├── network_embedding_pred.py ├── README.md ├── util.py ├── data ├── example2-test-pos.net ├── example2-val-pos.net ├── example2-test-neg.net ├── example2-val-neg.net ├── example-val-neg.net ├── example-val-pos.net └── example2-train.net ├── pnrl_r.py └── LICENSE /network_embedding_pred.py: -------------------------------------------------------------------------------- 1 | from gensim.models.word2vec import Word2Vec 2 | from sklearn import linear_model 3 | import numpy as np 4 | from sklearn.metrics import classification_report, roc_auc_score 5 | import random 6 | 7 | 8 | data = 'example' 9 | model_name = 'deepwalk' 10 | for i in range(5): 11 | i = str(i) 12 | model = Word2Vec.load_word2vec_format('data/'+ data + '_' + model_name + '_' +i+'.embeddings', binary=False) 13 | X_train = [] 14 | Y_train = [] 15 | X_test = [] 16 | Y_test = [] 17 | X_test_pos = [] 18 | X_test_neg = [] 19 | with open ('data/'+ data + '_train_' +i+'.net','rb') as f: 20 | for line in f: 21 | pair = line.strip().split() 22 | if pair[0] not in model.vocab or pair[1] not in model.vocab: 23 | continue 24 | else: 25 | head = model[pair[0]] 26 | tail = model[pair[1]] 27 | feature = np.multiply(head,tail) 28 | X_train.append(feature) 29 | Y_train.append(1) 30 | 31 | with open ('data/' + data + '_train_neg_' + i + '.net','rb') as f: 32 | for line in f: 33 | pair = line.strip().split() 34 | if pair[0] not in model.vocab or pair[1] not in model.vocab: 35 | continue 36 | else: 37 | head = model[pair[0]] 38 | tail = model[pair[1]] 39 | feature = np.multiply(head,tail) 40 | X_train.append(feature) 41 | Y_train.append(-1) 42 | 43 | clf = linear_model.SGDClassifier(loss='squared_hinge') 44 | 45 | X_train = np.array(X_train) 46 | Y_train = np.array(Y_train) 47 | 48 | clf.fit(X_train,Y_train) 49 | 50 | Y_unknown = [] 51 | Y_score_unknown = [] 52 | with open ('data/'+ data + '_test_' + i + '.net','rb') as f: 53 | for line in f: 54 | pair = line.strip().split() 55 | if pair[0] not in model.vocab or pair[1] not in model.vocab: 56 | Y_unknown.append(1) 57 | Y_score_unknown.append(0.5) 58 | else: 59 | head = model[pair[0]] 60 | tail = model[pair[1]] 61 | feature = np.multiply(head,tail) 62 | X_test.append(feature) 63 | X_test_pos.append(feature) 64 | Y_test.append(1) 65 | 66 | with open ('data/'+ data + '_test_neg_' + i + '.net','rb') as f: 67 | for line in f: 68 | pair = line.strip().split() 69 | if pair[0] not in model.vocab or pair[1] not in model.vocab: 70 | Y_unknown.append(-1) 71 | Y_score_unknown.append(0.5) 72 | else: 73 | head = model[pair[0]] 74 | tail = model[pair[1]] 75 | feature = np.multiply(head,tail) 76 | X_test.append(feature) 77 | X_test_neg.append(feature) 78 | Y_test.append(-1) 79 | 80 | X_test = np.array(X_test) 81 | Y_test = np.array(Y_test) 82 | Y_pred = clf.decision_function(X_test) 83 | Y_pred_pos = clf.decision_function(X_test_pos) 84 | Y_pred_neg = clf.decision_function(X_test_neg) 85 | for i in range(len(Y_pred)): 86 | Y_pred[i] = 1 / (1 + np.exp(-Y_pred[i])) 87 | print roc_auc_score(Y_test, Y_pred) 88 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # PNRL 2 | This repository provides reference codes of PNRL as described in the paper: 3 | 4 | >**Predictive Network Representation Learning for Link Prediction.** 5 | >**Zhitao Wang, Chengyao Chen and Wenjie Li.** 6 | >**SIGIR, 2017.** (https://dl.acm.org/citation.cfm?id=3080692) 7 | 8 | ## Environment 9 | The code is only tested in the environment with following setting: 10 |  1. python 2.7 11 |  2. keras (1.1.0) (Supporting Tensorflow Backend Now!) 12 |  3. numpy (1.11.1) 13 |  4. scikit-learn (0.16.1) 14 |  5. networkx (1.10) 15 | 16 | ## Run the code 17 | python pnrl_r.py 18 | 19 | ## Configuration 20 | You can change the path of data, learning rate, batch size, sample ratio and other parameters at Class Config() in pnrl_r.py 21 | 22 | ## Dataset 23 | All experimental datasets are public, you can find in the following links: 24 | * **Facebook**: J. McAuley and J. Leskovec. Learning to Discover Social Circles in Ego Networks. NIPS, 2012. https://snap.stanford.edu/data/egonets-Facebook.html 25 | * **Email**: R. Guimera, L. Danon, A. Diaz-Guilera, F. Giralt and A. Arenas, Physical Review E , vol. 68, 065103(R), (2003). http://deim.urv.cat/~alexandre.arenas/data/welcome.htm 26 | * **U.S. Power Grid**: D. J. Watts and S. H. Strogatz, Nature 393, 440-442 (1998). 27 | http://www-personal.umich.edu/~mejn/netdata/ 28 | * **Condensed Matter Collaborations**: M. E. J. Newman, The structure of scientific collaboration networks, Proc. Natl. Acad. Sci. USA 98, 404-409 (2001). http://www-personal.umich.edu/~mejn/netdata/ 29 | 30 | ## Data Format and Split 31 | Training, validation and testing graphs should be the format of edge lists (undirected): 32 | >node1_id node2_id 33 | >1 2 1.0 34 | >...... 35 | 36 | We regard the link prediction as binary classification, therefore the validation and testing graphs should have two files: 37 | * One for truly linked node-pair (Positive samples) 38 | * One for non-linked node-pair (Negative samples) 39 | 40 | Given an original edge list data (total num: N\*L), we randomly split these edges into N parts with same size L. We also need to randomly sample L non-linked pairs for N times as negative testing samplings. Then we can repeat N times cross-test over the processed data, N-1 parts for training and 1 part for testing each time. 41 | 42 | Particularly, DEEPWALK, LINE, NODE2VEC, PNRLC require to sample (N-1)\*L negative training samplings (the same size with positive training samplings) each time for classifier training. This is known as a Under-Sampling Strategy for imbanlance classification problem. 43 | 44 | 45 | ## Citing 46 | @inproceedings{Wang2017PNR, 47 | author = {Wang, Zhitao and Chen, Chengyao and Li, Wenjie}, 48 | title = {Predictive Network Representation Learning for Link Prediction}, 49 | booktitle = {Proceedings of the 40th International ACM SIGIR Conference on Research and Development in Information Retrieval}, 50 | series = {SIGIR '17}, 51 | year = {2017}, 52 | isbn = {978-1-4503-5022-8}, 53 | location = {Shinjuku, Tokyo, Japan}, 54 | url = {http://doi.acm.org/10.1145/3077136.3080692} 55 | } 56 | 57 | 58 | -------------------------------------------------------------------------------- /util.py: -------------------------------------------------------------------------------- 1 | import networkx as nx 2 | import math 3 | import numpy as np 4 | 5 | def load_training_graph(file, directed): 6 | if directed: 7 | return nx.read_edgelist(file, data=False, create_using = nx.DiGraph()) 8 | else: 9 | return nx.read_edgelist(file, data=False) 10 | 11 | def read_valset(pos_file, neg_file, graph_index, directed=False): 12 | print('Creating Validation edges set...') 13 | if directed: 14 | pos_val = nx.read_edgelist(pos_file, data=False, create_using = nx.DiGraph()) 15 | neg_val = nx.read_edgelist(neg_file, data=False, create_using = nx.DiGraph()) 16 | else: 17 | pos_val = nx.read_edgelist(pos_file, data=False) 18 | neg_val = nx.read_edgelist(neg_file, data=False) 19 | pos_val_set = pos_val.edges() 20 | neg_val_set = neg_val.edges() 21 | X_val_source = [] 22 | X_val_target = [] 23 | Y_val = [] 24 | for e in pos_val_set: 25 | if e[0] in graph_index and e[1] in graph_index: 26 | X_val_source.append(graph_index[e[0]]) 27 | X_val_target.append(graph_index[e[1]]) 28 | Y_val.append(1.) 29 | for e in neg_val_set: 30 | if e[0] in graph_index and e[1] in graph_index: 31 | X_val_source.append(graph_index[e[0]]) 32 | X_val_target.append(graph_index[e[1]]) 33 | Y_val.append(0.) 34 | X_val = [np.array(X_val_source), np.array(X_val_target)] 35 | Y_val = np.array(Y_val) 36 | return X_val, Y_val 37 | 38 | def creat_index(G): 39 | graph_index = {} 40 | i = 0 41 | for key in G.nodes(): 42 | graph_index[key] = i 43 | i += 1 44 | return graph_index 45 | 46 | def NegTable(G, graph_index): 47 | print('Creating negative sampling table...') 48 | nodes_size = len(G.nodes()) 49 | power = 0.75 50 | norm = sum([math.pow(G.degree(node), power) for node in G.nodes()]) # Normalizing constant 51 | table_size = int(1e8) # Length of the unigram table 52 | table = np.zeros(table_size, dtype=np.uint32) 53 | # print 'Filling unigram table' 54 | p = 0 # Cumulative probability 55 | i = 0 56 | for node in G.nodes(): 57 | p += float(math.pow(G.degree(node), power))/norm 58 | while i < table_size and float(i) / table_size < p: 59 | table[i] = graph_index[node] 60 | i += 1 61 | print('Finish') 62 | return table 63 | 64 | def neg_sample(neg_table, num_neg): 65 | indices = np.random.randint(low=0, high=len(neg_table), size=num_neg) 66 | return [neg_table[i] for i in indices] 67 | 68 | def neighbor_set(G): 69 | neighbor_set = {} 70 | non_neighbor_set = {} 71 | whole_set = set(G.nodes()) 72 | print('Creating neighbor set...') 73 | for node in G.nodes(): 74 | neighbours = nx.neighbors(G,node) 75 | neighbor_set[node] = list(neighbours) 76 | non_neighbor_set[node] = list(whole_set-set(neighbours)) 77 | print('Finish creating neighbor set') 78 | return neighbor_set, non_neighbor_set 79 | 80 | # def edge_sampling(neighbor_set, non_neighbor_set, graph_index, node, neg_table, num_neg): 81 | # if len(neighbor_set[node])==0: 82 | # return False 83 | # else: 84 | # linked = graph_index[random.choice(neighbor_set[node])] 85 | # nolinked = graph_index[random.choice(non_neighbor_set[node])] 86 | # source = graph_index[node] 87 | # neg = neg_sample(neg_table, num_neg) 88 | # return source, linked, nolinked, neg 89 | 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809 542 | 868 870 543 | 76 466 544 | 940 941 545 | 446 208 546 | -------------------------------------------------------------------------------- /data/example2-test-neg.net: -------------------------------------------------------------------------------- 1 | 974 1108 2 | 36 80 3 | 905 530 4 | 856 892 5 | 1016 935 6 | 593 693 7 | 890 351 8 | 143 618 9 | 73 996 10 | 88 226 11 | 1081 909 12 | 438 143 13 | 85 40 14 | 236 908 15 | 348 645 16 | 657 127 17 | 1006 322 18 | 400 354 19 | 184 1037 20 | 804 773 21 | 228 117 22 | 324 768 23 | 1000 189 24 | 596 858 25 | 545 845 26 | 902 636 27 | 693 499 28 | 942 135 29 | 346 784 30 | 903 173 31 | 456 1019 32 | 638 1072 33 | 94 989 34 | 20 830 35 | 849 14 36 | 192 799 37 | 742 670 38 | 591 858 39 | 215 545 40 | 373 1039 41 | 444 1129 42 | 687 45 43 | 626 151 44 | 290 91 45 | 616 125 46 | 457 531 47 | 520 170 48 | 517 565 49 | 186 469 50 | 591 777 51 | 897 288 52 | 83 365 53 | 88 1088 54 | 341 660 55 | 974 805 56 | 1103 4 57 | 94 385 58 | 192 376 59 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277 779 490 | 271 455 491 | 120 1022 492 | 709 1113 493 | 443 233 494 | 33 992 495 | 514 967 496 | 886 268 497 | 693 955 498 | 591 1098 499 | 768 821 500 | 146 225 501 | 1085 568 502 | 970 698 503 | 920 912 504 | 456 172 505 | 366 55 506 | 939 536 507 | 236 410 508 | 291 313 509 | 703 201 510 | 1067 186 511 | 1083 355 512 | 135 250 513 | 880 976 514 | 216 507 515 | 386 265 516 | 346 1072 517 | 180 507 518 | 640 136 519 | 940 498 520 | 91 960 521 | 189 883 522 | 375 806 523 | 716 526 524 | 228 1113 525 | 659 316 526 | 500 54 527 | 436 606 528 | 1010 835 529 | 401 78 530 | 874 111 531 | 906 390 532 | 96 632 533 | 828 571 534 | 645 615 535 | 348 88 536 | 382 110 537 | 648 805 538 | 816 27 539 | 330 632 540 | 334 164 541 | 296 126 542 | 498 721 543 | 511 183 544 | 1055 771 545 | 1065 738 546 | -------------------------------------------------------------------------------- /data/example2-val-neg.net: -------------------------------------------------------------------------------- 1 | 254 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131 722 366 | 149 821 367 | 36 775 368 | 660 254 369 | 122 824 370 | 217 532 371 | 1100 119 372 | 8 752 373 | 99 849 374 | 626 892 375 | 941 1127 376 | 349 226 377 | 249 125 378 | 270 177 379 | 343 886 380 | 649 484 381 | 497 657 382 | 1023 475 383 | 671 568 384 | 148 698 385 | 178 1076 386 | 234 504 387 | 632 1100 388 | 709 467 389 | 275 472 390 | 972 411 391 | 748 726 392 | 986 481 393 | 653 123 394 | 427 268 395 | 369 632 396 | 668 111 397 | 72 318 398 | 767 915 399 | 424 1055 400 | 235 1086 401 | 279 778 402 | 879 225 403 | 660 127 404 | 644 681 405 | 949 571 406 | 816 248 407 | 780 357 408 | 596 828 409 | 916 1024 410 | 345 441 411 | 1075 853 412 | 455 1001 413 | 391 751 414 | 341 113 415 | 548 216 416 | 272 957 417 | 552 893 418 | 1061 336 419 | 432 618 420 | 342 670 421 | 379 991 422 | 292 1099 423 | 82 499 424 | 133 3 425 | 816 363 426 | 175 363 427 | 452 3 428 | 680 356 429 | 440 323 430 | 7 802 431 | 993 984 432 | 969 957 433 | 170 488 434 | 334 685 435 | 1129 767 436 | 189 516 437 | 254 561 438 | 883 69 439 | 1105 753 440 | 222 121 441 | 966 936 442 | 712 455 443 | 436 878 444 | 832 305 445 | 550 455 446 | 335 856 447 | 209 384 448 | 515 537 449 | 464 356 450 | 1041 352 451 | 547 49 452 | 411 1030 453 | 1117 470 454 | 37 495 455 | 595 248 456 | 1088 411 457 | 1133 846 458 | 335 416 459 | 406 386 460 | 944 922 461 | 868 160 462 | 614 879 463 | 711 305 464 | 254 899 465 | 570 759 466 | 505 565 467 | 622 678 468 | 1009 951 469 | 720 606 470 | 431 6 471 | 43 18 472 | 739 987 473 | 789 285 474 | 101 919 475 | 713 19 476 | 994 676 477 | 746 554 478 | 273 1099 479 | 747 320 480 | 494 350 481 | 109 819 482 | 1023 720 483 | 136 696 484 | 645 843 485 | 95 636 486 | 35 119 487 | 597 651 488 | 336 495 489 | 315 1102 490 | 694 1129 491 | 977 1078 492 | 64 502 493 | 1060 741 494 | 368 304 495 | 604 952 496 | 716 599 497 | 175 78 498 | 903 969 499 | 371 772 500 | 375 323 501 | 654 41 502 | 193 3 503 | 717 30 504 | 142 514 505 | 922 156 506 | 14 786 507 | 990 576 508 | 35 52 509 | 32 645 510 | 448 350 511 | 743 999 512 | 704 1086 513 | 936 873 514 | 454 862 515 | 492 1071 516 | 222 114 517 | 449 119 518 | 91 743 519 | 1084 770 520 | 411 1090 521 | 434 912 522 | 857 171 523 | 198 490 524 | 734 607 525 | 1017 925 526 | 359 1030 527 | 210 608 528 | 942 578 529 | 191 132 530 | 359 774 531 | 656 305 532 | 330 204 533 | 553 305 534 | 235 267 535 | 88 81 536 | 24 450 537 | 414 180 538 | 345 737 539 | 551 682 540 | 874 756 541 | 38 738 542 | 979 725 543 | 610 1043 544 | 998 1024 545 | 593 466 546 | -------------------------------------------------------------------------------- /pnrl_r.py: -------------------------------------------------------------------------------- 1 | import numpy as np 2 | import math 3 | import random 4 | np.random.seed(13) 5 | from keras import backend as K 6 | from keras.models import Sequential, Model 7 | from keras.layers import Input, Embedding, LSTM, Dense, dot, concatenate, Reshape, Activation 8 | from keras.utils import np_utils 9 | from keras.utils.data_utils import get_file 10 | from keras.preprocessing.text import Tokenizer 11 | from keras.preprocessing.sequence import skipgrams,make_sampling_table 12 | from keras.optimizers import rmsprop, SGD, Adam 13 | from keras.regularizers import l2 14 | import networkx as nx 15 | from sklearn.metrics import classification_report, roc_auc_score 16 | import copy 17 | import gc 18 | from util import * 19 | 20 | class Config(object): 21 | """Model setting and data setting""" 22 | data_path = 'data/' 23 | data_name = 'example2' 24 | train_graph_file = data_path + data_name + '-train.net' # training file 25 | val_pos_file = data_path + data_name + '-val-pos.net' # validation positive file 26 | val_neg_file = data_path + data_name + '-val-neg.net' # validation negative file 27 | test_pos_file = data_path + data_name + '-test-pos.net' # validation positive file 28 | test_neg_file = data_path + data_name + '-test-neg.net' # validation negative file 29 | 30 | batch_size = 256 31 | neg_sample_num = 5 # max negative sampling 32 | dim_embedddings = 64 33 | 34 | hi_sample_beta = 0.2 35 | max_sample_iter = int(1/hi_sample_beta) # max iterations for hidden edge sample 36 | max_train_iter = 250 37 | 38 | p_threshold = 100 39 | 40 | 41 | def ranking_loss_bpr(y_true, y_pred): 42 | pos = y_pred[:,0] 43 | neg = y_pred[:,1] 44 | loss = -K.sigmoid(pos-neg) # use loss = K.maximum(1.0 + neg - pos, 0.0) if you want to use margin ranking loss 45 | return K.mean(loss) + 0 * y_true 46 | 47 | def ranking_loss_mm(y_true, y_pred): 48 | pos = y_pred[:,0] 49 | neg = y_pred[:,1] 50 | loss = K.maximum(1.0 + neg - pos, 0.0) 51 | return K.mean(loss) + 0 * y_true 52 | 53 | def ranking_loss_mse(y_true, y_pred): 54 | pos = y_pred[:,0] 55 | neg = y_pred[:,1] 56 | loss = (1/2)*K.square(pos-neg-1) 57 | return K.mean(loss) + 0 * y_true 58 | 59 | # def link_prediction(model, user_pair): 60 | # u1 = user_pair[0] 61 | # u2 = user_pair[1] 62 | # W = model.layers[5].get_weights()[0] 63 | # X = model.layers[3].get_weights()[0] 64 | # x = X[u1] 65 | # y = X[u2] 66 | # xW = np.dot(x,W) 67 | # xWy = np.sum(xW*y, axis=1) 68 | # return xWy 69 | def link_prediction(model, user_pair): 70 | u1 = user_pair[0] 71 | u2 = user_pair[1] 72 | W = model.layers[5].get_weights()[0] 73 | X = model.layers[1].get_weights()[0] 74 | x = X[u1] 75 | y = X[u2] 76 | xW = np.dot(x,W) 77 | xWy = np.sum(xW*y, axis=1) 78 | return xWy 79 | 80 | def PNRLR_Model(V, dim_embedddings=128): 81 | input_source = Input(shape=(1,), name='input_source') 82 | input_pos = Input(shape=(1,), name='input_pos') 83 | input_neg = Input(shape=(1,), name='input_neg') 84 | context_input = Input(shape=(1,), name='context_input') 85 | shared_embedding = Embedding(V, output_dim=dim_embedddings, input_length=1) 86 | X_source = shared_embedding(input_source) 87 | X_pos = shared_embedding(input_pos) 88 | X_neg = shared_embedding(input_neg) 89 | Y = Embedding(V, output_dim=dim_embedddings, input_length=1)(context_input) 90 | 91 | XY = dot([X_source, Y], axes=-1) 92 | res = Reshape((1,), input_shape=(1,1))(XY) 93 | nrl_output = Activation( activation='sigmoid', name='nrl_output')(res) 94 | model1 = Model(input=[input_source, context_input], output=[nrl_output]) 95 | # optimizer1 = SGD(lr=0.01, decay=1e-6, momentum=0.9, nesterov=True) 96 | optimizer1 = rmsprop() 97 | model1.compile(loss="binary_crossentropy", optimizer=optimizer1) 98 | 99 | reshape_layer = Reshape((dim_embedddings,), name='reshape_layer') 100 | X_S = reshape_layer(X_source) 101 | X_P = reshape_layer(X_pos) 102 | X_N = reshape_layer(X_neg) 103 | XW = Dense(dim_embedddings, activation='linear', W_regularizer=l2(0.01), bias=False,name='BiW')(X_S) 104 | pos_ouput = dot([XW, X_P], axes=-1) 105 | neg_output = dot([XW, X_N], axes=-1) 106 | lp_output = concatenate([pos_ouput, neg_output], axis=-1, name='lp_output') 107 | model2 = Model(input=[input_source, input_pos, input_neg], output=[lp_output]) 108 | optimizer2 = Adam() 109 | model2.compile(loss={'lp_output': ranking_loss_mm}, optimizer=optimizer2) 110 | return model1, model2 111 | 112 | def hidden_edge_sampling(sample_iter, sample_size, edges, neighbor_set): 113 | hi_edges = edges[sample_iter*sample_size : (sample_iter+1)*sample_size] 114 | ob_edges = edges[:sample_iter*sample_size] 115 | ob_edges.extend(edges[(sample_iter+1)*sample_size:]) 116 | ns = copy.deepcopy(neighbor_set) 117 | hi_ns = {} 118 | for e in hi_edges: 119 | if e[0] in hi_ns: 120 | hi_ns[e[0]].append(e[1]) 121 | else: 122 | hi_ns[e[0]] = [e[1]] 123 | ns[e[0]].remove(e[1]) 124 | if e[1] in hi_ns: 125 | hi_ns[e[1]].append(e[0]) 126 | else: 127 | hi_ns[e[1]] = [e[0]] 128 | ns[e[1]].remove(e[0]) 129 | return ob_edges, hi_edges, ns, hi_ns 130 | 131 | def train_batch_generation(graph_nodes, ob_ns, hi_ns, neg_ns, gindex, ntable, num_neg, batch_size): 132 | counter = 0 133 | X1_input1 = [] 134 | X1_input2 = [] 135 | Y1 = [] 136 | X2_input1 = [] 137 | X2_input2 = [] 138 | X2_input3 = [] 139 | Y2 = [] 140 | batch_data = [] 141 | for node in graph_nodes: 142 | if ob_ns[node]: 143 | X1_input1.append(gindex[node]) 144 | linked = gindex[random.choice(ob_ns[node])] 145 | X1_input2.append(linked) 146 | Y1.append(1.) 147 | neg = neg_sample(ntable, num_neg) 148 | for i in range(num_neg): 149 | X1_input1.append(gindex[node]) 150 | X1_input2.append(neg[i]) 151 | Y1.append(0.) 152 | if node in hi_ns: 153 | hi_linked = gindex[random.choice(hi_ns[node])] 154 | hi_nolinked = gindex[random.choice(neg_ns[node])] 155 | X2_input1.append(gindex[node]) 156 | X2_input2.append(hi_linked) 157 | X2_input3.append(hi_nolinked) 158 | Y2.append(1.) 159 | counter += 1 160 | if counter == batch_size: 161 | X1 = [np.array(X1_input1), np.array(X1_input2)] 162 | Y1 = np.array(Y1,dtype=np.int32) 163 | X2 = [np.array(X2_input1), np.array(X2_input2), np.array(X2_input3)] 164 | Y2 = np.array(Y2,dtype=np.int32) 165 | batch_data.append((X1, Y1, X2, Y2)) 166 | counter = 0 167 | X1_input1 = [] 168 | X1_input2 = [] 169 | Y1 = [] 170 | X2_input1 = [] 171 | X2_input2 = [] 172 | X2_input3 = [] 173 | Y2 = [] 174 | X1 = [np.array(X1_input1), np.array(X1_input2)] 175 | Y1 = np.array(Y1,dtype=np.int32) 176 | X2 = [np.array(X2_input1), np.array(X2_input2), np.array(X2_input3)] 177 | Y2 = np.array(Y2,dtype=np.int32) 178 | batch_data.append((X1, Y1, X2, Y2)) 179 | return batch_data 180 | 181 | def train(config): 182 | # Load settings 183 | batch_size = config.batch_size 184 | num_neg = config.neg_sample_num 185 | dim_embedddings = config.dim_embedddings 186 | max_sample_iter = config.max_sample_iter 187 | max_train_iter = config.max_train_iter 188 | p_threshold = config.p_threshold 189 | train_graph_file = config.train_graph_file 190 | val_pos_file = config.val_pos_file 191 | val_neg_file = config.val_neg_file 192 | test_pos_file = config.test_pos_file 193 | test_neg_file = config.test_neg_file 194 | # Read Data 195 | G = load_training_graph(train_graph_file, False) 196 | gindex = creat_index(G) 197 | edges = G.edges() 198 | ns_complete, neg_ns = neighbor_set(G) 199 | ntable = NegTable(G, gindex) 200 | V = len(gindex) + 1 201 | X_val, Y_val = read_valset(val_pos_file, val_neg_file, gindex, False) 202 | X_test, Y_test = read_valset(test_pos_file, test_neg_file, gindex, False) 203 | 204 | # Model initialization 205 | model1, model2 = PNRLR_Model(V, dim_embedddings) 206 | 207 | # Randomly shuffle data for training 208 | seed = random.randint(0, 10e6) 209 | random.seed(seed) 210 | random.shuffle(edges) 211 | 212 | best_val_auc = 0 213 | test_at_best_valid = 0 # validation for early stop 214 | patience = 0 # Early stop patience 215 | 216 | sample_size = int(len(edges)/max_sample_iter) 217 | for sample_iter in range(max_sample_iter): 218 | # Hidden edge sampling 219 | ob_edges, hi_edges, ob_ns, hi_ns = hidden_edge_sampling(sample_iter, sample_size, edges, ns_complete) 220 | print('Observed edges: %d, Hidden edges: %d' %(len(ob_edges), len(hi_edges))) 221 | 222 | # Training for the sampled hidden edges set and observed edges set 223 | for train_iter in range(max_train_iter): 224 | loss1 = 0. 225 | loss2 = 0. 226 | batch_data = train_batch_generation(G.nodes(), ob_ns, hi_ns, neg_ns, gindex, ntable, num_neg, batch_size) 227 | for batch in batch_data: 228 | (X1, Y1, X2, Y2) = batch 229 | loss1 += model1.train_on_batch(X1, Y1) 230 | loss2 += model2.train_on_batch(X2, Y2) 231 | Y_pred = link_prediction(model2, X_val) 232 | val_auc = roc_auc_score(Y_val, Y_pred) 233 | 234 | Y_pred = link_prediction(model2, X_test) 235 | test_auc = roc_auc_score(Y_test, Y_pred) 236 | 237 | if val_auc > best_val_auc: 238 | best_val_auc = val_auc 239 | test_at_best_valid = test_auc 240 | patience = 0 241 | else: 242 | patience += 1 243 | 244 | print('Training Iteration: %d/%d, Sample Iteration: %d/%d'%(train_iter+1, max_train_iter,sample_iter+1, max_sample_iter) ) 245 | print('Loss1: %f, Loss2: %f, Val AUC: %f, Test AUC: %f'%(loss1, loss2, val_auc, test_auc)) 246 | 247 | if patience == p_threshold: 248 | break; 249 | 250 | print ('Best Val AUC: %f; Test AUC at best valid model: %f'% (best_val_auc, test_at_best_valid)) 251 | 252 | result_file = config.data_name + '_res.txt' 253 | with open(result_file, 'a') as f: 254 | # for res_auc in auc_list: 255 | f.write('Test results at best valid of data ' + config.data_name + ' : \n') 256 | f.write('%.5f \n' %(test_at_best_valid,)) 257 | 258 | 259 | if __name__ == '__main__': 260 | config = Config() 261 | train(config) 262 | 263 | 264 | -------------------------------------------------------------------------------- /data/example-val-neg.net: -------------------------------------------------------------------------------- 1 | 1 896 2 | 6 43 3 | 6 1046 4 | 6 1086 5 | 7 156 6 | 7 628 7 | 7 1074 8 | 8 993 9 | 10 608 10 | 10 879 11 | 10 990 12 | 12 112 13 | 12 325 14 | 12 1101 15 | 13 309 16 | 13 354 17 | 13 923 18 | 15 986 19 | 15 1022 20 | 15 1110 21 | 16 162 22 | 18 730 23 | 21 263 24 | 22 10 25 | 23 13 26 | 24 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940 941 1 1076 | 940 946 1 1077 | 960 1122 1 1078 | 980 1068 1 1079 | 981 983 1 1080 | 990 1009 1 1081 | 995 1112 1 1082 | 1004 1067 1 1083 | 1024 1097 1 1084 | 1026 1045 1 1085 | 1032 1078 1 1086 | 1043 1098 1 1087 | 1069 1078 1 1088 | 1069 1105 1 1089 | 1087 1132 1 1090 | 1088 1089 1 1091 | 1096 1133 1 1092 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | GNU GENERAL PUBLIC LICENSE 2 | Version 3, 29 June 2007 3 | 4 | Copyright (C) 2007 Free Software Foundation, Inc. 5 | Everyone is permitted to copy and distribute verbatim copies 6 | of this license document, but changing it is not allowed. 7 | 8 | Preamble 9 | 10 | The GNU General Public License is a free, copyleft license for 11 | software and other kinds of works. 12 | 13 | The licenses for most software and other practical works are designed 14 | to take away your freedom to share and change the works. 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Interpretation of Sections 15 and 16. 613 | 614 | If the disclaimer of warranty and limitation of liability provided 615 | above cannot be given local legal effect according to their terms, 616 | reviewing courts shall apply local law that most closely approximates 617 | an absolute waiver of all civil liability in connection with the 618 | Program, unless a warranty or assumption of liability accompanies a 619 | copy of the Program in return for a fee. 620 | 621 | END OF TERMS AND CONDITIONS 622 | 623 | How to Apply These Terms to Your New Programs 624 | 625 | If you develop a new program, and you want it to be of the greatest 626 | possible use to the public, the best way to achieve this is to make it 627 | free software which everyone can redistribute and change under these terms. 628 | 629 | To do so, attach the following notices to the program. It is safest 630 | to attach them to the start of each source file to most effectively 631 | state the exclusion of warranty; and each file should have at least 632 | the "copyright" line and a pointer to where the full notice is found. 633 | 634 | 635 | Copyright (C) 636 | 637 | This program is free software: you can redistribute it and/or modify 638 | it under the terms of the GNU General Public License as published by 639 | the Free Software Foundation, either version 3 of the License, or 640 | (at your option) any later version. 641 | 642 | This program is distributed in the hope that it will be useful, 643 | but WITHOUT ANY WARRANTY; without even the implied warranty of 644 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 645 | GNU General Public License for more details. 646 | 647 | You should have received a copy of the GNU General Public License 648 | along with this program. If not, see . 649 | 650 | Also add information on how to contact you by electronic and paper mail. 651 | 652 | If the program does terminal interaction, make it output a short 653 | notice like this when it starts in an interactive mode: 654 | 655 | Copyright (C) 656 | This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. 657 | This is free software, and you are welcome to redistribute it 658 | under certain conditions; type `show c' for details. 659 | 660 | The hypothetical commands `show w' and `show c' should show the appropriate 661 | parts of the General Public License. Of course, your program's commands 662 | might be different; for a GUI interface, you would use an "about box". 663 | 664 | You should also get your employer (if you work as a programmer) or school, 665 | if any, to sign a "copyright disclaimer" for the program, if necessary. 666 | For more information on this, and how to apply and follow the GNU GPL, see 667 | . 668 | 669 | The GNU General Public License does not permit incorporating your program 670 | into proprietary programs. If your program is a subroutine library, you 671 | may consider it more useful to permit linking proprietary applications with 672 | the library. If this is what you want to do, use the GNU Lesser General 673 | Public License instead of this License. But first, please read 674 | . 675 | -------------------------------------------------------------------------------- /data/example2-train.net: -------------------------------------------------------------------------------- 1 | 344 568 2 | 344 541 3 | 344 38 4 | 344 155 5 | 344 49 6 | 344 564 7 | 344 939 8 | 344 181 9 | 344 116 10 | 344 489 11 | 344 339 12 | 344 549 13 | 345 38 14 | 345 350 15 | 346 155 16 | 346 54 17 | 346 551 18 | 346 287 19 | 346 399 20 | 346 375 21 | 346 231 22 | 346 254 23 | 347 590 24 | 347 38 25 | 347 946 26 | 347 748 27 | 347 944 28 | 347 945 29 | 347 942 30 | 347 943 31 | 347 940 32 | 347 941 33 | 347 356 34 | 347 743 35 | 340 846 36 | 340 268 37 | 340 31 38 | 340 761 39 | 340 51 40 | 340 52 41 | 340 935 42 | 340 354 43 | 340 241 44 | 340 365 45 | 340 228 46 | 340 237 47 | 340 362 48 | 340 658 49 | 340 934 50 | 341 578 51 | 341 884 52 | 341 573 53 | 341 571 54 | 341 62 55 | 341 44 56 | 341 183 57 | 341 938 58 | 341 736 59 | 341 364 60 | 341 937 61 | 341 890 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