gklearn

gklearn

This package contains 4 sub packages :

• c_ext : binders to C++ code

• ged : allows to compute graph edit distance between networkX graphs

• kernels : computation of graph kernels, ie graph similarity measure compatible with SVM

• notebooks : examples of code using this library

• utils : Diverse computation on graphs

• gklearn.kernels
  • gklearn.kernels.commonWalkKernel
    • commonwalkkernel()
    • find_all_walks()
    • find_all_walks_until_length()
    • find_walks()
    • wrapper_cw_exp()
    • wrapper_cw_geo()
  • gklearn.kernels.marginalizedKernel
    • marginalizedkernel()
    • wrapper_marg_do()
    • wrapper_untotter()
  • gklearn.kernels.randomWalkKernel
    • computeVK()
    • computeW()
    • filterGramMatrix()
    • func_fp()
    • getLabels()
    • randomwalkkernel()
    • wrapper_cg_labeled_do()
    • wrapper_cg_unlabled_do()
    • wrapper_fp_labeled_do()
    • wrapper_sd_do()
    • wrapper_se_do()
  • gklearn.kernels.spKernel
    • spkernel()
    • spkernel_do()
    • wrapper_getSPGraph()
    • wrapper_sp_do()
  • gklearn.kernels.structuralspKernel
    • getAllEdgeKernels()
    • getAllNodeKernels()
    • get_shortest_paths()
    • get_sps_as_trie()
    • ssp_do_trie()
    • structuralspkernel()
    • structuralspkernel_do()
    • traverseBothTriee()
    • traverseBothTriem()
    • traverseBothTrieu()
    • traverseBothTriev()
    • traverseTrie2e()
    • traverseTrie2m()
    • traverseTrie2u()
    • traverseTrie2v()
    • wrapper_getSP_naive()
    • wrapper_getSP_trie()
    • wrapper_ssp_do()
    • wrapper_ssp_do_trie()
  • gklearn.kernels.treeletKernel
    • find_all_paths()
    • find_paths()
    • get_canonkeys()
    • treeletkernel()
    • wrapper_get_canonkeys()
    • wrapper_treeletkernel_do()
  • gklearn.kernels.untilHPathKernel
    • find_all_path_as_trie()
    • find_all_paths_until_length()
    • paths2labelseqs()
    • untilhpathkernel()
    • wrapper_find_all_path_as_trie()
    • wrapper_find_all_paths_until_length()
    • wrapper_uhpath_do_kernelless()
    • wrapper_uhpath_do_naive()
    • wrapper_uhpath_do_trie()
  • gklearn.kernels.weisfeilerLehmanKernel
    • compute_kernel_matrix()
    • compute_subtree_kernel()
    • weisfeilerlehmankernel()
    • wl_iteration()
    • wrapper_compute_subtree_kernel()
    • wrapper_wl_iteration()
• gklearn.utils
  • gklearn.utils.graphdataset
    • get_dataset_attributes()
    • load_predefined_dataset()
  • gklearn.utils.graphfiles
    • loadCT()
    • loadDataset()
    • loadFromDS()
    • loadFromXML()
    • loadGXL()
    • loadMAT()
    • loadSDF()
    • loadTXT()
    • saveDataset()
    • saveGXL()
  • gklearn.utils.kernels
    • chi2_kernel()
    • cosine_kernel()
    • delta_kernel()
    • deltakernel()
    • exponential_kernel()
    • gaussian_kernel()
    • gaussiankernel()
    • highest_polynomial_kernel()
    • intersection_kernel()
    • inverse_multiquadratic_kernel()
    • kernelproduct()
    • kernelsum()
    • kronecker_delta_kernel()
    • laplacian_kernel()
    • linear_kernel()
    • linearkernel()
    • multiquadratic_kernel()
    • polynomial_kernel()
    • polynomialkernel()
    • sigmoid_kernel()
    • tanimoto_kernel()
  • gklearn.utils.model_selection_precomputed
    • compute_gram_matrices()
    • model_selection_for_precomputed_kernel()
    • parallel_trial_do()
    • printResultsInTable()
    • read_gram_matrices_from_file()
    • trial_do()
  • gklearn.utils.parallel
    • parallel_ged_mat()
    • parallel_gm()
    • parallel_me()
  • gklearn.utils.trie
    • Trie
      • Trie.deleteWord()
      • Trie.getNode()
      • Trie.insertWord()
      • Trie.load_from_json()
      • Trie.load_from_pickle()
      • Trie.save_to_json()
      • Trie.save_to_pickle()
      • Trie.searchWord()
      • Trie.searchWordPrefix()
      • Trie.to_json()
  • gklearn.utils.utils
    • SpecialLabel
      • SpecialLabel.DUMMY
    • check_json_serializable()
    • compute_distance_matrix()
    • compute_gram_matrices_by_class()
    • compute_vertex_kernels()
    • direct_product()
    • direct_product_graph()
    • dummy_edge()
    • dummy_node()
    • find_all_paths()
    • find_paths()
    • floydTransformation()
    • getSPGraph()
    • getSPLengths()
    • get_edge_labels()
    • get_graph_kernel_by_name()
    • get_mlti_dim_edge_attrs()
    • get_mlti_dim_node_attrs()
    • get_node_labels()
    • get_shortest_paths()
    • get_sp_graph()
    • graph_deepcopy()
    • graph_isIdentical()
    • is_basic_python_type()
    • normalize_gram_matrix()
    • nx_permute_nodes()
    • undefined_node()
    • untotterTransformation()