def classifier_domainadaptationsvm_modular(fm_train_dna=traindna,fm_test_dna=testdna, \
label_train_dna=label_traindna, \
label_test_dna=label_testdna,fm_train_dna2=traindna2,fm_test_dna2=testdna2, \
label_train_dna2=label_traindna2,label_test_dna2=label_testdna2,C=1,degree=3):
feats_train = StringCharFeatures(fm_train_dna, DNA)
feats_test = StringCharFeatures(fm_test_dna, DNA)
kernel = WeightedDegreeStringKernel(feats_train, feats_train, degree)
labels = Labels(label_train_dna)
svm = SVMLight(C, kernel, labels)
svm.train()
#svm.io.set_loglevel(MSG_DEBUG)
#####################################
#print "obtaining DA SVM from previously trained SVM"
feats_train2 = StringCharFeatures(fm_train_dna, DNA)
feats_test2 = StringCharFeatures(fm_test_dna, DNA)
kernel2 = WeightedDegreeStringKernel(feats_train, feats_train, degree)
labels2 = Labels(label_train_dna)
# we regularize against the previously obtained solution
dasvm = DomainAdaptationSVM(C, kernel2, labels2, svm, 1.0)
dasvm.train()
out = dasvm.apply(feats_test2).get_labels()
return out #,dasvm TODO
def classifier_domainadaptationsvm_modular(fm_train_dna=traindna,fm_test_dna=testdna, \
label_train_dna=label_traindna, \
label_test_dna=label_testdna,fm_train_dna2=traindna2,fm_test_dna2=testdna2, \
label_train_dna2=label_traindna2,label_test_dna2=label_testdna2,C=1,degree=3):
feats_train = StringCharFeatures(fm_train_dna, DNA)
feats_test = StringCharFeatures(fm_test_dna, DNA)
kernel = WeightedDegreeStringKernel(feats_train, feats_train, degree)
labels = BinaryLabels(label_train_dna)
svm = SVMLight(C, kernel, labels)
svm.train()
#svm.io.set_loglevel(MSG_DEBUG)
#####################################
#print("obtaining DA SVM from previously trained SVM")
feats_train2 = StringCharFeatures(fm_train_dna, DNA)
feats_test2 = StringCharFeatures(fm_test_dna, DNA)
kernel2 = WeightedDegreeStringKernel(feats_train, feats_train, degree)
labels2 = BinaryLabels(label_train_dna)
# we regularize against the previously obtained solution
dasvm = DomainAdaptationSVM(C, kernel2, labels2, svm, 1.0)
dasvm.train()
out = dasvm.apply_binary(feats_test2)
return out #,dasvm TODO
def create_domain_adaptation_svm(param, k, lab, presvm, weight):
'''
create SVM object with standard settings
@param param: parameter object
@param k: kernel
@param lab: label object
@return: svm object
'''
# create SVM
if param.flags.has_key(
"svm_type") and param.flags["svm_type"] == "liblineardual":
svm = DomainAdaptationSVMLinear(param.cost, k, lab, presvm, weight)
else:
svm = DomainAdaptationSVM(param.cost, k, lab, presvm, weight)
return set_svm_parameters(svm, param)
Math_init_random(1)
dasvm_manual_libsvm.train()
###############
# compare to LibLinear
dasvm_manual_liblinear = LibLinear(1.0, feat, lab)
dasvm_manual_liblinear.set_linear_term(linterm_manual)
dasvm_manual_liblinear.set_bias_enabled(False)
dasvm_manual_liblinear.train()
#############################################
# compute DA-SVMs in shogun (kernelized AND linear)
#############################################
dasvm_libsvm = DomainAdaptationSVM(1.0, wdk, lab, presvm_libsvm, B)
dasvm_libsvm.set_bias_enabled(False)
dasvm_libsvm.train()
dasvm_liblinear = DomainAdaptationSVMLinear(1.0, feat, lab, presvm_liblinear,
B)
dasvm_liblinear.io.set_loglevel(MSG_DEBUG)
dasvm_liblinear.set_bias_enabled(False)
dasvm_liblinear.train()
print "##############"
alphas = []
sv_ids = dasvm_libsvm.get_support_vectors()
for (j, sv_id) in enumerate(sv_ids):
alpha = dasvm_libsvm.get_alphas()[j]
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
"""
for task_id in train_data.keys():
print "task_id:", task_id
root = param.taxonomy.data
grey_nodes = [root]
# top-down processing of taxonomy
while len(grey_nodes) > 0:
node = grey_nodes.pop(0) # pop first item
# enqueue children
if node.children != None:
grey_nodes.extend(node.children)
#####################################################
# init data structures
#####################################################
# get data below current node
data = [train_data[key] for key in node.get_data_keys()]
print "data at current level"
for instance_set in data:
print instance_set[0].dataset
# initialize containers
examples = []
labels = []
# concatenate data
for instance_set in data:
print "train split_set:", instance_set[0].dataset.organism
for inst in instance_set:
examples.append(inst.example)
labels.append(inst.label)
# create shogun data objects
k = shogun_factory_new.create_kernel(examples, param)
lab = shogun_factory_new.create_labels(labels)
cost = param.cost
#cost = node.cost
print "using cost:", cost
#####################################################
# train predictors
#####################################################
# init predictor variable
svm = None
# set up SVM
if node.is_root():
print "training svm at top level"
svm = SVMLight(cost, k, lab)
else:
# regularize vs parent predictor
#weight = node.edge_weight
weight = param.transform
print "current edge_weight:", weight, " ,name:", node.name
parent_svm = node.parent.predictor
svm = DomainAdaptationSVM(cost, k, lab, parent_svm, weight)
#svm.set_train_factor(param.base_similarity)
if param.flags["normalize_cost"]:
norm_c_pos = param.cost / float(
len([l for l in lab.get_labels() if l == 1]))
norm_c_neg = param.cost / float(
len([l for l in lab.get_labels() if l == -1]))
svm.set_C(norm_c_neg, norm_c_pos)
# set epsilon
if param.flags.has_key("epsilon"):
svm.set_epsilon(param.flags["epsilon"])
# enable output
svm.io.enable_progress()
svm.io.set_loglevel(shogun.Classifier.MSG_INFO)
svm.set_train_factor(param.flags["train_factor"])
svm.train()
# attach svm to node
node.predictor = svm
# save some information
self.additional_information[node.name +
" svm obj"] = svm.get_objective()
self.additional_information[
node.name + " svm num sv"] = svm.get_num_support_vectors()
self.additional_information[node.name +
" runtime"] = svm.get_runtime()
#####################################################
# Wrap things up
#####################################################
# wrap up predictors for later use
predictors = {}
for leaf in root.get_leaves():
predictors[leaf.name] = leaf.predictor
assert (leaf.predictor != None)
# make sure we have the same keys (potentiall in a different order)
sym_diff_keys = set(train_data.keys()).symmetric_difference(
set(predictors.keys()))
assert len(
sym_diff_keys
) == 0, "symmetric difference between keys non-empty: " + str(
sym_diff_keys)
# save graph plot
mypath = "/fml/ag-raetsch/share/projects/multitask/graphs/"
filename = mypath + "graph_" + str(param.id)
root.plot(filename) #, plot_cost=True, plot_B=True)
return predictors
'AGCAGGAAGGGGGGGAGTC'] label_test_dna2 = numpy.array(5*[-1.0] + 5*[1.0]) C = 1.0 feats_train = StringCharFeatures(fm_train_dna, DNA) feats_test = StringCharFeatures(fm_test_dna, DNA) kernel = WeightedDegreeStringKernel(feats_train, feats_train, degree) labels = Labels(label_train_dna) svm = SVMLight(C, kernel, labels) svm.train() ##################################### print "obtaining DA SVM from previously trained SVM" feats_train2 = StringCharFeatures(fm_train_dna, DNA) feats_test2 = StringCharFeatures(fm_test_dna, DNA) kernel2 = WeightedDegreeStringKernel(feats_train, feats_train, degree) labels2 = Labels(label_train_dna) # we regularize against the previously obtained solution dasvm = DomainAdaptationSVM(C, kernel2, labels2, svm, 1.0) dasvm.train() out = dasvm.classify(feats_test2).get_labels() print out
objective = svm.get_objective() print "svmlight alphas:", numpy.array(alphas[0:5]) ############################################# # compute DA-SVMs in shogun ############################################# dasvm = DomainAdaptationSVM(1.0, wdk, lab, presvm, B) #dasvm = SVMLight(1.0, wdk, lab) Math_init_random(1) dasvm.train() #dasvm = SVMLight(1.0, wdk, lab) #dasvm.set_linear_term(numpy.double(p)) #dasvm.train() lin_da = dasvm.get_linear_term() daobj = dasvm.get_objective()
############### # compare to LibLinear dasvm_manual_liblinear = LibLinear(1.0, feat, lab) dasvm_manual_liblinear.set_linear_term(linterm_manual) dasvm_manual_liblinear.set_bias_enabled(False) dasvm_manual_liblinear.train() ############################################# # compute DA-SVMs in shogun (kernelized AND linear) ############################################# dasvm_libsvm = DomainAdaptationSVM(1.0, wdk, lab, presvm_libsvm, B) dasvm_libsvm.set_bias_enabled(False) dasvm_libsvm.train() dasvm_liblinear = DomainAdaptationSVMLinear(1.0, feat, lab, presvm_liblinear, B) dasvm_liblinear.io.set_loglevel(MSG_DEBUG) dasvm_liblinear.set_bias_enabled(False) dasvm_liblinear.train() print "##############" alphas = [] sv_ids = dasvm_libsvm.get_support_vectors() for (j, sv_id) in enumerate(sv_ids):
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
"""
for task_id in train_data.keys():
print "task_id:", task_id
root = param.taxonomy.data
grey_nodes = [root]
# top-down processing of taxonomy
for node in root.get_leaves():
#####################################################
# train predictor
#####################################################
parent_node = node.get_nearest_neighbor()
cost = param.cost
(examples, labels) = self.get_data(parent_node, train_data)
# create shogun data objects
k_parent = shogun_factory_new.create_kernel(examples, param)
lab_parent = shogun_factory_new.create_labels(labels)
parent_svm = SVMLight(cost, k_parent, lab_parent)
parent_svm.train()
#####################################################
# train predictors
#####################################################
(examples, labels) = self.get_data(node, train_data)
# create shogun data objects
k = shogun_factory_new.create_kernel(examples, param)
lab = shogun_factory_new.create_labels(labels)
# regularize vs parent predictor
weight = param.transform
print "current edge_weight:", weight, " ,name:", node.name
svm = DomainAdaptationSVM(cost, k, lab, parent_svm, weight)
svm.train()
# attach svm to node
node.predictor = svm
#####################################################
# Wrap things up
#####################################################
# wrap up predictors for later use
predictors = {}
for leaf in root.get_leaves():
predictors[leaf.name] = leaf.predictor
assert(leaf.predictor!=None)
sym_diff_keys = set(train_data.keys()).symmetric_difference(set(predictors.keys()))
assert len(sym_diff_keys)==0, "symmetric difference between keys non-empty: " + str(sym_diff_keys)
return predictors
alphas = svm.get_alphas() alphas_full = numpy.zeros(N) alphas_full[sv_idx] = alphas lin = svm.get_linear_term() print "AAAAAA", lin, type(lin) objective = svm.get_objective() print "svmlight alphas:", numpy.array(alphas[0:5]) ############################################# # compute DA-SVMs in shogun ############################################# dasvm = DomainAdaptationSVM(1.0, wdk, lab, presvm, B) #dasvm = SVMLight(1.0, wdk, lab) Math_init_random(1) dasvm.train() #dasvm = SVMLight(1.0, wdk, lab) #dasvm.set_linear_term(numpy.double(p)) #dasvm.train() lin_da = dasvm.get_linear_term() daobj = dasvm.get_objective() sv_idx_da = dasvm.get_support_vectors() alphas_da = dasvm.get_alphas()
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
"""
for task_id in train_data.keys():
print "task_id:", task_id
root = param.taxonomy.data
grey_nodes = [root]
# top-down processing of taxonomy
for node in root.get_leaves():
#####################################################
# train predictor
#####################################################
parent_node = node.get_nearest_neighbor()
cost = param.cost
(examples, labels) = self.get_data(parent_node, train_data)
# create shogun data objects
k_parent = shogun_factory_new.create_kernel(examples, param)
lab_parent = shogun_factory_new.create_labels(labels)
parent_svm = SVMLight(cost, k_parent, lab_parent)
parent_svm.train()
#####################################################
# train predictors
#####################################################
(examples, labels) = self.get_data(node, train_data)
# create shogun data objects
k = shogun_factory_new.create_kernel(examples, param)
lab = shogun_factory_new.create_labels(labels)
# regularize vs parent predictor
weight = param.transform
print "current edge_weight:", weight, " ,name:", node.name
svm = DomainAdaptationSVM(cost, k, lab, parent_svm, weight)
svm.train()
# attach svm to node
node.predictor = svm
#####################################################
# Wrap things up
#####################################################
# wrap up predictors for later use
predictors = {}
for leaf in root.get_leaves():
predictors[leaf.name] = leaf.predictor
assert (leaf.predictor != None)
sym_diff_keys = set(train_data.keys()).symmetric_difference(
set(predictors.keys()))
assert len(
sym_diff_keys
) == 0, "symmetric difference between keys non-empty: " + str(
sym_diff_keys)
return predictors
