 +497,43 @@ 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="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="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='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="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._node_ids = fluid.layers.data(
-            self.__data_name_prefix + "/node_ids",
+            self._data_name_prefix + "/node_ids",
             shape=[None],
             append_batch_size=False,
             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="int64",
@@ -545,12 +549,12 @@ class GraphWrapper(BaseGraphWrapper):
         """Create data holders for node features.
         """
         feat_holder = fluid.layers.data(
-            self.__data_name_prefix + '/node_feat/' + 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.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,
@@ -558,12 +562,12 @@ class GraphWrapper(BaseGraphWrapper):
         """Create edge holders for edge features.
         """
         feat_holder = fluid.layers.data(
-            self.__data_name_prefix + '/edge_feat/' + 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.edge_feat_tensor_dict[edge_feat_name] = feat_holder
         self._holder_list.append(feat_holder)
 
     def to_feed(self, graph):
@@ -594,20 +598,21 @@ 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'] = 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 + '/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'] = 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 + '/node_feat/' +
                       key] = node_feat[key]
 
-        for key in self._edge_feat_tensor_dict:
-            feed_dict[self.__data_name_prefix + '/edge_feat/' +
+        for key in self.edge_feat_tensor_dict:
+            feed_dict[self._data_name_prefix + '/edge_feat/' +
                       key] = edge_feat[key]
 
         return feed_dict

pgl/contrib/heter_graph_wrapper.py → pgl/heter_graph_wrapper.py

@@ -64,8 +64,8 @@ class HeterGraphWrapper(object):
 
             import paddle.fluid as fluid
             import numpy as np
-            from pgl.contrib import heter_graph
-            from pgl.contrib import heter_graph_wrapper
+            from pgl import heter_graph
+            from pgl import heter_graph_wrapper
             num_nodes = 4
             node_types = [(0, 'user'), (1, 'item'), (2, 'item'), (3, 'user')]
             edges = {

pgl/contrib/redis_hetergraph.py → pgl/redis_hetergraph.py

@@ -28,7 +28,7 @@ import pgl.graph as pgraph
 import pickle as pkl
 from pgl.utils.logger import log
 import pgl.graph_kernel as graph_kernel
-from pgl.contrib import heter_graph
+from pgl import heter_graph
 import pgl.redis_graph as rg
 
 

pgl/sample.py

@@ -24,10 +24,29 @@ from pgl import graph_kernel
 
 __all__ = [
     'graphsage_sample', 'node2vec_sample', 'deepwalk_sample',
-    'metapath_randomwalk'
+    'metapath_randomwalk', 'pinsage_sample'
 ]
 
 
+def traverse(item):
+    """traverse the list or numpy"""
+    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, weights=None):
+    """flatten the sub-lists to one list"""
+    nodes = list(set(traverse(nodes)))
+    eids = list(traverse(eids))
+    if weights is not None:
+        weights = list(traverse(weights))
+    return nodes, eids, weights
+
+
 def edge_hash(src, dst):
     """edge_hash
     """
@@ -88,7 +107,6 @@ def graphsage_sample(graph, nodes, samples, ignore_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
 
@@ -317,3 +335,146 @@ def metapath_randomwalk(graph,
         cur_nodes = np.array(nxt_cur_nodes)
 
     return walk
+
+
+def random_walk_with_start_prob(graph, nodes, max_depth, proba=0.5):
+    """Implement of random walk with the probability of returning the origin node.
+
+    This function get random walks path for given nodes and depth.
+
+    Args:
+        nodes: Walk starting from nodes
+        max_depth: Max walking depth
+        proba: the proba to return the origin node
+
+    Return:
+        A list of walks.
+    """
+    walk = []
+    # init
+    for node in nodes:
+        walk.append([node])
+
+    walk_ids = np.arange(0, len(nodes))
+    cur_nodes = np.array(nodes)
+    nodes = np.array(nodes)
+    for l in range(max_depth):
+        # select the walks not end
+        if l >= 1:
+            return_proba = np.random.rand(cur_nodes.shape[0])
+            proba_mask = (return_proba < proba)
+            cur_nodes[proba_mask] = nodes[proba_mask]
+        outdegree = graph.outdegree(cur_nodes)
+        mask = (outdegree != 0)
+        if np.any(mask):
+            cur_walk_ids = walk_ids[mask]
+            outdegree = outdegree[mask]
+        else:
+            # stop when all nodes have no successor, wait start next loop to get precesssor
+            continue
+        succ = graph.successor(cur_nodes[mask])
+        sample_index = np.floor(
+            np.random.rand(outdegree.shape[0]) * outdegree).astype("int64")
+
+        nxt_cur_nodes = cur_nodes
+        for s, ind, walk_id in zip(succ, sample_index, cur_walk_ids):
+            walk[walk_id].append(s[ind])
+            nxt_cur_nodes[walk_id] = s[ind]
+        cur_nodes = np.array(nxt_cur_nodes)
+    return walk
+
+
+def pinsage_sample(graph,
+                   nodes,
+                   samples,
+                   top_k=10,
+                   proba=0.5,
+                   norm_bais=1.0,
+                   ignore_edges=set()):
+    """Implement of graphsage sample.
+    
+    Reference paper: .
+
+    Args:
+        graph: A pgl graph instance
+        nodes: Sample starting from nodes
+        samples: A list, number of neighbors in each layer
+        top_k: select the top_k visit count nodes to construct the edges 
+        proba: the probability to return the origin node 
+        norm_bais: the normlization for the visit count
+        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
+    edges, weights = [], []
+    layer_nodes, layer_edges, layer_weights = [], [], []
+    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_edges = [edges] + layer_edges
+            layer_edges_weight = [weights] + layer_weights
+            continue
+        walks = random_walk_with_start_prob(
+            graph, start_nodes, samples[layer_idx], proba=proba)
+        walks = [walk[1:] for walk in walks]
+        pred_edges = []
+        pred_weights = []
+        pred_nodes = []
+        for node, walk in zip(start_nodes, walks):
+            walk_nodes = []
+            walk_weights = []
+            count_sum = 0
+
+            for random_walk_node in walk:
+                if len(ignore_edge_set) > 0 and random_walk_node != node and \
+                    edge_hash(random_walk_node, node) in ignore_edge_set:
+                    continue
+                walk_nodes.append(random_walk_node)
+            unique, counts = np.unique(walk_nodes, return_counts=True)
+            frequencies = np.asarray((unique, counts)).T
+            frequencies = frequencies[np.argsort(frequencies[:, 1])]
+            frequencies = frequencies[-1 * top_k:, :]
+            for random_walk_node, random_count in zip(
+                    frequencies[:, 0].tolist(), frequencies[:, 1].tolist()):
+                pred_nodes.append(random_walk_node)
+                pred_edges.append((random_walk_node, node))
+                walk_weights.append(random_count)
+                count_sum += random_count
+            count_sum += len(walk_weights) * norm_bais
+            walk_weights = (np.array(walk_weights) + norm_bais) / (count_sum)
+            pred_weights.extend(walk_weights.tolist())
+        last_node_set = set(nodes)
+        nodes, edges, weights = flat_node_and_edge([nodes, pred_nodes], \
+            [edges, pred_edges], [weights, pred_weights])
+
+        layer_edges = [edges] + layer_edges
+        layer_weights = [weights] + layer_weights
+        layer_nodes = [nodes] + layer_nodes
+
+        start_nodes = list(set(nodes) - last_node_set)
+        start = time.time()
+
+    feed_dict = {}
+
+    subgraphs = []
+
+    for i in range(num_layers):
+        edge_feat_dict = {
+            "weight": np.array(
+                layer_weights[i], dtype='float32')
+        }
+        subgraphs.append(
+            graph.subgraph(
+                nodes=layer_nodes[0],
+                edges=layer_edges[i],
+                edge_feats=edge_feat_dict))
+        subgraphs[i].node_feat["index"] = np.array(
+            layer_nodes[0], dtype="int64")
+
+    return subgraphs

pgl/tests/test_hetergraph.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.
+"""test_hetergraph"""
+
+import time
+import unittest
+import json
+import os
+
+import numpy as np
+from pgl.sample import metapath_randomwalk
+from pgl.graph import Graph
+from pgl import heter_graph
+
+
+class HeterGraphTest(unittest.TestCase):
+    """HeterGraph test
+    """
+
+    @classmethod
+    def setUpClass(cls):
+        np.random.seed(1)
+        edges = {}
+        # for test no successor
+        edges['c2p'] = [(1, 4), (0, 5), (1, 9), (1, 8), (2, 8), (2, 5), (3, 6),
+                        (3, 7), (3, 4), (3, 8)]
+        edges['p2c'] = [(v, u) for u, v in edges['c2p']]
+        edges['p2a'] = [(4, 10), (4, 11), (4, 12), (4, 14), (4, 13), (6, 12),
+                        (6, 11), (6, 14), (7, 12), (7, 11), (8, 14), (9, 10)]
+        edges['a2p'] = [(v, u) for u, v in edges['p2a']]
+
+        # for test speed
+        #  edges['c2p'] = [(0, 4), (0, 5), (1, 9), (1,8), (2,8), (2,5), (3,6), (3,7), (3,4), (3,8)]
+        #  edges['p2c'] = [(v,u) for u, v in edges['c2p']]
+        #  edges['p2a'] = [(4,10), (4,11), (4,12), (4,14), (5,13), (6,13), (6,11), (6,14), (7,12), (7,11), (8,14), (9,13)]
+        #  edges['a2p'] = [(v,u) for u, v in edges['p2a']]
+
+        node_types = ['c' for _ in range(4)] + ['p' for _ in range(6)
+                                                ] + ['a' for _ in range(5)]
+        node_types = [(i, t) for i, t in enumerate(node_types)]
+
+        cls.graph = heter_graph.HeterGraph(
+            num_nodes=len(node_types), edges=edges, node_types=node_types)
+
+    def test_num_nodes_by_type(self):
+        print()
+        n_types = {'c': 4, 'p': 6, 'a': 5}
+        for nt in n_types:
+            num_nodes = self.graph.num_nodes_by_type(nt)
+            self.assertEqual(num_nodes, n_types[nt])
+
+    def test_node_batch_iter(self):
+        print()
+        batch_size = 2
+        ground = [[4, 5], [6, 7], [8, 9]]
+        for idx, nodes in enumerate(
+                self.graph.node_batch_iter(
+                    batch_size=batch_size, shuffle=False, n_type='p')):
+            self.assertEqual(len(nodes), batch_size)
+            self.assertListEqual(list(nodes), ground[idx])
+
+    def test_sample_nodes(self):
+        print()
+        p_ground = [4, 5, 6, 7, 8, 9]
+        sample_num = 10
+        nodes = self.graph.sample_nodes(sample_num=sample_num, n_type='p')
+
+        self.assertEqual(len(nodes), sample_num)
+        for n in nodes:
+            self.assertIn(n, p_ground)
+
+        # test n_type == None
+        ground = [i for i in range(15)]
+        nodes = self.graph.sample_nodes(sample_num=sample_num, n_type=None)
+        self.assertEqual(len(nodes), sample_num)
+        for n in nodes:
+            self.assertIn(n, ground)
+
+
+if __name__ == "__main__":
+    unittest.main()

pgl/tests/test_metapath_randomwalk.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.
+"""test_metapath_randomwalk"""
+import time
+import unittest
+import json
+import os
+
+import numpy as np
+from pgl.sample import metapath_randomwalk
+from pgl.graph import Graph
+from pgl import heter_graph
+
+np.random.seed(1)
+
+
+class MetapathRandomwalkTest(unittest.TestCase):
+    """metapath_randomwalk test
+    """
+
+    def setUp(self):
+        edges = {}
+        # for test no successor
+        edges['c2p'] = [(1, 4), (0, 5), (1, 9), (1, 8), (2, 8), (2, 5), (3, 6),
+                        (3, 7), (3, 4), (3, 8)]
+        edges['p2c'] = [(v, u) for u, v in edges['c2p']]
+        edges['p2a'] = [(4, 10), (4, 11), (4, 12), (4, 14), (4, 13), (6, 12),
+                        (6, 11), (6, 14), (7, 12), (7, 11), (8, 14), (9, 10)]
+        edges['a2p'] = [(v, u) for u, v in edges['p2a']]
+
+        # for test speed
+        #  edges['c2p'] = [(0, 4), (0, 5), (1, 9), (1,8), (2,8), (2,5), (3,6), (3,7), (3,4), (3,8)]
+        #  edges['p2c'] = [(v,u) for u, v in edges['c2p']]
+        #  edges['p2a'] = [(4,10), (4,11), (4,12), (4,14), (5,13), (6,13), (6,11), (6,14), (7,12), (7,11), (8,14), (9,13)]
+        #  edges['a2p'] = [(v,u) for u, v in edges['p2a']]
+
+        self.node_types = ['c' for _ in range(4)] + [
+            'p' for _ in range(6)
+        ] + ['a' for _ in range(5)]
+        node_types = [(i, t) for i, t in enumerate(self.node_types)]
+
+        self.graph = heter_graph.HeterGraph(
+            num_nodes=len(node_types), edges=edges, node_types=node_types)
+
+    def test_metapath_randomwalk(self):
+        meta_path = 'c2p-p2a-a2p-p2c'
+        path = ['c', 'p', 'a', 'p', 'c']
+        start_nodes = [0, 1, 2, 3]
+        walk_len = 10
+        walks = metapath_randomwalk(
+            graph=self.graph,
+            start_nodes=start_nodes,
+            metapath=meta_path,
+            walk_length=walk_len)
+
+        self.assertEqual(len(walks), 4)
+
+        for walk in walks:
+            for i in range(len(walk)):
+                idx = i % (len(path) - 1)
+                self.assertEqual(self.node_types[walk[i]], path[idx])
+
+
+if __name__ == "__main__":
+    unittest.main()

pgl/utils/mp_reader.py

@@ -25,6 +25,8 @@ except:
 import numpy as np
 import time
 import paddle.fluid as fluid
+from queue import Queue
+import threading
 
 
 def serialize_data(data):
@@ -129,22 +131,39 @@ def multiprocess_reader(readers, use_pipe=True, queue_size=1000, pipe_size=10):
             p.start()
 
         reader_num = len(readers)
-        finish_num = 0
         conn_to_remove = []
         finish_flag = np.zeros(len(conns), dtype="int32")
+        start = time.time()
+
+        def queue_worker(sub_conn, que):
+            while True:
+                buff = sub_conn.recv()
+                sample = deserialize_data(buff)
+                if sample is None:
+                    que.put(None)
+                    sub_conn.close()
+                    break
+                que.put(sample)
+
+        thread_pool = []
+        output_queue = Queue(maxsize=reader_num)
+        for i in range(reader_num):
+            t = threading.Thread(
+                target=queue_worker, args=(conns[i], output_queue))
+            t.daemon = True
+            t.start()
+            thread_pool.append(t)
+
+        finish_num = 0
         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
+            sample = output_queue.get()
+            if sample is None:
+                finish_num += 1
+            else:
+                yield sample
+
+        for thread in thread_pool:
+            thread.join()
 
     if use_pipe:
         return pipe_reader