pyg-nightly 2.7.0.dev20241119__py3-none-any.whl → 2.7.0.dev20241120__py3-none-any.whl

torch_geometric/datasets/tag_dataset.py

@@ -0,0 +1,350 @@
+import os
+import os.path as osp
+from collections.abc import Sequence
+from typing import Dict, List, Optional, Union
+
+import numpy as np
+import torch
+from torch import Tensor
+from tqdm import tqdm
+
+from torch_geometric.data import InMemoryDataset, download_google_url
+from torch_geometric.data.data import BaseData
+
+try:
+    from pandas import DataFrame, read_csv
+    WITH_PANDAS = True
+except ImportError:
+    WITH_PANDAS = False
+
+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.
+    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.
+
+    Args:
+        root (str): Root directory where the dataset should be saved.
+        dataset (InMemoryDataset): The name of the dataset
+            (:obj:`"ogbn-products"`, :obj:`"ogbn-arxiv"`).
+        tokenizer_name (str): The tokenizer name for language model,
+            Be sure to use same tokenizer name as your `model id` of model repo
+            on huggingface.co.
+        text (List[str]): list of raw text associate with node, the order of
+            list should be align with node list
+        split_idx (Optional[Dict[str, torch.Tensor]]): Optional dictionary,
+            for saving split index, it is required that if your dataset doesn't
+            have get_split_idx function
+        tokenize_batch_size (int): batch size of tokenizing text, the
+            tokenizing process will run on cpu, default: 256
+        token_on_disk (bool): save token as .pt file on disk or not,
+            default: False
+        text_on_disk (bool): save given text(list of str) as dataframe on disk
+            or not, default: False
+        force_reload (bool): default: False
+    .. note::
+        See `example/llm_plus_gnn/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:
+        # list the vars you want to pass in before run download & process
+        self.name = dataset.name
+        self.text = text
+        self.tokenizer_name = tokenizer_name
+        from transformers import AutoTokenizer
+        self.tokenizer = AutoTokenizer.from_pretrained(tokenizer_name)
+        if self.tokenizer.pad_token_id is None:
+            self.tokenizer.pad_token_id = self.tokenizer.eos_token_id
+        if self.tokenizer.pad_token is None:
+            self.tokenizer.pad_token = self.tokenizer.eos_token
+
+        self.dir_name = '_'.join(dataset.name.split('-'))
+        self.root = osp.join(root, self.dir_name)
+        missing_str_list = []
+        if not WITH_PANDAS:
+            missing_str_list.append('pandas')
+        if len(missing_str_list) > 0:
+            missing_str = ' '.join(missing_str_list)
+            error_out = f"`pip install {missing_str}` to use this dataset."
+            raise ImportError(error_out)
+        if hasattr(dataset, 'get_idx_split'):
+            self.split_idx = dataset.get_idx_split()
+        elif split_idx is not None:
+            self.split_idx = split_idx
+        else:
+            raise ValueError("TAGDataset need split idx for generating "
+                             "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)
+        self.text_on_disk = text_on_disk
+        # init will call download and process
+        super().__init__(self.root, transform=None, pre_transform=None,
+                         pre_filter=None, force_reload=force_reload)
+        # after processing and download
+        # Dataset has to have BaseData as _data
+        assert dataset._data is not None
+        self._data = dataset._data  # reassign reference
+        assert self._data is not None
+        assert dataset._data.y is not None
+        assert isinstance(self._data, BaseData)
+        assert self._data.num_nodes is not None
+        assert isinstance(dataset._data.num_nodes, int)
+        assert isinstance(self._data.num_nodes, int)
+        self._n_id = torch.arange(self._data.num_nodes)
+        is_good_tensor = self.load_gold_mask()
+        self._is_gold = is_good_tensor.squeeze()
+        self._data['is_gold'] = is_good_tensor
+        if self.text is not None and len(self.text) != self._data.num_nodes:
+            raise ValueError("The number of text sequence in 'text' should be "
+                             "equal to number of nodes!")
+        self.token_on_disk = token_on_disk
+        self.tokenize_batch_size = tokenize_batch_size
+        self._token = self.tokenize_graph(self.tokenize_batch_size)
+        self.__num_classes__ = dataset.num_classes
+
+    @property
+    def num_classes(self) -> int:
+        return self.__num_classes__
+
+    @property
+    def raw_file_names(self) -> List[str]:
+        file_names = []
+        for root, _, files in os.walk(osp.join(self.root, 'raw')):
+            for file in files:
+                file_names.append(file)
+        return file_names
+
+    @property
+    def processed_file_names(self) -> List[str]:
+        return [
+            'geometric_data_processed.pt', 'pre_filter.pt',
+            'pre_transformed.pt'
+        ]
+
+    @property
+    def token(self) -> Dict[str, Tensor]:
+        if self._token is None:  # lazy load
+            self._token = self.tokenize_graph()
+        return self._token
+
+    # load is_gold after init
+    @property
+    def is_gold(self) -> Tensor:
+        if self._is_gold is None:
+            print('lazy load is_gold!!')
+            self._is_gold = self.load_gold_mask()
+        return self._is_gold
+
+    def get_n_id(self, node_idx: IndexType) -> Tensor:
+        if self._n_id is None:
+            assert self._data is not None
+            assert self._data.num_nodes is not None
+            assert isinstance(self._data.num_nodes, int)
+            self._n_id = torch.arange(self._data.num_nodes)
+        return self._n_id[node_idx]
+
+    def load_gold_mask(self) -> Tensor:
+        r"""Use original train split as gold split, generating is_gold mask
+        for picking ground truth labels and pseudo labels.
+        """
+        train_split_idx = self.get_idx_split()['train']
+        assert self._data is not None
+        assert self._data.num_nodes is not None
+        assert isinstance(self._data.num_nodes, int)
+        is_good_tensor = torch.zeros(self._data.num_nodes,
+                                     dtype=torch.bool).view(-1, 1)
+        is_good_tensor[train_split_idx] = True
+        return is_good_tensor
+
+    def get_gold(self, node_idx: IndexType) -> Tensor:
+        r"""Get gold mask for given node_idx.
+
+        Args:
+            node_idx (torch.tensor): a tensor contain node idx
+        """
+        if self._is_gold is None:
+            self._is_gold = self.is_gold
+        return self._is_gold[node_idx]
+
+    def get_idx_split(self) -> Dict[str, Tensor]:
+        return self.split_idx
+
+    def download(self) -> None:
+        print('downloading raw text')
+        raw_text_path = download_google_url(id=self.raw_text_id[self.name],
+                                            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'])
+
+    def process(self) -> None:
+        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'])
+        elif self.name in self.raw_text_id:
+            self.download()
+        else:
+            print('The dataset is not ogbn-products nor ogbn-arxiv,'
+                  'please pass in your raw text string list to `text`')
+        if self.text is None:
+            raise ValueError("The TAGDataset only have ogbn-products and "
+                             "ogbn-arxiv raw text in default "
+                             "The raw text of each node is not specified"
+                             "Please pass in 'text' 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')
+        if osp.exists(node_text_path):
+            print(f'The raw text is existed at {node_text_path}')
+        else:
+            print(f'Saving raw text file at {node_text_path}')
+            os.makedirs(f'{self.root}/raw', exist_ok=True)
+            text_df = DataFrame(text, columns=['text'])
+            text_df.to_csv(osp.join(node_text_path), compression='gzip',
+                           index=False)
+
+    def tokenize_graph(self, batch_size: int = 256) -> 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
+        Returns:
+            Dict[str, torch.Tensor]: tokenized graph
+        """
+        data_len = 0
+        if self.text is not None:
+            data_len = len(self.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)
+        # 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)
+
+        if token_files_exist and self.token_on_disk:
+            print('Found tokenized file, loading may take several minutes...')
+            all_encoded_token = {
+                k: torch.load(os.path.join(path, f'{k}.pt'), weights_only=True)
+                for k in token_keys
+                if os.path.exists(os.path.join(path, f'{k}.pt'))
+            }
+            return all_encoded_token
+
+        all_encoded_token = {k: [] for k in token_keys}
+        pbar = tqdm(total=data_len)
+
+        pbar.set_description('Tokenizing Text Attributed Graph')
+        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")
+            for k in token.keys():
+                all_encoded_token[k].append(token[k])
+            pbar.update(end_index - i)
+        pbar.close()
+
+        all_encoded_token = {
+            k: torch.cat(v)
+            for k, v in all_encoded_token.items() if len(v) > 0
+        }
+        if self.token_on_disk:
+            os.makedirs(path, exist_ok=True)
+            print('Saving tokens on Disk')
+            for k, tensor in all_encoded_token.items():
+                torch.save(tensor, os.path.join(path, f'{k}.pt'))
+                print('Token saved:', os.path.join(path, f'{k}.pt'))
+        os.environ["TOKENIZERS_PARALLELISM"] = 'true'  # supressing warning
+        return all_encoded_token
+
+    def __repr__(self) -> str:
+        return f'{self.__class__.__name__}()'
+
+    class TextDataset(torch.utils.data.Dataset):
+        r"""This nested dataset provides textual data for each node in
+        the graph. Factory method to create TextDataset from TAGDataset.
+
+        Args:
+            tag_dataset (TAGDataset): the parent dataset
+        """
+        def __init__(self, tag_dataset: 'TAGDataset') -> None:
+            self.tag_dataset = tag_dataset
+            self.token = tag_dataset.token
+            assert tag_dataset._data is not None
+            self._data = tag_dataset._data
+
+            assert tag_dataset._data.y is not None
+            self.labels = tag_dataset._data.y
+
+        def get_token(self, node_idx: IndexType) -> Dict[str, Tensor]:
+            r"""This function will be called in __getitem__().
+
+            Args:
+                node_idx (IndexType): selected node idx in each batch
+            Returns:
+                items (Dict[str, Tensor]): input for LM
+            """
+            items = {k: v[node_idx] for k, v in self.token.items()}
+            return items
+
+        # for LM training
+        def __getitem__(
+                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
+            iterate batch in the dataloader, make sure all following
+            key value pairs are present in the return dict.
+
+            Args:
+                node_id (List[int]): list of node idx for selecting tokens,
+                    labels etc. when iterating data loader for LM
+            Returns:
+                items (dict): input k,v pairs for Language model training and
+                    inference
+            """
+            item: Dict[str, Union[Tensor, Dict[str, Tensor]]] = {}
+            item['input'] = self.get_token(node_id)
+            item['labels'] = self.labels[node_id]
+            item['is_gold'] = self.tag_dataset.get_gold(node_id)
+            item['n_id'] = self.tag_dataset.get_n_id(node_id)
+            return item
+
+        def __len__(self) -> int:
+            assert self._data.num_nodes is not None
+            return self._data.num_nodes
+
+        def get(self, idx: int) -> BaseData:
+            return self._data
+
+        def __repr__(self) -> str:
+            return f'{self.__class__.__name__}()'
+
+    def to_text_dataset(self) -> TextDataset:
+        r"""Factory Build text dataset from Text Attributed Graph Dataset
+        each data point is node's associated text token.
+        """
+        return TAGDataset.TextDataset(self)

torch_geometric/nn/attention/__init__.py

@@ -1,3 +1,7 @@
 from .performer import PerformerAttention
+from .qformer import QFormer
 
-__all__ = ['PerformerAttention']
+__all__ = [
+    'PerformerAttention',
+    'QFormer',
+]

torch_geometric/nn/attention/qformer.py

@@ -0,0 +1,71 @@
+from typing import Callable
+
+import torch
+
+
+class QFormer(torch.nn.Module):
+    r"""The Querying Transformer (Q-Former) from
+    `"BLIP-2: Bootstrapping Language-Image Pre-training
+    with Frozen Image Encoders and Large Language Models"
+    <https://arxiv.org/pdf/2301.12597>`_ paper.
+
+    Args:
+        input_dim (int): The number of features in the input.
+        hidden_dim (int): The dimension of the fnn in the encoder layer.
+        output_dim (int): The final output dimension.
+        num_heads (int): The number of multi-attention-heads.
+        num_layers (int): The number of sub-encoder-layers in the encoder.
+        dropout (int): The dropout value in each encoder layer.
+
+
+    .. note::
+        This is a simplified version of the original Q-Former implementation.
+    """
+    def __init__(
+            self,
+            input_dim: int,
+            hidden_dim: int,
+            output_dim: int,
+            num_heads: int,
+            num_layers: int,
+            dropout: float = 0.0,
+            activation: Callable = torch.nn.ReLU(),
+    ) -> None:
+
+        super().__init__()
+        self.num_layers = num_layers
+        self.num_heads = num_heads
+
+        self.layer_norm = torch.nn.LayerNorm(input_dim)
+        self.encoder_layer = torch.nn.TransformerEncoderLayer(
+            d_model=input_dim,
+            nhead=num_heads,
+            dim_feedforward=hidden_dim,
+            dropout=dropout,
+            activation=activation,
+            batch_first=True,
+        )
+        self.encoder = torch.nn.TransformerEncoder(
+            self.encoder_layer,
+            num_layers=num_layers,
+        )
+        self.project = torch.nn.Linear(input_dim, output_dim)
+
+    def forward(self, x: torch.Tensor) -> torch.Tensor:
+        r"""Forward pass.
+
+        Args:
+            x (torch.Tensor): Input sequence to the encoder layer.
+                :math:`\mathbf{X} \in \mathbb{R}^{B \times N \times F}`, with
+                batch-size :math:`B`, sequence length :math:`N`,
+                and feature dimension :math:`F`.
+        """
+        x = self.layer_norm(x)
+        x = self.encoder(x)
+        out = self.project(x)
+        return out
+
+    def __repr__(self) -> str:
+        return (f'{self.__class__.__name__}('
+                f'num_heads={self.num_heads}, '
+                f'num_layers={self.num_layers})')

torch_geometric/nn/models/__init__.py

@@ -29,7 +29,8 @@ from .pmlp import PMLP
 from .neural_fingerprint import NeuralFingerprint
 from .visnet import ViSNet
 from .g_retriever import GRetriever
-
+from .molecule_gpt import MoleculeGPT
+from .glem import GLEM
 # Deprecated:
 from torch_geometric.explain.algorithm.captum import (to_captum_input,
                                                       captum_output_to_dicts)
@@ -77,4 +78,6 @@ __all__ = classes = [
     'NeuralFingerprint',
     'ViSNet',
     'GRetriever',
+    'MoleculeGPT',
+    'GLEM',
 ]