| @@ -37,15 +37,15 @@ def structuralspkernel(*args, | |||
| n_jobs=None, | |||
| chunksize=None, | |||
| verbose=True): | |||
| """Calculate mean average structural shortest path kernels between graphs. | |||
| """Compute mean average structural shortest path kernels between graphs. | |||
| Parameters | |||
| ---------- | |||
| 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 | |||
| Two graphs between which the kernel is calculated. | |||
| Two graphs between which the kernel is computed. | |||
| node_label : string | |||
| Node attribute used as label. The default node label is atom. | |||
| @@ -215,7 +215,7 @@ def structuralspkernel(*args, | |||
| from itertools import combinations_with_replacement | |||
| itr = combinations_with_replacement(range(0, len(Gn)), 2) | |||
| if verbose: | |||
| iterator = tqdm(itr, desc='calculating kernels', file=sys.stdout) | |||
| iterator = tqdm(itr, desc='Computing kernels', file=sys.stdout) | |||
| else: | |||
| iterator = itr | |||
| if compute_method == 'trie': | |||
| @@ -241,7 +241,7 @@ def structuralspkernel(*args, | |||
| # combinations_with_replacement(splist, 2), | |||
| # combinations_with_replacement(range(0, len(Gn)), 2)) | |||
| # for i, j, kernel in tqdm( | |||
| # pool.map(do_partial, itr), desc='calculating kernels', | |||
| # pool.map(do_partial, itr), desc='Computing kernels', | |||
| # file=sys.stdout): | |||
| # Kmatrix[i][j] = kernel | |||
| # Kmatrix[j][i] = kernel | |||
| @@ -263,7 +263,7 @@ def structuralspkernel(*args, | |||
| # with closing(Pool(n_jobs)) as pool: | |||
| # for i, j, kernel in tqdm( | |||
| # pool.imap_unordered(do_partial, itr, 1000), | |||
| # desc='calculating kernels', | |||
| # desc='Computing kernels', | |||
| # file=sys.stdout): | |||
| # Kmatrix[i][j] = kernel | |||
| # Kmatrix[j][i] = kernel | |||
| @@ -335,7 +335,7 @@ def structuralspkernel_do(g1, g2, spl1, spl2, ds_attrs, node_label, edge_label, | |||
| if len(p1) == len(p2): | |||
| kernel += 1 | |||
| try: | |||
| kernel = kernel / (len(spl1) * len(spl2)) # calculate mean average | |||
| kernel = kernel / (len(spl1) * len(spl2)) # Compute mean average | |||
| except ZeroDivisionError: | |||
| print(spl1, spl2) | |||
| print(g1.nodes(data=True)) | |||
| @@ -429,7 +429,7 @@ def ssp_do_trie(g1, g2, trie1, trie2, ds_attrs, node_label, edge_label, | |||
| # # compute graph kernels | |||
| # traverseBothTrie(trie1[0].root, trie2[0], kernel) | |||
| # | |||
| # kernel = kernel[0] / (trie1[1] * trie2[1]) # calculate mean average | |||
| # kernel = kernel[0] / (trie1[1] * trie2[1]) # Compute mean average | |||
| # # traverse all paths in graph1. Deep-first search is applied. | |||
| # def traverseBothTrie(root, trie2, kernel, vk_dict, ek_dict, pcurrent=[]): | |||
| @@ -485,7 +485,7 @@ def ssp_do_trie(g1, g2, trie1, trie2, ds_attrs, node_label, edge_label, | |||
| else: | |||
| traverseBothTrieu(trie1[0].root, trie2[0], kernel, vk_dict, ek_dict) | |||
| kernel = kernel[0] / (trie1[1] * trie2[1]) # calculate mean average | |||
| kernel = kernel[0] / (trie1[1] * trie2[1]) # Compute mean average | |||
| return kernel | |||
| @@ -781,9 +781,9 @@ def get_shortest_paths(G, weight, directed): | |||
| Parameters | |||
| ---------- | |||
| G : NetworkX graphs | |||
| The graphs whose paths are calculated. | |||
| The graphs whose paths are computed. | |||
| weight : string/None | |||
| edge attribute used as weight to calculate the shortest path. | |||
| edge attribute used as weight to compute the shortest path. | |||
| directed: boolean | |||
| Whether graph is directed. | |||
| @@ -822,9 +822,9 @@ def get_sps_as_trie(G, weight, directed): | |||
| Parameters | |||
| ---------- | |||
| G : NetworkX graphs | |||
| The graphs whose paths are calculated. | |||
| The graphs whose paths are computed. | |||
| weight : string/None | |||
| edge attribute used as weight to calculate the shortest path. | |||
| edge attribute used as weight to compute the shortest path. | |||
| directed: boolean | |||
| Whether graph is directed. | |||