pyg-nightly 2.7.0.dev20250918__tar.gz → 2.7.0.dev20250920__tar.gz

{pyg_nightly-2.7.0.dev20250918 → pyg_nightly-2.7.0.dev20250920}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pyg-nightly
-Version: 2.7.0.dev20250918
+Version: 2.7.0.dev20250920
 Summary: Graph Neural Network Library for PyTorch
 Keywords: deep-learning,pytorch,geometric-deep-learning,graph-neural-networks,graph-convolutional-networks
 Author-email: Matthias Fey <matthias@pyg.org>

{pyg_nightly-2.7.0.dev20250918 → pyg_nightly-2.7.0.dev20250920}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend="flit_core.buildapi"
 
 [project]
 name="pyg-nightly"
-version="2.7.0.dev20250918"
+version="2.7.0.dev20250920"
 authors=[
     {name="Matthias Fey", email="matthias@pyg.org"},
 ]

{pyg_nightly-2.7.0.dev20250918 → pyg_nightly-2.7.0.dev20250920}/torch_geometric/__init__.py

@@ -31,7 +31,7 @@ from .lazy_loader import LazyLoader
 contrib = LazyLoader('contrib', globals(), 'torch_geometric.contrib')
 graphgym = LazyLoader('graphgym', globals(), 'torch_geometric.graphgym')
 
-__version__ = '2.7.0.dev20250918'
+__version__ = '2.7.0.dev20250920'
 
 __all__ = [
     'Index',

{pyg_nightly-2.7.0.dev20250918 → pyg_nightly-2.7.0.dev20250920}/torch_geometric/datasets/tag_dataset.py

@@ -1,3 +1,4 @@
+import csv
 import os
 import os.path as osp
 from collections.abc import Sequence
@@ -10,6 +11,7 @@ from tqdm import tqdm
 
 from torch_geometric.data import InMemoryDataset, download_google_url
 from torch_geometric.data.data import BaseData
+from torch_geometric.io import fs
 
 try:
     from pandas import DataFrame, read_csv
@@ -22,14 +24,16 @@ IndexType = Union[slice, Tensor, np.ndarray, Sequence]
 
 class TAGDataset(InMemoryDataset):
     r"""The Text Attributed Graph datasets from the
-    `"Learning on Large-scale Text-attributed Graphs via Variational Inference
-    " <https://arxiv.org/abs/2210.14709>`_ paper.
+    `"Learning on Large-scale Text-attributed Graphs via Variational Inference"
+    <https://arxiv.org/abs/2210.14709>`_ paper and `"Harnessing Explanations:
+    LLM-to-LM Interpreter for Enhanced Text-Attributed Graph Representation
+    Learning" <https://arxiv.org/abs/2305.19523>`_ paper.
     This dataset is aiming on transform `ogbn products`, `ogbn arxiv`
     into Text Attributed Graph that each node in graph is associate with a
-    raw text, that dataset can be adapt to DataLoader (for LM training) and
-    NeighborLoader(for GNN training). In addition, this class can be use as a
-    wrapper class by convert a InMemoryDataset with Tokenizer and text into
-    Text Attributed Graph.
+    raw text, LLM prediction and explanation, that dataset can be adapt to
+    DataLoader (for LM training) and NeighborLoader(for GNN training).
+    In addition, this class can be use as a wrapper class by convert a
+    InMemoryDataset with Tokenizer and text into Text Attributed Graph.
 
     Args:
         root (str): Root directory where the dataset should be saved.
@@ -51,22 +55,35 @@ class TAGDataset(InMemoryDataset):
             or not, default: False
         force_reload (bool): default: False
     .. note::
-        See `example/llm_plus_gnn/glem.py` for example usage
+        See `example/llm/glem.py` for example usage
     """
     raw_text_id = {
         'ogbn-arxiv': '1g3OOVhRyiyKv13LY6gbp8GLITocOUr_3',
         'ogbn-products': '1I-S176-W4Bm1iPDjQv3hYwQBtxE0v8mt'
     }
 
-    def __init__(self, root: str, dataset: InMemoryDataset,
-                 tokenizer_name: str, text: Optional[List[str]] = None,
-                 split_idx: Optional[Dict[str, Tensor]] = None,
-                 tokenize_batch_size: int = 256, token_on_disk: bool = False,
-                 text_on_disk: bool = False,
-                 force_reload: bool = False) -> None:
+    llm_prediction_url = 'https://github.com/XiaoxinHe/TAPE/raw/main/gpt_preds'
+
+    llm_explanation_id = {
+        'ogbn-arxiv': '1o8n2xRen-N_elF9NQpIca0iCHJgEJbRQ',
+    }
+
+    def __init__(
+        self,
+        root: str,
+        dataset: InMemoryDataset,
+        tokenizer_name: str,
+        text: Optional[List[str]] = None,
+        split_idx: Optional[Dict[str, Tensor]] = None,
+        tokenize_batch_size: int = 256,
+        token_on_disk: bool = False,
+        text_on_disk: bool = False,
+        force_reload: bool = False,
+    ) -> None:
         # list the vars you want to pass in before run download & process
         self.name = dataset.name
         self.text = text
+        self.llm_prediction_topk = 5
         self.tokenizer_name = tokenizer_name
         from transformers import AutoTokenizer
         self.tokenizer = AutoTokenizer.from_pretrained(tokenizer_name)
@@ -93,8 +110,9 @@ class TAGDataset(InMemoryDataset):
                              "is_gold mask, please pass splited index "
                              "in format of dictionaty with 'train', 'valid' "
                              "'test' index tensor to 'split_idx'")
-        if text is not None and text_on_disk:
-            self.save_node_text(text)
+        if text_on_disk:
+            if text is not None:
+                self.save_node_text(text)
         self.text_on_disk = text_on_disk
         # init will call download and process
         super().__init__(self.root, transform=None, pre_transform=None,
@@ -119,6 +137,10 @@ class TAGDataset(InMemoryDataset):
         self.token_on_disk = token_on_disk
         self.tokenize_batch_size = tokenize_batch_size
         self._token = self.tokenize_graph(self.tokenize_batch_size)
+        self._llm_explanation_token = self.tokenize_graph(
+            self.tokenize_batch_size, text_type='llm_explanation')
+        self._all_token = self.tokenize_graph(self.tokenize_batch_size,
+                                              text_type='all')
         self.__num_classes__ = dataset.num_classes
 
     @property
@@ -146,6 +168,19 @@ class TAGDataset(InMemoryDataset):
             self._token = self.tokenize_graph()
         return self._token
 
+    @property
+    def llm_explanation_token(self) -> Dict[str, Tensor]:
+        if self._llm_explanation_token is None:  # lazy load
+            self._llm_explanation_token = self.tokenize_graph(
+                text_type='llm_explanation')
+        return self._llm_explanation_token
+
+    @property
+    def all_token(self) -> Dict[str, Tensor]:
+        if self._all_token is None:  # lazy load
+            self._all_token = self.tokenize_graph(text_type='all')
+        return self._all_token
+
     # load is_gold after init
     @property
     def is_gold(self) -> Tensor:
@@ -194,10 +229,17 @@ class TAGDataset(InMemoryDataset):
                                             folder=f'{self.root}/raw',
                                             filename='node-text.csv.gz',
                                             log=True)
-        text_df = read_csv(raw_text_path)
-        self.text = list(text_df['text'])
+        self.text = list(read_csv(raw_text_path)['text'])
+        print('downloading llm explanations')
+        llm_explanation_path = download_google_url(
+            id=self.llm_explanation_id[self.name], folder=f'{self.root}/raw',
+            filename='node-gpt-response.csv.gz', log=True)
+        self.llm_explanation = list(read_csv(llm_explanation_path)['text'])
+        print('downloading llm predictions')
+        fs.cp(f'{self.llm_prediction_url}/{self.name}.csv', self.raw_dir)
 
     def process(self) -> None:
+        # process Title and Abstraction
         if osp.exists(osp.join(self.root, 'raw', 'node-text.csv.gz')):
             text_df = read_csv(osp.join(self.root, 'raw', 'node-text.csv.gz'))
             self.text = list(text_df['text'])
@@ -212,6 +254,42 @@ class TAGDataset(InMemoryDataset):
                              "The raw text of each node is not specified"
                              "Please pass in 'text' when convert your dataset "
                              "to Text Attribute Graph Dataset")
+        # process LLM explanation and prediction
+        llm_explanation_path = f'{self.raw_dir}/node-gpt-response.csv.gz'
+        llm_prediction_path = f'{self.raw_dir}/{self.name}.csv'
+        if osp.exists(llm_explanation_path) and osp.exists(
+                llm_prediction_path):
+            # load LLM explanation
+            self.llm_explanation = list(read_csv(llm_explanation_path)['text'])
+            # load LLM prediction
+            preds = []
+            with open(llm_prediction_path) as file:
+                reader = csv.reader(file)
+                for row in reader:
+                    inner_list = []
+                    for value in row:
+                        inner_list.append(int(value))
+                    preds.append(inner_list)
+
+            pl = torch.zeros(len(preds), self.llm_prediction_topk,
+                             dtype=torch.long)
+            for i, pred in enumerate(preds):
+                pl[i][:len(pred)] = torch.tensor(
+                    pred[:self.llm_prediction_topk], dtype=torch.long) + 1
+        elif self.name in self.llm_explanation_id:
+            self.download()
+        else:
+            print(
+                'The dataset is not ogbn-arxiv,'
+                'please pass in your llm explanation list to `llm_explanation`'
+                'and llm prediction list to `llm_prediction`')
+        if self.llm_explanation is None or pl is None:
+            raise ValueError(
+                "The TAGDataset only have ogbn-arxiv LLM explanations"
+                "and predictions in default. The llm explanation and"
+                "prediction of each node is not specified."
+                "Please pass in 'llm_explanation' and 'llm_prediction' when"
+                "convert your dataset to Text Attribute Graph Dataset")
 
     def save_node_text(self, text: List[str]) -> None:
         node_text_path = osp.join(self.root, 'raw', 'node-text.csv.gz')
@@ -224,22 +302,39 @@ class TAGDataset(InMemoryDataset):
             text_df.to_csv(osp.join(node_text_path), compression='gzip',
                            index=False)
 
-    def tokenize_graph(self, batch_size: int = 256) -> Dict[str, Tensor]:
+    def tokenize_graph(self, batch_size: int = 256,
+                       text_type: str = 'raw_text') -> Dict[str, Tensor]:
         r"""Tokenizing the text associate with each node, running in cpu.
 
         Args:
             batch_size (Optional[int]): batch size of list of text for
                 generating emebdding
+            text_type (Optional[str]): type of text
         Returns:
             Dict[str, torch.Tensor]: tokenized graph
         """
+        assert text_type in ['raw_text', 'llm_explanation', 'all']
+        if text_type == 'raw_text':
+            _text = self.text
+        elif text_type == 'llm_explanation':
+            _text = self.llm_explanation
+        elif text_type == 'all':
+            if self.text is None or self.llm_explanation is None:
+                raise ValueError("The TAGDataset need text and llm explanation"
+                                 "for tokenizing all text")
+            _text = [
+                f'{raw_txt} Explanation: {exp_txt}'
+                for raw_txt, exp_txt in zip(self.text, self.llm_explanation)
+            ]
+
         data_len = 0
-        if self.text is not None:
-            data_len = len(self.text)
+        if _text is not None:
+            data_len = len(_text)
         else:
             raise ValueError("The TAGDataset need text for tokenization")
         token_keys = ['input_ids', 'token_type_ids', 'attention_mask']
-        path = os.path.join(self.processed_dir, 'token', self.tokenizer_name)
+        path = os.path.join(self.processed_dir, 'token', text_type,
+                            self.tokenizer_name)
         # Check if the .pt files already exist
         token_files_exist = any(
             os.path.exists(os.path.join(path, f'{k}.pt')) for k in token_keys)
@@ -256,12 +351,12 @@ class TAGDataset(InMemoryDataset):
         all_encoded_token = {k: [] for k in token_keys}
         pbar = tqdm(total=data_len)
 
-        pbar.set_description('Tokenizing Text Attributed Graph')
+        pbar.set_description(f'Tokenizing Text Attributed Graph {text_type}')
         for i in range(0, data_len, batch_size):
             end_index = min(data_len, i + batch_size)
-            token = self.tokenizer(self.text[i:min(i + batch_size, data_len)],
-                                   padding='max_length', truncation=True,
-                                   max_length=512, return_tensors="pt")
+            token = self.tokenizer(_text[i:end_index], padding='max_length',
+                                   truncation=True, max_length=512,
+                                   return_tensors="pt")
             for k in token.keys():
                 all_encoded_token[k].append(token[k])
             pbar.update(end_index - i)
@@ -289,10 +384,18 @@ class TAGDataset(InMemoryDataset):
 
         Args:
             tag_dataset (TAGDataset): the parent dataset
+            text_type (str): type of text
         """
-        def __init__(self, tag_dataset: 'TAGDataset') -> None:
+        def __init__(self, tag_dataset: 'TAGDataset',
+                     text_type: str = 'raw_text') -> None:
+            assert text_type in ['raw_text', 'llm_explanation', 'all']
             self.tag_dataset = tag_dataset
-            self.token = tag_dataset.token
+            if text_type == 'raw_text':
+                self.token = tag_dataset.token
+            elif text_type == 'llm_explanation':
+                self.token = tag_dataset.llm_explanation_token
+            elif text_type == 'all':
+                self.token = tag_dataset.all_token
             assert tag_dataset._data is not None
             self._data = tag_dataset._data
 
@@ -312,7 +415,8 @@ class TAGDataset(InMemoryDataset):
 
         # for LM training
         def __getitem__(
-                self, node_id: IndexType
+            self,
+            node_id: IndexType,
         ) -> Dict[str, Union[Tensor, Dict[str, Tensor]]]:
             r"""This function will override the function in
             torch.utils.data.Dataset, and will be called when you
@@ -343,8 +447,8 @@ class TAGDataset(InMemoryDataset):
         def __repr__(self) -> str:
             return f'{self.__class__.__name__}()'
 
-    def to_text_dataset(self) -> TextDataset:
+    def to_text_dataset(self, text_type: str = 'raw_text') -> TextDataset:
         r"""Factory Build text dataset from Text Attributed Graph Dataset
         each data point is node's associated text token.
         """
-        return TAGDataset.TextDataset(self)
+        return TAGDataset.TextDataset(self, text_type)

{pyg_nightly-2.7.0.dev20250918 → pyg_nightly-2.7.0.dev20250920}/torch_geometric/metrics/link_pred.py

@@ -53,7 +53,7 @@ class LinkPredMetricData:
 
         # Flatten both prediction and ground-truth indices, and determine
         # overlaps afterwards via `torch.searchsorted`.
-        max_index = max(  # type: ignore
+        max_index = max(
             self.pred_index_mat.max()
             if self.pred_index_mat.numel() > 0 else 0,
             self.edge_label_index[1].max()
@@ -820,9 +820,10 @@ class LinkPredPersonalization(_LinkPredMetric):
             right = pred[col.cpu()].to(device)
 
             # Use offset to work around applying `isin` along a specific dim:
-            i = max(left.max(), right.max()) + 1  # type: ignore
-            i = torch.arange(0, i * row.size(0), i, device=device).view(-1, 1)
-            isin = torch.isin(left + i, right + i)
+            i = max(int(left.max()), int(right.max())) + 1
+            idx = torch.arange(0, i * row.size(0), i, device=device)
+            idx = idx.view(-1, 1)
+            isin = torch.isin(left + idx, right + idx)
 
             # Compute personalization via average inverse cosine similarity:
             cos = isin.sum(dim=-1) / pred.size(1)