Exemple #1
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 public FKFeatures(FKFeatures orig) : this(modshogunPINVOKE.new_FKFeatures__SWIG_2(FKFeatures.getCPtr(orig)), true)
 {
     if (modshogunPINVOKE.SWIGPendingException.Pending)
     {
         throw modshogunPINVOKE.SWIGPendingException.Retrieve();
     }
 }
Exemple #2
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 internal static HandleRef getCPtr(FKFeatures obj)
 {
     return((obj == null) ? new HandleRef(null, IntPtr.Zero) : obj.swigCPtr);
 }
Exemple #3
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 internal static HandleRef getCPtr(FKFeatures obj) {
   return (obj == null) ? new HandleRef(null, IntPtr.Zero) : obj.swigCPtr;
 }
Exemple #4
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 public FKFeatures(FKFeatures orig) : this(modshogunPINVOKE.new_FKFeatures__SWIG_2(FKFeatures.getCPtr(orig)), true) {
   if (modshogunPINVOKE.SWIGPendingException.Pending) throw modshogunPINVOKE.SWIGPendingException.Retrieve();
 }
    internal static ArrayList run(IList para)
    {
        bool reverse = false;
        modshogun.init_shogun_with_defaults();
        int N = (int)((int?)para[0]);
        int M = (int)((int?)para[1]);
        double pseudo = (double)((double?)para[2]);
        int order = (int)((int?)para[3]);
        int gap = (int)((int?)para[4]);

        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 label_train_dna = Load.load_labels("../data/label_train_dna.dat");

        ArrayList fm_hmm_pos_builder = new ArrayList();
        ArrayList fm_hmm_neg_builder = new ArrayList();
        for(int i = 0; i < label_train_dna.Columns; i++)
        {
            if (label_train_dna.get(i) == 1)
            {
                fm_hmm_pos_builder.Add(fm_train_dna[i]);
            }
            else
            {
                fm_hmm_neg_builder.Add(fm_train_dna[i]);
            }
        }

        int pos_size = fm_hmm_pos_builder.Count;
        int neg_size = fm_hmm_neg_builder.Count;
        string[] fm_hmm_pos = new string[pos_size];
        string[] fm_hmm_neg = new string[neg_size];
        for (int i = 0; i < pos_size; i++)
        {
            fm_hmm_pos[i] = (string)fm_hmm_pos_builder[i];
        }
        for (int i = 0; i < neg_size; i++)
        {
            fm_hmm_pos[i] = (string)fm_hmm_neg_builder[i];
        }

        StringCharFeatures charfeat = new StringCharFeatures(fm_hmm_pos, DNA);
        StringWordFeatures hmm_pos_train = new StringWordFeatures(charfeat.get_alphabet());
        hmm_pos_train.obtain_from_char(charfeat, order-1, order, gap, reverse);

        HMM pos = new HMM(hmm_pos_train, N, M, pseudo);
        pos.baum_welch_viterbi_train(BW_NORMAL);

        charfeat = new StringCharFeatures(fm_hmm_neg, DNA);
        StringWordFeatures hmm_neg_train = new StringWordFeatures(charfeat.get_alphabet());
        hmm_neg_train.obtain_from_char(charfeat, order-1, order, gap, reverse);

        HMM neg = new HMM(hmm_neg_train, N, M, pseudo);
        neg.baum_welch_viterbi_train(BW_NORMAL);

        charfeat = new StringCharFeatures(fm_train_dna, DNA);
        StringWordFeatures wordfeats_train = new StringWordFeatures(charfeat.get_alphabet());
        wordfeats_train.obtain_from_char(charfeat, order-1, order, gap, reverse);

        charfeat = new StringCharFeatures(fm_test_dna, DNA);
        StringWordFeatures wordfeats_test = new StringWordFeatures(charfeat.get_alphabet());
        wordfeats_test.obtain_from_char(charfeat, order-1, order, gap, reverse);

        pos.set_observations(wordfeats_train);
        neg.set_observations(wordfeats_train);
        FKFeatures feats_train = new FKFeatures(10, pos, neg);
        feats_train.set_opt_a(-1);
        PolyKernel kernel = new PolyKernel(feats_train, feats_train, 1, true);
        DoubleMatrix km_train = kernel.get_kernel_matrix();

        HMM pos_clone = new HMM(pos);
        HMM neg_clone = new HMM(neg);
        pos_clone.set_observations(wordfeats_test);
        neg_clone.set_observations(wordfeats_test);
        FKFeatures feats_test = new FKFeatures(10, pos_clone, neg_clone);
        feats_test.set_a(feats_train.get_a());
        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;
    }