diff --git a/lang/zh/gklearn/preimage/random_preimage_generator.py b/lang/zh/gklearn/preimage/random_preimage_generator.py new file mode 100644 index 0000000..cb28519 --- /dev/null +++ b/lang/zh/gklearn/preimage/random_preimage_generator.py @@ -0,0 +1,389 @@ +#!/usr/bin/env python3 +# -*- coding: utf-8 -*- +""" +Created on Fri May 29 14:29:52 2020 + +@author: ljia +""" + +import numpy as np +import time +import sys +from tqdm import tqdm +import multiprocessing +import networkx as nx +from multiprocessing import Pool +from functools import partial +from gklearn.preimage import PreimageGenerator +from gklearn.preimage.utils import compute_k_dis +from gklearn.utils import Timer +from gklearn.utils.utils import get_graph_kernel_by_name +# from gklearn.utils.dataset import Dataset + + +class RandomPreimageGenerator(PreimageGenerator): + + def __init__(self, dataset=None): + PreimageGenerator.__init__(self, dataset=dataset) + # arguments to set. + self.__k = 5 # number of nearest neighbors of phi in D_N. + self.__r_max = 10 # maximum number of iterations. + self.__l = 500 # numbers of graphs generated for each graph in D_k U {g_i_hat}. + self.__alphas = None # weights of linear combinations of points in kernel space. + self.__parallel = True + self.__n_jobs = multiprocessing.cpu_count() + self.__time_limit_in_sec = 0 + self.__max_itrs = 20 + # values to compute. + self.__runtime_generate_preimage = None + self.__runtime_total = None + self.__preimage = None + self.__best_from_dataset = None + self.__k_dis_preimage = None + self.__k_dis_dataset = None + self.__itrs = 0 + self.__converged = False # @todo + self.__num_updates = 0 + # values that can be set or to be computed. + self.__gram_matrix_unnorm = None + self.__runtime_precompute_gm = None + + + def set_options(self, **kwargs): + self._kernel_options = kwargs.get('kernel_options', {}) + self._graph_kernel = kwargs.get('graph_kernel', None) + self._verbose = kwargs.get('verbose', 2) + self.__k = kwargs.get('k', 5) + self.__r_max = kwargs.get('r_max', 10) + self.__l = kwargs.get('l', 500) + self.__alphas = kwargs.get('alphas', None) + self.__parallel = kwargs.get('parallel', True) + self.__n_jobs = kwargs.get('n_jobs', multiprocessing.cpu_count()) + self.__time_limit_in_sec = kwargs.get('time_limit_in_sec', 0) + self.__max_itrs = kwargs.get('max_itrs', 20) + self.__gram_matrix_unnorm = kwargs.get('gram_matrix_unnorm', None) + self.__runtime_precompute_gm = kwargs.get('runtime_precompute_gm', None) + + + def run(self): + self._graph_kernel = get_graph_kernel_by_name(self._kernel_options['name'], + node_labels=self._dataset.node_labels, + edge_labels=self._dataset.edge_labels, + node_attrs=self._dataset.node_attrs, + edge_attrs=self._dataset.edge_attrs, + ds_infos=self._dataset.get_dataset_infos(keys=['directed']), + kernel_options=self._kernel_options) + + # record start time. + start = time.time() + + # 1. precompute gram matrix. + if self.__gram_matrix_unnorm is None: + gram_matrix, run_time = self._graph_kernel.compute(self._dataset.graphs, **self._kernel_options) + self.__gram_matrix_unnorm = self._graph_kernel.gram_matrix_unnorm + end_precompute_gm = time.time() + self.__runtime_precompute_gm = end_precompute_gm - start + else: + if self.__runtime_precompute_gm is None: + raise Exception('Parameter "runtime_precompute_gm" must be given when using pre-computed Gram matrix.') + self._graph_kernel.gram_matrix_unnorm = self.__gram_matrix_unnorm + if self._kernel_options['normalize']: + self._graph_kernel.gram_matrix = self._graph_kernel.normalize_gm(np.copy(self.__gram_matrix_unnorm)) + else: + self._graph_kernel.gram_matrix = np.copy(self.__gram_matrix_unnorm) + end_precompute_gm = time.time() + start -= self.__runtime_precompute_gm + + # 2. compute k nearest neighbors of phi in D_N. + if self._verbose >= 2: + print('\nstart computing k nearest neighbors of phi in D_N...\n') + D_N = self._dataset.graphs + if self.__alphas is None: + self.__alphas = [1 / len(D_N)] * len(D_N) + k_dis_list = [] # distance between g_star and each graph. + term3 = 0 + for i1, a1 in enumerate(self.__alphas): + for i2, a2 in enumerate(self.__alphas): + term3 += a1 * a2 * self._graph_kernel.gram_matrix[i1, i2] + for idx in range(len(D_N)): + k_dis_list.append(compute_k_dis(idx, range(0, len(D_N)), self.__alphas, self._graph_kernel.gram_matrix, term3=term3, withterm3=True)) + + # sort. + sort_idx = np.argsort(k_dis_list) + dis_gs = [k_dis_list[idis] for idis in sort_idx[0:self.__k]] # the k shortest distances. + nb_best = len(np.argwhere(dis_gs == dis_gs[0]).flatten().tolist()) + g0hat_list = [D_N[idx].copy() for idx in sort_idx[0:nb_best]] # the nearest neighbors of phi in D_N + self.__best_from_dataset = g0hat_list[0] # get the first best graph if there are muitlple. + self.__k_dis_dataset = dis_gs[0] + + if self.__k_dis_dataset == 0: # get the exact pre-image. + end_generate_preimage = time.time() + self.__runtime_generate_preimage = end_generate_preimage - end_precompute_gm + self.__runtime_total = end_generate_preimage - start + self.__preimage = self.__best_from_dataset.copy() + self.__k_dis_preimage = self.__k_dis_dataset + if self._verbose: + print() + print('=============================================================================') + print('The exact pre-image is found from the input dataset.') + print('-----------------------------------------------------------------------------') + print('Distance in kernel space for the best graph from dataset and for preimage:', self.__k_dis_dataset) + print('Time to pre-compute Gram matrix:', self.__runtime_precompute_gm) + print('Time to generate pre-images:', self.__runtime_generate_preimage) + print('Total time:', self.__runtime_total) + print('=============================================================================') + print() + return + + dhat = dis_gs[0] # the nearest distance + Gk = [D_N[ig].copy() for ig in sort_idx[0:self.__k]] # the k nearest neighbors + Gs_nearest = [nx.convert_node_labels_to_integers(g) for g in Gk] # [g.copy() for g in Gk] + + # 3. start iterations. + if self._verbose >= 2: + print('starting iterations...') + gihat_list = [] + dihat_list = [] + r = 0 + dis_of_each_itr = [dhat] + if self.__parallel: + self._kernel_options['parallel'] = None + self.__itrs = 0 + self.__num_updates = 0 + timer = Timer(self.__time_limit_in_sec) + while not self.__termination_criterion_met(timer, self.__itrs, r): + print('\n- r =', r) + found = False + dis_bests = dis_gs + dihat_list + + # compute numbers of edges to be inserted/deleted. + # @todo what if the log is negetive? how to choose alpha (scalar)? + fdgs_list = np.array(dis_bests) + if np.min(fdgs_list) < 1: # in case the log is negetive. + fdgs_list /= np.min(fdgs_list) + fdgs_list = [int(item) for item in np.ceil(np.log(fdgs_list))] + if np.min(fdgs_list) < 1: # in case the log is smaller than 1. + fdgs_list = np.array(fdgs_list) + 1 + # expand the number of modifications to increase the possiblity. + nb_vpairs_list = [nx.number_of_nodes(g) * (nx.number_of_nodes(g) - 1) for g in (Gs_nearest + gihat_list)] + nb_vpairs_min = np.min(nb_vpairs_list) + idx_fdgs_max = np.argmax(fdgs_list) + fdgs_max_old = fdgs_list[idx_fdgs_max] + fdgs_max = fdgs_max_old + nb_modif = 1 + for idx, nb in enumerate(range(nb_vpairs_min, nb_vpairs_min - fdgs_max, -1)): + nb_modif *= nb / (fdgs_max - idx) + while fdgs_max < nb_vpairs_min and nb_modif < self.__l: + fdgs_max += 1 + nb_modif *= (nb_vpairs_min - fdgs_max + 1) / fdgs_max + nb_increase = int(fdgs_max - fdgs_max_old) + if nb_increase > 0: + fdgs_list += 1 + + + for ig, gs in enumerate(Gs_nearest + gihat_list): + if self._verbose >= 2: + print('-- computing', ig + 1, 'graphs out of', len(Gs_nearest) + len(gihat_list)) + gnew, dhat, found = self.__generate_l_graphs(gs, fdgs_list[ig], dhat, ig, found, term3) + + if found: + r = 0 + gihat_list = [gnew] + dihat_list = [dhat] + else: + r += 1 + + dis_of_each_itr.append(dhat) + self.__itrs += 1 + if self._verbose >= 2: + print('Total number of iterations is', self.__itrs, '.') + print('The preimage is updated', self.__num_updates, 'times.') + print('The shortest distances for previous iterations are', dis_of_each_itr, '.') + + + # get results and print. + end_generate_preimage = time.time() + self.__runtime_generate_preimage = end_generate_preimage - end_precompute_gm + self.__runtime_total = end_generate_preimage - start + self.__preimage = (g0hat_list[0] if len(gihat_list) == 0 else gihat_list[0]) + self.__k_dis_preimage = dhat + if self._verbose: + print() + print('=============================================================================') + print('Finished generation of preimages.') + print('-----------------------------------------------------------------------------') + print('Distance in kernel space for the best graph from dataset:', self.__k_dis_dataset) + print('Distance in kernel space for the preimage:', self.__k_dis_preimage) + print('Total number of iterations for optimizing:', self.__itrs) + print('Total number of updating preimage:', self.__num_updates) + print('Time to pre-compute Gram matrix:', self.__runtime_precompute_gm) + print('Time to generate pre-images:', self.__runtime_generate_preimage) + print('Total time:', self.__runtime_total) + print('=============================================================================') + print() + + + def __generate_l_graphs(self, g_init, fdgs, dhat, ig, found, term3): + if self.__parallel: + gnew, dhat, found = self.__generate_l_graphs_parallel(g_init, fdgs, dhat, ig, found, term3) + else: + gnew, dhat, found = self.__generate_l_graphs_series(g_init, fdgs, dhat, ig, found, term3) + return gnew, dhat, found + + + def __generate_l_graphs_series(self, g_init, fdgs, dhat, ig, found, term3): + gnew = None + updated = False + for trial in range(0, self.__l): + if self._verbose >= 2: + print('---', trial + 1, 'trial out of', self.__l) + + gtemp, dnew = self.__do_trial(g_init, fdgs, term3, trial) + + # get the better graph preimage. + if dnew <= dhat: # @todo: the new distance is smaller or also equal? + if dhat - dnew > 1e-6: + if self._verbose >= 2: + print('trial =', str(trial)) + print('\nI am smaller!') + print('index (as in D_k U {gihat} =', str(ig)) + print('distance:', dhat, '->', dnew) + updated = True + else: + if self._verbose >= 2: + print('I am equal!') + dhat = dnew + gnew = gtemp.copy() + found = True # found better or equally good graph. + + if updated: + self.__num_updates += 1 + + return gnew, dhat, found + + + def __generate_l_graphs_parallel(self, g_init, fdgs, dhat, ig, found, term3): + gnew = None + len_itr = self.__l + gnew_list = [None] * len_itr + dnew_list = [None] * len_itr + itr = range(0, len_itr) + n_jobs = multiprocessing.cpu_count() + if len_itr < 100 * n_jobs: + chunksize = int(len_itr / n_jobs) + 1 + else: + chunksize = 100 + do_fun = partial(self._generate_graph_parallel, g_init, fdgs, term3) + pool = Pool(processes=n_jobs) + if self._verbose >= 2: + iterator = tqdm(pool.imap_unordered(do_fun, itr, chunksize), + desc='Generating l graphs', file=sys.stdout) + else: + iterator = pool.imap_unordered(do_fun, itr, chunksize) + for idx, gnew, dnew in iterator: + gnew_list[idx] = gnew + dnew_list[idx] = dnew + pool.close() + pool.join() + + # check if get the better graph preimage. + idx_min = np.argmin(dnew_list) + dnew = dnew_list[idx_min] + if dnew <= dhat: # @todo: the new distance is smaller or also equal? + if dhat - dnew > 1e-6: # @todo: use a proportion and watch out for 0. + if self._verbose >= 2: + print('I am smaller!') + print('index (as in D_k U {gihat}) =', str(ig)) + print('distance:', dhat, '->', dnew, '\n') + self.__num_updates += 1 + else: + if self._verbose >= 2: + print('I am equal!') + dhat = dnew + gnew = gnew_list[idx_min] + found = True # found better graph. + + return gnew, dhat, found + + + def _generate_graph_parallel(self, g_init, fdgs, term3, itr): + trial = itr + gtemp, dnew = self.__do_trial(g_init, fdgs, term3, trial) + return trial, gtemp, dnew + + + def __do_trial(self, g_init, fdgs, term3, trial): + # add and delete edges. + gtemp = g_init.copy() + seed = (trial + int(time.time())) % (2 ** 32 - 1) + rdm_state = np.random.RandomState(seed=seed) + # which edges to change. + # @todo: should we use just half of the adjacency matrix for undirected graphs? + nb_vpairs = nx.number_of_nodes(g_init) * (nx.number_of_nodes(g_init) - 1) + # @todo: what if fdgs is bigger than nb_vpairs? + idx_change = rdm_state.randint(0, high=nb_vpairs, size=(fdgs if + fdgs < nb_vpairs else nb_vpairs)) +# print(idx_change) + for item in idx_change: + node1 = int(item / (nx.number_of_nodes(g_init) - 1)) + node2 = (item - node1 * (nx.number_of_nodes(g_init) - 1)) + if node2 >= node1: # skip the self pair. + node2 += 1 + # @todo: is the randomness correct? + if not gtemp.has_edge(node1, node2): + gtemp.add_edge(node1, node2) + else: + gtemp.remove_edge(node1, node2) + + # compute new distances. + kernels_to_gtmp, _ = self._graph_kernel.compute(gtemp, self._dataset.graphs, **self._kernel_options) + kernel_gtmp, _ = self._graph_kernel.compute(gtemp, gtemp, **self._kernel_options) + if self._kernel_options['normalize']: + kernels_to_gtmp = [kernels_to_gtmp[i] / np.sqrt(self.__gram_matrix_unnorm[i, i] * kernel_gtmp) for i in range(len(kernels_to_gtmp))] # normalize + kernel_gtmp = 1 + # @todo: not correct kernel value + gram_with_gtmp = np.concatenate((np.array([kernels_to_gtmp]), np.copy(self._graph_kernel.gram_matrix)), axis=0) + gram_with_gtmp = np.concatenate((np.array([[kernel_gtmp] + kernels_to_gtmp]).T, gram_with_gtmp), axis=1) + dnew = compute_k_dis(0, range(1, 1 + len(self._dataset.graphs)), self.__alphas, gram_with_gtmp, term3=term3, withterm3=True) + + return gtemp, dnew + + + def get_results(self): + results = {} + results['runtime_precompute_gm'] = self.__runtime_precompute_gm + results['runtime_generate_preimage'] = self.__runtime_generate_preimage + results['runtime_total'] = self.__runtime_total + results['k_dis_dataset'] = self.__k_dis_dataset + results['k_dis_preimage'] = self.__k_dis_preimage + results['itrs'] = self.__itrs + results['num_updates'] = self.__num_updates + return results + + + def __termination_criterion_met(self, timer, itr, r): + if timer.expired() or (itr >= self.__max_itrs if self.__max_itrs >= 0 else False): +# if self.__state == AlgorithmState.TERMINATED: +# self.__state = AlgorithmState.INITIALIZED + return True + return (r >= self.__r_max if self.__r_max >= 0 else False) +# return converged or (itrs_without_update > self.__max_itrs_without_update if self.__max_itrs_without_update >= 0 else False) + + + @property + def preimage(self): + return self.__preimage + + + @property + def best_from_dataset(self): + return self.__best_from_dataset + + + @property + def gram_matrix_unnorm(self): + return self.__gram_matrix_unnorm + + @gram_matrix_unnorm.setter + def gram_matrix_unnorm(self, value): + self.__gram_matrix_unnorm = value \ No newline at end of file