| @@ -24,7 +24,7 @@ from gklearn.kernels import GraphKernel | |||||
| from gklearn.utils import Trie | from gklearn.utils import Trie | ||||
| class PathUpToH(GraphKernel): # @todo: add function for k_func == None | |||||
| class PathUpToH(GraphKernel): # @todo: add function for k_func is None | |||||
| def __init__(self, **kwargs): | def __init__(self, **kwargs): | ||||
| GraphKernel.__init__(self) | GraphKernel.__init__(self) | ||||
| @@ -43,7 +43,7 @@ class PathUpToH(GraphKernel): # @todo: add function for k_func == None | |||||
| itr_kernel = combinations_with_replacement(range(0, len(self._graphs)), 2) | itr_kernel = combinations_with_replacement(range(0, len(self._graphs)), 2) | ||||
| if self._verbose >= 2: | if self._verbose >= 2: | ||||
| iterator_ps = tqdm(range(0, len(self._graphs)), desc='getting paths', file=sys.stdout) | iterator_ps = tqdm(range(0, len(self._graphs)), desc='getting paths', file=sys.stdout) | ||||
| iterator_kernel = tqdm(itr_kernel, desc='calculating kernels', file=sys.stdout) | |||||
| iterator_kernel = tqdm(itr_kernel, desc='Computing kernels', file=sys.stdout) | |||||
| else: | else: | ||||
| iterator_ps = range(0, len(self._graphs)) | iterator_ps = range(0, len(self._graphs)) | ||||
| iterator_kernel = itr_kernel | iterator_kernel = itr_kernel | ||||
| @@ -69,7 +69,7 @@ class PathUpToH(GraphKernel): # @todo: add function for k_func == None | |||||
| def _compute_gm_imap_unordered(self): | def _compute_gm_imap_unordered(self): | ||||
| self.__add_dummy_labels(self._graphs) | self.__add_dummy_labels(self._graphs) | ||||
| # get all paths of all graphs before calculating kernels to save time, | |||||
| # get all paths of all graphs before computing kernels to save time, | |||||
| # but this may cost a lot of memory for large datasets. | # but this may cost a lot of memory for large datasets. | ||||
| pool = Pool(self._n_jobs) | pool = Pool(self._n_jobs) | ||||
| itr = zip(self._graphs, range(0, len(self._graphs))) | itr = zip(self._graphs, range(0, len(self._graphs))) | ||||
| @@ -123,7 +123,7 @@ class PathUpToH(GraphKernel): # @todo: add function for k_func == None | |||||
| if self._verbose >= 2: | if self._verbose >= 2: | ||||
| iterator_ps = tqdm(g_list, desc='getting paths', file=sys.stdout) | iterator_ps = tqdm(g_list, desc='getting paths', file=sys.stdout) | ||||
| iterator_kernel = tqdm(range(len(g_list)), desc='calculating kernels', file=sys.stdout) | |||||
| iterator_kernel = tqdm(range(len(g_list)), desc='Computing kernels', file=sys.stdout) | |||||
| else: | else: | ||||
| iterator_ps = g_list | iterator_ps = g_list | ||||
| iterator_kernel = range(len(g_list)) | iterator_kernel = range(len(g_list)) | ||||
| @@ -149,7 +149,7 @@ class PathUpToH(GraphKernel): # @todo: add function for k_func == None | |||||
| def _compute_kernel_list_imap_unordered(self, g1, g_list): | def _compute_kernel_list_imap_unordered(self, g1, g_list): | ||||
| self.__add_dummy_labels(g_list + [g1]) | self.__add_dummy_labels(g_list + [g1]) | ||||
| # get all paths of all graphs before calculating kernels to save time, | |||||
| # get all paths of all graphs before computing kernels to save time, | |||||
| # but this may cost a lot of memory for large datasets. | # but this may cost a lot of memory for large datasets. | ||||
| pool = Pool(self._n_jobs) | pool = Pool(self._n_jobs) | ||||
| itr = zip(g_list, range(0, len(g_list))) | itr = zip(g_list, range(0, len(g_list))) | ||||
| @@ -190,7 +190,7 @@ class PathUpToH(GraphKernel): # @todo: add function for k_func == None | |||||
| itr = range(len(g_list)) | itr = range(len(g_list)) | ||||
| len_itr = len(g_list) | len_itr = len(g_list) | ||||
| parallel_me(do_fun, func_assign, kernel_list, itr, len_itr=len_itr, | parallel_me(do_fun, func_assign, kernel_list, itr, len_itr=len_itr, | ||||
| init_worker=init_worker, glbv=(paths_g1, paths_g_list), method='imap_unordered', n_jobs=self._n_jobs, itr_desc='calculating kernels', verbose=self._verbose) | |||||
| init_worker=init_worker, glbv=(paths_g1, paths_g_list), method='imap_unordered', n_jobs=self._n_jobs, itr_desc='Computing kernels', verbose=self._verbose) | |||||
| return kernel_list | return kernel_list | ||||
| @@ -218,7 +218,7 @@ class PathUpToH(GraphKernel): # @todo: add function for k_func == None | |||||
| def __kernel_do_trie(self, trie1, trie2): | def __kernel_do_trie(self, trie1, trie2): | ||||
| """Calculate path graph kernels up to depth d between 2 graphs using trie. | |||||
| """Compute path graph kernels up to depth d between 2 graphs using trie. | |||||
| Parameters | Parameters | ||||
| ---------- | ---------- | ||||
| @@ -335,7 +335,7 @@ class PathUpToH(GraphKernel): # @todo: add function for k_func == None | |||||
| def __kernel_do_naive(self, paths1, paths2): | def __kernel_do_naive(self, paths1, paths2): | ||||
| """Calculate path graph kernels up to depth d between 2 graphs naively. | |||||
| """Compute path graph kernels up to depth d between 2 graphs naively. | |||||
| Parameters | Parameters | ||||
| ---------- | ---------- | ||||