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all_preproc.m
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all_preproc.m
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init_shogun
% Explicit examples on how to use the different preprocs
addpath('tools');
fm_train_real=load_matrix('../data/fm_train_real.dat');
fm_test_real=load_matrix('../data/fm_test_real.dat');
fm_train_word=load_matrix('../data/fm_train_word.dat');
fm_test_word=load_matrix('../data/fm_test_word.dat');
fm_train_dna=load_matrix('../data/fm_train_dna.dat');
fm_test_dna=load_matrix('../data/fm_test_dna.dat');
%LogPlusOne
disp('LogPlusOne')
feats_train=RealFeatures(fm_train_real);
feats_test=RealFeatures(fm_test_real);
preproc=LogPlusOne();
preproc.init(feats_train);
feats_train.add_preproc(preproc);
feats_train.apply_preproc();
feats_test.add_preproc(preproc);
feats_test.apply_preproc();
width=1.4;
size_cache=10;
kernel=Chi2Kernel(feats_train, feats_train, width, size_cache);
km_train=kernel.get_kernel_matrix();
kernel.init(feats_train, feats_test);
km_test=kernel.get_kernel_matrix();
%NormOne
disp('NormOne')
feats_train=RealFeatures(fm_train_real);
feats_test=RealFeatures(fm_test_real);
preproc=NormOne();
preproc.init(feats_train);
feats_train.add_preproc(preproc);
feats_train.apply_preproc();
feats_test.add_preproc(preproc);
feats_test.apply_preproc();
width=1.4;
size_cache=10;
kernel=Chi2Kernel(feats_train, feats_train, width, size_cache);
km_train=kernel.get_kernel_matrix();
kernel.init(feats_train, feats_test);
km_test=kernel.get_kernel_matrix();
%PruneVarSubMean
disp('PruneVarSubMean')
feats_train=RealFeatures(fm_train_real);
feats_test=RealFeatures(fm_test_real);
preproc=PruneVarSubMean();
preproc.init(feats_train);
feats_train.add_preproc(preproc);
feats_train.apply_preproc();
feats_test.add_preproc(preproc);
feats_test.apply_preproc();
width=1.4;
size_cache=10;
kernel=Chi2Kernel(feats_train, feats_train, width, size_cache);
km_train=kernel.get_kernel_matrix();
kernel.init(feats_train, feats_test);
km_test=kernel.get_kernel_matrix();
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% complex string features
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%CommWordString
disp('CommWordString')
order=3;
gap=0;
reverse=false;
charfeat=StringCharFeatures(DNA);
charfeat.set_string_features(fm_train_dna);
feats_train=StringWordFeatures(charfeat.get_alphabet());
feats_train.obtain_from_char(charfeat, order-1, order, gap, reverse);
preproc=SortWordString();
preproc.init(feats_train);
feats_train.add_preproc(preproc);
feats_train.apply_preproc();
charfeat=StringCharFeatures(DNA);
charfeat.set_string_features(fm_test_dna);
feats_test=StringWordFeatures(charfeat.get_alphabet());
feats_test.obtain_from_char(charfeat, order-1, order, gap, reverse);
feats_test.add_preproc(preproc);
feats_test.apply_preproc();
use_sign=false;
kernel=CommWordStringKernel(feats_train, feats_train, use_sign);
km_train=kernel.get_kernel_matrix();
kernel.init(feats_train, feats_test);
km_test=kernel.get_kernel_matrix();
%CommUlongString
disp('CommUlongString')
order=3;
gap=0;
reverse=false;
charfeat=StringCharFeatures(DNA);
charfeat.set_string_features(fm_train_dna);
feats_train=StringUlongFeatures(charfeat.get_alphabet());
feats_train.obtain_from_char(charfeat, order-1, order, gap, reverse);
charfeat=StringCharFeatures(DNA);
charfeat.set_string_features(fm_test_dna);
feats_test=StringUlongFeatures(charfeat.get_alphabet());
feats_test.obtain_from_char(charfeat, order-1, order, gap, reverse);
preproc=SortUlongString();
preproc.init(feats_train);
feats_train.add_preproc(preproc);
feats_train.apply_preproc();
feats_test.add_preproc(preproc);
feats_test.apply_preproc();
use_sign=false;
kernel=CommUlongStringKernel(feats_train, feats_train, use_sign);
km_train=kernel.get_kernel_matrix();
kernel.init(feats_train, feats_test);
km_test=kernel.get_kernel_matrix();