SauravMaheshkar commited on
Commit
46a85c5
1 Parent(s): 836b957

feat: add link generation script

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Files changed (1) hide show
  1. link_gen.py +108 -0
link_gen.py ADDED
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+ import dgl
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+ from dgl.data import CiteseerGraphDataset
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+ import torch
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+ import pickle
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+ from copy import deepcopy
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+ import scipy.sparse as sp
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+ import numpy as np
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+ import os
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+
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+
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+ def mask_test_edges(adj_orig, val_frac, test_frac):
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+
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+ # Remove diagonal elements
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+ adj = deepcopy(adj_orig)
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+ # set diag as all zero
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+ adj.setdiag(0)
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+ adj.eliminate_zeros()
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+ # Check that diag is zero:
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+ # assert np.diag(adj.todense()).sum() == 0
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+
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+ adj_triu = sp.triu(adj, 1)
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+ edges = sparse_to_tuple(adj_triu)[0]
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+ num_test = int(np.floor(edges.shape[0] * test_frac))
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+ num_val = int(np.floor(edges.shape[0] * val_frac))
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+
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+ all_edge_idx = list(range(edges.shape[0]))
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+ np.random.shuffle(all_edge_idx)
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+ val_edge_idx = all_edge_idx[:num_val]
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+ test_edge_idx = all_edge_idx[num_val : (num_val + num_test)]
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+ test_edges = edges[test_edge_idx]
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+ val_edges = edges[val_edge_idx]
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+ train_edges = edges[all_edge_idx[num_val + num_test :]]
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+
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+ noedge_mask = np.ones(adj.shape) - adj
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+ noedges = np.asarray(sp.triu(noedge_mask, 1).nonzero()).T
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+ all_edge_idx = list(range(noedges.shape[0]))
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+ np.random.shuffle(all_edge_idx)
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+ val_edge_idx = all_edge_idx[:num_val]
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+ test_edge_idx = all_edge_idx[num_val : (num_val + num_test)]
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+ test_edges_false = noedges[test_edge_idx]
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+ val_edges_false = noedges[val_edge_idx]
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+
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+ data = np.ones(train_edges.shape[0])
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+ adj_train = sp.csr_matrix(
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+ (data, (train_edges[:, 0], train_edges[:, 1])), shape=adj.shape
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+ )
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+ adj_train = adj_train + adj_train.T
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+
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+ train_mask = np.ones(adj_train.shape)
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+ for edges_tmp in [val_edges, val_edges_false, test_edges, test_edges_false]:
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+ for e in edges_tmp:
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+ assert e[0] < e[1]
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+ train_mask[edges_tmp.T[0], edges_tmp.T[1]] = 0
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+ train_mask[edges_tmp.T[1], edges_tmp.T[0]] = 0
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+
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+ train_edges = np.asarray(sp.triu(adj_train, 1).nonzero()).T
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+ train_edges_false = np.asarray(
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+ (sp.triu(train_mask, 1) - sp.triu(adj_train, 1)).nonzero()
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+ ).T
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+
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+ # NOTE: all these edge lists only contain single direction of edge!
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+ return (
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+ train_edges,
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+ train_edges_false,
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+ val_edges,
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+ val_edges_false,
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+ test_edges,
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+ test_edges_false,
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+ )
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+
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+
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+ def sparse_to_tuple(sparse_mx):
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+ if not sp.isspmatrix_coo(sparse_mx):
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+ sparse_mx = sparse_mx.tocoo()
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+ coords = np.vstack((sparse_mx.row, sparse_mx.col)).transpose()
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+ values = sparse_mx.data
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+ shape = sparse_mx.shape
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+ return coords, values, shape
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+
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+
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+ if __name__ == "__main__":
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+ os.mkdir("links")
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+ os.mkdir("pretrain_labels")
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+ g = CiteseerGraphDataset()[0]
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+ total_pos_edges = torch.randperm(g.num_edges())
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+ adj_train = g.adjacency_matrix(scipy_fmt="csr")
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+ (
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+ train_edges,
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+ train_edges_false,
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+ val_edges,
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+ val_edges_false,
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+ test_edges,
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+ test_edges_false,
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+ ) = mask_test_edges(adj_train, 0.1, 0.2)
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+ tvt_edges_file = "links/citeseer_tvtEdges.pkl"
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+ pickle.dump(
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+ (
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+ train_edges,
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+ train_edges_false,
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+ val_edges,
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+ val_edges_false,
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+ test_edges,
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+ test_edges_false,
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+ ),
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+ open(tvt_edges_file, "wb"),
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+ )
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+ node_assignment = dgl.metis_partition_assignment(g, 10)
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+ torch.save(node_assignment, "pretrain_labels/metis_label_citeseer.pt")