| @@ -30,15 +30,15 @@ def commonwalkkernel(*args, | |||
| n_jobs=None, | |||
| chunksize=None, | |||
| verbose=True): | |||
| """Calculate common walk graph kernels between graphs. | |||
| """Compute common walk graph 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 symbolic label. The default node label is 'atom'. | |||
| edge_label : string | |||
| @@ -133,7 +133,7 @@ def commonwalkkernel(*args, | |||
| # | |||
| # for i, j, kernel in tqdm( | |||
| # pool.imap_unordered(do_partial, itr, chunksize), | |||
| # desc='calculating kernels', | |||
| # desc='computing kernels', | |||
| # file=sys.stdout): | |||
| # Kmatrix[i][j] = kernel | |||
| # Kmatrix[j][i] = kernel | |||
| @@ -145,14 +145,14 @@ def commonwalkkernel(*args, | |||
| # # direct product graph method - exponential | |||
| # itr = combinations_with_replacement(range(0, len(Gn)), 2) | |||
| # if compute_method == 'exp': | |||
| # for i, j in tqdm(itr, desc='calculating kernels', file=sys.stdout): | |||
| # for i, j in tqdm(itr, desc='Computing kernels', file=sys.stdout): | |||
| # Kmatrix[i][j] = _commonwalkkernel_exp(Gn[i], Gn[j], node_label, | |||
| # edge_label, weight) | |||
| # Kmatrix[j][i] = Kmatrix[i][j] | |||
| # | |||
| # # direct product graph method - geometric | |||
| # elif compute_method == 'geo': | |||
| # for i, j in tqdm(itr, desc='calculating kernels', file=sys.stdout): | |||
| # for i, j in tqdm(itr, desc='Computing kernels', file=sys.stdout): | |||
| # Kmatrix[i][j] = _commonwalkkernel_geo(Gn[i], Gn[j], node_label, | |||
| # edge_label, weight) | |||
| # Kmatrix[j][i] = Kmatrix[i][j] | |||
| @@ -161,7 +161,7 @@ def commonwalkkernel(*args, | |||
| # # search all paths use brute force. | |||
| # elif compute_method == 'brute': | |||
| # n = int(n) | |||
| # # get all paths of all graphs before calculating kernels to save time, but this may cost a lot of memory for large dataset. | |||
| # # get all paths of all graphs before computing kernels to save time, but this may cost a lot of memory for large dataset. | |||
| # all_walks = [ | |||
| # find_all_walks_until_length(Gn[i], n, node_label, edge_label) | |||
| # for i in range(0, len(Gn)) | |||
| @@ -185,13 +185,13 @@ def commonwalkkernel(*args, | |||
| def _commonwalkkernel_exp(g1, g2, node_label, edge_label, beta): | |||
| """Calculate walk graph kernels up to n between 2 graphs using exponential | |||
| """Compute walk graph kernels up to n between 2 graphs using exponential | |||
| series. | |||
| Parameters | |||
| ---------- | |||
| 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 attribute used as label. | |||
| edge_label : string | |||
| @@ -259,13 +259,13 @@ def wrapper_cw_exp(node_label, edge_label, beta, itr): | |||
| def _commonwalkkernel_geo(g1, g2, node_label, edge_label, gamma): | |||
| """Calculate common walk graph kernels up to n between 2 graphs using | |||
| """Compute common walk graph kernels up to n between 2 graphs using | |||
| geometric series. | |||
| Parameters | |||
| ---------- | |||
| 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 attribute used as label. | |||
| edge_label : string | |||
| @@ -304,7 +304,7 @@ def _commonwalkkernel_brute(walks1, | |||
| node_label='atom', | |||
| edge_label='bond_type', | |||
| labeled=True): | |||
| """Calculate walk graph kernels up to n between 2 graphs. | |||
| """Compute walk graph kernels up to n between 2 graphs. | |||
| Parameters | |||
| ---------- | |||