# Copyright (c) 2019 PaddlePaddle Authors. All Rights Reserved # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # # http://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. # See the License for the specific language governing permissions and # limitations under the License. """ This file implement the training process of GATNE model. """ import os import argparse import time import numpy as np import logging import pickle as pkl import pgl from pgl.utils import paddle_helper import paddle import paddle.fluid as fluid import paddle.fluid.layers as fl from utils import * import Dataset import model as Model from sklearn.metrics import (auc, f1_score, precision_recall_curve, roc_auc_score) def set_seed(seed): """Set random seed. """ random.seed(seed) np.random.seed(seed) def produce_model(exe, program, dataset, model, feed_dict): """Output the learned model parameters for testing. """ edge_types = dataset.edge_types num_nodes = dataset.graph[edge_types[0]].num_nodes edge_types_count = len(edge_types) neg_num = dataset.config['neg_num'] final_model = {} feed_dict['train_inputs'] = np.array( [n for n in range(num_nodes)], dtype=np.int64).reshape(-1, ) feed_dict['train_labels'] = np.array( [n for n in range(num_nodes)], dtype=np.int64).reshape(-1, 1, 1) feed_dict['train_negs'] = np.tile(feed_dict['train_labels'], (1, neg_num)).reshape(-1, neg_num, 1) for i in range(edge_types_count): feed_dict['train_types'] = np.array( [i for _ in range(num_nodes)], dtype=np.int64).reshape(-1, 1) edge_node_embed = exe.run(program, feed=feed_dict, fetch_list=[model.last_node_embed], return_numpy=True)[0] final_model[edge_types[i]] = edge_node_embed return final_model def evaluate(final_model, edge_types, data): """Calculate the AUC score, F1 score and PR score of the final model """ edge_types_count = len(edge_types) AUC, F1, PR = [], [], [] true_edge_data_by_type = data[0] fake_edge_data_by_type = data[1] for i in range(edge_types_count): try: local_model = final_model[edge_types[i]] true_edges = true_edge_data_by_type[edge_types[i]] fake_edges = fake_edge_data_by_type[edge_types[i]] except Exception as e: logging.warn('edge type not exists. %s' % str(e)) continue tmp_auc, tmp_f1, tmp_pr = calculate_score(local_model, true_edges, fake_edges) AUC.append(tmp_auc) F1.append(tmp_f1) PR.append(tmp_pr) return {'AUC': np.mean(AUC), 'F1': np.mean(F1), 'PR': np.mean(PR)} def calculate_score(model, true_edges, fake_edges): """Calculate the AUC score, F1 score and PR score of specified edge type """ true_list = list() prediction_list = list() true_num = 0 for edge in true_edges: tmp_score = get_score(model, edge) if tmp_score is not None: true_list.append(1) prediction_list.append(tmp_score) true_num += 1 for edge in fake_edges: tmp_score = get_score(model, edge) if tmp_score is not None: true_list.append(0) prediction_list.append(tmp_score) sorted_pred = prediction_list[:] sorted_pred.sort() threshold = sorted_pred[-true_num] y_pred = np.zeros(len(prediction_list), dtype=np.int32) for i in range(len(prediction_list)): if prediction_list[i] >= threshold: y_pred[i] = 1 y_true = np.array(true_list) y_scores = np.array(prediction_list) ps, rs, _ = precision_recall_curve(y_true, y_scores) return roc_auc_score(y_true, y_scores), f1_score(y_true, y_pred), auc(rs, ps) def get_score(local_model, edge): """Calculate the cosine similarity score between two nodes. """ try: vector1 = local_model[edge[0]] vector2 = local_model[edge[1]] return np.dot(vector1, vector2) / (np.linalg.norm(vector1) * np.linalg.norm(vector2)) except Exception as e: logging.warn('get_score warning: %s' % str(e)) return None pass def run_epoch(epoch, config, dataset, data, train_prog, test_prog, model, feed_dict, exe, for_test=False): """Run training process of every epoch. """ total_loss = [] for idx, batch_data in enumerate(data): feed_dict['train_inputs'] = batch_data[0] feed_dict['train_labels'] = batch_data[1] feed_dict['train_negs'] = batch_data[2] feed_dict['train_types'] = batch_data[3] loss, lr = exe.run(train_prog, feed=feed_dict, fetch_list=[model.loss, model.lr], return_numpy=True) total_loss.append(loss[0]) if (idx + 1) % 500 == 0: avg_loss = np.mean(total_loss) logging.info("epoch %d | step %d | lr %.4f | train_loss %f " % (epoch, idx + 1, lr, avg_loss)) total_loss = [] return avg_loss def save_model(program, exe, dataset, model, feed_dict, filename): """Save model. """ final_model = produce_model(exe, program, dataset, model, feed_dict) logging.info('saving model in %s' % (filename)) pkl.dump(final_model, open(filename, 'wb')) def test(program, exe, dataset, model, feed_dict): """Testing and validating. """ final_model = produce_model(exe, program, dataset, model, feed_dict) valid_result = evaluate(final_model, dataset.edge_types, dataset.valid_data) test_result = evaluate(final_model, dataset.edge_types, dataset.test_data) logging.info("valid_AUC %.4f | valid_PR %.4f | valid_F1 %.4f" % (valid_result['AUC'], valid_result['PR'], valid_result['F1'])) logging.info("test_AUC %.4f | test_PR %.4f | test_F1 %.4f" % (test_result['AUC'], test_result['PR'], test_result['F1'])) return test_result def main(config): """main function for training GATNE model. """ logging.info(config) set_seed(config['seed']) dataset = getattr( Dataset, config['data_loader']['type'])(config['data_loader']['args']) edge_types = dataset.graph.edge_types_info() logging.info(['total edge types: ', edge_types]) # train_pairs is a list of tuple: [(src1, dst1, neg, e1), (src2, dst2, neg, e2)] # e(int), edge num count, for select which edge embedding train_pairs_file = config['data_loader']['args']['data_path'] + \ config['data_loader']['args']['train_pairs_file'] if os.path.exists(train_pairs_file): logging.info('loading train pairs from pkl file %s' % train_pairs_file) train_pairs = pkl.load(open(train_pairs_file, 'rb')) else: logging.info('generating walks') all_walks = dataset.generate_walks() logging.info('generating train pairs') train_pairs = dataset.generate_pairs(all_walks) logging.info('dumping train pairs to %s' % (train_pairs_file)) pkl.dump(train_pairs, open(train_pairs_file, 'wb')) logging.info('total train pairs: %d' % (len(train_pairs))) data = dataset.fetch_batch(train_pairs, config['data_loader']['args']['batch_size']) place = fluid.CUDAPlace(0) if config['use_cuda'] else fluid.CPUPlace() train_program = fluid.Program() startup_program = fluid.Program() test_program = fluid.Program() with fluid.program_guard(train_program, startup_program): model = getattr(Model, config['model']['type'])( config['model']['args'], dataset, place) test_program = train_program.clone(for_test=True) with fluid.program_guard(train_program, startup_program): global_steps = len(data) * config['trainer']['args']['epochs'] model.backward(global_steps, config['optimizer']['args']) # train exe = fluid.Executor(place) exe.run(startup_program) feed_dict = model.gw.to_feed(dataset.graph) logging.info('test before training...') test(test_program, exe, dataset, model, feed_dict) logging.info('training...') for epoch in range(1, 1 + config['trainer']['args']['epochs']): train_result = run_epoch(epoch, config['trainer']['args'], dataset, data, train_program, test_program, model, feed_dict, exe) logging.info('validating and testing...') test_result = test(test_program, exe, dataset, model, feed_dict) filename = os.path.join(config['trainer']['args']['save_dir'], 'dict_embed_model_epoch_%d.pkl' % (epoch)) save_model(test_program, exe, dataset, model, feed_dict, filename) logging.info( "final_test_AUC %.4f | final_test_PR %.4f | fianl_test_F1 %.4f" % ( test_result['AUC'], test_result['PR'], test_result['F1'])) logging.info('training finished') if __name__ == "__main__": parser = argparse.ArgumentParser(description='GATNE') parser.add_argument( '-c', '--config', default=None, type=str, help='config file path (default: None)') parser.add_argument( '-n', '--taskname', default=None, type=str, help='task name(default: None)') args = parser.parse_args() if args.config: # load config file config = Config(args.config, isCreate=True, isSave=True) config = config() else: raise AssertionError( "Configuration file need to be specified. Add '-c config.yaml', for example." ) log_format = '%(asctime)s-%(levelname)s-%(name)s: %(message)s' logging.basicConfig( level=getattr(logging, config['log_level'].upper()), format=log_format) main(config)