Python CommUlongStringKernel.init Examples

Example #1

def kernel_comm_ulong_string_modular(fm_train_dna=traindat,
                                     fm_test_dna=testdat,
                                     order=3,
                                     gap=0,
                                     reverse=False):

    from shogun.Kernel import CommUlongStringKernel
    from shogun.Features import StringUlongFeatures, StringCharFeatures, DNA
    from shogun.PreProc import SortUlongString

    charfeat = StringCharFeatures(DNA)
    charfeat.set_features(fm_train_dna)
    feats_train = StringUlongFeatures(charfeat.get_alphabet())
    feats_train.obtain_from_char(charfeat, order - 1, order, gap, reverse)
    preproc = SortUlongString()
    preproc.init(feats_train)
    feats_train.add_preproc(preproc)
    feats_train.apply_preproc()

    charfeat = StringCharFeatures(DNA)
    charfeat.set_features(fm_test_dna)
    feats_test = StringUlongFeatures(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 = 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()
    return km_train, km_test, kernel

Example #2

File: preprocessor_sortulongstring_modular.py Project: ashish-sadh/shogun

def preprocessor_sortulongstring_modular (fm_train_dna=traindna,fm_test_dna=testdna,order=3,gap=0,reverse=False,use_sign=False):

	from shogun.Kernel import CommUlongStringKernel
	from shogun.Features import StringCharFeatures, StringUlongFeatures, DNA
	from shogun.Preprocessor import SortUlongString


	charfeat=StringCharFeatures(DNA)
	charfeat.set_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_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_preprocessor(preproc)
	feats_train.apply_preprocessor()
	feats_test.add_preprocessor(preproc)
	feats_test.apply_preprocessor()

	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()
	return km_train,km_test,kernel

Example #3

File: kernel_comm_ulong_string_modular.py Project: memimo/shogun-liblinear

def comm_ulong_string ():
	print 'CommUlongString'
	from shogun.Kernel import CommUlongStringKernel
	from shogun.Features import StringUlongFeatures, StringCharFeatures, DNA
	from shogun.PreProc import SortUlongString
	order=3
	gap=0
	reverse=False

	charfeat=StringCharFeatures(DNA)
	charfeat.set_features(fm_train_dna)
	feats_train=StringUlongFeatures(charfeat.get_alphabet())
	feats_train.obtain_from_char(charfeat, order-1, order, gap, reverse)
	preproc=SortUlongString()
	preproc.init(feats_train)
	feats_train.add_preproc(preproc)
	feats_train.apply_preproc()


	charfeat=StringCharFeatures(DNA)
	charfeat.set_features(fm_test_dna)
	feats_test=StringUlongFeatures(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=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()