Add gpt example (#115)

examples/gpt/README.md

@@ -0,0 +1,33 @@
+# Using GPT to Reason on Graphs
+
+This simple example shows how to leverage GPT to make inference on large graphs.
+
+### 1. Prepare the graph dataset & environment
+In this example, we use the dataset
+[arxiv_2023](https://github.com/TRAIS-Lab/LLM-Structured-Data/tree/main/dataset/arxiv_2023)
+and download it to the path `../data/arxiv_2023`.
+
+Then, export your OPENAI_API_KEY as the environment variable in your shell:
+
+```bash
+export OPENAI_API_KEY='YOUR_API_KEY'
+```
+
+### 2. Run the code
+Configure the parameters in the data loader and run the code.
+```bash
+python arxiv.py
+```
+This example tests the inference performance of GPT on a large graph with the link prediction task as the default task. 
+
+First, we sample a 2-hop ego-subgraph from the original graph. The subgraph is sampled by the `LinkNeighborLoader` with a mini-batch sampler that samples a fixed number of neighbors for each edge and is formed as PyG's `edge_index`.
+
+Then, the sampled subgraph along with node features (e.g. in this example the title for the paper node) is fed into GPT to infer whether a requested edge is in the original graph or not. 
+
+**Note**: GPT has a limitation on its context size, and thus limits the size of the sampled subgraph, which is determined by the parameter `num_neighbors` in the data loader. If the sampled subgraph is too large, please try to decrease the `num_neighbors` to reduce the size of the subgraph.
+
+### Appendix:
+1. **Dataset**: You can also use other datasets and modify the preprocessing code, but don't forget to transform the graph format into PyG's `edge_index`.
+2. **Prompts**: Use the parameter `reason: Bool` to decide whether to see the reasoning process of GPT. You can also design your own prompts to make inference on graphs instead of using our template. 
+3. **Node classification**: We also provide a template prompt for node classification task, and design your method to leverage the label informatiion. 
+**Note**: We've tried directly passing the labels for nodes in an ego-subgraph to predict the label of the center node, and GPT's prediction behavior in this case is close to voting via neighbors.

examples/gpt/arxiv.py

@@ -0,0 +1,76 @@
+# Copyright 2022 Alibaba Group Holding Limited. All Rights Reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+# ==============================================================================
+
+import time
+import torch
+
+from tqdm import tqdm
+
+import graphlearn_torch as glt
+from utils import get_gpt_response, link_prediction
+
+
+def run(glt_ds, raw_text, reason):
+  neg_sampling = glt.sampler.NegativeSampling('binary')
+  train_loader = glt.loader.LinkNeighborLoader(glt_ds,
+                                              [12, 6],
+                                              neg_sampling=neg_sampling,
+                                              batch_size=2,
+                                              drop_last=True,
+                                              shuffle=True,
+                                              device=torch.device('cpu'))
+  print(f'Building graphlearn_torch NeighborLoader Done.')
+
+  for batch in tqdm(train_loader):
+    batch_titles = raw_text[batch.node]
+    if batch.edge_index.shape[1] < 5:
+      continue
+
+    # print(batch)
+    # print(batch.edge_label_index)
+    message = link_prediction(batch, batch_titles, reason=reason)
+
+    # print(message)
+    response = get_gpt_response(
+      message=message
+    )
+
+    print(f"response: {response}")
+
+
+if __name__ == '__main__':
+  import pandas as pd
+  root = '../data/arxiv_2023/raw/'
+  titles = pd.read_csv(root + "titles.csv.gz").to_numpy()
+  ids = torch.from_numpy(pd.read_csv(root + "ids.csv.gz").to_numpy())
+  edge_index = torch.from_numpy(pd.read_csv(root + "edges.csv.gz").to_numpy())
+
+  print('Build graphlearn_torch dataset...')
+  start = time.time()
+  glt_dataset = glt.data.Dataset()
+  glt_dataset.init_graph(
+    edge_index=edge_index.T,
+    graph_mode='CPU',
+    directed=True
+  )
+  glt_dataset.init_node_features(
+    node_feature_data=ids,
+    sort_func=glt.data.sort_by_in_degree,
+    split_ratio=0
+  )
+
+  print(f'Build graphlearn_torch csr_topo and feature cost {time.time() - start} s.')
+
+  run(glt_dataset, titles, reason=False)

examples/gpt/utils.py

@@ -0,0 +1,67 @@
+# Copyright 2022 Alibaba Group Holding Limited. 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.
+# ==============================================================================
+
+from openai import OpenAI
+
+
+def get_gpt_response(message, model="gpt-4-1106-preview"):
+    client = OpenAI()
+    chat_completion = client.chat.completions.create(
+        messages=[
+            {
+                "role" : "user",
+                "content": message,
+            }
+        ],
+        model=model,
+    )
+    return chat_completion.choices[0].message.content
+
+
+def node_classification(batch):
+  message = "This is a directed subgraph of arxiv citation network with " + str(batch.x.shape[0]) + " nodes numbered from 0 to " + str(batch.x.shape[0]-1) + ".\n"
+  message += "The subgraph has " + str(batch.edge_index.shape[1]) + " edges.\n"
+  for i in range(1, batch.x.shape[0]):
+    feature_str = ','.join(f'{it:.3f}' for it in batch.x[i].tolist())
+    message += "The feature of node " + str(i) + " is [" + feature_str + "] "
+    message += "and the node label is " + str(batch.y[i].item()) + ".\n"
+  message += "The edges of the subgraph are " + str(batch.edge_index.T.tolist()) + ' where the first number indicates source node and the second destination node.\n'
+  message += "Question: predict the label for node 0, whose feature is [" + ','.join(f'{it:.3f}' for it in batch.x[0].tolist()) + "]. Give the label only and don't show any reasoning process.\n\n"
+
+  return message
+
+
+def link_prediction(batch, titles, reason=False):
+  message = "This is a directed subgraph of arxiv citation network with " + str(batch.x.shape[0]) + " nodes numbered from 0 to " + str(batch.x.shape[0]-1) + ".\n"
+  graph = batch.edge_index.T.unique(dim=0).tolist()
+  message += "The titles of each paper:\n"
+  for i in range(batch.x.shape[0]):
+    message += "node " + str(i) + " is '" + titles[i][0] + "'\n" 
+  message += "The sampled subgraph of the network is " + str(graph) + ' where the first number indicates source node and the second destination node.\n'
+  message += "Hint: the direction of the edge can indicate some information of temporality.\n"
+  message += "\nAccording to principles of citation network construction and the given subgraph structure, answer the following questions:\n"
+
+  # In batch.edge_label_index.T.tolist(), index 0 and 1 are positive samples,
+  #                                       index 2 and 3 are negative samples.
+  message += "Question 1: predict whether there tends to form an edge "+str(batch.edge_label_index.T.tolist()[1])+".\n"
+  message += "Question 2: predict whether there tends to form an edge "+str(batch.edge_label_index.T.tolist()[3])+".\n"
+  message += "Question 3: predict whether there tends to form an edge "+str(batch.edge_label_index.T.tolist()[2])+".\n"
+  message += "Question 4: predict whether there tends to form an edge "+str(batch.edge_label_index.T.tolist()[0])+".\n"
+  if reason:
+    message += "Answer yes or no and show reasoning process.\n\n"
+  else:
+    message += "Answer yes or no and don't show any reasoning process.\n\n"
+
+  return message

graphlearn_torch/python/sampler/neighbor_sampler.py

@@ -62,6 +62,7 @@ def __init__(self,
     self._inducer = None
     self._sampler_lock = threading.Lock()
     self.is_sampler_initialized = False
+    self.is_neg_sampler_initialized = False
 
     if seed is not None:
       pywrap.RandomSeedManager.getInstance().setSeed(seed)
@@ -113,7 +114,7 @@ def lazy_init_sampler(self):
 
 
   def lazy_init_neg_sampler(self):
-    if not self.is_sampler_initialized and self.with_neg:
+    if not self.is_neg_sampler_initialized and self.with_neg:
       with self._sampler_lock:
         if self._neg_sampler is None:
           if self._g_cls == 'homo':
@@ -122,7 +123,7 @@ def lazy_init_neg_sampler(self):
               mode=self.device.type.upper(),
               edge_dir=self.edge_dir
             )
-            self.is_sampler_initialized = True
+            self.is_neg_sampler_initialized = True
           else: # hetero
             self._neg_sampler = {}
             for etype, g in self.graph.items():
@@ -131,7 +132,7 @@ def lazy_init_neg_sampler(self):
                 mode=self.device.type.upper(),
                 edge_dir=self.edge_dir
               )
-            self.is_sampler_initialized = True
+            self.is_neg_sampler_initialized = True
 
   def lazy_init_subgraph_op(self):
     if self._subgraph_op is None:

setup.py

@@ -30,7 +30,7 @@
 WITH_CUDA = os.getenv('WITH_CUDA', 'ON')
 
 sys.path.append(os.path.join(ROOT_PATH, 'graphlearn_torch', 'python', 'utils'))
-from build import glt_ext_module, glt_v6d_ext_module
+from build_glt import glt_ext_module, glt_v6d_ext_module
 
 GLT_V6D_EXT_NAME = "py_graphlearn_torch_vineyard"
 GLT_EXT_NAME = "py_graphlearn_torch"