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