evaluate_link_prediction.py

import logging
import time
import sys
import os
import numpy as np
import warnings
import json
import torch.nn as nn

from models.TGAT import TGAT
from models.MemoryModel import MemoryModel, compute_src_dst_node_time_shifts
from models.CAWN import CAWN
from models.TCL import TCL
from models.GraphMixer import GraphMixer
from models.DyGFormer import DyGFormer
from models.modules import MergeLayer
from utils.utils import set_random_seed, convert_to_gpu, get_parameter_sizes
from utils.utils import get_neighbor_sampler, NegativeEdgeSampler
from evaluate_models_utils import evaluate_model_link_prediction, evaluate_edge_bank_link_prediction
from utils.DataLoader import get_idx_data_loader, get_link_prediction_data
from utils.EarlyStopping import EarlyStopping
from utils.load_configs import get_link_prediction_args

if __name__ == "__main__":

    warnings.filterwarnings('ignore')

    # get arguments
    args = get_link_prediction_args(is_evaluation=True)

    # get data for training, validation and testing
    node_raw_features, edge_raw_features, full_data, train_data, val_data, test_data, new_node_val_data, new_node_test_data = \
        get_link_prediction_data(dataset_name=args.dataset_name, val_ratio=args.val_ratio, test_ratio=args.test_ratio)

    # initialize validation and test neighbor sampler to retrieve temporal graph
    full_neighbor_sampler = get_neighbor_sampler(data=full_data, sample_neighbor_strategy=args.sample_neighbor_strategy,
                                                 time_scaling_factor=args.time_scaling_factor, seed=1)

    # initialize negative samplers, set seeds for validation and testing so negatives are the same across different runs
    # in the inductive setting, negatives are sampled only amongst other new nodes
    if args.negative_sample_strategy != 'random':
        val_neg_edge_sampler = NegativeEdgeSampler(src_node_ids=full_data.src_node_ids, dst_node_ids=full_data.dst_node_ids,
                                                   interact_times=full_data.node_interact_times, last_observed_time=train_data.node_interact_times[-1],
                                                   negative_sample_strategy=args.negative_sample_strategy, seed=0)
        new_node_val_neg_edge_sampler = NegativeEdgeSampler(src_node_ids=new_node_val_data.src_node_ids, dst_node_ids=new_node_val_data.dst_node_ids,
                                                            interact_times=new_node_val_data.node_interact_times, last_observed_time=train_data.node_interact_times[-1],
                                                            negative_sample_strategy=args.negative_sample_strategy, seed=1)
        test_neg_edge_sampler = NegativeEdgeSampler(src_node_ids=full_data.src_node_ids, dst_node_ids=full_data.dst_node_ids,
                                                    interact_times=full_data.node_interact_times, last_observed_time=val_data.node_interact_times[-1],
                                                    negative_sample_strategy=args.negative_sample_strategy, seed=2)
        new_node_test_neg_edge_sampler = NegativeEdgeSampler(src_node_ids=new_node_test_data.src_node_ids, dst_node_ids=new_node_test_data.dst_node_ids,
                                                             interact_times=new_node_test_data.node_interact_times, last_observed_time=val_data.node_interact_times[-1],
                                                             negative_sample_strategy=args.negative_sample_strategy, seed=3)
    else:
        val_neg_edge_sampler = NegativeEdgeSampler(src_node_ids=full_data.src_node_ids, dst_node_ids=full_data.dst_node_ids, seed=0)
        new_node_val_neg_edge_sampler = NegativeEdgeSampler(src_node_ids=new_node_val_data.src_node_ids, dst_node_ids=new_node_val_data.dst_node_ids, seed=1)
        test_neg_edge_sampler = NegativeEdgeSampler(src_node_ids=full_data.src_node_ids, dst_node_ids=full_data.dst_node_ids, seed=2)
        new_node_test_neg_edge_sampler = NegativeEdgeSampler(src_node_ids=new_node_test_data.src_node_ids, dst_node_ids=new_node_test_data.dst_node_ids, seed=3)

    # get data loaders
    val_idx_data_loader = get_idx_data_loader(indices_list=list(range(len(val_data.src_node_ids))), batch_size=args.batch_size, shuffle=False)
    new_node_val_idx_data_loader = get_idx_data_loader(indices_list=list(range(len(new_node_val_data.src_node_ids))), batch_size=args.batch_size, shuffle=False)
    test_idx_data_loader = get_idx_data_loader(indices_list=list(range(len(test_data.src_node_ids))), batch_size=args.batch_size, shuffle=False)
    new_node_test_idx_data_loader = get_idx_data_loader(indices_list=list(range(len(new_node_test_data.src_node_ids))), batch_size=args.batch_size, shuffle=False)

    # we separately evaluate EdgeBank, since EdgeBank does not contain any trainable parameters and has a different evaluation pipeline
    if args.model_name == 'EdgeBank':
        evaluate_edge_bank_link_prediction(args=args, train_data=train_data, val_data=val_data, test_idx_data_loader=test_idx_data_loader,
                                           test_neg_edge_sampler=test_neg_edge_sampler, test_data=test_data)

    else:
        val_metric_all_runs, new_node_val_metric_all_runs, test_metric_all_runs, new_node_test_metric_all_runs = [], [], [], []

        for run in range(args.num_runs):

            set_random_seed(seed=run)

            args.seed = run
            args.load_model_name = f'{args.model_name}_seed{args.seed}'
            args.save_result_name = f'{args.negative_sample_strategy}_negative_sampling_{args.model_name}_seed{args.seed}'

            # set up logger
            logging.basicConfig(level=logging.INFO)
            logger = logging.getLogger()
            logger.setLevel(logging.DEBUG)
            os.makedirs(f"./logs/{args.model_name}/{args.dataset_name}/{args.save_result_name}/", exist_ok=True)
            # create file handler that logs debug and higher level messages
            fh = logging.FileHandler(f"./logs/{args.model_name}/{args.dataset_name}/{args.save_result_name}/{str(time.time())}.log")
            fh.setLevel(logging.DEBUG)
            # create console handler with a higher log level
            ch = logging.StreamHandler()
            ch.setLevel(logging.WARNING)
            # create formatter and add it to the handlers
            formatter = logging.Formatter('%(asctime)s - %(name)s - %(levelname)s - %(message)s')
            fh.setFormatter(formatter)
            ch.setFormatter(formatter)
            # add the handlers to logger
            logger.addHandler(fh)
            logger.addHandler(ch)

            run_start_time = time.time()
            logger.info(f"********** Run {run + 1} starts. **********")

            logger.info(f'configuration is {args}')

            # create model
            if args.model_name == 'TGAT':
                dynamic_backbone = TGAT(node_raw_features=node_raw_features, edge_raw_features=edge_raw_features, neighbor_sampler=full_neighbor_sampler,
                                        time_feat_dim=args.time_feat_dim, num_layers=args.num_layers, num_heads=args.num_heads, dropout=args.dropout, device=args.device)
            elif args.model_name in ['JODIE', 'DyRep', 'TGN']:
                # four floats that represent the mean and standard deviation of source and destination node time shifts in the training data, which is used for JODIE
                src_node_mean_time_shift, src_node_std_time_shift, dst_node_mean_time_shift_dst, dst_node_std_time_shift = \
                    compute_src_dst_node_time_shifts(train_data.src_node_ids, train_data.dst_node_ids, train_data.node_interact_times)
                dynamic_backbone = MemoryModel(node_raw_features=node_raw_features, edge_raw_features=edge_raw_features, neighbor_sampler=full_neighbor_sampler,
                                               time_feat_dim=args.time_feat_dim, model_name=args.model_name, num_layers=args.num_layers, num_heads=args.num_heads,
                                               dropout=args.dropout, src_node_mean_time_shift=src_node_mean_time_shift, src_node_std_time_shift=src_node_std_time_shift,
                                               dst_node_mean_time_shift_dst=dst_node_mean_time_shift_dst, dst_node_std_time_shift=dst_node_std_time_shift, device=args.device)
            elif args.model_name == 'CAWN':
                dynamic_backbone = CAWN(node_raw_features=node_raw_features, edge_raw_features=edge_raw_features, neighbor_sampler=full_neighbor_sampler,
                                        time_feat_dim=args.time_feat_dim, position_feat_dim=args.position_feat_dim, walk_length=args.walk_length,
                                        num_walk_heads=args.num_walk_heads, dropout=args.dropout, device=args.device)
            elif args.model_name == 'TCL':
                dynamic_backbone = TCL(node_raw_features=node_raw_features, edge_raw_features=edge_raw_features, neighbor_sampler=full_neighbor_sampler,
                                       time_feat_dim=args.time_feat_dim, num_layers=args.num_layers, num_heads=args.num_heads,
                                       num_depths=args.num_neighbors + 1, dropout=args.dropout, device=args.device)
            elif args.model_name == 'GraphMixer':
                dynamic_backbone = GraphMixer(node_raw_features=node_raw_features, edge_raw_features=edge_raw_features, neighbor_sampler=full_neighbor_sampler,
                                              time_feat_dim=args.time_feat_dim, num_tokens=args.num_neighbors, num_layers=args.num_layers, dropout=args.dropout, device=args.device)
            elif args.model_name == 'DyGFormer':
                dynamic_backbone = DyGFormer(node_raw_features=node_raw_features, edge_raw_features=edge_raw_features, neighbor_sampler=full_neighbor_sampler,
                                             time_feat_dim=args.time_feat_dim, channel_embedding_dim=args.channel_embedding_dim, patch_size=args.patch_size,
                                             num_layers=args.num_layers, num_heads=args.num_heads, dropout=args.dropout,
                                             max_input_sequence_length=args.max_input_sequence_length, device=args.device)
            else:
                raise ValueError(f"Wrong value for model_name {args.model_name}!")
            link_predictor = MergeLayer(input_dim1=node_raw_features.shape[1], input_dim2=node_raw_features.shape[1],
                                        hidden_dim=node_raw_features.shape[1], output_dim=1)
            model = nn.Sequential(dynamic_backbone, link_predictor)
            logger.info(f'model -> {model}')
            logger.info(f'model name: {args.model_name}, #parameters: {get_parameter_sizes(model) * 4} B, '
                        f'{get_parameter_sizes(model) * 4 / 1024} KB, {get_parameter_sizes(model) * 4 / 1024 / 1024} MB.')

            # load the saved model
            load_model_folder = f"./saved_models/{args.model_name}/{args.dataset_name}/{args.load_model_name}"
            early_stopping = EarlyStopping(patience=0, save_model_folder=load_model_folder,
                                           save_model_name=args.load_model_name, logger=logger, model_name=args.model_name)
            early_stopping.load_checkpoint(model, map_location='cpu')

            model = convert_to_gpu(model, device=args.device)
            # put the node raw messages of memory-based models on device
            if args.model_name in ['JODIE', 'DyRep', 'TGN']:
                for node_id, node_raw_messages in model[0].memory_bank.node_raw_messages.items():
                    new_node_raw_messages = []
                    for node_raw_message in node_raw_messages:
                        new_node_raw_messages.append((node_raw_message[0].to(args.device), node_raw_message[1]))
                    model[0].memory_bank.node_raw_messages[node_id] = new_node_raw_messages

            loss_func = nn.BCELoss()

            # evaluate the best model
            logger.info(f'get final performance on dataset {args.dataset_name}...')

            # the saved best model of memory-based models cannot perform validation since the stored memory has been updated by validation data
            if args.model_name not in ['JODIE', 'DyRep', 'TGN']:
                val_losses, val_metrics = evaluate_model_link_prediction(model_name=args.model_name,
                                                                         model=model,
                                                                         neighbor_sampler=full_neighbor_sampler,
                                                                         evaluate_idx_data_loader=val_idx_data_loader,
                                                                         evaluate_neg_edge_sampler=val_neg_edge_sampler,
                                                                         evaluate_data=val_data,
                                                                         loss_func=loss_func,
                                                                         num_neighbors=args.num_neighbors,
                                                                         time_gap=args.time_gap)

                new_node_val_losses, new_node_val_metrics = evaluate_model_link_prediction(model_name=args.model_name,
                                                                                           model=model,
                                                                                           neighbor_sampler=full_neighbor_sampler,
                                                                                           evaluate_idx_data_loader=new_node_val_idx_data_loader,
                                                                                           evaluate_neg_edge_sampler=new_node_val_neg_edge_sampler,
                                                                                           evaluate_data=new_node_val_data,
                                                                                           loss_func=loss_func,
                                                                                           num_neighbors=args.num_neighbors,
                                                                                           time_gap=args.time_gap)

            if args.model_name in ['JODIE', 'DyRep', 'TGN']:
                # the memory in the best model has seen the validation edges, we need to backup the memory for new testing nodes
                val_backup_memory_bank = model[0].memory_bank.backup_memory_bank()

            test_losses, test_metrics = evaluate_model_link_prediction(model_name=args.model_name,
                                                                       model=model,
                                                                       neighbor_sampler=full_neighbor_sampler,
                                                                       evaluate_idx_data_loader=test_idx_data_loader,
                                                                       evaluate_neg_edge_sampler=test_neg_edge_sampler,
                                                                       evaluate_data=test_data,
                                                                       loss_func=loss_func,
                                                                       num_neighbors=args.num_neighbors,
                                                                       time_gap=args.time_gap)

            if args.model_name in ['JODIE', 'DyRep', 'TGN']:
                # reload validation memory bank for new testing nodes
                model[0].memory_bank.reload_memory_bank(val_backup_memory_bank)

            new_node_test_losses, new_node_test_metrics = evaluate_model_link_prediction(model_name=args.model_name,
                                                                                         model=model,
                                                                                         neighbor_sampler=full_neighbor_sampler,
                                                                                         evaluate_idx_data_loader=new_node_test_idx_data_loader,
                                                                                         evaluate_neg_edge_sampler=new_node_test_neg_edge_sampler,
                                                                                         evaluate_data=new_node_test_data,
                                                                                         loss_func=loss_func,
                                                                                         num_neighbors=args.num_neighbors,
                                                                                         time_gap=args.time_gap)
            # store the evaluation metrics at the current run
            val_metric_dict, new_node_val_metric_dict, test_metric_dict, new_node_test_metric_dict = {}, {}, {}, {}

            if args.model_name not in ['JODIE', 'DyRep', 'TGN']:
                logger.info(f'validate loss: {np.mean(val_losses):.4f}')
                for metric_name in val_metrics[0].keys():
                    average_val_metric = np.mean([val_metric[metric_name] for val_metric in val_metrics])
                    logger.info(f'validate {metric_name}, {average_val_metric:.4f}')
                    val_metric_dict[metric_name] = average_val_metric

                logger.info(f'new node validate loss: {np.mean(new_node_val_losses):.4f}')
                for metric_name in new_node_val_metrics[0].keys():
                    average_new_node_val_metric = np.mean([new_node_val_metric[metric_name] for new_node_val_metric in new_node_val_metrics])
                    logger.info(f'new node validate {metric_name}, {average_new_node_val_metric:.4f}')
                    new_node_val_metric_dict[metric_name] = average_new_node_val_metric

            logger.info(f'test loss: {np.mean(test_losses):.4f}')
            for metric_name in test_metrics[0].keys():
                average_test_metric = np.mean([test_metric[metric_name] for test_metric in test_metrics])
                logger.info(f'test {metric_name}, {average_test_metric:.4f}')
                test_metric_dict[metric_name] = average_test_metric

            logger.info(f'new node test loss: {np.mean(new_node_test_losses):.4f}')
            for metric_name in new_node_test_metrics[0].keys():
                average_new_node_test_metric = np.mean([new_node_test_metric[metric_name] for new_node_test_metric in new_node_test_metrics])
                logger.info(f'new node test {metric_name}, {average_new_node_test_metric:.4f}')
                new_node_test_metric_dict[metric_name] = average_new_node_test_metric

            single_run_time = time.time() - run_start_time
            logger.info(f'Run {run + 1} cost {single_run_time:.2f} seconds.')

            if args.model_name not in ['JODIE', 'DyRep', 'TGN']:
                val_metric_all_runs.append(val_metric_dict)
                new_node_val_metric_all_runs.append(new_node_val_metric_dict)
            test_metric_all_runs.append(test_metric_dict)
            new_node_test_metric_all_runs.append(new_node_test_metric_dict)

            # avoid the overlap of logs
            if run < args.num_runs - 1:
                logger.removeHandler(fh)
                logger.removeHandler(ch)

            # save model result
            if args.model_name not in ['JODIE', 'DyRep', 'TGN']:
                result_json = {
                    "validate metrics": {metric_name: f'{val_metric_dict[metric_name]:.4f}' for metric_name in val_metric_dict},
                    "new node validate metrics": {metric_name: f'{new_node_val_metric_dict[metric_name]:.4f}' for metric_name in new_node_val_metric_dict},
                    "test metrics": {metric_name: f'{test_metric_dict[metric_name]:.4f}' for metric_name in test_metric_dict},
                    "new node test metrics": {metric_name: f'{new_node_test_metric_dict[metric_name]:.4f}' for metric_name in new_node_test_metric_dict}
                }
            else:
                result_json = {
                    "test metrics": {metric_name: f'{test_metric_dict[metric_name]:.4f}' for metric_name in test_metric_dict},
                    "new node test metrics": {metric_name: f'{new_node_test_metric_dict[metric_name]:.4f}' for metric_name in new_node_test_metric_dict}
                }
            result_json = json.dumps(result_json, indent=4)

            save_result_folder = f"./saved_results/{args.model_name}/{args.dataset_name}"
            os.makedirs(save_result_folder, exist_ok=True)
            save_result_path = os.path.join(save_result_folder, f"{args.save_result_name}.json")
            with open(save_result_path, 'w') as file:
                file.write(result_json)
            logger.info(f'save negative sampling results at {save_result_path}')

        # store the average metrics at the log of the last run
        logger.info(f'metrics over {args.num_runs} runs:')

        if args.model_name not in ['JODIE', 'DyRep', 'TGN']:
            for metric_name in val_metric_all_runs[0].keys():
                logger.info(f'validate {metric_name}, {[val_metric_single_run[metric_name] for val_metric_single_run in val_metric_all_runs]}')
                logger.info(f'average validate {metric_name}, {np.mean([val_metric_single_run[metric_name] for val_metric_single_run in val_metric_all_runs]):.4f} '
                            f'± {np.std([val_metric_single_run[metric_name] for val_metric_single_run in val_metric_all_runs], ddof=1):.4f}')

            for metric_name in new_node_val_metric_all_runs[0].keys():
                logger.info(f'new node validate {metric_name}, {[new_node_val_metric_single_run[metric_name] for new_node_val_metric_single_run in new_node_val_metric_all_runs]}')
                logger.info(f'average new node validate {metric_name}, {np.mean([new_node_val_metric_single_run[metric_name] for new_node_val_metric_single_run in new_node_val_metric_all_runs]):.4f} '
                            f'± {np.std([new_node_val_metric_single_run[metric_name] for new_node_val_metric_single_run in new_node_val_metric_all_runs], ddof=1):.4f}')

        for metric_name in test_metric_all_runs[0].keys():
            logger.info(f'test {metric_name}, {[test_metric_single_run[metric_name] for test_metric_single_run in test_metric_all_runs]}')
            logger.info(f'average test {metric_name}, {np.mean([test_metric_single_run[metric_name] for test_metric_single_run in test_metric_all_runs]):.4f} '
                        f'± {np.std([test_metric_single_run[metric_name] for test_metric_single_run in test_metric_all_runs], ddof=1):.4f}')

        for metric_name in new_node_test_metric_all_runs[0].keys():
            logger.info(f'new node test {metric_name}, {[new_node_test_metric_single_run[metric_name] for new_node_test_metric_single_run in new_node_test_metric_all_runs]}')
            logger.info(f'average new node test {metric_name}, {np.mean([new_node_test_metric_single_run[metric_name] for new_node_test_metric_single_run in new_node_test_metric_all_runs]):.4f} '
                        f'± {np.std([new_node_test_metric_single_run[metric_name] for new_node_test_metric_single_run in new_node_test_metric_all_runs], ddof=1):.4f}')

    sys.exit()