graph_saint.py

from typing import Optional

import os.path as osp

import torch
from tqdm import tqdm
from torch_sparse import SparseTensor


class GraphSAINTSampler(torch.utils.data.DataLoader):
    r"""The GraphSAINT sampler base class from the `"GraphSAINT: Graph
    Sampling Based Inductive Learning Method"
    <https://arxiv.org/abs/1907.04931>`_ paper.
    Given a graph in a :obj:`data` object, this class samples nodes and
    constructs subgraphs that can be processed in a mini-batch fashion.
    Normalization coefficients for each mini-batch are given via
    :obj:`node_norm` and :obj:`edge_norm` data attributes.

    .. note::

        See :class:`~torch_geometric.loader.GraphSAINTNodeSampler`,
        :class:`~torch_geometric.loader.GraphSAINTEdgeSampler` and
        :class:`~torch_geometric.loader.GraphSAINTRandomWalkSampler` for
        currently supported samplers.
        For an example of using GraphSAINT sampling, see
        `examples/graph_saint.py <https://github.com/pyg-team/
        pytorch_geometric/blob/master/examples/graph_saint.py>`_.

    Args:
        data (torch_geometric.data.Data): The graph data object.
        batch_size (int): The approximate number of samples per batch.
        num_steps (int, optional): The number of iterations per epoch.
            (default: :obj:`1`)
        sample_coverage (int): How many samples per node should be used to
            compute normalization statistics. (default: :obj:`0`)
        save_dir (string, optional): If set, will save normalization
            statistics to the :obj:`save_dir` directory for faster re-use.
            (default: :obj:`None`)
        log (bool, optional): If set to :obj:`False`, will not log any
            pre-processing progress. (default: :obj:`True`)
        **kwargs (optional): Additional arguments of
            :class:`torch.utils.data.DataLoader`, such as :obj:`batch_size` or
            :obj:`num_workers`.
    """
    def __init__(self, data, batch_size: int, num_steps: int = 1,
                 sample_coverage: int = 0, save_dir: Optional[str] = None,
                 log: bool = True, **kwargs):

        if 'collate_fn' in kwargs:
            del kwargs['collate_fn']

        assert data.edge_index is not None
        assert 'node_norm' not in data
        assert 'edge_norm' not in data
        assert not data.edge_index.is_cuda

        self.num_steps = num_steps
        self.__batch_size__ = batch_size
        self.sample_coverage = sample_coverage
        self.save_dir = save_dir
        self.log = log

        self.N = N = data.num_nodes
        self.E = data.num_edges

        self.adj = SparseTensor(
            row=data.edge_index[0], col=data.edge_index[1],
            value=torch.arange(self.E, device=data.edge_index.device),
            sparse_sizes=(N, N))

        self.data = data

        super().__init__(self, batch_size=1, collate_fn=self.__collate__,
                         **kwargs)

        if self.sample_coverage > 0:
            path = osp.join(save_dir or '', self.__filename__)
            if save_dir is not None and osp.exists(path):  # pragma: no cover
                self.node_norm, self.edge_norm = torch.load(path)
            else:
                self.node_norm, self.edge_norm = self.__compute_norm__()
                if save_dir is not None:  # pragma: no cover
                    torch.save((self.node_norm, self.edge_norm), path)

    @property
    def __filename__(self):
        return f'{self.__class__.__name__.lower()}_{self.sample_coverage}.pt'

    def __len__(self):
        return self.num_steps

    def __sample_nodes__(self, batch_size):
        raise NotImplementedError

    def __getitem__(self, idx):
        node_idx = self.__sample_nodes__(self.__batch_size__).unique()
        adj, _ = self.adj.saint_subgraph(node_idx)
        return node_idx, adj

    def __collate__(self, data_list):
        assert len(data_list) == 1
        node_idx, adj = data_list[0]

        data = self.data.__class__()
        data.num_nodes = node_idx.size(0)
        row, col, edge_idx = adj.coo()
        data.edge_index = torch.stack([row, col], dim=0)

        for key, item in self.data:
            if key in ['edge_index', 'num_nodes']:
                continue
            if isinstance(item, torch.Tensor) and item.size(0) == self.N:
                data[key] = item[node_idx]
            elif isinstance(item, torch.Tensor) and item.size(0) == self.E:
                data[key] = item[edge_idx]
            else:
                data[key] = item

        if self.sample_coverage > 0:
            data.node_norm = self.node_norm[node_idx]
            data.edge_norm = self.edge_norm[edge_idx]

        return data

    def __compute_norm__(self):
        node_count = torch.zeros(self.N, dtype=torch.float)
        edge_count = torch.zeros(self.E, dtype=torch.float)

        loader = torch.utils.data.DataLoader(self, batch_size=200,
                                             collate_fn=lambda x: x,
                                             num_workers=self.num_workers)

        if self.log:  # pragma: no cover
            pbar = tqdm(total=self.N * self.sample_coverage)
            pbar.set_description('Compute GraphSAINT normalization')

        num_samples = total_sampled_nodes = 0
        while total_sampled_nodes < self.N * self.sample_coverage:
            for data in loader:
                for node_idx, adj in data:
                    edge_idx = adj.storage.value()
                    node_count[node_idx] += 1
                    edge_count[edge_idx] += 1
                    total_sampled_nodes += node_idx.size(0)

                    if self.log:  # pragma: no cover
                        pbar.update(node_idx.size(0))
            num_samples += self.num_steps

        if self.log:  # pragma: no cover
            pbar.close()

        row, _, edge_idx = self.adj.coo()
        t = torch.empty_like(edge_count).scatter_(0, edge_idx, node_count[row])
        edge_norm = (t / edge_count).clamp_(0, 1e4)
        edge_norm[torch.isnan(edge_norm)] = 0.1

        node_count[node_count == 0] = 0.1
        node_norm = num_samples / node_count / self.N

        return node_norm, edge_norm


class GraphSAINTNodeSampler(GraphSAINTSampler):
    r"""The GraphSAINT node sampler class (see
    :class:`~torch_geometric.loader.GraphSAINTSampler`).
    """
    def __sample_nodes__(self, batch_size):
        edge_sample = torch.randint(0, self.E, (batch_size, self.batch_size),
                                    dtype=torch.long)

        return self.adj.storage.row()[edge_sample]


class GraphSAINTEdgeSampler(GraphSAINTSampler):
    r"""The GraphSAINT edge sampler class (see
    :class:`~torch_geometric.loader.GraphSAINTSampler`).
    """
    def __sample_nodes__(self, batch_size):
        row, col, _ = self.adj.coo()

        deg_in = 1. / self.adj.storage.colcount()
        deg_out = 1. / self.adj.storage.rowcount()
        prob = (1. / deg_in[row]) + (1. / deg_out[col])

        # Parallel multinomial sampling (without replacement)
        # https://github.com/pytorch/pytorch/issues/11931#issuecomment-625882503
        rand = torch.rand(batch_size, self.E).log() / (prob + 1e-10)
        edge_sample = rand.topk(self.batch_size, dim=-1).indices

        source_node_sample = col[edge_sample]
        target_node_sample = row[edge_sample]

        return torch.cat([source_node_sample, target_node_sample], -1)


class GraphSAINTRandomWalkSampler(GraphSAINTSampler):
    r"""The GraphSAINT random walk sampler class (see
    :class:`~torch_geometric.loader.GraphSAINTSampler`).

    Args:
        walk_length (int): The length of each random walk.
    """
    def __init__(self, data, batch_size: int, walk_length: int,
                 num_steps: int = 1, sample_coverage: int = 0,
                 save_dir: Optional[str] = None, log: bool = True, **kwargs):
        self.walk_length = walk_length
        super().__init__(data, batch_size, num_steps, sample_coverage,
                         save_dir, log, **kwargs)

    @property
    def __filename__(self):
        return (f'{self.__class__.__name__.lower()}_{self.walk_length}_'
                f'{self.sample_coverage}.pt')

    def __sample_nodes__(self, batch_size):
        start = torch.randint(0, self.N, (batch_size, ), dtype=torch.long)
        node_idx = self.adj.random_walk(start.flatten(), self.walk_length)
        return node_idx.view(-1)