Python Kernel.CombinedKernel类代码示例

def evaluation_cross_validation_multiclass_storage(traindat=traindat, label_traindat=label_traindat):
    from shogun.Evaluation import CrossValidation, CrossValidationResult
    from shogun.Evaluation import CrossValidationPrintOutput
    from shogun.Evaluation import CrossValidationMKLStorage, CrossValidationMulticlassStorage
    from shogun.Evaluation import MulticlassAccuracy, F1Measure
    from shogun.Evaluation import StratifiedCrossValidationSplitting
    from shogun.Features import MulticlassLabels
    from shogun.Features import RealFeatures, CombinedFeatures
    from shogun.Kernel import GaussianKernel, CombinedKernel
    from shogun.Classifier import MKLMulticlass
    from shogun.Mathematics import Statistics, MSG_DEBUG

    # training data, combined features all on same data
    features=RealFeatures(traindat)
    comb_features=CombinedFeatures()
    comb_features.append_feature_obj(features)
    comb_features.append_feature_obj(features)
    comb_features.append_feature_obj(features)
    labels=MulticlassLabels(label_traindat)
    
    # kernel, different Gaussians combined
    kernel=CombinedKernel()
    kernel.append_kernel(GaussianKernel(10, 0.1))
    kernel.append_kernel(GaussianKernel(10, 1))
    kernel.append_kernel(GaussianKernel(10, 2))

    # create mkl using libsvm, due to a mem-bug, interleaved is not possible
    svm=MKLMulticlass(1.0,kernel,labels);
    svm.set_kernel(kernel);

    # splitting strategy for 5 fold cross-validation (for classification its better
    # to use "StratifiedCrossValidation", but the standard
    # "StratifiedCrossValidationSplitting" is also available
    splitting_strategy=StratifiedCrossValidationSplitting(labels, 5)

    # evaluation method
    evaluation_criterium=MulticlassAccuracy()

    # cross-validation instance
    cross_validation=CrossValidation(svm, comb_features, labels,
        splitting_strategy, evaluation_criterium)
    cross_validation.set_autolock(False)

    # append cross vlaidation output classes
    #cross_validation.add_cross_validation_output(CrossValidationPrintOutput())
    #mkl_storage=CrossValidationMKLStorage()
    #cross_validation.add_cross_validation_output(mkl_storage)
    multiclass_storage=CrossValidationMulticlassStorage()
    multiclass_storage.append_binary_evaluation(F1Measure())
    cross_validation.add_cross_validation_output(multiclass_storage)
    cross_validation.set_num_runs(3)
    
    # perform cross-validation
    result=cross_validation.evaluate()

    roc_0_0_0 = multiclass_storage.get_fold_ROC(0,0,0)
    #print roc_0_0_0
    auc_0_0_0 = multiclass_storage.get_fold_evaluation_result(0,0,0,0)
    #print auc_0_0_0
    return roc_0_0_0, auc_0_0_0

def evaluation_cross_validation_mkl_weight_storage(traindat=traindat, label_traindat=label_traindat):
    from shogun.Evaluation import CrossValidation, CrossValidationResult
    from shogun.Evaluation import CrossValidationPrintOutput
    from shogun.Evaluation import CrossValidationMKLStorage
    from shogun.Evaluation import ContingencyTableEvaluation, ACCURACY
    from shogun.Evaluation import StratifiedCrossValidationSplitting
    from shogun.Features import BinaryLabels
    from shogun.Features import RealFeatures, CombinedFeatures
    from shogun.Kernel import GaussianKernel, CombinedKernel
    from shogun.Classifier import LibSVM, MKLClassification
    from shogun.Mathematics import Statistics

    # training data, combined features all on same data
    features=RealFeatures(traindat)
    comb_features=CombinedFeatures()
    comb_features.append_feature_obj(features)
    comb_features.append_feature_obj(features)
    comb_features.append_feature_obj(features)
    labels=BinaryLabels(label_traindat)
    
    # kernel, different Gaussians combined
    kernel=CombinedKernel()
    kernel.append_kernel(GaussianKernel(10, 0.1))
    kernel.append_kernel(GaussianKernel(10, 1))
    kernel.append_kernel(GaussianKernel(10, 2))

    # create mkl using libsvm, due to a mem-bug, interleaved is not possible
    svm=MKLClassification(LibSVM());
    svm.set_interleaved_optimization_enabled(False);
    svm.set_kernel(kernel);

    # splitting strategy for 5 fold cross-validation (for classification its better
    # to use "StratifiedCrossValidation", but the standard
    # "StratifiedCrossValidationSplitting" is also available
    splitting_strategy=StratifiedCrossValidationSplitting(labels, 5)

    # evaluation method
    evaluation_criterium=ContingencyTableEvaluation(ACCURACY)

    # cross-validation instance
    cross_validation=CrossValidation(svm, comb_features, labels,
        splitting_strategy, evaluation_criterium)
    cross_validation.set_autolock(False)

    # append cross vlaidation output classes
    #cross_validation.add_cross_validation_output(CrossValidationPrintOutput())
    mkl_storage=CrossValidationMKLStorage()
    cross_validation.add_cross_validation_output(mkl_storage)
    cross_validation.set_num_runs(3)
    
    # perform cross-validation
    result=cross_validation.evaluate()

    # print mkl weights
    weights=mkl_storage.get_mkl_weights()

def statistics_linear_time_mmd_kernel_choice():
	from shogun.Features import RealFeatures, CombinedFeatures
	from shogun.Kernel import GaussianKernel, CombinedKernel
	from shogun.Statistics import LinearTimeMMD
	from shogun.Statistics import BOOTSTRAP, MMD1_GAUSSIAN

	# note that the linear time statistic is designed for much larger datasets
	n=50000
	dim=5
	difference=2

	# data is standard normal distributed. only one dimension of Y has a mean
	# shift of difference
	(X,Y)=gen_data.create_mean_data(n,dim,difference)
	
	# concatenate since MMD class takes data as one feature object
	# (it is possible to give two, but then data is copied)
	Z=concatenate((X,Y), axis=1)
	print "dimension means of X", [mean(x) for x in X]
	print "dimension means of Y", [mean(x) for x in Y]

	# create kernels/features to choose from
	# here: just a bunch of Gaussian Kernels with different widths
	# real sigmas are 2^-5, ..., 2^10
	sigmas=array([pow(2,x) for x in range(-5,10)])
	
	# shogun has a different parametrization of the Gaussian kernel
	shogun_sigmas=array([x*x*2 for x in sigmas])
	
	# We will use multiple kernels
	kernel=CombinedKernel()
	
	# two separate feature objects here, could also be one with appended data
	features=CombinedFeatures()
	
	# all kernels work on same features
	for i in range(len(sigmas)):
		kernel.append_kernel(GaussianKernel(10, shogun_sigmas[i]))
		features.append_feature_obj(RealFeatures(Z))
	
	mmd=LinearTimeMMD(kernel,features, n)
	
	print "start learning kernel weights"
	mmd.set_opt_regularization_eps(10E-5)
	mmd.set_opt_low_cut(10E-5)
	mmd.set_opt_max_iterations(1000)
	mmd.set_opt_epsilon(10E-7)
	mmd.optimize_kernel_weights()
	weights=kernel.get_subkernel_weights()
	print "learned weights:", weights
	#pyplot.plot(array(range(len(sigmas))), weights)
	#pyplot.show()
	print "index of max weight", weights.argmax()

def statistics_linear_time_mmd_kernel_choice():
	from shogun.Features import RealFeatures, CombinedFeatures
	from shogun.Features import DataGenerator
	from shogun.Kernel import GaussianKernel, CombinedKernel
	from shogun.Statistics import LinearTimeMMD
	from shogun.Statistics import BOOTSTRAP, MMD1_GAUSSIAN

	# note that the linear time statistic is designed for much larger datasets
	n=50000
	dim=5
	difference=2

	# use data generator class to produce example data
	# in pratice, this generate data function could be replaced by a method
	# that obtains data from a stream
	data=DataGenerator.generate_mean_data(n,dim,difference)
	
	print "dimension means of X", mean(data.T[0:n].T)
	print "dimension means of Y", mean(data.T[n:2*n+1].T)

	# create kernels/features to choose from
	# here: just a bunch of Gaussian Kernels with different widths
	# real sigmas are 2^-5, ..., 2^10
	sigmas=array([pow(2,x) for x in range(-5,10)])
	
	# shogun has a different parametrization of the Gaussian kernel
	shogun_sigmas=array([x*x*2 for x in sigmas])
	
	# We will use multiple kernels
	kernel=CombinedKernel()
	
	# two separate feature objects here, could also be one with appended data
	features=CombinedFeatures()
	
	# all kernels work on same features
	for i in range(len(sigmas)):
		kernel.append_kernel(GaussianKernel(10, shogun_sigmas[i]))
		features.append_feature_obj(RealFeatures(data))
	
	mmd=LinearTimeMMD(kernel,features, n)
	
	print "start learning kernel weights"
	mmd.set_opt_regularization_eps(10E-5)
	mmd.set_opt_low_cut(10E-5)
	mmd.set_opt_max_iterations(1000)
	mmd.set_opt_epsilon(10E-7)
	mmd.optimize_kernel_weights()
	weights=kernel.get_subkernel_weights()
	print "learned weights:", weights
	#pyplot.plot(array(range(len(sigmas))), weights)
	#pyplot.show()
	print "index of max weight", weights.argmax()

def training_run(options):
    """Conduct a training run and return a trained SVM kernel"""
    settings = MotifFinderSettings(kirmes_ini.MOTIF_LENGTH, options.window_width, options.replace)
    positives = MotifFinder(finder_settings=settings)
    positives.setFastaFile(options.positives)
    positives.setMotifs(options.pgff)
    pmotifs, ppositions = positives.getResults()
    negatives = MotifFinder(finder_settings=settings)
    negatives.setFastaFile(options.negatives)
    negatives.setMotifs(options.ngff)
    nmotifs, npositions = negatives.getResults()

    wds_kparams = kirmes_ini.WDS_KERNEL_PARAMETERS
    wds_svm = EasySVM.EasySVM(wds_kparams)
    num_positives = len(pmotifs.values()[0])
    num_negatives = len(nmotifs.values()[0])
    # Creating Kernel Objects
    kernel = CombinedKernel()
    features = CombinedFeatures()
    kernel_array = []
    motifs = pmotifs.keys()
    motifs.sort()
    # Adding Kmer Kernels
    for motif in motifs:
        all_examples = pmotifs[motif] + nmotifs[motif]
        motif_features = wds_svm.createFeatures(all_examples)
        wds_kernel = WeightedDegreePositionStringKernel(motif_features, motif_features, wds_kparams["degree"])
        wds_kernel.set_shifts(wds_kparams["shift"] * ones(wds_kparams["seqlength"], dtype=int32))
        features.append_feature_obj(motif_features)
        kernel_array.append(wds_kernel)
        kernel.append_kernel(wds_kernel)
    rbf_svm = EasySVM.EasySVM(kirmes_ini.RBF_KERNEL_PARAMETERS)
    positions = array(ppositions + npositions, dtype=float64).T
    position_features = rbf_svm.createFeatures(positions)
    features.append_feature_obj(position_features)
    motif_labels = append(ones(num_positives), -ones(num_negatives))
    complete_labels = Labels(motif_labels)
    rbf_kernel = GaussianKernel(position_features, position_features, kirmes_ini.RBF_KERNEL_PARAMETERS["width"])
    kernel_array.append(rbf_kernel)
    kernel.append_kernel(rbf_kernel)
    # Kernel init
    kernel.init(features, features)
    kernel.set_cache_size(kirmes_ini.K_CACHE_SIZE)
    svm = LibSVM(kirmes_ini.K_COMBINED_C, kernel, complete_labels)
    svm.parallel.set_num_threads(kirmes_ini.K_NUM_THREADS)
    # Training
    svm.train()
    if not os.path.exists(options.output_path):
        os.mkdir(options.output_path)
    html = {}
    if options.contrib:
        html["contrib"] = contrib(svm, kernel, motif_labels, kernel_array, motifs)
    if options.logos:
        html["poims"] = poims(svm, kernel, kernel_array, motifs, options.output_path)
    if options.query:
        html["query"] = evaluate(options, svm, kernel, features, motifs)
    htmlize(html, options.output_html)

def get_weighted_spectrum_kernel(subfeats_list, options):
	"""build weighted spectrum kernel with non-redundant k-mer list (removing reverse complement)

	Arguments:
	subfeats_list -- list of sub-feature objects
	options -- object containing option data 

	Return:
	CombinedFeatures of StringWord(Ulong)Features, CombinedKernel of CommWord(Ulong)StringKernel 
	"""
	kmerlen = options.kmerlen
	kmerlen2 = options.kmerlen2

	subkernels = 0
	kernel = CombinedKernel()
	feats = CombinedFeatures()

	for subfeats in subfeats_list:
		feats.append_feature_obj(subfeats)

	for k in xrange(kmerlen, kmerlen2+1):
		if k <= 8:
			subkernel = CommWordStringKernel(10, False)
		else:
			subkernel = CommUlongStringKernel(10, False)

		kernel.append_kernel(subkernel)
		subkernels+=1

	kernel.init(feats, feats)

	kernel.set_subkernel_weights(numpy.array([1/float(subkernels)]*subkernels, numpy.dtype('float64')))

	return kernel

def create_empty_promoter_kernel(param):
    """
    creates an uninitialized promoter kernel
   
    @param param:
    """


    # centered WDK/WDK-shift
    if param["shifts"] == 0:
        kernel_center = WeightedDegreeStringKernel(param["degree"])
    else:
        kernel_center = WeightedDegreePositionStringKernel(10, param["degree"])
        shifts_vector = numpy.ones(param["center_offset"]*2, dtype=numpy.int32)*param["shifts"]
        kernel_center.set_shifts(shifts_vector)

    kernel_center.set_cache_size(param["kernel_cache"]/3)

    # border spetrum kernels
    size = param["kernel_cache"]/3
    use_sign = False
    kernel_left = WeightedCommWordStringKernel(size, use_sign)
    kernel_right = WeightedCommWordStringKernel(size, use_sign)

    # assemble combined kernel
    kernel = CombinedKernel()
    kernel.append_kernel(kernel_center)
    kernel.append_kernel(kernel_left)
    kernel.append_kernel(kernel_right)


    return kernel

def create_combined_kernel(kname, kparam, examples, train_mode, preproc):
    """A wrapper for creating combined kernels.

    kname, kparam and examples are lists.

    """
    num_kernels = len(kname)
    feats['combined'] = CombinedFeatures()
    kernel = CombinedKernel()

    for kix in xrange(num_kernels):
        cur_kname = '%s%d' % (kname[kix],kix)
        (cur_feats, cur_preproc) = create_features(kname[kix], examples[kix], kparam[kix], train_mode, preproc)
        feats[cur_kname] = cur_feats
        cur_kernel = create_kernel(kname[kix], kparam[kix], cur_feats)
        kernel.append_kernel(cur_kernel)

    return (feats,kernel)

    def train(self, data, labels):
        """
        model training 
        """

        # centered WDK/WDK-shift
        if self.param["shifts"] == 0:
            kernel_center = WeightedDegreeStringKernel(self.param["degree"])
        else:
            kernel_center = WeightedDegreePositionStringKernel(10, self.param["degree"])
            shifts_vector = numpy.ones(self.param["center_offset"]*2, dtype=numpy.int32)*self.param["shifts"]
            kernel_center.set_shifts(shifts_vector)

        kernel_center.set_cache_size(self.param["kernel_cache"]/3)

        # border spetrum kernels
        size = self.param["kernel_cache"]/3
        use_sign = False
        kernel_left = WeightedCommWordStringKernel(size, use_sign)
        kernel_right = WeightedCommWordStringKernel(size, use_sign)
        
        # assemble combined kernel
        kernel = CombinedKernel()
        kernel.append_kernel(kernel_center)
        kernel.append_kernel(kernel_left)
        kernel.append_kernel(kernel_right)

        ## building features 
        feat = create_features(data, self.param["center_offset"], self.param["center_pos"])
        
        # init combined kernel
        kernel.init(feat, feat)

        print "len(labels) = %i" % (len(labels))
        lab = BinaryLabels(numpy.double(labels))
        self.svm = SVMLight(self.param["cost"], kernel, lab)

        # show debugging output
        self.svm.io.enable_progress()
        self.svm.io.set_loglevel(MSG_DEBUG)

        # optimization settings
        num_threads = 2
        self.svm.parallel.set_num_threads(num_threads)
        self.svm.set_epsilon(10e-8)

        self.svm.train()

        return self

def loadSVM(pickled_svm_filename, C, labels):
    """Loads a Shogun SVM object which was pickled by saveSVM"""
    from cPickle import Unpickler, PickleError
    from shogun.Kernel import CombinedKernel 
    pickle_file = open(pickled_svm_filename, 'rb')
    unpck = Unpickler(pickle_file)
    (version, num_sv, name, bias, alphas, svs) = unpck.load()
    if (version == __version__):
        svm = LibSVM(num_sv) # same as .create_new_model(num_sv)
        svm.set_bias(bias)
        svm.set_alphas(alphas)
        svm.set_support_vectors(svs)
        kernel = CombinedKernel() #not sure if this is even required
        kernel.set_name(name) # maybe not required
        svm.set_kernel(kernel)
    else: 
        print "File was pickled by another version of EasySVM.py or is not a kernel:"
        print "Received from ", pickled_svm_filename, ": ", version, "    expected: ", __version__
        raise PickleError
    return svm

def create_combined_wd_kernel(instances, param):
    """
    creates a combined wd kernel object
    """

    num_features = len(instances[0])

    # contruct combined features
    kernel = CombinedKernel()
    
    for idx in range(num_features): 
        
        param.kernel = "WeightedDegreeStringKernel"
        
        tmp_kernel = create_empty_kernel(param)
        kernel.append_kernel(tmp_kernel)

    combined_features = create_combined_wd_features(instances, feat_type="dna")

    kernel.init(combined_features, combined_features)
    
    return kernel

def mkl_binclass_modular(fm_train_real=traindat,
                         fm_test_real=testdat,
                         fm_label_twoclass=label_traindat):

    sc1 = StringCharFeatures(strings1, RAWBYTE)
    sc2 = StringCharFeatures(strings2, RAWBYTE)

    sfeats1 = StringWordFeatures(RAWBYTE)
    sfeats1.obtain_from_char(sc1, 0, 2, 0, False)
    skernel1 = CommWordStringKernel(10, False)
    skernel1.init(sfeats1, sfeats1)
    sfeats2 = StringWordFeatures(RAWBYTE)
    sfeats2.obtain_from_char(sc2, 0, 2, 0, False)
    skernel2 = CommWordStringKernel(10, False)
    skernel2.init(sfeats2, sfeats2)

    ffeats = RealFeatures(traindat)
    fkernel = LinearKernel(ffeats, ffeats)

    fffeats = RealFeatures(traindat)
    ffkernel = GaussianKernel(fffeats, fffeats, 1.0)

    # COMBINING LINADD FEATURES/KERNELS LEAD TO FAIL
    feats_train = CombinedFeatures()
    feats_train.append_feature_obj(ffeats)
    #feats_train.append_feature_obj(fffeats)
    feats_train.append_feature_obj(sfeats2)

    print feats_train.get_num_vectors()

    kernel = CombinedKernel()
    kernel.append_kernel(fkernel)
    #kernel.append_kernel(ffkernel)
    kernel.append_kernel(skernel2)
    kernel.init(feats_train, feats_train)

    labels = RegressionLabels(fm_label_twoclass)
    mkl = MKLRegression()

    mkl.set_mkl_norm(1)  #2,3
    mkl.set_C(1, 1)
    mkl.set_kernel(kernel)
    mkl.set_labels(labels)

    mkl.io.enable_file_and_line()
    mkl.io.set_loglevel(MSG_DEBUG)

feats_train.append_feature_obj(RealFeatures(traindata_real))
feats_train.append_feature_obj(RealFeatures(traindata_real))
feats_train.append_feature_obj(RealFeatures(traindata_real))
feats_train.append_feature_obj(RealFeatures(traindata_real))

feats_test = CombinedFeatures()
feats_test.append_feature_obj(RealFeatures(testdata_real))
feats_test.append_feature_obj(RealFeatures(testdata_real))
feats_test.append_feature_obj(RealFeatures(testdata_real))
feats_test.append_feature_obj(RealFeatures(testdata_real))
feats_test.append_feature_obj(RealFeatures(testdata_real))

labels = BinaryLabels(trainlab)

# and corresponding combined kernel
kernel = CombinedKernel()
kernel.append_kernel(GaussianKernel(10, s))
kernel.append_kernel(GaussianKernel(10, s))
kernel.append_kernel(GaussianKernel(10, s))
kernel.append_kernel(GaussianKernel(10, s))
kernel.append_kernel(GaussianKernel(10, s))
kernel.init(feats_train, feats_train)

# Create a classifier
classifier=MKLClassification(LibSVM())
classifier.set_interleaved_optimization_enabled(False)
classifier.set_kernel(kernel)
classifier.set_labels(labels)
classifier.set_C(C, C)

param_tree_root=ModelSelectionParameters()

def kernel_combined_custom_poly_modular(fm_train_real = traindat,fm_test_real = testdat,fm_label_twoclass=label_traindat):
    from shogun.Features import CombinedFeatures, RealFeatures, BinaryLabels
    from shogun.Kernel import CombinedKernel, PolyKernel, CustomKernel
    from shogun.Classifier import LibSVM
   
    kernel = CombinedKernel()
    feats_train = CombinedFeatures()
    
    tfeats = RealFeatures(fm_train_real)
    tkernel = PolyKernel(10,3)
    tkernel.init(tfeats, tfeats)
    K = tkernel.get_kernel_matrix()
    kernel.append_kernel(CustomKernel(K))
        
    subkfeats_train = RealFeatures(fm_train_real)
    feats_train.append_feature_obj(subkfeats_train)
    subkernel = PolyKernel(10,2)
    kernel.append_kernel(subkernel)

    kernel.init(feats_train, feats_train)
    
    labels = BinaryLabels(fm_label_twoclass)
    svm = LibSVM(1.0, kernel, labels)
    svm.train()

    kernel = CombinedKernel()
    feats_pred = CombinedFeatures()

    pfeats = RealFeatures(fm_test_real)
    tkernel = PolyKernel(10,3)
    tkernel.init(tfeats, pfeats)
    K = tkernel.get_kernel_matrix()
    kernel.append_kernel(CustomKernel(K))

    subkfeats_test = RealFeatures(fm_test_real)
    feats_pred.append_feature_obj(subkfeats_test)
    subkernel = PolyKernel(10, 2)
    kernel.append_kernel(subkernel)
    kernel.init(feats_train, feats_pred)

    svm.set_kernel(kernel)
    svm.apply()
    km_train=kernel.get_kernel_matrix()
    return km_train,kernel

def mkl_multiclass_modular(fm_train_real, fm_test_real, label_train_multiclass,
	width, C, epsilon, num_threads, mkl_epsilon, mkl_norm):

	from shogun.Features import CombinedFeatures, RealFeatures, Labels
	from shogun.Kernel import CombinedKernel, GaussianKernel, LinearKernel,PolyKernel
	from shogun.Classifier import MKLMultiClass

	kernel = CombinedKernel()
	feats_train = CombinedFeatures()
	feats_test = CombinedFeatures()

	subkfeats_train = RealFeatures(fm_train_real)
	subkfeats_test = RealFeatures(fm_test_real)
	subkernel = GaussianKernel(10, width)
	feats_train.append_feature_obj(subkfeats_train)
	feats_test.append_feature_obj(subkfeats_test)
	kernel.append_kernel(subkernel)

	subkfeats_train = RealFeatures(fm_train_real)
	subkfeats_test = RealFeatures(fm_test_real)
	subkernel = LinearKernel()
	feats_train.append_feature_obj(subkfeats_train)
	feats_test.append_feature_obj(subkfeats_test)
	kernel.append_kernel(subkernel)

	subkfeats_train = RealFeatures(fm_train_real)
	subkfeats_test = RealFeatures(fm_test_real)
	subkernel = PolyKernel(10,2)
	feats_train.append_feature_obj(subkfeats_train)
	feats_test.append_feature_obj(subkfeats_test)
	kernel.append_kernel(subkernel)
	
	kernel.init(feats_train, feats_train)

	labels = Labels(label_train_multiclass)

	mkl = MKLMultiClass(C, kernel, labels)
	
	mkl.set_epsilon(epsilon);
	mkl.parallel.set_num_threads(num_threads)
	mkl.set_mkl_epsilon(mkl_epsilon)
	mkl.set_mkl_norm(mkl_norm)

	mkl.train()

	kernel.init(feats_train, feats_test)

	out =  mkl.classify().get_labels()
	return out