diff --git a/gklearn/kernels/weisfeiler_lehman.py b/gklearn/kernels/weisfeiler_lehman.py index 9fb7c83..1f52755 100644 --- a/gklearn/kernels/weisfeiler_lehman.py +++ b/gklearn/kernels/weisfeiler_lehman.py @@ -33,9 +33,9 @@ class WeisfeilerLehman(GraphKernel): # @todo: sp, edge user kernel. def _compute_gm_series(self): -# if self._verbose >= 2: -# import warnings -# warnings.warn('A part of the computation is parallelized.') +# if self._verbose >= 2: +# import warnings +# warnings.warn('A part of the computation is parallelized.') self._add_dummy_node_labels(self._graphs) @@ -64,6 +64,11 @@ class WeisfeilerLehman(GraphKernel): # @todo: sp, edge user kernel. if self._base_kernel == 'subtree': gram_matrix = np.zeros((len(self._graphs), len(self._graphs))) +# for i in range(len(self._graphs)): +# for j in range(i, len(self._graphs)): +# gram_matrix[i][j] = self.pairwise_kernel(self._graphs[i], self._graphs[j]) +# gram_matrix[j][i] = gram_matrix[i][j] + def init_worker(gn_toshare): global G_gn G_gn = gn_toshare @@ -79,9 +84,9 @@ class WeisfeilerLehman(GraphKernel): # @todo: sp, edge user kernel. def _compute_kernel_list_series(self, g1, g_list): # @todo: this should be better. -# if self._verbose >= 2: -# import warnings -# warnings.warn('A part of the computation is parallelized.') +# if self._verbose >= 2: +# import warnings +# warnings.warn('A part of the computation is parallelized.') self._add_dummy_node_labels(g_list + [g1]) @@ -131,7 +136,7 @@ class WeisfeilerLehman(GraphKernel): # @todo: sp, edge user kernel. def _wrapper_kernel_list_do(self, itr): - return self._kernel_do_exp(G_g1, G_g_list[itr]) + return itr, self.pairwise_kernel(G_g1, G_g_list[itr]) def _compute_single_kernel_series(self, g1, g2): # @todo: this should be better. @@ -157,7 +162,7 @@ class WeisfeilerLehman(GraphKernel): # @todo: sp, edge user kernel. def pairwise_kernel(self, g1, g2): - Gn = [g1, g2] + Gn = [g1.copy(), g2.copy()] # @todo: make sure it is a full deep copy. and faster! kernel = 0 # initial for height = 0 @@ -327,15 +332,15 @@ class WeisfeilerLehman(GraphKernel): # @todo: sp, edge user kernel. def _compute_gram_itr(self, gram_matrix, all_num_of_each_label): """Compute Gram matrix using the base kernel. """ -# if self._parallel == 'imap_unordered': -# # compute kernels. -# def init_worker(alllabels_toshare): -# global G_alllabels -# G_alllabels = alllabels_toshare -# do_partial = partial(self._wrapper_compute_subtree_kernel, gram_matrix) -# parallel_gm(do_partial, gram_matrix, Gn, init_worker=init_worker, -# glbv=(all_num_of_each_label,), n_jobs=self._n_jobs, verbose=self._verbose) -# elif self._parallel is None: +# if self._parallel == 'imap_unordered': +# # compute kernels. +# def init_worker(alllabels_toshare): +# global G_alllabels +# G_alllabels = alllabels_toshare +# do_partial = partial(self._wrapper_compute_subtree_kernel, gram_matrix) +# parallel_gm(do_partial, gram_matrix, Gn, init_worker=init_worker, +# glbv=(all_num_of_each_label,), n_jobs=self._n_jobs, verbose=self._verbose) +# elif self._parallel is None: for i in range(len(gram_matrix)): for j in range(i, len(gram_matrix)): gram_matrix[i][j] = self._compute_subtree_kernel(all_num_of_each_label[i], @@ -357,10 +362,10 @@ class WeisfeilerLehman(GraphKernel): # @todo: sp, edge user kernel. return kernel -# def _wrapper_compute_subtree_kernel(self, gram_matrix, itr): -# i = itr[0] -# j = itr[1] -# return i, j, self._compute_subtree_kernel(G_alllabels[i], G_alllabels[j], gram_matrix[i][j]) +# def _wrapper_compute_subtree_kernel(self, gram_matrix, itr): +# i = itr[0] +# j = itr[1] +# return i, j, self._compute_subtree_kernel(G_alllabels[i], G_alllabels[j], gram_matrix[i][j]) def _wl_spkernel_do(Gn, node_label, edge_label, height):