public static void Main() { modshogun.init_shogun_with_defaults(); int order = 3; int gap = 0; bool reverse = false; bool use_sign = false; String[] fm_train_dna = Load.load_dna("../data/fm_train_dna.dat"); String[] fm_test_dna = Load.load_dna("../data/fm_test_dna.dat"); StringCharFeatures charfeat = new StringCharFeatures(EAlphabet.DNA); charfeat.set_features(fm_train_dna); StringUlongFeatures feats_train = new StringUlongFeatures(charfeat.get_alphabet()); feats_train.obtain_from_char(charfeat, order-1, order, gap, reverse); SortUlongString preproc = new SortUlongString(); preproc.init(feats_train); feats_train.add_preprocessor(preproc); feats_train.apply_preprocessor(); StringCharFeatures charfeat_test = new StringCharFeatures(EAlphabet.DNA); charfeat_test.set_features(fm_test_dna); StringUlongFeatures feats_test = new StringUlongFeatures(charfeat.get_alphabet()); feats_test.obtain_from_char(charfeat_test, order-1, order, gap, reverse); feats_test.add_preprocessor(preproc); feats_test.apply_preprocessor(); CommUlongStringKernel kernel = new CommUlongStringKernel(feats_train, feats_train, use_sign); double[,] km_train = kernel.get_kernel_matrix(); kernel.init(feats_train, feats_test); double[,] km_test = kernel.get_kernel_matrix(); modshogun.exit_shogun(); }
public static void Main() { modshogun.init_shogun_with_defaults(); int order = 3; int gap = 0; bool reverse = false; bool use_sign = false; String[] fm_train_dna = Load.load_dna("../data/fm_train_dna.dat"); String[] fm_test_dna = Load.load_dna("../data/fm_test_dna.dat"); double[] fm_test_real = Load.load_labels("../data/fm_test_real.dat"); StringCharFeatures charfeat = new StringCharFeatures(EAlphabet.DNA); charfeat.set_features(fm_train_dna); StringWordFeatures feats_train = new StringWordFeatures(charfeat.get_alphabet()); feats_train.obtain_from_char(charfeat, order-1, order, gap, reverse); SortWordString preproc = new SortWordString(); preproc.init(feats_train); feats_train.add_preprocessor(preproc); feats_train.apply_preprocessor(); StringCharFeatures charfeat_test = new StringCharFeatures(EAlphabet.DNA); charfeat_test.set_features(fm_test_dna); StringWordFeatures feats_test = new StringWordFeatures(charfeat.get_alphabet()); feats_test.obtain_from_char(charfeat_test, order-1, order, gap, reverse); feats_test.add_preprocessor(preproc); feats_test.apply_preprocessor(); HammingWordDistance distance = new HammingWordDistance(feats_train, feats_train, use_sign); double[,] dm_train = distance.get_distance_matrix(); distance.init(feats_train, feats_test); double[,] dm_test = distance.get_distance_matrix(); }
static void Main(string[] argv) { modshogun.init_shogun_with_defaults(); int order = 3; int gap = 0; bool reverse = false; string[] fm_train_dna = Load.load_dna("../data/fm_train_dna.dat"); string[] fm_test_dna = Load.load_dna("../data/fm_test_dna.dat"); DoubleMatrix fm_test_real = Load.load_numbers("../data/fm_test_real.dat"); StringCharFeatures charfeat = new StringCharFeatures(DNA); charfeat.set_features(fm_train_dna); StringWordFeatures feats_train = new StringWordFeatures(charfeat.get_alphabet()); feats_train.obtain_from_char(charfeat, order-1, order, gap, reverse); SortWordString preproc = new SortWordString(); preproc.init(feats_train); feats_train.add_preprocessor(preproc); feats_train.apply_preprocessor(); StringCharFeatures charfeat_test = new StringCharFeatures(DNA); charfeat_test.set_features(fm_test_dna); StringWordFeatures feats_test = new StringWordFeatures(charfeat.get_alphabet()); feats_test.obtain_from_char(charfeat_test, order-1, order, gap, reverse); feats_test.add_preprocessor(preproc); feats_test.apply_preprocessor(); ManhattanWordDistance distance = new ManhattanWordDistance(feats_train, feats_train); DoubleMatrix dm_train = distance.get_distance_matrix(); distance.init(feats_train, feats_test); DoubleMatrix dm_test = distance.get_distance_matrix(); modshogun.exit_shogun(); }
public static void Main() { modshogun.init_shogun_with_defaults(); int order = 3; int gap = 0; bool reverse = false; String[] fm_train_dna = Load.load_dna("../data/fm_train_dna.dat"); String[] fm_test_dna = Load.load_dna("../data/fm_test_dna.dat"); double[,] fm_test_real = Load.load_numbers("../data/fm_test_real.dat"); StringCharFeatures charfeat = new StringCharFeatures(EAlphabet.DNA); charfeat.set_features(fm_train_dna); StringWordFeatures feats_train = new StringWordFeatures(charfeat.get_alphabet()); feats_train.obtain_from_char(charfeat, order - 1, order, gap, reverse); SortWordString preproc = new SortWordString(); preproc.init(feats_train); feats_train.add_preprocessor(preproc); feats_train.apply_preprocessor(); StringCharFeatures charfeat_test = new StringCharFeatures(EAlphabet.DNA); charfeat_test.set_features(fm_test_dna); StringWordFeatures feats_test = new StringWordFeatures(charfeat.get_alphabet()); feats_test.obtain_from_char(charfeat_test, order - 1, order, gap, reverse); feats_test.add_preprocessor(preproc); feats_test.apply_preprocessor(); ManhattanWordDistance distance = new ManhattanWordDistance(feats_train, feats_train); double[,] dm_train = distance.get_distance_matrix(); distance.init(feats_train, feats_test); double[,] dm_test = distance.get_distance_matrix(); foreach (double item in dm_train) { Console.Write(item); } foreach (double item in dm_test) { Console.Write(item); } modshogun.exit_shogun(); }
internal static ArrayList run(string[] strs) { modshogun.init_shogun_with_defaults(); StringCharFeatures f = new StringCharFeatures(strs, DNA); f.obtain_by_sliding_window(5,1); f.set_features(strs); DynamicIntArray positions = new DynamicIntArray(); positions.append_element(0); positions.append_element(6); positions.append_element(16); positions.append_element(25); //f.obtain_by_position_list(8,positions); ArrayList result = new ArrayList(); result.Add(f); modshogun.exit_shogun(); return result; }
public static void Main() { modshogun.init_shogun_with_defaults(); int order = 3; int gap = 0; bool reverse = false; bool use_sign = false; String[] fm_train_dna = Load.load_dna("../data/fm_train_dna.dat"); String[] fm_test_dna = Load.load_dna("../data/fm_test_dna.dat"); StringCharFeatures charfeat = new StringCharFeatures(EAlphabet.DNA); charfeat.set_features(fm_train_dna); StringUlongFeatures feats_train = new StringUlongFeatures(charfeat.get_alphabet()); feats_train.obtain_from_char(charfeat, order - 1, order, gap, reverse); SortUlongString preproc = new SortUlongString(); preproc.init(feats_train); feats_train.add_preprocessor(preproc); feats_train.apply_preprocessor(); StringCharFeatures charfeat_test = new StringCharFeatures(EAlphabet.DNA); charfeat_test.set_features(fm_test_dna); StringUlongFeatures feats_test = new StringUlongFeatures(charfeat.get_alphabet()); feats_test.obtain_from_char(charfeat_test, order - 1, order, gap, reverse); feats_test.add_preprocessor(preproc); feats_test.apply_preprocessor(); CommUlongStringKernel kernel = new CommUlongStringKernel(feats_train, feats_train, use_sign); double[,] km_train = kernel.get_kernel_matrix(); kernel.init(feats_train, feats_test); double[,] km_test = kernel.get_kernel_matrix(); modshogun.exit_shogun(); }
static void Main(string[] argv) { modshogun.init_shogun_with_defaults(); int num = 10; int order = 7; int gap = 0; bool reverse = false; string[] POS = new string[141]; for (int i = 0; i < 60; i++) { POS[i] = repeat("ACGT", 10); } for (int i = 61; i < 82; i++) { POS[i] = repeat("TTGT", 10); } for (int i = 83; i < 141; i++) { POS[i] = repeat("ACGT", 10); } string[] NEG = new string[141]; for (int i = 0; i < 60; i++) { NEG[i] = repeat("ACGT", 10); } for (int i = 61; i < 82; i++) { NEG[i] = repeat("TTGT", 10); } for (int i = 83; i < 141; i++) { NEG[i] = repeat("ACGT", 10); } string[] POSNEG = new string[282]; for (int i = 0; i < 141; i++) { POSNEG[i] = POS[i]; POSNEG[i + 141] = NEG[i]; } for(int i = 0; i < 10; i++) { Alphabet alpha = new Alphabet(DNA); StringCharFeatures traindat = new StringCharFeatures(alpha); traindat.set_features(POSNEG); StringWordFeatures trainudat = new StringWordFeatures(traindat.get_alphabet()); trainudat.obtain_from_char(traindat, order-1, order, gap, reverse); SortWordString pre = new SortWordString(); pre.init(trainudat); trainudat.add_preprocessor(pre); trainudat.apply_preprocessor(); CommWordStringKernel spec = new CommWordStringKernel(10, false); spec.set_normalizer(new IdentityKernelNormalizer()); spec.init(trainudat, trainudat); DoubleMatrix K = spec.get_kernel_matrix(); } modshogun.exit_shogun(); }