internal static ArrayList run(IList para)
{
int degree = 20;
modshogun.init_shogun_with_defaults();
double C = (double)((double?)para[0]);
double epsilon = (double)((double?)para[1]);
int num_threads = (int)((int?)para[2]);
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 feats_train = new StringCharFeatures(fm_train_dna, DNA);
StringCharFeatures feats_test = new StringCharFeatures(fm_test_dna, DNA);
Labels labels = new Labels(Load.load_labels("../data/label_train_dna.dat"));
WeightedDegreeStringKernel kernel = new WeightedDegreeStringKernel(feats_train, feats_train, degree);
SVMLight svm = new SVMLight(C, kernel, labels);
svm.set_epsilon(epsilon);
//svm.parallel.set_num_threads(num_threads);
svm.train();
kernel.init(feats_train, feats_test);
svm.apply().get_labels();
ArrayList result = new ArrayList();
result.Add(kernel);
modshogun.exit_shogun();
return result;
}
internal static ArrayList run(IList para)
{
modshogun.init_shogun_with_defaults();
int degree = (int)((int?)para[0]);
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 feats_train = new StringCharFeatures(fm_train_dna, DNA);
StringCharFeatures feats_test = new StringCharFeatures(fm_test_dna, DNA);
WeightedDegreeStringKernel kernel = new WeightedDegreeStringKernel(feats_train, feats_train, degree);
double[] w = new double[degree];
double sum = degree * (degree + 1)/2;
for (int i = 0; i < degree; i++)
{
w[i] = (degree - i)/sum;
}
DoubleMatrix weights = new DoubleMatrix(1, degree, w);
kernel.set_wd_weights(weights);
DoubleMatrix km_train = kernel.get_kernel_matrix();
kernel.init(feats_train, feats_test);
DoubleMatrix km_test = kernel.get_kernel_matrix();
ArrayList result = new ArrayList();
result.Add(km_train);
result.Add(km_test);
result.Add(kernel);
modshogun.exit_shogun();
return result;
}
static void Main(string[] argv)
{
modshogun.init_shogun_with_defaults();
int degree = 3;
int C = 1;
string[] fm_train_dna = {"CGCACGTACGTAGCTCGAT", "CGACGTAGTCGTAGTCGTA", "CGACGGGGGGGGGGTCGTA", "CGACCTAGTCGTAGTCGTA", "CGACCACAGTTATATAGTA", "CGACGTAGTCGTAGTCGTA", "CGACGTAGTTTTTTTCGTA", "CGACGTAGTCGTAGCCCCA", "CAAAAAAAAAAAAAAAATA", "CGACGGGGGGGGGGGCGTA"};
string[] fm_test_dna = {"AGCACGTACGTAGCTCGAT", "AGACGTAGTCGTAGTCGTA", "CAACGGGGGGGGGGTCGTA", "CGACCTAGTCGTAGTCGTA", "CGAACACAGTTATATAGTA", "CGACCTAGTCGTAGTCGTA", "CGACGTGGGGTTTTTCGTA", "CGACGTAGTCCCAGCCCCA", "CAAAAAAAAAAAACCAATA", "CGACGGCCGGGGGGGCGTA"};
StringCharFeatures feats_train = new StringCharFeatures(fm_train_dna, DNA);
StringCharFeatures feats_test = new StringCharFeatures(fm_test_dna, DNA);
WeightedDegreeStringKernel kernel = new WeightedDegreeStringKernel(feats_train, feats_train, degree);
double[][] label_train_dna = { new double[] { -1, -1, -1, -1, -1, 1, 1, 1, 1, 1 } };
Labels labels = new Labels(new DoubleMatrix(label_train_dna));
SVMLight svm = new SVMLight(C, kernel, labels);
svm.train();
DomainAdaptationSVM dasvm = new DomainAdaptationSVM(C, kernel, labels, svm, 1.0);
dasvm.train();
DoubleMatrix @out = dasvm.apply(feats_test).get_labels();
modshogun.exit_shogun();
}
internal static DoubleMatrix run(IList para)
{
int degree = 20;
modshogun.init_shogun_with_defaults();
double C = (double)((double?)para[0]);
double epsilon = (double)((double?)para[1]);
int num_threads = (int)((int?)para[2]);
string[] fm_train_dna = {"CGCACGTACGTAGCTCGAT", "CGACGTAGTCGTAGTCGTA", "CGACGGGGGGGGGGTCGTA", "CGACCTAGTCGTAGTCGTA", "CGACCACAGTTATATAGTA", "CGACGTAGTCGTAGTCGTA", "CGACGTAGTTTTTTTCGTA", "CGACGTAGTCGTAGCCCCA", "CAAAAAAAAAAAAAAAATA", "CGACGGGGGGGGGGGCGTA"};
string[] fm_test_dna = {"AGCACGTACGTAGCTCGAT", "AGACGTAGTCGTAGTCGTA", "CAACGGGGGGGGGGTCGTA", "CGACCTAGTCGTAGTCGTA", "CGAACACAGTTATATAGTA", "CGACCTAGTCGTAGTCGTA", "CGACGTGGGGTTTTTCGTA", "CGACGTAGTCCCAGCCCCA", "CAAAAAAAAAAAACCAATA", "CGACGGCCGGGGGGGCGTA"};
StringCharFeatures feats_train = new StringCharFeatures(fm_train_dna, DNA);
StringCharFeatures feats_test = new StringCharFeatures(fm_test_dna, DNA);
WeightedDegreeStringKernel kernel = new WeightedDegreeStringKernel(feats_train, feats_train, degree);
double[][] label_train_dna = { new double[] { -1, -1, -1, -1, -1, 1, 1, 1, 1, 1 } };
Labels labels = new Labels(new DoubleMatrix(label_train_dna));
SVMLight svm = new SVMLight(C, kernel, labels);
svm.set_qpsize(3);
svm.set_linear_term(new DoubleMatrix(new double[][] {{-1,-2,-3,-4,-5,-6,-7,-8,-7,-6}}));
svm.set_epsilon(epsilon);
//svm.parallel.set_num_threads(num_threads);
svm.train();
kernel.init(feats_train, feats_test);
DoubleMatrix @out = svm.apply().get_labels();
modshogun.exit_shogun();
return @out;
}
public static void Main()
{
modshogun.init_shogun_with_defaults();
int degree = 3;
string[] fm_train_dna = Load.load_dna("../data/fm_train_dna.dat");
string[] fm_test_dna = Load.load_dna("../data/fm_test_dna.dat");
foreach (string item in fm_train_dna)
{
Console.WriteLine(item);
}
StringCharFeatures feats_train = new StringCharFeatures(fm_train_dna, EAlphabet.DNA);
StringCharFeatures feats_test = new StringCharFeatures(fm_test_dna, EAlphabet.DNA);
WeightedDegreeStringKernel kernel = new WeightedDegreeStringKernel(feats_train, feats_train, degree);
double [] w = new double[degree];
double sum = degree * (degree + 1) / 2;
for (int i = 0; i < degree; i++)
{
w[i] = (degree - i) / sum;
}
kernel.set_wd_weights(w);
double[,] km_train = kernel.get_kernel_matrix();
kernel.init(feats_train, feats_test);
double[,] km_test = kernel.get_kernel_matrix();
foreach (double item in km_train)
{
Console.Write(item);
}
foreach (double item in km_test)
{
Console.Write(item);
}
modshogun.exit_shogun();
}
public static void Main()
{
modshogun.init_shogun_with_defaults();
int degree = 3;
string[] fm_train_dna = Load.load_dna("../data/fm_train_dna.dat");
string[] fm_test_dna = Load.load_dna("../data/fm_test_dna.dat");
foreach(string item in fm_train_dna) {
Console.WriteLine(item);
}
StringCharFeatures feats_train = new StringCharFeatures(fm_train_dna, EAlphabet.DNA);
StringCharFeatures feats_test = new StringCharFeatures(fm_test_dna, EAlphabet.DNA);
WeightedDegreeStringKernel kernel = new WeightedDegreeStringKernel(feats_train, feats_train, degree);
double [] w = new double[degree];
double sum = degree * (degree + 1)/2;
for (int i = 0; i < degree; i++) {
w[i] = (degree - i)/sum;
}
kernel.set_wd_weights(w);
double[,] km_train = kernel.get_kernel_matrix();
kernel.init(feats_train, feats_test);
double[,] km_test = kernel.get_kernel_matrix();
foreach(double item in km_train) {
Console.Write(item);
}
foreach(double item in km_test) {
Console.Write(item);
}
modshogun.exit_shogun();
}
internal static HandleRef getCPtr(WeightedDegreeStringKernel obj)
{
return((obj == null) ? new HandleRef(null, IntPtr.Zero) : obj.swigCPtr);
}
internal static HandleRef getCPtr(WeightedDegreeStringKernel obj) {
return (obj == null) ? new HandleRef(null, IntPtr.Zero) : obj.swigCPtr;
}
