Source code for dgl.data.knowledge_graph

from __future__ import absolute_import

import os, sys
import pickle as pkl

import networkx as nx

import numpy as np
import scipy.sparse as sp

from .. import backend as F
from ..convert import graph as dgl_graph
from ..utils import retry_method_with_fix

from .dgl_dataset import DGLBuiltinDataset
from .utils import (
    _get_dgl_url,
    deprecate_function,
    deprecate_property,
    download,
    extract_archive,
    generate_mask_tensor,
    get_download_dir,
    load_graphs,
    load_info,
    makedirs,
    save_graphs,
    save_info,
)


class KnowledgeGraphDataset(DGLBuiltinDataset):
    """KnowledgeGraph link prediction dataset

    The dataset contains a graph depicting the connectivity of a knowledge
    base. Currently, the knowledge bases from the
    `RGCN paper <https://arxiv.org/pdf/1703.06103.pdf>`_ supported are
    FB15k-237, FB15k, wn18

    Parameters
    -----------
    name : str
        Name can be 'FB15k-237', 'FB15k' or 'wn18'.
    reverse : bool
        Whether add reverse edges. Default: True.
    raw_dir : str
        Raw file directory to download/contains the input data directory.
        Default: ~/.dgl/
    force_reload : bool
        Whether to reload the dataset. Default: False
    verbose : bool
        Whether to print out progress information. Default: True.
    transform : callable, optional
        A transform that takes in a :class:`~dgl.DGLGraph` object and returns
        a transformed version. The :class:`~dgl.DGLGraph` object will be
        transformed before every access.
    """

    def __init__(
        self,
        name,
        reverse=True,
        raw_dir=None,
        force_reload=False,
        verbose=True,
        transform=None,
    ):
        self._name = name
        self.reverse = reverse
        url = _get_dgl_url("dataset/") + "{}.tgz".format(name)
        super(KnowledgeGraphDataset, self).__init__(
            name,
            url=url,
            raw_dir=raw_dir,
            force_reload=force_reload,
            verbose=verbose,
            transform=transform,
        )

    def download(self):
        r"""Automatically download data and extract it."""
        tgz_path = os.path.join(self.raw_dir, self.name + ".tgz")
        download(self.url, path=tgz_path)
        extract_archive(tgz_path, self.raw_path)

    def process(self):
        """
        The original knowledge base is stored in triplets.
        This function will parse these triplets and build the DGLGraph.
        """
        root_path = self.raw_path
        entity_path = os.path.join(root_path, "entities.dict")
        relation_path = os.path.join(root_path, "relations.dict")
        train_path = os.path.join(root_path, "train.txt")
        valid_path = os.path.join(root_path, "valid.txt")
        test_path = os.path.join(root_path, "test.txt")
        entity_dict = _read_dictionary(entity_path)
        relation_dict = _read_dictionary(relation_path)
        train = np.asarray(
            _read_triplets_as_list(train_path, entity_dict, relation_dict)
        )
        valid = np.asarray(
            _read_triplets_as_list(valid_path, entity_dict, relation_dict)
        )
        test = np.asarray(
            _read_triplets_as_list(test_path, entity_dict, relation_dict)
        )
        num_nodes = len(entity_dict)
        num_rels = len(relation_dict)
        if self.verbose:
            print("# entities: {}".format(num_nodes))
            print("# relations: {}".format(num_rels))
            print("# training edges: {}".format(train.shape[0]))
            print("# validation edges: {}".format(valid.shape[0]))
            print("# testing edges: {}".format(test.shape[0]))

        # for compatability
        self._train = train
        self._valid = valid
        self._test = test

        self._num_nodes = num_nodes
        self._num_rels = num_rels
        # build graph
        g, data = build_knowledge_graph(
            num_nodes, num_rels, train, valid, test, reverse=self.reverse
        )
        (
            etype,
            ntype,
            train_edge_mask,
            valid_edge_mask,
            test_edge_mask,
            train_mask,
            val_mask,
            test_mask,
        ) = data
        g.edata["train_edge_mask"] = train_edge_mask
        g.edata["valid_edge_mask"] = valid_edge_mask
        g.edata["test_edge_mask"] = test_edge_mask
        g.edata["train_mask"] = train_mask
        g.edata["val_mask"] = val_mask
        g.edata["test_mask"] = test_mask
        g.edata["etype"] = etype
        g.ndata["ntype"] = ntype
        self._g = g

    @property
    def graph_path(self):
        return os.path.join(self.save_path, self.save_name + ".bin")

    @property
    def info_path(self):
        return os.path.join(self.save_path, self.save_name + ".pkl")

    def has_cache(self):
        if os.path.exists(self.graph_path) and os.path.exists(self.info_path):
            return True

        return False

    def __getitem__(self, idx):
        assert idx == 0, "This dataset has only one graph"
        if self._transform is None:
            return self._g
        else:
            return self._transform(self._g)

    def __len__(self):
        return 1

    def save(self):
        """save the graph list and the labels"""
        save_graphs(str(self.graph_path), self._g)
        save_info(
            str(self.info_path),
            {"num_nodes": self.num_nodes, "num_rels": self.num_rels},
        )

    def load(self):
        graphs, _ = load_graphs(str(self.graph_path))

        info = load_info(str(self.info_path))
        self._num_nodes = info["num_nodes"]
        self._num_rels = info["num_rels"]
        self._g = graphs[0]
        train_mask = self._g.edata["train_edge_mask"].numpy()
        val_mask = self._g.edata["valid_edge_mask"].numpy()
        test_mask = self._g.edata["test_edge_mask"].numpy()

        # convert mask tensor into bool tensor if possible
        self._g.edata["train_edge_mask"] = generate_mask_tensor(
            self._g.edata["train_edge_mask"].numpy()
        )
        self._g.edata["valid_edge_mask"] = generate_mask_tensor(
            self._g.edata["valid_edge_mask"].numpy()
        )
        self._g.edata["test_edge_mask"] = generate_mask_tensor(
            self._g.edata["test_edge_mask"].numpy()
        )
        self._g.edata["train_mask"] = generate_mask_tensor(
            self._g.edata["train_mask"].numpy()
        )
        self._g.edata["val_mask"] = generate_mask_tensor(
            self._g.edata["val_mask"].numpy()
        )
        self._g.edata["test_mask"] = generate_mask_tensor(
            self._g.edata["test_mask"].numpy()
        )

        # for compatability (with 0.4.x) generate train_idx, valid_idx and test_idx
        etype = self._g.edata["etype"].numpy()
        self._etype = etype
        u, v = self._g.all_edges(form="uv")
        u = u.numpy()
        v = v.numpy()
        train_idx = np.nonzero(train_mask == 1)
        self._train = np.column_stack(
            (u[train_idx], etype[train_idx], v[train_idx])
        )
        valid_idx = np.nonzero(val_mask == 1)
        self._valid = np.column_stack(
            (u[valid_idx], etype[valid_idx], v[valid_idx])
        )
        test_idx = np.nonzero(test_mask == 1)
        self._test = np.column_stack(
            (u[test_idx], etype[test_idx], v[test_idx])
        )

        if self.verbose:
            print("# entities: {}".format(self.num_nodes))
            print("# relations: {}".format(self.num_rels))
            print("# training edges: {}".format(self._train.shape[0]))
            print("# validation edges: {}".format(self._valid.shape[0]))
            print("# testing edges: {}".format(self._test.shape[0]))

    @property
    def num_nodes(self):
        return self._num_nodes

    @property
    def num_rels(self):
        return self._num_rels

    @property
    def save_name(self):
        return self.name + "_dgl_graph"


def _read_dictionary(filename):
    d = {}
    with open(filename, "r+") as f:
        for line in f:
            line = line.strip().split("\t")
            d[line[1]] = int(line[0])
    return d


def _read_triplets(filename):
    with open(filename, "r+") as f:
        for line in f:
            processed_line = line.strip().split("\t")
            yield processed_line


def _read_triplets_as_list(filename, entity_dict, relation_dict):
    l = []
    for triplet in _read_triplets(filename):
        s = entity_dict[triplet[0]]
        r = relation_dict[triplet[1]]
        o = entity_dict[triplet[2]]
        l.append([s, r, o])
    return l


def build_knowledge_graph(
    num_nodes, num_rels, train, valid, test, reverse=True
):
    """Create a DGL Homogeneous graph with heterograph info stored as node or edge features."""
    src = []
    rel = []
    dst = []
    raw_subg = {}
    raw_subg_eset = {}
    raw_subg_etype = {}
    raw_reverse_sugb = {}
    raw_reverse_subg_eset = {}
    raw_reverse_subg_etype = {}

    # here there is noly one node type
    s_type = "node"
    d_type = "node"

    def add_edge(s, r, d, reverse, edge_set):
        r_type = str(r)
        e_type = (s_type, r_type, d_type)
        if raw_subg.get(e_type, None) is None:
            raw_subg[e_type] = ([], [])
            raw_subg_eset[e_type] = []
            raw_subg_etype[e_type] = []
        raw_subg[e_type][0].append(s)
        raw_subg[e_type][1].append(d)
        raw_subg_eset[e_type].append(edge_set)
        raw_subg_etype[e_type].append(r)

        if reverse is True:
            r_type = str(r + num_rels)
            re_type = (d_type, r_type, s_type)
            if raw_reverse_sugb.get(re_type, None) is None:
                raw_reverse_sugb[re_type] = ([], [])
                raw_reverse_subg_etype[re_type] = []
                raw_reverse_subg_eset[re_type] = []
            raw_reverse_sugb[re_type][0].append(d)
            raw_reverse_sugb[re_type][1].append(s)
            raw_reverse_subg_eset[re_type].append(edge_set)
            raw_reverse_subg_etype[re_type].append(r + num_rels)

    for edge in train:
        s, r, d = edge
        assert r < num_rels
        add_edge(s, r, d, reverse, 1)  # train set

    for edge in valid:
        s, r, d = edge
        assert r < num_rels
        add_edge(s, r, d, reverse, 2)  # valid set

    for edge in test:
        s, r, d = edge
        assert r < num_rels
        add_edge(s, r, d, reverse, 3)  # test set

    subg = []
    fg_s = []
    fg_d = []
    fg_etype = []
    fg_settype = []
    for e_type, val in raw_subg.items():
        s, d = val
        s = np.asarray(s)
        d = np.asarray(d)
        etype = raw_subg_etype[e_type]
        etype = np.asarray(etype)
        settype = raw_subg_eset[e_type]
        settype = np.asarray(settype)

        fg_s.append(s)
        fg_d.append(d)
        fg_etype.append(etype)
        fg_settype.append(settype)

    settype = np.concatenate(fg_settype)
    if reverse is True:
        settype = np.concatenate([settype, np.full((settype.shape[0]), 0)])
    train_edge_mask = generate_mask_tensor(settype == 1)
    valid_edge_mask = generate_mask_tensor(settype == 2)
    test_edge_mask = generate_mask_tensor(settype == 3)

    for e_type, val in raw_reverse_sugb.items():
        s, d = val
        s = np.asarray(s)
        d = np.asarray(d)
        etype = raw_reverse_subg_etype[e_type]
        etype = np.asarray(etype)
        settype = raw_reverse_subg_eset[e_type]
        settype = np.asarray(settype)

        fg_s.append(s)
        fg_d.append(d)
        fg_etype.append(etype)
        fg_settype.append(settype)

    s = np.concatenate(fg_s)
    d = np.concatenate(fg_d)
    g = dgl_graph((s, d), num_nodes=num_nodes)
    etype = np.concatenate(fg_etype)
    settype = np.concatenate(fg_settype)
    etype = F.tensor(etype, dtype=F.data_type_dict["int64"])
    train_edge_mask = train_edge_mask
    valid_edge_mask = valid_edge_mask
    test_edge_mask = test_edge_mask
    train_mask = (
        generate_mask_tensor(settype == 1)
        if reverse is True
        else train_edge_mask
    )
    valid_mask = (
        generate_mask_tensor(settype == 2)
        if reverse is True
        else valid_edge_mask
    )
    test_mask = (
        generate_mask_tensor(settype == 3)
        if reverse is True
        else test_edge_mask
    )
    ntype = F.full_1d(
        num_nodes, 0, dtype=F.data_type_dict["int64"], ctx=F.cpu()
    )

    return g, (
        etype,
        ntype,
        train_edge_mask,
        valid_edge_mask,
        test_edge_mask,
        train_mask,
        valid_mask,
        test_mask,
    )


[docs]class FB15k237Dataset(KnowledgeGraphDataset): r"""FB15k237 link prediction dataset. FB15k-237 is a subset of FB15k where inverse relations are removed. When creating the dataset, a reverse edge with reversed relation types are created for each edge by default. FB15k237 dataset statistics: - Nodes: 14541 - Number of relation types: 237 - Number of reversed relation types: 237 - Label Split: - Train: 272115 - Valid: 17535 - Test: 20466 Parameters ---------- reverse : bool Whether to add reverse edge. Default True. raw_dir : str Raw file directory to download/contains the input data directory. Default: ~/.dgl/ force_reload : bool Whether to reload the dataset. Default: False verbose : bool Whether to print out progress information. Default: True. transform : callable, optional A transform that takes in a :class:`~dgl.DGLGraph` object and returns a transformed version. The :class:`~dgl.DGLGraph` object will be transformed before every access. Attributes ---------- num_nodes: int Number of nodes num_rels: int Number of relation types Examples ---------- >>> dataset = FB15k237Dataset() >>> g = dataset.graph >>> e_type = g.edata['e_type'] >>> >>> # get data split >>> train_mask = g.edata['train_mask'] >>> val_mask = g.edata['val_mask'] >>> test_mask = g.edata['test_mask'] >>> >>> train_set = th.arange(g.num_edges())[train_mask] >>> val_set = th.arange(g.num_edges())[val_mask] >>> >>> # build train_g >>> train_edges = train_set >>> train_g = g.edge_subgraph(train_edges, relabel_nodes=False) >>> train_g.edata['e_type'] = e_type[train_edges]; >>> >>> # build val_g >>> val_edges = th.cat([train_edges, val_edges]) >>> val_g = g.edge_subgraph(val_edges, relabel_nodes=False) >>> val_g.edata['e_type'] = e_type[val_edges]; >>> >>> # Train, Validation and Test """ def __init__( self, reverse=True, raw_dir=None, force_reload=False, verbose=True, transform=None, ): name = "FB15k-237" super(FB15k237Dataset, self).__init__( name, reverse, raw_dir, force_reload, verbose, transform )
[docs] def __getitem__(self, idx): r"""Gets the graph object Parameters ----------- idx: int Item index, FB15k237Dataset has only one graph object Return ------- :class:`dgl.DGLGraph` The graph contains - ``edata['e_type']``: edge relation type - ``edata['train_edge_mask']``: positive training edge mask - ``edata['val_edge_mask']``: positive validation edge mask - ``edata['test_edge_mask']``: positive testing edge mask - ``edata['train_mask']``: training edge set mask (include reversed training edges) - ``edata['val_mask']``: validation edge set mask (include reversed validation edges) - ``edata['test_mask']``: testing edge set mask (include reversed testing edges) - ``ndata['ntype']``: node type. All 0 in this dataset """ return super(FB15k237Dataset, self).__getitem__(idx)
[docs] def __len__(self): r"""The number of graphs in the dataset.""" return super(FB15k237Dataset, self).__len__()
[docs]class FB15kDataset(KnowledgeGraphDataset): r"""FB15k link prediction dataset. The FB15K dataset was introduced in `Translating Embeddings for Modeling Multi-relational Data <http://papers.nips.cc/paper/5071-translating-embeddings-for-modeling-multi-relational-data.pdf>`_. It is a subset of Freebase which contains about 14,951 entities with 1,345 different relations. When creating the dataset, a reverse edge with reversed relation types are created for each edge by default. FB15k dataset statistics: - Nodes: 14,951 - Number of relation types: 1,345 - Number of reversed relation types: 1,345 - Label Split: - Train: 483142 - Valid: 50000 - Test: 59071 Parameters ---------- reverse : bool Whether to add reverse edge. Default True. raw_dir : str Raw file directory to download/contains the input data directory. Default: ~/.dgl/ force_reload : bool Whether to reload the dataset. Default: False verbose : bool Whether to print out progress information. Default: True. transform : callable, optional A transform that takes in a :class:`~dgl.DGLGraph` object and returns a transformed version. The :class:`~dgl.DGLGraph` object will be transformed before every access. Attributes ---------- num_nodes: int Number of nodes num_rels: int Number of relation types Examples ---------- >>> dataset = FB15kDataset() >>> g = dataset.graph >>> e_type = g.edata['e_type'] >>> >>> # get data split >>> train_mask = g.edata['train_mask'] >>> val_mask = g.edata['val_mask'] >>> >>> train_set = th.arange(g.num_edges())[train_mask] >>> val_set = th.arange(g.num_edges())[val_mask] >>> >>> # build train_g >>> train_edges = train_set >>> train_g = g.edge_subgraph(train_edges, relabel_nodes=False) >>> train_g.edata['e_type'] = e_type[train_edges]; >>> >>> # build val_g >>> val_edges = th.cat([train_edges, val_edges]) >>> val_g = g.edge_subgraph(val_edges, relabel_nodes=False) >>> val_g.edata['e_type'] = e_type[val_edges]; >>> >>> # Train, Validation and Test >>> """ def __init__( self, reverse=True, raw_dir=None, force_reload=False, verbose=True, transform=None, ): name = "FB15k" super(FB15kDataset, self).__init__( name, reverse, raw_dir, force_reload, verbose, transform )
[docs] def __getitem__(self, idx): r"""Gets the graph object Parameters ----------- idx: int Item index, FB15kDataset has only one graph object Return ------- :class:`dgl.DGLGraph` The graph contains - ``edata['e_type']``: edge relation type - ``edata['train_edge_mask']``: positive training edge mask - ``edata['val_edge_mask']``: positive validation edge mask - ``edata['test_edge_mask']``: positive testing edge mask - ``edata['train_mask']``: training edge set mask (include reversed training edges) - ``edata['val_mask']``: validation edge set mask (include reversed validation edges) - ``edata['test_mask']``: testing edge set mask (include reversed testing edges) - ``ndata['ntype']``: node type. All 0 in this dataset """ return super(FB15kDataset, self).__getitem__(idx)
[docs] def __len__(self): r"""The number of graphs in the dataset.""" return super(FB15kDataset, self).__len__()
[docs]class WN18Dataset(KnowledgeGraphDataset): r"""WN18 link prediction dataset. The WN18 dataset was introduced in `Translating Embeddings for Modeling Multi-relational Data <http://papers.nips.cc/paper/5071-translating-embeddings-for-modeling-multi-relational-data.pdf>`_. It included the full 18 relations scraped from WordNet for roughly 41,000 synsets. When creating the dataset, a reverse edge with reversed relation types are created for each edge by default. WN18 dataset statistics: - Nodes: 40943 - Number of relation types: 18 - Number of reversed relation types: 18 - Label Split: - Train: 141442 - Valid: 5000 - Test: 5000 Parameters ---------- reverse : bool Whether to add reverse edge. Default True. raw_dir : str Raw file directory to download/contains the input data directory. Default: ~/.dgl/ force_reload : bool Whether to reload the dataset. Default: False verbose : bool Whether to print out progress information. Default: True. transform : callable, optional A transform that takes in a :class:`~dgl.DGLGraph` object and returns a transformed version. The :class:`~dgl.DGLGraph` object will be transformed before every access. Attributes ---------- num_nodes: int Number of nodes num_rels: int Number of relation types Examples ---------- >>> dataset = WN18Dataset() >>> g = dataset.graph >>> e_type = g.edata['e_type'] >>> >>> # get data split >>> train_mask = g.edata['train_mask'] >>> val_mask = g.edata['val_mask'] >>> >>> train_set = th.arange(g.num_edges())[train_mask] >>> val_set = th.arange(g.num_edges())[val_mask] >>> >>> # build train_g >>> train_edges = train_set >>> train_g = g.edge_subgraph(train_edges, relabel_nodes=False) >>> train_g.edata['e_type'] = e_type[train_edges]; >>> >>> # build val_g >>> val_edges = th.cat([train_edges, val_edges]) >>> val_g = g.edge_subgraph(val_edges, relabel_nodes=False) >>> val_g.edata['e_type'] = e_type[val_edges]; >>> >>> # Train, Validation and Test >>> """ def __init__( self, reverse=True, raw_dir=None, force_reload=False, verbose=True, transform=None, ): name = "wn18" super(WN18Dataset, self).__init__( name, reverse, raw_dir, force_reload, verbose, transform )
[docs] def __getitem__(self, idx): r"""Gets the graph object Parameters ----------- idx: int Item index, WN18Dataset has only one graph object Return ------- :class:`dgl.DGLGraph` The graph contains - ``edata['e_type']``: edge relation type - ``edata['train_edge_mask']``: positive training edge mask - ``edata['val_edge_mask']``: positive validation edge mask - ``edata['test_edge_mask']``: positive testing edge mask - ``edata['train_mask']``: training edge set mask (include reversed training edges) - ``edata['val_mask']``: validation edge set mask (include reversed validation edges) - ``edata['test_mask']``: testing edge set mask (include reversed testing edges) - ``ndata['ntype']``: node type. All 0 in this dataset """ return super(WN18Dataset, self).__getitem__(idx)
[docs] def __len__(self): r"""The number of graphs in the dataset.""" return super(WN18Dataset, self).__len__()
def load_data(dataset): r"""Load knowledge graph dataset for RGCN link prediction tasks It supports three datasets: wn18, FB15k and FB15k-237 Parameters ---------- dataset: str The name of the dataset to load. Return ------ The dataset object. """ if dataset == "wn18": return WN18Dataset() elif dataset == "FB15k": return FB15kDataset() elif dataset == "FB15k-237": return FB15k237Dataset()