Python StringWordFeatures.apply_preproc方法代码示例

本文整理汇总了Python中shogun.Features.StringWordFeatures.apply_preproc方法的典型用法代码示例。如果您正苦于以下问题：Python StringWordFeatures.apply_preproc方法的具体用法？Python StringWordFeatures.apply_preproc怎么用？Python StringWordFeatures.apply_preproc使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类shogun.Features.StringWordFeatures的用法示例。

在下文中一共展示了StringWordFeatures.apply_preproc方法的9个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。

示例1: sort_word_string

# 需要导入模块: from shogun.Features import StringWordFeatures [as 别名]
# 或者: from shogun.Features.StringWordFeatures import apply_preproc [as 别名]
def sort_word_string ():
	print 'CommWordString'

	from shogun.Kernel import CommWordStringKernel
	from shogun.Features import StringCharFeatures, StringWordFeatures, DNA
	from shogun.PreProc import SortWordString

	order=3
	gap=0
	reverse=False

	charfeat=StringCharFeatures(fm_train_dna, 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(fm_test_dna, 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()

开发者ID:memimo，项目名称:shogun-liblinear，代码行数:34，代码来源:preproc_sortwordstring_modular.py

示例2: distance_canberraword_modular

# 需要导入模块: from shogun.Features import StringWordFeatures [as 别名]
# 或者: from shogun.Features.StringWordFeatures import apply_preproc [as 别名]
def distance_canberraword_modular (fm_train_dna=traindna,fm_test_dna=testdna,order=3,gap=0,reverse=False):
	from shogun.Features import StringCharFeatures, StringWordFeatures, DNA
	from shogun.Preprocessor import SortWordString
	from shogun.Distance import CanberraWordDistance
	
	charfeat=StringCharFeatures(DNA)
	charfeat.set_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_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()

	distance=CanberraWordDistance(feats_train, feats_train)

	dm_train=distance.get_distance_matrix()
	distance.init(feats_train, feats_test)
	dm_test=distance.get_distance_matrix()
	return distance,dm_train,dm_test

开发者ID:alesis，项目名称:shogun，代码行数:29，代码来源:distance_canberraword_modular.py

示例3: manhattan_word_distance

# 需要导入模块: from shogun.Features import StringWordFeatures [as 别名]
# 或者: from shogun.Features.StringWordFeatures import apply_preproc [as 别名]
def manhattan_word_distance ():
	print 'ManhattanWordDistance'

	from shogun.Features import StringCharFeatures, StringWordFeatures, DNA
	from shogun.PreProc import SortWordString
	from shogun.Distance import ManhattanWordDistance

	order=3
	gap=0
	reverse=False

	charfeat=StringCharFeatures(DNA)
	charfeat.set_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_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()

	distance=ManhattanWordDistance(feats_train, feats_train)

	dm_train=distance.get_distance_matrix()
	distance.init(feats_train, feats_test)
	dm_test=distance.get_distance_matrix()

开发者ID:memimo，项目名称:shogun-liblinear，代码行数:34，代码来源:distance_manhattenword_modular.py

示例4: preproc_sortwordstring_modular

# 需要导入模块: from shogun.Features import StringWordFeatures [as 别名]
# 或者: from shogun.Features.StringWordFeatures import apply_preproc [as 别名]
def preproc_sortwordstring_modular (fm_train_dna=traindna,fm_test_dna=testdna,order=3,gap=0,reverse=False,use_sign=False):

	from shogun.Kernel import CommWordStringKernel
	from shogun.Features import StringCharFeatures, StringWordFeatures, DNA
	from shogun.Preprocessor import SortWordString

	charfeat=StringCharFeatures(fm_train_dna, 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(fm_test_dna, 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()

	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()

	return km_train,km_test,kernel

开发者ID:alesis，项目名称:shogun，代码行数:29，代码来源:preproc_sortwordstring_modular.py

示例5: init_sensor

# 需要导入模块: from shogun.Features import StringWordFeatures [as 别名]
# 或者: from shogun.Features.StringWordFeatures import apply_preproc [as 别名]
    def init_sensor(self, kernel, svs):
        f = StringCharFeatures(svs, DNA)

        kname = kernel['name']
        if  kname == 'spectrum':
            wf = StringWordFeatures(f.get_alphabet())
            wf.obtain_from_char(f, kernel['order'] - 1, kernel['order'], 0, False)

            pre = SortWordString()
            pre.init(wf)
            wf.add_preproc(pre)
            wf.apply_preproc()
            f = wf

            k = CommWordStringKernel(0, False)
            k.set_use_dict_diagonal_optimization(kernel['order'] < 8)
            self.preproc = pre

        elif kname == 'wdshift':
                k = WeightedDegreePositionStringKernel(0, kernel['order'])
                k.set_normalizer(IdentityKernelNormalizer())
                k.set_shifts(kernel['shift'] *
                        numpy.ones(f.get_max_vector_length(), dtype=numpy.int32))
                k.set_position_weights(1.0 / f.get_max_vector_length() *
                        numpy.ones(f.get_max_vector_length(), dtype=numpy.float64))
        else:
            raise "Currently, only wdshift and spectrum kernels supported"

        self.kernel = k
        self.train_features = f

        return (self.kernel, self.train_features)

开发者ID:AsherBond，项目名称:shogun，代码行数:34，代码来源:signal_sensor.py

示例6: create_hashed_features_spectrum

# 需要导入模块: from shogun.Features import StringWordFeatures [as 别名]
# 或者: from shogun.Features.StringWordFeatures import apply_preproc [as 别名]
def create_hashed_features_spectrum(param, data):
    """
    creates hashed dot features for the spectrum kernel
    """

    # extract parameters
    order = param["degree_spectrum"]

    # fixed parameters
    gap = 0
    reverse = True 
    normalize = True

    # create features
    feats_char = StringCharFeatures(data, DNA)
    feats_word = StringWordFeatures(feats_char.get_alphabet())
    feats_word.obtain_from_char(feats_char, order-1, order, gap, reverse)

    # create preproc
    preproc = SortWordString()
    preproc.init(feats_word)
    feats_word.add_preproc(preproc)
    feats_word.apply_preproc()

    # finish 
    feats = ImplicitWeightedSpecFeatures(feats_word, normalize)

    return feats

开发者ID:cwidmer，项目名称:multitask，代码行数:30，代码来源:shogun_factory_new.py

示例7: perform_clustering

# 需要导入模块: from shogun.Features import StringWordFeatures [as 别名]
# 或者: from shogun.Features.StringWordFeatures import apply_preproc [as 别名]
def perform_clustering(mss_id):

    import numpy
    import expenv
    
    mss = expenv.MultiSplitSet.get(mss_id)
    


    from method_mhc_mkl import SequencesHandler
    from shogun.Distance import EuclidianDistance, HammingWordDistance
    from shogun.Features import StringCharFeatures, StringWordFeatures, PROTEIN
    from shogun.Clustering import Hierarchical
    from shogun.PreProc import SortWordString
    
    order = 1
    gap = 0
    reverse = False
    
    seq_handler = SequencesHandler()
    
    data = [seq_handler.get_seq(ss.dataset.organism) for ss in mss.split_sets] 

    charfeat=StringCharFeatures(PROTEIN)
    charfeat.set_features(data)
    feats=StringWordFeatures(charfeat.get_alphabet())
    feats.obtain_from_char(charfeat, order-1, order, gap, reverse)
    preproc=SortWordString()
    preproc.init(feats)
    feats.add_preproc(preproc)
    feats.apply_preproc()

    
    use_sign = False

    distance = HammingWordDistance(feats, feats, use_sign)
    #distance = EuclidianDistance()
    
    merges=4
    hierarchical=Hierarchical(merges, distance)
    hierarchical.train()

    hierarchical.get_merge_distances()
    hierarchical.get_cluster_pairs()
    
    
    return hierarchical

开发者ID:cwidmer，项目名称:multitask，代码行数:49，代码来源:mhc_stuff.py

示例8: tests_check_commwordkernel_memleak_modular

# 需要导入模块: from shogun.Features import StringWordFeatures [as 别名]
# 或者: from shogun.Features.StringWordFeatures import apply_preproc [as 别名]
def tests_check_commwordkernel_memleak_modular(num, order, gap, reverse):
	import gc
	from shogun.Features import Alphabet,StringCharFeatures,StringWordFeatures,DNA
	from shogun.Preprocessor import SortWordString, MSG_DEBUG
	from shogun.Kernel import CommWordStringKernel, IdentityKernelNormalizer
	from numpy import mat

	POS=[num*'ACGT', num*'ACGT', num*'ACGT',num*'ACGT', num*'ACGT', 
	num*'ACGT',num*'ACGT', num*'ACGT', num*'ACGT',num*'ACGT', num*'ACGT', 
	num*'ACGT',num*'ACGT', num*'ACGT', num*'ACGT',num*'ACGT', num*'ACGT', 
	num*'ACGT',num*'ACGT', num*'ACGT', num*'ACGT',num*'ACGT', num*'ACGT', 
	num*'ACGT',num*'ACGT', num*'ACGT', num*'ACGT',num*'ACGT', num*'ACGT', 
	num*'ACGT',num*'ACGT', num*'ACGT', num*'ACGT',num*'ACGT', num*'ACGT', 
	num*'ACGT',num*'ACGT', num*'ACGT', num*'ACGT',num*'ACGT', num*'ACGT', 
	num*'ACGT',num*'ACGT', num*'ACGT', num*'ACGT',num*'ACGT', num*'ACGT', 
	num*'ACGT',num*'ACGT', num*'ACGT', num*'ACGT',num*'ACGT', num*'ACGT', 
	num*'ACGT',num*'ACGT', num*'ACGT', num*'ACGT',num*'ACGT', num*'ACGT', 
	num*'ACGT',num*'TTGT', num*'TTGT', num*'TTGT',num*'TTGT', num*'TTGT', 
	num*'TTGT',num*'TTGT', num*'TTGT', num*'TTGT',num*'TTGT', num*'TTGT', 
	num*'TTGT',num*'TTGT', num*'TTGT', num*'TTGT',num*'TTGT', num*'TTGT', 
	num*'TTGT',num*'TTGT', num*'TTGT', num*'TTGT',num*'ACGT', num*'ACGT', 
	num*'ACGT',num*'ACGT', num*'ACGT', num*'ACGT',num*'ACGT', num*'ACGT', 
	num*'ACGT',num*'ACGT', num*'ACGT', num*'ACGT',num*'ACGT', num*'ACGT', 
	num*'ACGT',num*'ACGT', num*'ACGT', num*'ACGT',num*'ACGT', num*'ACGT', 
	num*'ACGT',num*'ACGT', num*'ACGT', num*'ACGT',num*'ACGT', num*'ACGT', 
	num*'ACGT',num*'ACGT', num*'ACGT', num*'ACGT',num*'ACGT', num*'ACGT', 
	num*'ACGT',num*'ACGT', num*'ACGT', num*'ACGT',num*'ACGT', num*'ACGT', 
	num*'ACGT',num*'ACGT', num*'ACGT', num*'ACGT',num*'ACGT', num*'ACGT', 
	num*'ACGT',num*'ACGT', num*'ACGT', num*'ACGT',num*'ACGT', num*'ACGT', 
	num*'ACGT',num*'ACGT', num*'ACGT', num*'ACGT',num*'ACGT', num*'ACGT', 
	num*'ACGT',num*'ACGT', num*'ACGT', num*'ACGT']
	NEG=[num*'ACGT', num*'ACGT', num*'ACGT',num*'ACGT', num*'ACGT', 
	num*'ACGT',num*'ACGT', num*'ACGT', num*'ACGT',num*'ACGT', num*'ACGT', 
	num*'ACGT',num*'ACGT', num*'ACGT', num*'ACGT',num*'ACGT', num*'ACGT', 
	num*'ACGT',num*'ACGT', num*'ACGT', num*'ACGT',num*'ACGT', num*'ACGT', 
	num*'ACGT',num*'ACGT', num*'ACGT', num*'ACGT',num*'ACGT', num*'ACGT', 
	num*'ACGT',num*'ACGT', num*'ACGT', num*'ACGT',num*'ACGT', num*'ACGT', 
	num*'ACGT',num*'ACGT', num*'ACGT', num*'ACGT',num*'ACGT', num*'ACGT', 
	num*'ACGT',num*'ACGT', num*'ACGT', num*'ACGT',num*'ACGT', num*'ACGT', 
	num*'ACGT',num*'ACGT', num*'ACGT', num*'ACGT',num*'ACGT', num*'ACGT', 
	num*'ACGT',num*'ACGT', num*'ACGT', num*'ACGT',num*'ACGT', num*'ACGT', 
	num*'ACGT',num*'TTGT', num*'TTGT', num*'TTGT',num*'TTGT', num*'TTGT', 
	num*'TTGT',num*'TTGT', num*'TTGT', num*'TTGT',num*'TTGT', num*'TTGT', 
	num*'TTGT',num*'TTGT', num*'TTGT', num*'TTGT',num*'TTGT', num*'TTGT', 
	num*'TTGT',num*'TTGT', num*'TTGT', num*'TTGT',num*'ACGT', num*'ACGT', 
	num*'ACGT',num*'ACGT', num*'ACGT', num*'ACGT',num*'ACGT', num*'ACGT', 
	num*'ACGT',num*'ACGT', num*'ACGT', num*'ACGT',num*'ACGT', num*'ACGT', 
	num*'ACGT',num*'ACGT', num*'ACGT', num*'ACGT',num*'ACGT', num*'ACGT', 
	num*'ACGT',num*'ACGT', num*'ACGT', num*'ACGT',num*'ACGT', num*'ACGT', 
	num*'ACGT',num*'ACGT', num*'ACGT', num*'ACGT',num*'ACGT', num*'ACGT', 
	num*'ACGT',num*'ACGT', num*'ACGT', num*'ACGT',num*'ACGT', num*'ACGT', 
	num*'ACGT',num*'ACGT', num*'ACGT', num*'ACGT',num*'ACGT', num*'ACGT', 
	num*'ACGT',num*'ACGT', num*'ACGT', num*'ACGT',num*'ACGT', num*'ACGT', 
	num*'ACGT',num*'ACGT', num*'ACGT', num*'ACGT',num*'ACGT', num*'ACGT', 
	num*'ACGT',num*'ACGT', num*'ACGT', num*'ACGT']

	for i in xrange(10):
		alpha=Alphabet(DNA)
		traindat=StringCharFeatures(alpha)
		traindat.set_features(POS+NEG)
		trainudat=StringWordFeatures(traindat.get_alphabet());
		trainudat.obtain_from_char(traindat, order-1, order, gap, reverse)
		#trainudat.io.set_loglevel(MSG_DEBUG)
		pre = SortWordString()
		#pre.io.set_loglevel(MSG_DEBUG)
		pre.init(trainudat)
		trainudat.add_preproc(pre)
		trainudat.apply_preproc()
		spec = CommWordStringKernel(10, False)
		spec.set_normalizer(IdentityKernelNormalizer())
		spec.init(trainudat, trainudat)
		K=spec.get_kernel_matrix()

	del POS
	del NEG
	del order
	del gap
	del reverse
	return K

开发者ID:alesis，项目名称:shogun，代码行数:81，代码来源:tests_check_commwordkernel_memleak_modular.py

示例9: xrange

# 需要导入模块: from shogun.Features import StringWordFeatures [as 别名]
# 或者: from shogun.Features.StringWordFeatures import apply_preproc [as 别名]
100*'ACGT',100*'ACGT', 100*'ACGT', 100*'ACGT',100*'ACGT', 100*'ACGT', 
100*'ACGT',100*'ACGT', 100*'ACGT', 100*'ACGT',100*'ACGT', 100*'ACGT', 
100*'ACGT',100*'ACGT', 100*'ACGT', 100*'ACGT',100*'ACGT', 100*'ACGT', 
100*'ACGT',100*'ACGT', 100*'ACGT', 100*'ACGT']
order=7
gap=0
reverse=False

for i in xrange(10):
    alpha=Alphabet(DNA)
    traindat=StringCharFeatures(alpha)
    traindat.set_features(POS+NEG)
    trainudat=StringWordFeatures(traindat.get_alphabet());
    trainudat.obtain_from_char(traindat, order-1, order, gap, reverse)
    #trainudat.io.set_loglevel(MSG_DEBUG)
    pre = SortWordString()
    #pre.io.set_loglevel(MSG_DEBUG)
    pre.init(trainudat)
    trainudat.add_preproc(pre)
    trainudat.apply_preproc()
    spec = CommWordStringKernel(10, False)
    spec.set_normalizer(IdentityKernelNormalizer())
    spec.init(trainudat, trainudat)
    K=mat(spec.get_kernel_matrix())

del POS
del NEG
del order
del gap
del reverse

开发者ID:memimo，项目名称:shogun-liblinear，代码行数:32，代码来源:tests_check_commwordkernel_memleak_modular.py

注：本文中的shogun.Features.StringWordFeatures.apply_preproc方法示例由纯净天空整理自Github/MSDocs等开源代码及文档管理平台，相关代码片段筛选自各路编程大神贡献的开源项目，源码版权归原作者所有，传播和使用请参考对应项目的License；未经允许，请勿转载。