#!/usr/bin/env python3 # -*- coding: utf-8 -*- """ Created on Thu Aug 20 16:09:51 2020 @author: ljia @references: [1] S Vichy N Vishwanathan, Nicol N Schraudolph, Risi Kondor, and Karsten M Borgwardt. Graph kernels. Journal of Machine Learning Research, 11(Apr):1201–1242, 2010. """ import sys from gklearn.utils import get_iters import numpy as np import networkx as nx from scipy import optimize from gklearn.utils.parallel import parallel_gm, parallel_me from gklearn.kernels import RandomWalkMeta from gklearn.utils.utils import compute_vertex_kernels class FixedPoint(RandomWalkMeta): def __init__(self, **kwargs): super().__init__(**kwargs) self._node_kernels = kwargs.get('node_kernels', None) self._edge_kernels = kwargs.get('edge_kernels', None) self._node_labels = kwargs.get('node_labels', []) self._edge_labels = kwargs.get('edge_labels', []) self._node_attrs = kwargs.get('node_attrs', []) self._edge_attrs = kwargs.get('edge_attrs', []) def _compute_gm_series(self): self._check_edge_weight(self._graphs, self._verbose) self._check_graphs(self._graphs) lmda = self._weight # Compute Gram matrix. gram_matrix = np.zeros((len(self._graphs), len(self._graphs))) # Reindex nodes using consecutive integers for the convenience of kernel computation. iterator = get_iters(self._graphs, desc='Reindex vertices', file=sys.stdout,verbose=(self._verbose >= 2)) self._graphs = [nx.convert_node_labels_to_integers(g, first_label=0, label_attribute='label_orignal') for g in iterator] if self._p is None and self._q is None: # p and q are uniform distributions as default. from itertools import combinations_with_replacement itr = combinations_with_replacement(range(0, len(self._graphs)), 2) len_itr = int(len(self._graphs) * (len(self._graphs) + 1) / 2) iterator = get_iters(itr, desc='Computing kernels', file=sys.stdout, length=len_itr, verbose=(self._verbose >= 2)) for i, j in iterator: kernel = self._kernel_do(self._graphs[i], self._graphs[j], lmda) gram_matrix[i][j] = kernel gram_matrix[j][i] = kernel else: # @todo pass return gram_matrix def _compute_gm_imap_unordered(self): self._check_edge_weight(self._graphs, self._verbose) self._check_graphs(self._graphs) # Compute Gram matrix. gram_matrix = np.zeros((len(self._graphs), len(self._graphs))) # @todo: parallel this. # Reindex nodes using consecutive integers for the convenience of kernel computation. iterator = get_iters(self._graphs, desc='Reindex vertices', file=sys.stdout, verbose=(self._verbose >= 2)) self._graphs = [nx.convert_node_labels_to_integers(g, first_label=0, label_attribute='label_orignal') for g in iterator] if self._p is None and self._q is None: # p and q are uniform distributions as default. def init_worker(gn_toshare): global G_gn G_gn = gn_toshare do_fun = self._wrapper_kernel_do parallel_gm(do_fun, gram_matrix, self._graphs, init_worker=init_worker, glbv=(self._graphs,), n_jobs=self._n_jobs, verbose=self._verbose) else: # @todo pass return gram_matrix def _compute_kernel_list_series(self, g1, g_list): self._check_edge_weight(g_list + [g1], self._verbose) self._check_graphs(g_list + [g1]) lmda = self._weight # compute kernel list. kernel_list = [None] * len(g_list) # Reindex nodes using consecutive integers for the convenience of kernel computation. g1 = nx.convert_node_labels_to_integers(g1, first_label=0, label_attribute='label_orignal') iterator = get_iters(g_list, desc='Reindex vertices', file=sys.stdout, verbose=(self._verbose >= 2)) g_list = [nx.convert_node_labels_to_integers(g, first_label=0, label_attribute='label_orignal') for g in iterator] if self._p is None and self._q is None: # p and q are uniform distributions as default. iterator = get_iters(range(len(g_list)), desc='Computing kernels', file=sys.stdout, length=len(g_list), verbose=(self._verbose >= 2)) for i in iterator: kernel = self._kernel_do(g1, g_list[i], lmda) kernel_list[i] = kernel else: # @todo pass return kernel_list def _compute_kernel_list_imap_unordered(self, g1, g_list): self._check_edge_weight(g_list + [g1], self._verbose) self._check_graphs(g_list + [g1]) # compute kernel list. kernel_list = [None] * len(g_list) # Reindex nodes using consecutive integers for the convenience of kernel computation. g1 = nx.convert_node_labels_to_integers(g1, first_label=0, label_attribute='label_orignal') # @todo: parallel this. iterator = get_iters(g_list, desc='Reindex vertices', file=sys.stdout, verbose=(self._verbose >= 2)) g_list = [nx.convert_node_labels_to_integers(g, first_label=0, label_attribute='label_orignal') for g in iterator] if self._p is None and self._q is None: # p and q are uniform distributions as default. def init_worker(g1_toshare, g_list_toshare): global G_g1, G_g_list G_g1 = g1_toshare G_g_list = g_list_toshare do_fun = self._wrapper_kernel_list_do def func_assign(result, var_to_assign): var_to_assign[result[0]] = result[1] itr = range(len(g_list)) len_itr = len(g_list) parallel_me(do_fun, func_assign, kernel_list, itr, len_itr=len_itr, init_worker=init_worker, glbv=(g1, g_list), method='imap_unordered', n_jobs=self._n_jobs, itr_desc='Computing kernels', verbose=self._verbose) else: # @todo pass return kernel_list def _wrapper_kernel_list_do(self, itr): return itr, self._kernel_do(G_g1, G_g_list[itr], self._weight) def _compute_single_kernel_series(self, g1, g2): self._check_edge_weight([g1] + [g2], self._verbose) self._check_graphs([g1] + [g2]) lmda = self._weight # Reindex nodes using consecutive integers for the convenience of kernel computation. g1 = nx.convert_node_labels_to_integers(g1, first_label=0, label_attribute='label_orignal') g2 = nx.convert_node_labels_to_integers(g2, first_label=0, label_attribute='label_orignal') if self._p is None and self._q is None: # p and q are uniform distributions as default. kernel = self._kernel_do(g1, g2, lmda) else: # @todo pass return kernel def _kernel_do(self, g1, g2, lmda): # Frist, compute kernels between all pairs of nodes using the method borrowed # from FCSP. It is faster than directly computing all edge kernels # when $d_1d_2>2$, where $d_1$ and $d_2$ are vertex degrees of the # graphs compared, which is the most case we went though. For very # sparse graphs, this would be slow. vk_dict = self._compute_vertex_kernels(g1, g2) # Compute the weight matrix of the direct product graph. w_times, w_dim = self._compute_weight_matrix(g1, g2, vk_dict) # use uniform distribution if there is no prior knowledge. p_times_uni = 1 / w_dim p_times = np.full((w_dim, 1), p_times_uni) x = optimize.fixed_point(self._func_fp, p_times, args=(p_times, lmda, w_times), xtol=1e-06, maxiter=1000) # use uniform distribution if there is no prior knowledge. q_times = np.full((1, w_dim), p_times_uni) return np.dot(q_times, x) def _wrapper_kernel_do(self, itr): i = itr[0] j = itr[1] return i, j, self._kernel_do(G_gn[i], G_gn[j], self._weight) def _func_fp(self, x, p_times, lmda, w_times): haha = w_times * x haha = lmda * haha haha = p_times + haha return p_times + lmda * np.dot(w_times, x) def _compute_vertex_kernels(self, g1, g2): """Compute vertex kernels between vertices of two graphs. """ return compute_vertex_kernels(g1, g2, self._node_kernels, node_labels=self._node_labels, node_attrs=self._node_attrs) # @todo: move if out to make it faster. # @todo: node/edge kernels use direct function rather than dicts. def _compute_weight_matrix(self, g1, g2, vk_dict): """Compute the weight matrix of the direct product graph. """ # Define edge kernels. def compute_ek_11(e1, e2, ke): e1_labels = [e1[2][el] for el in self._edge_labels] e2_labels = [e2[2][el] for el in self._edge_labels] e1_attrs = [e1[2][ea] for ea in self._edge_attrs] e2_attrs = [e2[2][ea] for ea in self._edge_attrs] return ke(e1_labels, e2_labels, e1_attrs, e2_attrs) def compute_ek_10(e1, e2, ke): e1_labels = [e1[2][el] for el in self._edge_labels] e2_labels = [e2[2][el] for el in self._edge_labels] return ke(e1_labels, e2_labels) def compute_ek_01(e1, e2, ke): e1_attrs = [e1[2][ea] for ea in self._edge_attrs] e2_attrs = [e2[2][ea] for ea in self._edge_attrs] return ke(e1_attrs, e2_attrs) def compute_ek_00(e1, e2, ke): return 1 # Select the proper edge kernel. if len(self._edge_labels) > 0: # edge symb and non-synb labeled if len(self._edge_attrs) > 0: ke = self._edge_kernels['mix'] ek_temp = compute_ek_11 # edge symb labeled else: ke = self._edge_kernels['symb'] ek_temp = compute_ek_10 else: # edge non-synb labeled if len(self._edge_attrs) > 0: ke = self._edge_kernels['nsymb'] ek_temp = compute_ek_01 # edge unlabeled else: ke = None ek_temp = compute_ek_00 # @todo: check how much slower is this. # Compute the weight matrix. w_dim = nx.number_of_nodes(g1) * nx.number_of_nodes(g2) w_times = np.zeros((w_dim, w_dim)) if vk_dict: # node labeled if self._ds_infos['directed']: for e1 in g1.edges(data=True): for e2 in g2.edges(data=True): w_idx = (e1[0] * nx.number_of_nodes(g2) + e2[0], e1[1] * nx.number_of_nodes(g2) + e2[1]) w_times[w_idx] = vk_dict[(e1[0], e2[0])] * ek_temp(e1, e2, ke) * vk_dict[(e1[1], e2[1])] else: # undirected for e1 in g1.edges(data=True): for e2 in g2.edges(data=True): w_idx = (e1[0] * nx.number_of_nodes(g2) + e2[0], e1[1] * nx.number_of_nodes(g2) + e2[1]) w_times[w_idx] = vk_dict[(e1[0], e2[0])] * ek_temp(e1, e2, ke) * vk_dict[(e1[1], e2[1])] + vk_dict[(e1[0], e2[1])] * ek_temp(e1, e2, ke) * vk_dict[(e1[1], e2[0])] w_times[w_idx[1], w_idx[0]] = w_times[w_idx[0], w_idx[1]] w_idx2 = (e1[0] * nx.number_of_nodes(g2) + e2[1], e1[1] * nx.number_of_nodes(g2) + e2[0]) w_times[w_idx2[0], w_idx2[1]] = w_times[w_idx[0], w_idx[1]] w_times[w_idx2[1], w_idx2[0]] = w_times[w_idx[0], w_idx[1]] else: # node unlabeled if self._ds_infos['directed']: for e1 in g1.edges(data=True): for e2 in g2.edges(data=True): w_idx = (e1[0] * nx.number_of_nodes(g2) + e2[0], e1[1] * nx.number_of_nodes(g2) + e2[1]) w_times[w_idx] = ek_temp(e1, e2, ke) else: # undirected for e1 in g1.edges(data=True): for e2 in g2.edges(data=True): w_idx = (e1[0] * nx.number_of_nodes(g2) + e2[0], e1[1] * nx.number_of_nodes(g2) + e2[1]) w_times[w_idx] = ek_temp(e1, e2, ke) w_times[w_idx[1], w_idx[0]] = w_times[w_idx[0], w_idx[1]] w_idx2 = (e1[0] * nx.number_of_nodes(g2) + e2[1], e1[1] * nx.number_of_nodes(g2) + e2[0]) w_times[w_idx2[0], w_idx2[1]] = w_times[w_idx[0], w_idx[1]] w_times[w_idx2[1], w_idx2[0]] = w_times[w_idx[0], w_idx[1]] return w_times, w_dim