import functools from libs import * from pygraph.kernels.spKernel import spkernel from pygraph.utils.kernels import deltakernel, kernelsum from sklearn.metrics.pairwise import rbf_kernel # dslist = [ # {'name': 'Acyclic', 'dataset': '../datasets/acyclic/dataset_bps.ds', 'task': 'regression'}, # node symb # # {'name': 'COIL-DEL', 'dataset': '../datasets/COIL-DEL/COIL-DEL_A.txt'}, # edge symb, node nsymb # {'name': 'PAH', 'dataset': '../datasets/PAH/dataset.ds',}, # unlabeled # {'name': 'MAO', 'dataset': '../datasets/MAO/dataset.ds',}, # node/edge symb # {'name': 'MUTAG', 'dataset': '../datasets/MUTAG/MUTAG.mat', # 'extra_params': {'am_sp_al_nl_el': [0, 0, 3, 1, 2]}}, # node/edge symb # {'name': 'Alkane', 'dataset': '../datasets/Alkane/dataset.ds', 'task': 'regression', # 'dataset_y': '../datasets/Alkane/dataset_boiling_point_names.txt',}, # contains single node graph, node symb # # {'name': 'BZR', 'dataset': '../datasets/BZR_txt/BZR_A_sparse.txt'}, # node symb/nsymb # # {'name': 'COX2', 'dataset': '../datasets/COX2_txt/COX2_A_sparse.txt'}, # node symb/nsymb # {'name': 'Mutagenicity', 'dataset': '../datasets/Mutagenicity/Mutagenicity_A.txt'}, # node/edge symb # {'name': 'ENZYMES', 'dataset': '../datasets/ENZYMES_txt/ENZYMES_A_sparse.txt'}, # node symb/nsymb # # {'name': 'Fingerprint', 'dataset': '../datasets/Fingerprint/Fingerprint_A.txt'}, # {'name': 'Letter-med', 'dataset': '../datasets/Letter-med/Letter-med_A.txt'}, # # {'name': 'DHFR', 'dataset': '../datasets/DHFR_txt/DHFR_A_sparse.txt'}, # node symb/nsymb # # {'name': 'SYNTHETIC', 'dataset': '../datasets/SYNTHETIC_txt/SYNTHETIC_A_sparse.txt'}, # node symb/nsymb # # {'name': 'MSRC9', 'dataset': '../datasets/MSRC_9_txt/MSRC_9_A.txt'}, # node symb # # {'name': 'MSRC21', 'dataset': '../datasets/MSRC_21_txt/MSRC_21_A.txt'}, # node symb # # {'name': 'FIRSTMM_DB', 'dataset': '../datasets/FIRSTMM_DB/FIRSTMM_DB_A.txt'}, # node symb/nsymb ,edge nsymb # # {'name': 'PROTEINS', 'dataset': '../datasets/PROTEINS_txt/PROTEINS_A_sparse.txt'}, # node symb/nsymb # # {'name': 'PROTEINS_full', 'dataset': '../datasets/PROTEINS_full_txt/PROTEINS_full_A_sparse.txt'}, # node symb/nsymb # {'name': 'D&D', 'dataset': '../datasets/D&D/DD.mat', # 'extra_params': {'am_sp_al_nl_el': [0, 1, 2, 1, -1]}}, # node symb # # {'name': 'AIDS', 'dataset': '../datasets/AIDS/AIDS_A.txt'}, # node symb/nsymb, edge symb # # {'name': 'NCI1', 'dataset': '../datasets/NCI1/NCI1.mat', # # 'extra_params': {'am_sp_al_nl_el': [1, 1, 2, 0, -1]}}, # node symb # # {'name': 'NCI109', 'dataset': '../datasets/NCI109/NCI109.mat', # # 'extra_params': {'am_sp_al_nl_el': [1, 1, 2, 0, -1]}}, # node symb # # {'name': 'NCI-HIV', 'dataset': '../datasets/NCI-HIV/AIDO99SD.sdf', # # 'dataset_y': '../datasets/NCI-HIV/aids_conc_may04.txt',}, # node/edge symb # # # not working below # # {'name': 'PTC_FM', 'dataset': '../datasets/PTC/Train/FM.ds',}, # # {'name': 'PTC_FR', 'dataset': '../datasets/PTC/Train/FR.ds',}, # # {'name': 'PTC_MM', 'dataset': '../datasets/PTC/Train/MM.ds',}, # # {'name': 'PTC_MR', 'dataset': '../datasets/PTC/Train/MR.ds',}, # ] import ast ds = ast.literal_eval(sys.argv[1]) estimator = spkernel mixkernel = functools.partial(kernelsum, deltakernel, rbf_kernel) param_grid_precomputed = { 'node_kernels': [{ 'symb': deltakernel, 'nsymb': rbf_kernel, 'mix': mixkernel }] } param_grid = [{ 'C': np.logspace(-10, 10, num=41, base=10) }, { 'alpha': np.logspace(-10, 10, num=41, base=10) }] print() print(ds['name']) model_selection_for_precomputed_kernel( ds['dataset'], estimator, param_grid_precomputed, (param_grid[1] if ('task' in ds and ds['task'] == 'regression') else param_grid[0]), (ds['task'] if 'task' in ds else 'classification'), NUM_TRIALS=30, datafile_y=(ds['dataset_y'] if 'dataset_y' in ds else None), extra_params=(ds['extra_params'] if 'extra_params' in ds else None), ds_name=ds['name']) # %lprun -f spkernel \ # model_selection_for_precomputed_kernel( \ # ds['dataset'], estimator, param_grid_precomputed, \ # (param_grid[1] if ('task' in ds and ds['task'] == 'regression') else param_grid[0]), \ # (ds['task'] if 'task' in ds else 'classification'), NUM_TRIALS=30, \ # datafile_y=(ds['dataset_y'] if 'dataset_y' in ds else None), \ # extra_params=(ds['extra_params'] if 'extra_params' in ds else None)) print() # import functools # from libs import * # from pygraph.kernels.spKernel import spkernel # from pygraph.utils.kernels import deltakernel, kernelsum # from sklearn.metrics.pairwise import rbf_kernel # dslist = [ # {'name': 'Acyclic', 'dataset': '../datasets/acyclic/dataset_bps.ds', 'task': 'regression'}, # node symb # # {'name': 'COIL-DEL', 'dataset': '../datasets/COIL-DEL/COIL-DEL_A.txt'}, # edge symb, node nsymb # # {'name': 'PAH', 'dataset': '../datasets/PAH/dataset.ds',}, # unlabeled # # {'name': 'MAO', 'dataset': '../datasets/MAO/dataset.ds',}, # node/edge symb # # {'name': 'MUTAG', 'dataset': '../datasets/MUTAG/MUTAG.mat', # # 'extra_params': {'am_sp_al_nl_el': [0, 0, 3, 1, 2]}}, # node/edge symb # # {'name': 'Alkane', 'dataset': '../datasets/Alkane/dataset.ds', 'task': 'regression', # # 'dataset_y': '../datasets/Alkane/dataset_boiling_point_names.txt',}, # contains single node graph, node symb # # {'name': 'BZR', 'dataset': '../datasets/BZR_txt/BZR_A_sparse.txt'}, # node symb/nsymb # # {'name': 'COX2', 'dataset': '../datasets/COX2_txt/COX2_A_sparse.txt'}, # node symb/nsymb # # {'name': 'Mutagenicity', 'dataset': '../datasets/Mutagenicity/Mutagenicity_A.txt'}, # node/edge symb # # {'name': 'ENZYMES', 'dataset': '../datasets/ENZYMES_txt/ENZYMES_A_sparse.txt'}, # node symb/nsymb # # {'name': 'Fingerprint', 'dataset': '../datasets/Fingerprint/Fingerprint_A.txt'}, # # {'name': 'Letter-med', 'dataset': '../datasets/Letter-med/Letter-med_A.txt'}, # # {'name': 'DHFR', 'dataset': '../datasets/DHFR_txt/DHFR_A_sparse.txt'}, # node symb/nsymb # # {'name': 'SYNTHETIC', 'dataset': '../datasets/SYNTHETIC_txt/SYNTHETIC_A_sparse.txt'}, # node symb/nsymb # # {'name': 'MSRC9', 'dataset': '../datasets/MSRC_9_txt/MSRC_9_A.txt'}, # node symb # # {'name': 'MSRC21', 'dataset': '../datasets/MSRC_21_txt/MSRC_21_A.txt'}, # node symb # # {'name': 'FIRSTMM_DB', 'dataset': '../datasets/FIRSTMM_DB/FIRSTMM_DB_A.txt'}, # node symb/nsymb ,edge nsymb # # {'name': 'PROTEINS', 'dataset': '../datasets/PROTEINS_txt/PROTEINS_A_sparse.txt'}, # node symb/nsymb # # {'name': 'PROTEINS_full', 'dataset': '../datasets/PROTEINS_full_txt/PROTEINS_full_A_sparse.txt'}, # node symb/nsymb # # {'name': 'D&D', 'dataset': '../datasets/D&D/DD.mat', # # 'extra_params': {'am_sp_al_nl_el': [0, 1, 2, 1, -1]}}, # node symb # # {'name': 'AIDS', 'dataset': '../datasets/AIDS/AIDS_A.txt'}, # node symb/nsymb, edge symb # # {'name': 'NCI1', 'dataset': '../datasets/NCI1/NCI1.mat', # # 'extra_params': {'am_sp_al_nl_el': [1, 1, 2, 0, -1]}}, # node symb # # {'name': 'NCI109', 'dataset': '../datasets/NCI109/NCI109.mat', # # 'extra_params': {'am_sp_al_nl_el': [1, 1, 2, 0, -1]}}, # node symb # # {'name': 'NCI-HIV', 'dataset': '../datasets/NCI-HIV/AIDO99SD.sdf', # # 'dataset_y': '../datasets/NCI-HIV/aids_conc_may04.txt',}, # node/edge symb # # # not working below # # {'name': 'PTC_FM', 'dataset': '../datasets/PTC/Train/FM.ds',}, # # {'name': 'PTC_FR', 'dataset': '../datasets/PTC/Train/FR.ds',}, # # {'name': 'PTC_MM', 'dataset': '../datasets/PTC/Train/MM.ds',}, # # {'name': 'PTC_MR', 'dataset': '../datasets/PTC/Train/MR.ds',}, # ] # estimator = spkernel # mixkernel = functools.partial(kernelsum, deltakernel, rbf_kernel) # param_grid_precomputed = {'node_kernels': [{'symb': deltakernel, 'nsymb': rbf_kernel, 'mix': mixkernel}]} # param_grid = [{'C': np.logspace(-10, 10, num = 41, base = 10)}, # {'alpha': np.logspace(-10, 10, num = 41, base = 10)}] # for ds in dslist: # print() # print(ds['name']) # model_selection_for_precomputed_kernel( # ds['dataset'], estimator, param_grid_precomputed, # (param_grid[1] if ('task' in ds and ds['task'] == 'regression') else param_grid[0]), # (ds['task'] if 'task' in ds else 'classification'), NUM_TRIALS=30, # datafile_y=(ds['dataset_y'] if 'dataset_y' in ds else None), # extra_params=(ds['extra_params'] if 'extra_params' in ds else None), # ds_name=ds['name']) # # %lprun -f spkernel \ # # model_selection_for_precomputed_kernel( \ # # ds['dataset'], estimator, param_grid_precomputed, \ # # (param_grid[1] if ('task' in ds and ds['task'] == 'regression') else param_grid[0]), \ # # (ds['task'] if 'task' in ds else 'classification'), NUM_TRIALS=30, \ # # datafile_y=(ds['dataset_y'] if 'dataset_y' in ds else None), \ # # extra_params=(ds['extra_params'] if 'extra_params' in ds else None)) # print()