utils.py

"""
Utility functions for link prediction
Most code is adapted from authors' implementation of RGCN link prediction:
https://github.com/MichSchli/RelationPrediction

"""

import dgl
import numpy as np
import tensorflow as tf

#######################################################################
#
# Utility function for building training and testing graphs
#
#######################################################################


def get_adj_and_degrees(num_nodes, triplets):
    """Get adjacency list and degrees of the graph"""
    adj_list = [[] for _ in range(num_nodes)]
    for i, triplet in enumerate(triplets):
        adj_list[triplet[0]].append([i, triplet[2]])
        adj_list[triplet[2]].append([i, triplet[0]])

    degrees = np.array([len(a) for a in adj_list])
    adj_list = [np.array(a) for a in adj_list]
    return adj_list, degrees


def sample_edge_neighborhood(adj_list, degrees, n_triplets, sample_size):
    """Sample edges by neighborhool expansion.

    This guarantees that the sampled edges form a connected graph, which
    may help deeper GNNs that require information from more than one hop.
    """
    edges = np.zeros((sample_size), dtype=np.int32)

    # initialize
    sample_counts = np.array([d for d in degrees])
    picked = np.array([False for _ in range(n_triplets)])
    seen = np.array([False for _ in degrees])

    for i in range(0, sample_size):
        weights = sample_counts * seen

        if np.sum(weights) == 0:
            weights = np.ones_like(weights)
            weights[np.where(sample_counts == 0)] = 0

        probabilities = (weights) / np.sum(weights)
        chosen_vertex = np.random.choice(
            np.arange(degrees.shape[0]), p=probabilities
        )
        chosen_adj_list = adj_list[chosen_vertex]
        seen[chosen_vertex] = True

        chosen_edge = np.random.choice(np.arange(chosen_adj_list.shape[0]))
        chosen_edge = chosen_adj_list[chosen_edge]
        edge_number = chosen_edge[0]

        while picked[edge_number]:
            chosen_edge = np.random.choice(np.arange(chosen_adj_list.shape[0]))
            chosen_edge = chosen_adj_list[chosen_edge]
            edge_number = chosen_edge[0]

        edges[i] = edge_number
        other_vertex = chosen_edge[1]
        picked[edge_number] = True
        sample_counts[chosen_vertex] -= 1
        sample_counts[other_vertex] -= 1
        seen[other_vertex] = True

    return edges


def sample_edge_uniform(adj_list, degrees, n_triplets, sample_size):
    """Sample edges uniformly from all the edges."""
    all_edges = np.arange(n_triplets)
    return np.random.choice(all_edges, sample_size, replace=False)


def generate_sampled_graph_and_labels(
    triplets,
    sample_size,
    split_size,
    num_rels,
    adj_list,
    degrees,
    negative_rate,
    sampler="uniform",
):
    """Get training graph and signals
    First perform edge neighborhood sampling on graph, then perform negative
    sampling to generate negative samples
    """
    # perform edge neighbor sampling
    if sampler == "uniform":
        edges = sample_edge_uniform(
            adj_list, degrees, len(triplets), sample_size
        )
    elif sampler == "neighbor":
        edges = sample_edge_neighborhood(
            adj_list, degrees, len(triplets), sample_size
        )
    else:
        raise ValueError("Sampler type must be either 'uniform' or 'neighbor'.")

    # relabel nodes to have consecutive node ids
    edges = triplets[edges]
    src, rel, dst = edges.transpose()
    uniq_v, edges = np.unique((src, dst), return_inverse=True)
    src, dst = np.reshape(edges, (2, -1))
    relabeled_edges = np.stack((src, rel, dst)).transpose()

    # negative sampling
    samples, labels = negative_sampling(
        relabeled_edges, len(uniq_v), negative_rate
    )

    # further split graph, only half of the edges will be used as graph
    # structure, while the rest half is used as unseen positive samples
    split_size = int(sample_size * split_size)
    graph_split_ids = np.random.choice(
        np.arange(sample_size), size=split_size, replace=False
    )
    src = src[graph_split_ids]
    dst = dst[graph_split_ids]
    rel = rel[graph_split_ids]

    # build DGL graph
    print("# sampled nodes: {}".format(len(uniq_v)))
    print("# sampled edges: {}".format(len(src) * 2))
    g, rel, norm = build_graph_from_triplets(
        len(uniq_v), num_rels, (src, rel, dst)
    )
    return g, uniq_v, rel, norm, samples, labels


def comp_deg_norm(g):
    g = g.local_var()
    in_deg = g.in_degrees(range(g.number_of_nodes())).float().numpy()
    norm = 1.0 / in_deg
    norm[np.isinf(norm)] = 0
    return norm


def build_graph_from_triplets(num_nodes, num_rels, triplets):
    """Create a DGL graph. The graph is bidirectional because RGCN authors
    use reversed relations.
    This function also generates edge type and normalization factor
    (reciprocal of node incoming degree)
    """
    g = dgl.DGLGraph()
    g.add_nodes(num_nodes)
    src, rel, dst = triplets
    src, dst = np.concatenate((src, dst)), np.concatenate((dst, src))
    rel = np.concatenate((rel, rel + num_rels))
    edges = sorted(zip(dst, src, rel))
    dst, src, rel = np.array(edges).transpose()
    g.add_edges(src, dst)
    norm = comp_deg_norm(g)
    print("# nodes: {}, # edges: {}".format(num_nodes, len(src)))
    return g, rel, norm


def build_test_graph(num_nodes, num_rels, edges):
    src, rel, dst = edges.transpose()
    print("Test graph:")
    return build_graph_from_triplets(num_nodes, num_rels, (src, rel, dst))


def negative_sampling(pos_samples, num_entity, negative_rate):
    size_of_batch = len(pos_samples)
    num_to_generate = size_of_batch * negative_rate
    neg_samples = np.tile(pos_samples, (negative_rate, 1))
    labels = np.zeros(size_of_batch * (negative_rate + 1), dtype=np.float32)
    labels[:size_of_batch] = 1
    values = np.random.randint(num_entity, size=num_to_generate)
    choices = np.random.uniform(size=num_to_generate)
    subj = choices > 0.5
    obj = choices <= 0.5
    neg_samples[subj, 0] = values[subj]
    neg_samples[obj, 2] = values[obj]

    return np.concatenate((pos_samples, neg_samples)), labels