def kernel_io_modular (fm_train_real=traindat,fm_test_real=testdat,width=1.9):
from shogun.Features import RealFeatures
from shogun.Kernel import GaussianKernel
from shogun.Library import AsciiFile, BinaryFile
feats_train=RealFeatures(fm_train_real)
feats_test=RealFeatures(fm_test_real)
kernel=GaussianKernel(feats_train, feats_train, width)
km_train=kernel.get_kernel_matrix()
f=AsciiFile("gaussian_train.ascii","w")
kernel.save(f)
del f
kernel.init(feats_train, feats_test)
km_test=kernel.get_kernel_matrix()
f=AsciiFile("gaussian_test.ascii","w")
kernel.save(f)
del f
#clean up
import os
os.unlink("gaussian_test.ascii")
os.unlink("gaussian_train.ascii")
return km_train, km_test, kernel
def kernel_io_modular(fm_train_real=traindat, fm_test_real=testdat, width=1.9):
from shogun.Features import RealFeatures
from shogun.Kernel import GaussianKernel
from shogun.IO import AsciiFile, BinaryFile
feats_train = RealFeatures(fm_train_real)
feats_test = RealFeatures(fm_test_real)
kernel = GaussianKernel(feats_train, feats_train, width)
km_train = kernel.get_kernel_matrix()
f = AsciiFile("gaussian_train.ascii", "w")
kernel.save(f)
del f
kernel.init(feats_train, feats_test)
km_test = kernel.get_kernel_matrix()
f = AsciiFile("gaussian_test.ascii", "w")
kernel.save(f)
del f
#clean up
import os
os.unlink("gaussian_test.ascii")
os.unlink("gaussian_train.ascii")
return km_train, km_test, kernel
def mkl_binclass_modular (train_data, testdata, train_labels, test_labels, d1, d2):
# create some Gaussian train/test matrix
tfeats = RealFeatures(train_data)
tkernel = GaussianKernel(128, d1)
tkernel.init(tfeats, tfeats)
K_train = tkernel.get_kernel_matrix()
pfeats = RealFeatures(test_data)
tkernel.init(tfeats, pfeats)
K_test = tkernel.get_kernel_matrix()
# create combined train features
feats_train = CombinedFeatures()
feats_train.append_feature_obj(RealFeatures(train_data))
# and corresponding combined kernel
kernel = CombinedKernel()
kernel.append_kernel(CustomKernel(K_train))
kernel.append_kernel(GaussianKernel(128, d2))
kernel.init(feats_train, feats_train)
# train mkl
labels = Labels(train_labels)
mkl = MKLClassification()
# not to use svmlight
mkl.set_interleaved_optimization_enabled(0)
# which norm to use for MKL
mkl.set_mkl_norm(2)
# set cost (neg, pos)
mkl.set_C(1, 1)
# set kernel and labels
mkl.set_kernel(kernel)
mkl.set_labels(labels)
# train
mkl.train()
# test
# create combined test features
feats_pred = CombinedFeatures()
feats_pred.append_feature_obj(RealFeatures(test_data))
# and corresponding combined kernel
kernel = CombinedKernel()
kernel.append_kernel(CustomKernel(K_test))
kernel.append_kernel(GaussianKernel(128, d2))
kernel.init(feats_train, feats_pred)
# and classify
mkl.set_kernel(kernel)
output = mkl.apply().get_labels()
output = [1.0 if i>0 else -1.0 for i in output]
accu = len(where(output == test_labels)[0]) / float(len(output))
return accu
def kernel_gaussian_modular (fm_train_real=traindat,fm_test_real=testdat, width=1.3): from shogun.Features import RealFeatures from shogun.Kernel import GaussianKernel feats_train=RealFeatures(fm_train_real) feats_test=RealFeatures(fm_test_real) kernel=GaussianKernel(feats_train, feats_train, width) km_train=kernel.get_kernel_matrix() kernel.init(feats_train, feats_test) km_test=kernel.get_kernel_matrix() return km_train,km_test,kernel
def gaussian (): print 'Gaussian' from shogun.Features import RealFeatures from shogun.Kernel import GaussianKernel feats_train=RealFeatures(fm_train_real) feats_test=RealFeatures(fm_test_real) width=1.9 kernel=GaussianKernel(feats_train, feats_train, width) km_train=kernel.get_kernel_matrix() kernel.init(feats_train, feats_test) km_test=kernel.get_kernel_matrix()
