#!/usr/bin/env python3 # -*- coding: utf-8 -*- """ Created on Wed Mar 6 16:03:11 2019 pre-image @author: ljia """ import sys import numpy as np import multiprocessing from tqdm import tqdm import networkx as nx import matplotlib.pyplot as plt sys.path.insert(0, "../") from pygraph.kernels.marginalizedKernel import marginalizedkernel from pygraph.utils.graphfiles import loadDataset ds = {'name': 'MUTAG', 'dataset': '../datasets/MUTAG/MUTAG.mat', 'extra_params': {'am_sp_al_nl_el': [0, 0, 3, 1, 2]}} # node/edge symb DN, y_all = loadDataset(ds['dataset'], extra_params=ds['extra_params']) DN = DN[0:10] lmbda = 0.03 # termination probalility r_max = 10 # recursions l = 500 alpha_range = np.linspace(0.1, 0.9, 9) k = 5 # k nearest neighbors # randomly select two molecules np.random.seed(1) idx1, idx2 = np.random.randint(0, len(DN), 2) g1 = DN[idx1] g2 = DN[idx2] # compute k_list = [] # kernel between each graph and itself. k_g1_list = [] # kernel between each graph and g1 k_g2_list = [] # kernel between each graph and g2 for ig, g in tqdm(enumerate(DN), desc='computing self kernels', file=sys.stdout): ktemp = marginalizedkernel([g, g1, g2], node_label='atom', edge_label=None, p_quit=lmbda, n_iteration=20, remove_totters=False, n_jobs=multiprocessing.cpu_count(), verbose=False) k_list.append(ktemp[0][0, 0]) k_g1_list.append(ktemp[0][0, 1]) k_g2_list.append(ktemp[0][0, 2]) g_best = [] dis_best = [] # for each alpha for alpha in alpha_range: print('alpha =', alpha) # compute k nearest neighbors of phi in DN. dis_list = [] # distance between g_star and each graph. for ig, g in tqdm(enumerate(DN), desc='computing distances', file=sys.stdout): dtemp = k_list[ig] - 2 * (alpha * k_g1_list[ig] + (1 - alpha) * k_g2_list[ig]) + (alpha * alpha * k_list[idx1] + alpha * (1 - alpha) * k_g2_list[idx1] + (1 - alpha) * alpha * k_g1_list[idx2] + (1 - alpha) * (1 - alpha) * k_list[idx2]) dis_list.append(dtemp) # sort sort_idx = np.argsort(dis_list) dis_gs = [dis_list[idis] for idis in sort_idx[0:k]] g0hat = DN[sort_idx[0]] # the nearest neighbor of phi in DN if dis_gs[0] == 0: # the exact pre-image. print('The exact pre-image is found from the input dataset.') g_pimg = g0hat break dhat = dis_gs[0] # the nearest distance Dk = [DN[ig] for ig in sort_idx[0:k]] # the k nearest neighbors gihat_list = [] i = 1 r = 1 while r < r_max: print('r =', r) found = False for ig, gs in enumerate(Dk + gihat_list): # nx.draw_networkx(gs) # plt.show() fdgs = int(np.abs(np.ceil(np.log(alpha * dis_gs[ig])))) # @todo ??? for trail in tqdm(range(0, l), desc='l loop', file=sys.stdout): # add and delete edges. gtemp = gs.copy() np.random.seed() # which edges to change. idx_change = np.random.randint(0, nx.number_of_nodes(gs) * (nx.number_of_nodes(gs) - 1), fdgs) for item in idx_change: node1 = int(item / (nx.number_of_nodes(gs) - 1)) node2 = (item - node1 * (nx.number_of_nodes(gs) - 1)) if node2 >= node1: node2 += 1 # @todo: is the randomness correct? if not gtemp.has_edge(node1, node2): gtemp.add_edges_from([(node1, node2, {'bond_type': 0})]) # nx.draw_networkx(gs) # plt.show() # nx.draw_networkx(gtemp) # plt.show() else: gtemp.remove_edge(node1, node2) # nx.draw_networkx(gs) # plt.show() # nx.draw_networkx(gtemp) # plt.show() # nx.draw_networkx(gtemp) # plt.show() # compute distance between phi and the new generated graph. knew = marginalizedkernel([gtemp, g1, g2], node_label='atom', edge_label=None, p_quit=lmbda, n_iteration=20, remove_totters=False, n_jobs=multiprocessing.cpu_count(), verbose=False) dnew = knew[0][0, 0] - 2 * (alpha * knew[0][0, 1] + (1 - alpha) * knew[0][0, 2]) + (alpha * alpha * k_list[idx1] + alpha * (1 - alpha) * k_g2_list[idx1] + (1 - alpha) * alpha * k_g1_list[idx2] + (1 - alpha) * (1 - alpha) * k_list[idx2]) if dnew <= dhat: # the new distance is smaller print('I am smaller!') dhat = dnew gnew = gtemp.copy() found = True # found better graph. if found: gihat_list = [gnew] dis_gs.append(dhat) else: r += 1 dis_best.append(dhat) g_best += ([g0hat] if len(gihat_list) == 0 else gihat_list) for idx, item in enumerate(alpha_range): print('when alpha is', item, 'the shortest distance is', dis_best[idx]) print('the corresponding pre-image is') nx.draw_networkx(g_best[idx]) plt.show()