#!/usr/bin/env python3 # -*- coding: utf-8 -*- """ Created on Wed Oct 20 11:48:02 2020 @author: ljia """ # This script tests the influence of the ratios between node costs and edge costs on the stability of the GED computation, where the base edit costs are [1, 1, 1, 1, 1, 1]. import os import multiprocessing import pickle import logging from gklearn.utils import Dataset from gklearn.ged.util import compute_geds def get_dataset(ds_name): # The node/edge labels that will not be used in the computation. if ds_name == 'MAO': irrelevant_labels = {'node_attrs': ['x', 'y', 'z'], 'edge_labels': ['bond_stereo']} elif ds_name == 'Monoterpenoides': irrelevant_labels = {'edge_labels': ['valence']} elif ds_name == 'MUTAG': irrelevant_labels = {'edge_labels': ['label_0']} elif ds_name == 'AIDS_symb': irrelevant_labels = {'node_attrs': ['chem', 'charge', 'x', 'y'], 'edge_labels': ['valence']} # Initialize a Dataset. dataset = Dataset() # Load predefined dataset. dataset.load_predefined_dataset(ds_name) # Remove irrelevant labels. dataset.remove_labels(**irrelevant_labels) print('dataset size:', len(dataset.graphs)) return dataset def xp_compute_ged_matrix(ds_name, num_solutions, ratio, trial): save_dir = 'outputs/edit_costs.num_sols.ratios.IPFP/' if not os.path.exists(save_dir): os.makedirs(save_dir) save_file_suffix = '.' + ds_name + '.num_sols_' + str(num_solutions) + '.ratio_' + "{:.2f}".format(ratio) + '.trial_' + str(trial) """**1. Get dataset.**""" dataset = get_dataset(ds_name) """**2. Set parameters.**""" # Parameters for GED computation. ged_options = {'method': 'IPFP', # use IPFP huristic. 'initialization_method': 'RANDOM', # or 'NODE', etc. # when bigger than 1, then the method is considered mIPFP. 'initial_solutions': int(num_solutions * 4), 'edit_cost': 'CONSTANT', # use CONSTANT cost. # the distance between non-symbolic node/edge labels is computed by euclidean distance. 'attr_distance': 'euclidean', 'ratio_runs_from_initial_solutions': 0.25, # parallel threads. Do not work if mpg_options['parallel'] = False. 'threads': multiprocessing.cpu_count(), 'init_option': 'EAGER_WITHOUT_SHUFFLED_COPIES' } edit_cost_constants = [i * ratio for i in [1, 1, 1]] + [1, 1, 1] # edit_cost_constants = [item * 0.01 for item in edit_cost_constants] # pickle.dump(edit_cost_constants, open(save_dir + "edit_costs" + save_file_suffix + ".pkl", "wb")) options = ged_options.copy() options['edit_cost_constants'] = edit_cost_constants options['node_labels'] = dataset.node_labels options['edge_labels'] = dataset.edge_labels options['node_attrs'] = dataset.node_attrs options['edge_attrs'] = dataset.edge_attrs parallel = True # if num_solutions == 1 else False """**5. Compute GED matrix.**""" ged_mat = 'error' try: ged_vec_init, ged_mat, n_edit_operations = compute_geds(dataset.graphs, options=options, parallel=parallel, verbose=True) except Exception as exp: print('An exception occured when running this experiment:') LOG_FILENAME = save_dir + 'error.txt' logging.basicConfig(filename=LOG_FILENAME, level=logging.DEBUG) logging.exception('save_file_suffix') print(repr(exp)) """**6. Get results.**""" pickle.dump(ged_mat, open(save_dir + 'ged_matrix' + save_file_suffix + '.pkl', 'wb')) if __name__ == '__main__': for ds_name in ['MAO', 'Monoterpenoides', 'MUTAG', 'AIDS_symb']: print() print('Dataset:', ds_name) for num_solutions in [1, 10, 20, 30, 40, 50, 60, 70, 80, 90, 100]: print() print('# of solutions:', num_solutions) for ratio in [0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10]: print() print('Ratio:', ratio) for trial in range(1, 101): print() print('Trial:', trial) xp_compute_ged_matrix(ds_name, num_solutions, ratio, trial)