#!/usr/bin/env python3 # -*- coding: utf-8 -*- """ Created on Thu Nov 22 17:02:28 2018 @author: ljia """ import functools from libs import * import multiprocessing from pygraph.kernels.randomWalkKernel import randomwalkkernel from pygraph.utils.kernels import deltakernel, gaussiankernel, kernelproduct import numpy as np dslist = [ {'name': 'Acyclic', 'dataset': '../datasets/acyclic/dataset_bps.ds', 'task': 'regression'}, # node 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': 'MAO', 'dataset': '../datasets/MAO/dataset.ds', }, # node/edge symb {'name': 'PAH', 'dataset': '../datasets/PAH/dataset.ds', }, # unlabeled {'name': 'MUTAG', 'dataset': '../datasets/MUTAG/MUTAG.mat', 'extra_params': {'am_sp_al_nl_el': [0, 0, 3, 1, 2]}}, # node/edge symb {'name': 'Letter-med', 'dataset': '../datasets/Letter-med/Letter-med_A.txt'}, # node nsymb {'name': 'ENZYMES', 'dataset': '../datasets/ENZYMES_txt/ENZYMES_A_sparse.txt'}, # node symb/nsymb # {'name': 'Mutagenicity', 'dataset': '../datasets/Mutagenicity/Mutagenicity_A.txt'}, # # node/edge symb # {'name': 'D&D', 'dataset': '../datasets/D&D/DD.mat', # 'extra_params': {'am_sp_al_nl_el': [0, 1, 2, 1, -1]}}, # node symb # {'name': 'COIL-DEL', 'dataset': '../datasets/COIL-DEL/COIL-DEL_A.txt'}, # edge symb, node nsymb # # # {'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': 'Fingerprint', 'dataset': '../datasets/Fingerprint/Fingerprint_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, missing values # {'name': 'MSRC21', 'dataset': '../datasets/MSRC_21_txt/MSRC_21_A.txt'}, # node symb, missing values # # {'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': '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 = randomwalkkernel 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']) for compute_method in ['sylvester', 'conjugate', 'fp', 'spectral']: if compute_method == 'sylvester': param_grid_precomputed = {'compute_method': ['sylvester'], # 'weight': np.linspace(0.01, 0.10, 10)} 'weight': np.logspace(-1, -10, num=10, base=10)} elif compute_method == 'conjugate': mixkernel = functools.partial(kernelproduct, deltakernel, gaussiankernel) param_grid_precomputed = {'compute_method': ['conjugate'], 'node_kernels': [{'symb': deltakernel, 'nsymb': gaussiankernel, 'mix': mixkernel}], 'edge_kernels': [{'symb': deltakernel, 'nsymb': gaussiankernel, 'mix': mixkernel}], 'weight': np.logspace(-1, -10, num=10, base=10)} elif compute_method == 'fp': mixkernel = functools.partial(kernelproduct, deltakernel, gaussiankernel) param_grid_precomputed = {'compute_method': ['fp'], 'node_kernels': [{'symb': deltakernel, 'nsymb': gaussiankernel, 'mix': mixkernel}], 'edge_kernels': [{'symb': deltakernel, 'nsymb': gaussiankernel, 'mix': mixkernel}], 'weight': np.logspace(-3, -10, num=8, base=10)} elif compute_method == 'spectral': param_grid_precomputed = {'compute_method': ['spectral'], 'weight': np.logspace(-1, -10, num=10, base=10), 'sub_kernel': ['geo', 'exp']} 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'], n_jobs=multiprocessing.cpu_count(), read_gm_from_file=False) print()