#!/usr/bin/env python3 # -*- coding: utf-8 -*- """ Created on Thu Sep 5 15:59:00 2019 @author: ljia """ import numpy as np import networkx as nx import matplotlib.pyplot as plt import time import random #from tqdm import tqdm #import os import sys sys.path.insert(0, "../") from pygraph.utils.graphfiles import loadDataset from iam import iam_upgraded from utils import remove_edges, compute_kernel, get_same_item_indices from ged import ged_median ############################################################################### # tests on different numbers of median-sets. def test_iam_median_nb(): ds = {'name': 'MUTAG', 'dataset': '../datasets/MUTAG/MUTAG_A.txt', 'extra_params': {}} # node/edge symb Gn, y_all = loadDataset(ds['dataset'], extra_params=ds['extra_params']) # Gn = Gn[0:50] remove_edges(Gn) gkernel = 'marginalizedkernel' # lmbda = 0.03 # termination probalility # r_max = 10 # iteration limit for pre-image. # alpha_range = np.linspace(0.5, 0.5, 1) # k = 5 # k nearest neighbors # epsilon = 1e-6 # InitIAMWithAllDk = True # parameters for GED function ged_cost='CHEM_1' ged_method='IPFP' saveGXL='gedlib' # parameters for IAM function c_ei=1 c_er=1 c_es=1 ite_max_iam = 50 epsilon_iam = 0.001 removeNodes = False connected_iam = False # number of graphs; we what to compute the median of these graphs. nb_median_range = [2, 3, 4, 5, 10, 20, 30, 40, 50, 100] # find out all the graphs classified to positive group 1. idx_dict = get_same_item_indices(y_all) Gn = [Gn[i] for i in idx_dict[1]] # # compute Gram matrix. # time0 = time.time() # km = compute_kernel(Gn, gkernel, True) # time_km = time.time() - time0 # # write Gram matrix to file. # np.savez('results/gram_matrix_marg_itr10_pq0.03_mutag_positive.gm', gm=km, gmtime=time_km) time_list = [] dis_ks_min_list = [] sod_gs_list = [] sod_gs_min_list = [] nb_updated_list = [] nb_updated_k_list = [] g_best = [] for nb_median in nb_median_range: print('\n-------------------------------------------------------') print('number of median graphs =', nb_median) random.seed(1) idx_rdm = random.sample(range(len(Gn)), nb_median) print('graphs chosen:', idx_rdm) Gn_median = [Gn[idx].copy() for idx in idx_rdm] Gn_candidate = [g.copy() for g in Gn_median] # for g in Gn_median: # nx.draw(g, labels=nx.get_node_attributes(g, 'atom'), with_labels=True) ## plt.savefig("results/preimage_mix/mutag.png", format="PNG") # plt.show() # plt.clf() ################################################################### gmfile = np.load('results/gram_matrix_marg_itr10_pq0.03_mutag_positive.gm.npz') km_tmp = gmfile['gm'] time_km = gmfile['gmtime'] # modify mixed gram matrix. km = np.zeros((len(Gn) + nb_median, len(Gn) + nb_median)) for i in range(len(Gn)): for j in range(i, len(Gn)): km[i, j] = km_tmp[i, j] km[j, i] = km[i, j] for i in range(len(Gn)): for j, idx in enumerate(idx_rdm): km[i, len(Gn) + j] = km[i, idx] km[len(Gn) + j, i] = km[i, idx] for i, idx1 in enumerate(idx_rdm): for j, idx2 in enumerate(idx_rdm): km[len(Gn) + i, len(Gn) + j] = km[idx1, idx2] ################################################################### alpha_range = [1 / nb_median] * nb_median time0 = time.time() ghat_new_list, dis_min = iam_upgraded(Gn_median, Gn_candidate, c_ei=c_ei, c_er=c_er, c_es=c_es, ite_max=ite_max_iam, epsilon=epsilon_iam, removeNodes=removeNodes, connected=connected_iam, params_ged={'ged_cost': ged_cost, 'ged_method': ged_method, 'saveGXL': saveGXL}) time_total = time.time() - time0 print('\ntime: ', time_total) time_list.append(time_total) print('\nsmallest distance in kernel space: ', dhat) dis_ks_min_list.append(dhat) g_best.append(ghat_list) print('\nnumber of updates of the best graph: ', nb_updated) nb_updated_list.append(nb_updated) print('\nnumber of updates of k nearest graphs: ', nb_updated_k) nb_updated_k_list.append(nb_updated_k) # show the best graph and save it to file. print('the shortest distance is', dhat) print('one of the possible corresponding pre-images is') nx.draw(ghat_list[0], labels=nx.get_node_attributes(ghat_list[0], 'atom'), with_labels=True) plt.show() plt.savefig('results/preimage_iam/mutag_median_nb' + str(nb_median) + '.png', format="PNG") plt.clf() # print(ghat_list[0].nodes(data=True)) # print(ghat_list[0].edges(data=True)) # compute the corresponding sod in graph space. sod_tmp, _ = ged_median([ghat_list[0]], Gn_median, ged_cost=ged_cost, ged_method=ged_method, saveGXL=saveGXL) sod_gs_list.append(sod_tmp) sod_gs_min_list.append(np.min(sod_tmp)) print('\nsmallest sod in graph space: ', np.min(sod_tmp)) print('\nsods in graph space: ', sod_gs_list) print('\nsmallest sod in graph space for each set of median graphs: ', sod_gs_min_list) print('\nsmallest distance in kernel space for each set of median graphs: ', dis_ks_min_list) print('\nnumber of updates of the best graph for each set of median graphs by IAM: ', nb_updated_list) print('\nnumber of updates of k nearest graphs for each set of median graphs by IAM: ', nb_updated_k_list) print('\ntimes:', time_list) ############################################################################### if __name__ == '__main__': ############################################################################### # tests on different numbers of median-sets. test_iam_median_nb()