def svm_light (): print 'SVMLight' from shogun.Features import StringCharFeatures, Labels, DNA from shogun.Kernel import WeightedDegreeStringKernel try: from shogun.Classifier import SVMLight except ImportError: print 'No support for SVMLight available.' return feats_train=StringCharFeatures(DNA) feats_train.set_features(fm_train_dna) feats_test=StringCharFeatures(DNA) feats_test.set_features(fm_test_dna) degree=20 kernel=WeightedDegreeStringKernel(feats_train, feats_train, degree) C=1.2 epsilon=1e-5 num_threads=1 labels=Labels(label_train_dna) svm=SVMLight(C, kernel, labels) svm.set_epsilon(epsilon) svm.parallel.set_num_threads(num_threads) svm.train() kernel.init(feats_train, feats_test) svm.classify().get_labels()
def classifier_svmlight_modular(fm_train_dna=traindat,
fm_test_dna=testdat,
label_train_dna=label_traindat,
C=1.2,
epsilon=1e-5,
num_threads=1):
from shogun.Features import StringCharFeatures, Labels, DNA
from shogun.Kernel import WeightedDegreeStringKernel
try:
from shogun.Classifier import SVMLight
except ImportError:
print 'No support for SVMLight available.'
return
feats_train = StringCharFeatures(DNA)
feats_train.set_features(fm_train_dna)
feats_test = StringCharFeatures(DNA)
feats_test.set_features(fm_test_dna)
degree = 20
kernel = WeightedDegreeStringKernel(feats_train, feats_train, degree)
labels = Labels(label_train_dna)
svm = SVMLight(C, kernel, labels)
svm.set_epsilon(epsilon)
svm.parallel.set_num_threads(num_threads)
svm.train()
kernel.init(feats_train, feats_test)
svm.classify().get_labels()
return kernel
def classifier_svmlight_linear_term_modular(fm_train_dna=traindna,fm_test_dna=testdna, \
label_train_dna=label_traindna,degree=3, \
C=10,epsilon=1e-5,num_threads=1):
from shogun.Features import StringCharFeatures, Labels, DNA
from shogun.Kernel import WeightedDegreeStringKernel
from shogun.Classifier import SVMLight
feats_train=StringCharFeatures(DNA)
feats_train.set_features(fm_train_dna)
feats_test=StringCharFeatures(DNA)
feats_test.set_features(fm_test_dna)
kernel=WeightedDegreeStringKernel(feats_train, feats_train, degree)
labels=Labels(label_train_dna)
svm=SVMLight(C, kernel, labels)
svm.set_qpsize(3)
svm.set_linear_term(-numpy.array([1,2,3,4,5,6,7,8,7,6], dtype=numpy.double));
svm.set_epsilon(epsilon)
svm.parallel.set_num_threads(num_threads)
svm.train()
kernel.init(feats_train, feats_test)
out = svm.classify().get_labels()
return out,kernel
def do_batch_linadd (): print 'SVMlight batch' from shogun.Features import StringCharFeatures, Labels, DNA from shogun.Kernel import WeightedDegreeStringKernel try: from shogun.Classifier import SVMLight except ImportError: print 'No support for SVMLight available.' return feats_train=StringCharFeatures(DNA) feats_train.set_features(fm_train_dna) feats_test=StringCharFeatures(DNA) feats_test.set_features(fm_test_dna) degree=20 kernel=WeightedDegreeStringKernel(feats_train, feats_train, degree) C=1 epsilon=1e-5 num_threads=2 labels=Labels(label_train_dna) svm=SVMLight(C, kernel, labels) svm.set_epsilon(epsilon) svm.parallel.set_num_threads(num_threads) svm.train() kernel.init(feats_train, feats_test) #print 'SVMLight Objective: %f num_sv: %d' % \ # (svm.get_objective(), svm.get_num_support_vectors()) svm.set_batch_computation_enabled(False) svm.set_linadd_enabled(False) svm.classify().get_labels() svm.set_batch_computation_enabled(True) svm.classify().get_labels()
def classifier_svmlight_batch_linadd_modular(fm_train_dna, fm_test_dna, label_train_dna, degree, C, epsilon, num_threads): from shogun.Features import StringCharFeatures, Labels, DNA from shogun.Kernel import WeightedDegreeStringKernel, MSG_DEBUG try: from shogun.Classifier import SVMLight except ImportError: print 'No support for SVMLight available.' return feats_train=StringCharFeatures(DNA) #feats_train.io.set_loglevel(MSG_DEBUG) feats_train.set_features(fm_train_dna) feats_test=StringCharFeatures(DNA) feats_test.set_features(fm_test_dna) degree=20 kernel=WeightedDegreeStringKernel(feats_train, feats_train, degree) labels=Labels(label_train_dna) svm=SVMLight(C, kernel, labels) svm.set_epsilon(epsilon) svm.parallel.set_num_threads(num_threads) svm.train() kernel.init(feats_train, feats_test) #print 'SVMLight Objective: %f num_sv: %d' % \ # (svm.get_objective(), svm.get_num_support_vectors()) svm.set_batch_computation_enabled(False) svm.set_linadd_enabled(False) svm.classify().get_labels() svm.set_batch_computation_enabled(True) labels = svm.classify().get_labels() return labels, svm
print 'SVMLight' from shogun.Features import StringCharFeatures, Labels, DNA from shogun.Kernel import WeightedDegreeStringKernel from shogun.Classifier import SVMLight feats_train=StringCharFeatures(DNA) feats_train.set_features(fm_train_dna) feats_test=StringCharFeatures(DNA) feats_test.set_features(fm_test_dna) kernel=WeightedDegreeStringKernel(feats_train, feats_train, degree) C=10 epsilon=1e-5 num_threads=1 labels=Labels(label_train_dna) svm=SVMLight(C, kernel, labels) svm.set_qpsize(3) svm.set_linear_term(-numpy.array([1,2,3,4,5,6,7,8,7,6], dtype=numpy.double)); svm.set_epsilon(epsilon) svm.parallel.set_num_threads(num_threads) svm.train() kernel.init(feats_train, feats_test) out = svm.classify().get_labels()
sv_id = int(old_svm.get_support_vectors()[j])
alpha = old_svm.get_alpha(j)
inner_sum = inner_sum + alpha * kv.kernel(sv_id, idx)
inner.append(inner_sum)
#general case
p[idx] = B * tmp_lab[idx] * inner_sum - 1.0
################
#checking inner term
presvm.set_bias(0.0)
tmp_out = presvm.classify(feat).get_labels()
for i in xrange(len(examples)):
#print inner[i], tmp_out[i]
assert(abs(inner[i]-tmp_out[i])<= 0.001)
svm = SVMLight(1.0, wdk, lab)
svm.set_linear_term(p)
Math_init_random(1)
svm.train()
###############
#compare to LibSVM
for j in xrange(old_svm.get_num_support_vectors()):
sv_id = int(old_svm.get_support_vectors()[j])
alpha = old_svm.get_alpha(j)
inner_sum = inner_sum + alpha * kv.kernel(sv_id, idx)
inner.append(inner_sum)
#general case
p[idx] = B * tmp_lab[idx] * inner_sum - 1.0
################
#checking inner term
presvm.set_bias(0.0)
tmp_out = presvm.classify(feat).get_labels()
for i in xrange(len(examples)):
#print inner[i], tmp_out[i]
assert (abs(inner[i] - tmp_out[i]) <= 0.001)
svm = SVMLight(1.0, wdk, lab)
svm.set_linear_term(p)
Math_init_random(1)
svm.train()
###############
#compare to LibSVM
svm2 = LibSVM(1.0, wdk, lab)
