| @@ -32,15 +32,15 @@ def weisfeilerlehmankernel(*args, | |||||
| n_jobs=None, | n_jobs=None, | ||||
| chunksize=None, | chunksize=None, | ||||
| verbose=True): | verbose=True): | ||||
| """Calculate Weisfeiler-Lehman kernels between graphs. | |||||
| """Compute Weisfeiler-Lehman kernels between graphs. | |||||
| Parameters | Parameters | ||||
| ---------- | ---------- | ||||
| Gn : List of NetworkX graph | Gn : List of NetworkX graph | ||||
| List of graphs between which the kernels are calculated. | |||||
| List of graphs between which the kernels are computed. | |||||
| G1, G2 : NetworkX graphs | G1, G2 : NetworkX graphs | ||||
| Two graphs between which the kernel is calculated. | |||||
| Two graphs between which the kernel is computed. | |||||
| node_label : string | node_label : string | ||||
| Node attribute used as label. The default node label is atom. | Node attribute used as label. The default node label is atom. | ||||
| @@ -115,12 +115,12 @@ def weisfeilerlehmankernel(*args, | |||||
| def _wl_kernel_do(Gn, node_label, edge_label, height, parallel, n_jobs, chunksize, verbose): | def _wl_kernel_do(Gn, node_label, edge_label, height, parallel, n_jobs, chunksize, verbose): | ||||
| """Calculate Weisfeiler-Lehman kernels between graphs. | |||||
| """Compute Weisfeiler-Lehman kernels between graphs. | |||||
| Parameters | Parameters | ||||
| ---------- | ---------- | ||||
| Gn : List of NetworkX graph | Gn : List of NetworkX graph | ||||
| List of graphs between which the kernels are calculated. | |||||
| List of graphs between which the kernels are computed. | |||||
| node_label : string | node_label : string | ||||
| node attribute used as label. | node attribute used as label. | ||||
| edge_label : string | edge_label : string | ||||
| @@ -146,7 +146,7 @@ def _wl_kernel_do(Gn, node_label, edge_label, height, parallel, n_jobs, chunksiz | |||||
| # number of occurence of each label in G | # number of occurence of each label in G | ||||
| all_num_of_each_label.append(dict(Counter(labels_ori))) | all_num_of_each_label.append(dict(Counter(labels_ori))) | ||||
| # calculate subtree kernel with the 0th iteration and add it to the final kernel | |||||
| # Compute subtree kernel with the 0th iteration and add it to the final kernel | |||||
| compute_kernel_matrix(Kmatrix, all_num_of_each_label, Gn, parallel, n_jobs, chunksize, False) | compute_kernel_matrix(Kmatrix, all_num_of_each_label, Gn, parallel, n_jobs, chunksize, False) | ||||
| # iterate each height | # iterate each height | ||||
| @@ -255,7 +255,7 @@ def _wl_kernel_do(Gn, node_label, edge_label, height, parallel, n_jobs, chunksiz | |||||
| # all_labels_ori.update(labels_comp) | # all_labels_ori.update(labels_comp) | ||||
| all_num_of_each_label.append(dict(Counter(labels_comp))) | all_num_of_each_label.append(dict(Counter(labels_comp))) | ||||
| # calculate subtree kernel with h iterations and add it to the final kernel | |||||
| # Compute subtree kernel with h iterations and add it to the final kernel | |||||
| compute_kernel_matrix(Kmatrix, all_num_of_each_label, Gn, parallel, n_jobs, chunksize, False) | compute_kernel_matrix(Kmatrix, all_num_of_each_label, Gn, parallel, n_jobs, chunksize, False) | ||||
| return Kmatrix | return Kmatrix | ||||
| @@ -316,7 +316,7 @@ def compute_kernel_matrix(Kmatrix, all_num_of_each_label, Gn, parallel, n_jobs, | |||||
| do_partial = partial(wrapper_compute_subtree_kernel, Kmatrix) | do_partial = partial(wrapper_compute_subtree_kernel, Kmatrix) | ||||
| parallel_gm(do_partial, Kmatrix, Gn, init_worker=init_worker, | parallel_gm(do_partial, Kmatrix, Gn, init_worker=init_worker, | ||||
| glbv=(all_num_of_each_label,), n_jobs=n_jobs, chunksize=chunksize, verbose=verbose) | glbv=(all_num_of_each_label,), n_jobs=n_jobs, chunksize=chunksize, verbose=verbose) | ||||
| elif parallel == None: | |||||
| elif parallel is None: | |||||
| for i in range(len(Kmatrix)): | for i in range(len(Kmatrix)): | ||||
| for j in range(i, len(Kmatrix)): | for j in range(i, len(Kmatrix)): | ||||
| Kmatrix[i][j] = compute_subtree_kernel(all_num_of_each_label[i], | Kmatrix[i][j] = compute_subtree_kernel(all_num_of_each_label[i], | ||||
| @@ -345,12 +345,12 @@ def wrapper_compute_subtree_kernel(Kmatrix, itr): | |||||
| def _wl_spkernel_do(Gn, node_label, edge_label, height): | def _wl_spkernel_do(Gn, node_label, edge_label, height): | ||||
| """Calculate Weisfeiler-Lehman shortest path kernels between graphs. | |||||
| """Compute Weisfeiler-Lehman shortest path kernels between graphs. | |||||
| Parameters | Parameters | ||||
| ---------- | ---------- | ||||
| Gn : List of NetworkX graph | Gn : List of NetworkX graph | ||||
| List of graphs between which the kernels are calculated. | |||||
| List of graphs between which the kernels are computed. | |||||
| node_label : string | node_label : string | ||||
| node attribute used as label. | node attribute used as label. | ||||
| edge_label : string | edge_label : string | ||||
| @@ -413,7 +413,7 @@ def _wl_spkernel_do(Gn, node_label, edge_label, height): | |||||
| for node in G.nodes(data = True): | for node in G.nodes(data = True): | ||||
| node[1][node_label] = set_compressed[set_multisets[node[0]]] | node[1][node_label] = set_compressed[set_multisets[node[0]]] | ||||
| # calculate subtree kernel with h iterations and add it to the final kernel | |||||
| # Compute subtree kernel with h iterations and add it to the final kernel | |||||
| for i in range(0, len(Gn)): | for i in range(0, len(Gn)): | ||||
| for j in range(i, len(Gn)): | for j in range(i, len(Gn)): | ||||
| for e1 in Gn[i].edges(data = True): | for e1 in Gn[i].edges(data = True): | ||||
| @@ -427,12 +427,12 @@ def _wl_spkernel_do(Gn, node_label, edge_label, height): | |||||
| def _wl_edgekernel_do(Gn, node_label, edge_label, height): | def _wl_edgekernel_do(Gn, node_label, edge_label, height): | ||||
| """Calculate Weisfeiler-Lehman edge kernels between graphs. | |||||
| """Compute Weisfeiler-Lehman edge kernels between graphs. | |||||
| Parameters | Parameters | ||||
| ---------- | ---------- | ||||
| Gn : List of NetworkX graph | Gn : List of NetworkX graph | ||||
| List of graphs between which the kernels are calculated. | |||||
| List of graphs between which the kernels are computed. | |||||
| node_label : string | node_label : string | ||||
| node attribute used as label. | node attribute used as label. | ||||
| edge_label : string | edge_label : string | ||||
| @@ -491,7 +491,7 @@ def _wl_edgekernel_do(Gn, node_label, edge_label, height): | |||||
| for node in G.nodes(data = True): | for node in G.nodes(data = True): | ||||
| node[1][node_label] = set_compressed[set_multisets[node[0]]] | node[1][node_label] = set_compressed[set_multisets[node[0]]] | ||||
| # calculate subtree kernel with h iterations and add it to the final kernel | |||||
| # Compute subtree kernel with h iterations and add it to the final kernel | |||||
| for i in range(0, len(Gn)): | for i in range(0, len(Gn)): | ||||
| for j in range(i, len(Gn)): | for j in range(i, len(Gn)): | ||||
| for e1 in Gn[i].edges(data = True): | for e1 in Gn[i].edges(data = True): | ||||
| @@ -504,12 +504,12 @@ def _wl_edgekernel_do(Gn, node_label, edge_label, height): | |||||
| def _wl_userkernel_do(Gn, node_label, edge_label, height, base_kernel): | def _wl_userkernel_do(Gn, node_label, edge_label, height, base_kernel): | ||||
| """Calculate Weisfeiler-Lehman kernels based on user-defined kernel between graphs. | |||||
| """Compute Weisfeiler-Lehman kernels based on user-defined kernel between graphs. | |||||
| Parameters | Parameters | ||||
| ---------- | ---------- | ||||
| Gn : List of NetworkX graph | Gn : List of NetworkX graph | ||||
| List of graphs between which the kernels are calculated. | |||||
| List of graphs between which the kernels are computed. | |||||
| node_label : string | node_label : string | ||||
| node attribute used as label. | node attribute used as label. | ||||
| edge_label : string | edge_label : string | ||||
| @@ -564,7 +564,7 @@ def _wl_userkernel_do(Gn, node_label, edge_label, height, base_kernel): | |||||
| for node in G.nodes(data = True): | for node in G.nodes(data = True): | ||||
| node[1][node_label] = set_compressed[set_multisets[node[0]]] | node[1][node_label] = set_compressed[set_multisets[node[0]]] | ||||
| # calculate kernel with h iterations and add it to the final kernel | |||||
| # Compute kernel with h iterations and add it to the final kernel | |||||
| Kmatrix += base_kernel(Gn, node_label, edge_label) | Kmatrix += base_kernel(Gn, node_label, edge_label) | ||||
| return Kmatrix | return Kmatrix | ||||