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