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 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()
weights = []
i = 0
for subfeats in subfeats_list:
feats.append_feature_obj(subfeats)
combine_kcount = Counter()
for i in xrange(subfeats.get_num_vectors()):
fv = list(subfeats.get_feature_vector(i))
combine_kcount += Counter(fv)
number = len(combine_kcount)
klen = kmerlen + i
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)
# here the weight for each k-mer is uniform
'''
subkernels = 8
numpy.array([1 / float(subkernels)] * subkernels, numpy.dtype('float64'))
array([ 0.125, 0.125, 0.125, 0.125, 0.125, 0.125, 0.125, 0.125])
'''
kernel.set_subkernel_weights(
numpy.array([1 / float(subkernels)] * subkernels,
numpy.dtype('float64')))
return kernel
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
c2.build_values(-4.0, 4.0, R_EXP);
param_tree_root.append_child(c2)
splitting_strategy = StratifiedCrossValidationSplitting(labels, 50)
evaluation_criterium = ContingencyTableEvaluation(ACCURACY)
cross_validation = CrossValidation(classifier, feats_train, labels, splitting_strategy, evaluation_criterium)
model_selection = GridSearchModelSelection(param_tree_root, cross_validation)
best_parameters = model_selection.select_model(True)
print "Best parameters: ",
best_parameters.print_tree()
best_parameters.apply_to_machine(classifier)
classifier.train()
w=kernel.get_subkernel_weights()
kernel.set_subkernel_weights(w)
# Plot ROC curve
subplot(111)
ROC_evaluation=ROCEvaluation()
ROC_evaluation.evaluate(classifier.apply(feats_train),Labels(trainlab))
roc = ROC_evaluation.get_ROC()
plot(roc[0], roc[1])
fill_between(roc[0],roc[1],0,alpha=0.1)
grid(True)
xlabel('FPR')
ylabel('TPR')
title('Train ROC (Width=%.3f, C1=%.3f, C2=%.3f) ROC curve = %.3f' % (10, classifier.get_C1(), classifier.get_C2(), ROC_evaluation.get_auROC()),size=10)
savefig("data/iri/mkl.png")
"""
subplot(222)
def _train(self, train_data, param):
"""
training procedure using training examples and labels
@param train_data: Data relevant to SVM training
@type train_data: dict<str, list<instances> >
@param param: Parameters for the training procedure
@type param: ParameterSvm
"""
# merge data sets
data = PreparedMultitaskData(train_data, shuffle=False)
# create shogun data objects
base_wdk = shogun_factory.create_empty_kernel(param)
lab = shogun_factory.create_labels(data.labels)
combined_kernel = CombinedKernel()
combined_kernel.io.set_loglevel(shogun.Kernel.MSG_INFO)
base_features = shogun_factory.create_features(data.examples)
combined_features = CombinedFeatures()
# set normalizer
normalizer = MultitaskKernelNormalizer(data.task_vector_nums)
# load data
#f = file("/fml/ag-raetsch/home/cwidmer/Documents/phd/projects/multitask/data/mhc/MHC_Distanzen/MHC_Distanzen/ALL_PseudoSeq_BlosumEnc_pearson.txt")
f = file(
"/fml/ag-raetsch/home/cwidmer/Documents/phd/projects/multitask/data/mhc/MHC_Distanzen/MHC_Distanzen/All_PseudoSeq_Hamming.txt"
)
#f = file("/fml/ag-raetsch/home/cwidmer/Documents/phd/projects/multitask/data/mhc/MHC_Distanzen/MHC_Distanzen/ALL_PseudoSeq_BlosumEnc_euklid.txt")
#f = file("/fml/ag-raetsch/home/cwidmer/Documents/phd/projects/multitask/data/mhc/MHC_Distanzen/MHC_Distanzen/ALL_RAxML.txt")
num_lines = int(f.readline().strip())
task_distances = numpy.zeros((num_lines, num_lines))
name_to_id = {}
for (i, line) in enumerate(f):
tokens = line.strip().split("\t")
name = str(tokens[0])
name_to_id[name] = i
entry = numpy.array([v for (j, v) in enumerate(tokens) if j != 0])
assert len(entry) == num_lines, "len_entry %i, num_lines %i" % (
len(entry), num_lines)
task_distances[i, :] = entry
# cut relevant submatrix
active_ids = [name_to_id[name] for name in data.get_task_names()]
tmp_distances = task_distances[active_ids, :]
tmp_distances = tmp_distances[:, active_ids]
print "distances ", tmp_distances.shape
# normalize distances
task_distances = task_distances / numpy.max(tmp_distances)
similarities = numpy.zeros(
(data.get_num_tasks(), data.get_num_tasks()))
# convert distance to similarity
for task_name_lhs in data.get_task_names():
for task_name_rhs in data.get_task_names():
# convert similarity with simple transformation
similarity = param.base_similarity - task_distances[
name_to_id[task_name_lhs], name_to_id[task_name_rhs]]
normalizer.set_task_similarity(data.name_to_id(task_name_lhs),
data.name_to_id(task_name_rhs),
similarity)
# save for later
similarities[data.name_to_id(task_name_lhs),
data.name_to_id(task_name_rhs)] = similarity
# set normalizer
base_wdk.set_normalizer(normalizer)
#base_wdk.init_normalizer()
combined_features.append_feature_obj(base_features)
combined_kernel.append_kernel(base_wdk)
##################################################
# intra-domain blocks
intra_block_vec = PairiiVec()
for task_id in data.get_task_ids():
intra_block_vec.push_back(Pairii(task_id, task_id))
# create mask-based normalizer
normalizer = MultitaskKernelMaskPairNormalizer(data.task_vector_nums,
intra_block_vec)
kernel = shogun_factory.create_empty_kernel(param)
kernel.set_normalizer(normalizer)
# append current kernel to CombinedKernel
combined_kernel.append_kernel(kernel)
# append features
combined_features.append_feature_obj(base_features)
# set mixing factor (used if MKL is OFF)
assert (param.base_similarity <= 1)
assert (param.base_similarity >= 0)
combined_kernel.set_subkernel_weights(
[param.base_similarity, 1 - param.base_similarity])
combined_kernel.init(combined_features, combined_features)
svm = None
print "using MKL:", (param.transform >= 1.0)
if param.transform >= 1.0:
svm = MKLClassification()
svm.set_mkl_norm(param.transform)
#svm.set_solver_type(ST_CPLEX) #ST_GLPK) #DIRECT) #NEWTON)#ST_CPLEX) #auto
svm.set_C(param.cost, param.cost)
svm.set_kernel(combined_kernel)
svm.set_labels(lab)
else:
# create SVM (disable unsupported optimizations)
combined_kernel.set_cache_size(500)
svm = SVMLight(param.cost, combined_kernel, lab)
# set up SVM
num_threads = 8
svm.io.enable_progress()
svm.io.set_loglevel(shogun.Classifier.MSG_DEBUG)
svm.parallel.set_num_threads(num_threads)
svm.set_linadd_enabled(False)
svm.set_batch_computation_enabled(False)
print "WARNING: custom epsilon set"
svm.set_epsilon(0.05)
# normalize cost
norm_c_pos = param.cost / float(len([l
for l in data.labels if l == 1]))
norm_c_neg = param.cost / float(
len([l for l in data.labels if l == -1]))
svm.set_C(norm_c_neg, norm_c_pos)
# start training
svm.train()
# save additional information
self.additional_information["svm objective"] = svm.get_objective()
self.additional_information["num sv"] = svm.get_num_support_vectors()
self.additional_information["similarities"] = similarities
self.additional_information[
"post_weights"] = combined_kernel.get_subkernel_weights()
# wrap up predictors
svms = {}
# use a reference to the same svm several times
for task_name in data.get_task_names():
task_num = data.name_to_id(task_name)
# save svm and task_num
svms[task_name] = (task_num, combined_kernel, svm)
return svms