def structure_discrete_hmsvm_bmrm (m_data_dict=data_dict):
from modshogun import RealMatrixFeatures, SequenceLabels, HMSVMModel, Sequence, TwoStateModel
from modshogun import StructuredAccuracy, SMT_TWO_STATE
try:
from modshogun import DualLibQPBMSOSVM
except ImportError:
print("DualLibQPBMSOSVM not available")
exit(0)
labels_array = m_data_dict['label'][0]
idxs = numpy.nonzero(labels_array == -1)
labels_array[idxs] = 0
labels = SequenceLabels(labels_array, 250, 500, 2)
features = RealMatrixFeatures(m_data_dict['signal'].astype(float), 250, 500)
num_obs = 4 # given by the data file used
model = HMSVMModel(features, labels, SMT_TWO_STATE, num_obs)
sosvm = DualLibQPBMSOSVM(model, labels, 5000.0)
sosvm.train()
#print sosvm.get_w()
predicted = sosvm.apply(features)
evaluator = StructuredAccuracy()
acc = evaluator.evaluate(predicted, labels)
def structure_discrete_hmsvm_bmrm(m_data_dict=data_dict):
from modshogun import RealMatrixFeatures, SequenceLabels, HMSVMModel, Sequence, TwoStateModel
from modshogun import StructuredAccuracy, SMT_TWO_STATE
try:
from modshogun import DualLibQPBMSOSVM
except ImportError:
print("DualLibQPBMSOSVM not available")
exit(0)
labels_array = m_data_dict['label'][0]
idxs = numpy.nonzero(labels_array == -1)
labels_array[idxs] = 0
labels = SequenceLabels(labels_array, 250, 500, 2)
features = RealMatrixFeatures(m_data_dict['signal'].astype(float), 250,
500)
num_obs = 4 # given by the data file used
model = HMSVMModel(features, labels, SMT_TWO_STATE, num_obs)
sosvm = DualLibQPBMSOSVM(model, labels, 5000.0)
sosvm.train()
#print sosvm.get_w()
predicted = sosvm.apply(features)
evaluator = StructuredAccuracy()
acc = evaluator.evaluate(predicted, labels)
def structure_factor_graph_model(tr_samples=samples,
tr_labels=labels,
w=w_all,
ftype=ftype_all):
from modshogun import SOSVMHelper, LabelsFactory
from modshogun import FactorGraphModel, MAPInference, TREE_MAX_PROD
from modshogun import DualLibQPBMSOSVM, StochasticSOSVM
# create model
model = FactorGraphModel(tr_samples, tr_labels, TREE_MAX_PROD, False)
w_truth = [w[0].copy(), w[1].copy(), w[2].copy()]
w[0] = np.zeros(8)
w[1] = np.zeros(4)
w[2] = np.zeros(2)
ftype[0].set_w(w[0])
ftype[1].set_w(w[1])
ftype[2].set_w(w[2])
model.add_factor_type(ftype[0])
model.add_factor_type(ftype[1])
model.add_factor_type(ftype[2])
# --- training with BMRM ---
bmrm = DualLibQPBMSOSVM(model, tr_labels, 0.01)
#bmrm.set_verbose(True)
bmrm.train()
#print 'learned weights:'
#print bmrm.get_w()
#print 'ground truth weights:'
#print w_truth
# evaluation
lbs_bmrm = LabelsFactory.to_structured(bmrm.apply())
acc_loss = 0.0
ave_loss = 0.0
for i in xrange(num_samples):
y_pred = lbs_bmrm.get_label(i)
y_truth = tr_labels.get_label(i)
acc_loss = acc_loss + model.delta_loss(y_truth, y_pred)
ave_loss = acc_loss / num_samples
#print('BMRM: Average training error is %.4f' % ave_loss)
# show primal objs and dual objs
#hbm = bmrm.get_helper()
#print hbm.get_primal_values()
#print hbm.get_eff_passes()
#print hbm.get_train_errors()
# --- training with SGD ---
sgd = StochasticSOSVM(model, tr_labels)
#sgd.set_verbose(True)
sgd.set_lambda(0.01)
sgd.train()
def structure_plif_hmsvm_bmrm (num_examples, example_length, num_features, num_noise_features): from modshogun import RealMatrixFeatures, TwoStateModel, DualLibQPBMSOSVM, StructuredAccuracy model = TwoStateModel.simulate_data(num_examples, example_length, num_features, num_noise_features) sosvm = DualLibQPBMSOSVM(model, model.get_labels(), 5000.0) sosvm.train() #print sosvm.get_w() predicted = sosvm.apply(model.get_features()) evaluator = StructuredAccuracy() acc = evaluator.evaluate(predicted, model.get_labels())
def structure_factor_graph_model(tr_samples = samples, tr_labels = labels, w = w_all, ftype = ftype_all):
from modshogun import SOSVMHelper, LabelsFactory
from modshogun import FactorGraphModel, MAPInference, TREE_MAX_PROD
from modshogun import DualLibQPBMSOSVM, StochasticSOSVM
# create model
model = FactorGraphModel(tr_samples, tr_labels, TREE_MAX_PROD, False)
w_truth = [w[0].copy(), w[1].copy(), w[2].copy()]
w[0] = np.zeros(8)
w[1] = np.zeros(4)
w[2] = np.zeros(2)
ftype[0].set_w(w[0])
ftype[1].set_w(w[1])
ftype[2].set_w(w[2])
model.add_factor_type(ftype[0])
model.add_factor_type(ftype[1])
model.add_factor_type(ftype[2])
# --- training with BMRM ---
bmrm = DualLibQPBMSOSVM(model, tr_labels, 0.01)
#bmrm.set_verbose(True)
bmrm.train()
#print 'learned weights:'
#print bmrm.get_w()
#print 'ground truth weights:'
#print w_truth
# evaluation
eva_bmrm = bmrm.apply()
lbs_bmrm = LabelsFactory.to_structured(eva_bmrm)
acc_loss = 0.0
ave_loss = 0.0
for i in xrange(num_samples):
y_pred = lbs_bmrm.get_label(i)
y_truth = tr_labels.get_label(i)
acc_loss = acc_loss + model.delta_loss(y_truth, y_pred)
ave_loss = acc_loss / num_samples
#print('BMRM: Average training error is %.4f' % ave_loss)
# show primal objs and dual objs
#hbm = bmrm.get_helper()
#print hbm.get_primal_values()
#print hbm.get_eff_passes()
#print hbm.get_train_errors()
# --- training with SGD ---
sgd = StochasticSOSVM(model, tr_labels)
#sgd.set_verbose(True)
sgd.set_lambda(0.01)
sgd.train()
def structure_plif_hmsvm_bmrm (num_examples, example_length, num_features, num_noise_features):
from modshogun import RealMatrixFeatures, TwoStateModel, StructuredAccuracy
try:
from modshogun import DualLibQPBMSOSVM
except ImportError:
print("DualLibQPBMSOSVM not available")
exit(0)
model = TwoStateModel.simulate_data(num_examples, example_length, num_features, num_noise_features)
sosvm = DualLibQPBMSOSVM(model, model.get_labels(), 5000.0)
sosvm.set_store_train_info(False)
sosvm.train()
#print sosvm.get_w()
predicted = sosvm.apply(model.get_features())
evaluator = StructuredAccuracy()
acc = evaluator.evaluate(predicted, model.get_labels())
def structure_multiclass_bmrm(fm_train_real=traindat,
label_train_multiclass=label_traindat):
from modshogun import RealFeatures
from modshogun import SOSVMHelper
from modshogun import BMRM, PPBMRM, P3BMRM
from modshogun import MulticlassModel, MulticlassSOLabels, DualLibQPBMSOSVM, RealNumber
labels = MulticlassSOLabels(label_train_multiclass)
features = RealFeatures(fm_train_real.T)
model = MulticlassModel(features, labels)
sosvm = DualLibQPBMSOSVM(model, labels, 1.0)
# BMRM
sosvm.set_solver(BMRM)
sosvm.set_verbose(True)
sosvm.train()
out = sosvm.apply()
count = 0
for i in xrange(out.get_num_labels()):
yi_pred = RealNumber.obtain_from_generic(out.get_label(i))
if yi_pred.value == label_train_multiclass[i]:
count = count + 1
#print("BMRM: Correct classification rate: %0.2f" % ( 100.0*count/out.get_num_labels() ))
#hp = sosvm.get_helper()
#print hp.get_primal_values()
#print hp.get_train_errors()
# PPBMRM
w = np.zeros(model.get_dim())
sosvm.set_w(w)
sosvm.set_solver(PPBMRM)
sosvm.set_verbose(True)
sosvm.train()
out = sosvm.apply()
count = 0
for i in xrange(out.get_num_labels()):
yi_pred = RealNumber.obtain_from_generic(out.get_label(i))
if yi_pred.value == label_train_multiclass[i]:
count = count + 1
#print("PPBMRM: Correct classification rate: %0.2f" % ( 100.0*count/out.get_num_labels() ))
# P3BMRM
w = np.zeros(model.get_dim())
sosvm.set_w(w)
sosvm.set_solver(P3BMRM)
sosvm.set_verbose(True)
sosvm.train()
out = sosvm.apply()
count = 0
for i in xrange(out.get_num_labels()):
yi_pred = RealNumber.obtain_from_generic(out.get_label(i))
if yi_pred.value == label_train_multiclass[i]:
count = count + 1
def structure_multiclass_bmrm(fm_train_real=traindat,label_train_multiclass=label_traindat):
from modshogun import RealFeatures
from modshogun import SOSVMHelper
from modshogun import BMRM, PPBMRM, P3BMRM
from modshogun import MulticlassModel, MulticlassSOLabels, DualLibQPBMSOSVM, RealNumber
labels = MulticlassSOLabels(label_train_multiclass)
features = RealFeatures(fm_train_real.T)
model = MulticlassModel(features, labels)
sosvm = DualLibQPBMSOSVM(model, labels, 1.0)
# BMRM
sosvm.set_solver(BMRM)
sosvm.set_verbose(True)
sosvm.train()
out = sosvm.apply()
count = 0
for i in xrange(out.get_num_labels()):
yi_pred = RealNumber.obtain_from_generic(out.get_label(i))
if yi_pred.value == label_train_multiclass[i]:
count = count + 1
#print("BMRM: Correct classification rate: %0.2f" % ( 100.0*count/out.get_num_labels() ))
#hp = sosvm.get_helper()
#print hp.get_primal_values()
#print hp.get_train_errors()
# PPBMRM
w = np.zeros(model.get_dim())
sosvm.set_w(w)
sosvm.set_solver(PPBMRM)
sosvm.set_verbose(True)
sosvm.train()
out = sosvm.apply()
count = 0
for i in xrange(out.get_num_labels()):
yi_pred = RealNumber.obtain_from_generic(out.get_label(i))
if yi_pred.value == label_train_multiclass[i]:
count = count + 1
#print("PPBMRM: Correct classification rate: %0.2f" % ( 100.0*count/out.get_num_labels() ))
# P3BMRM
w = np.zeros(model.get_dim())
sosvm.set_w(w)
sosvm.set_solver(P3BMRM)
sosvm.set_verbose(True)
sosvm.train()
out = sosvm.apply()
count = 0
for i in xrange(out.get_num_labels()):
yi_pred = RealNumber.obtain_from_generic(out.get_label(i))
if yi_pred.value == label_train_multiclass[i]:
count = count + 1
model = MulticlassModel(features, labels)
lambda_ = 1e1
sosvm = DualLibQPBMSOSVM(model, labels, lambda_)
sosvm.set_cleanAfter(10) # number of iterations that cutting plane has to be inactive for to be removed
sosvm.set_cleanICP(True) # enables inactive cutting plane removal feature
sosvm.set_TolRel(0.001) # set relative tolerance
sosvm.set_verbose(True) # enables verbosity of the solver
sosvm.set_cp_models(16) # set number of cutting plane models
sosvm.set_solver(BMRM) # select training algorithm
# sosvm.set_solver(PPBMRM)
# sosvm.set_solver(P3BMRM)
sosvm.train()
res = sosvm.get_result()
Fps = np.array(res.get_hist_Fp_vector())
Fds = np.array(res.get_hist_Fp_vector())
wdists = np.array(res.get_hist_wdist_vector())
plt.figure()
plt.subplot(221)
plt.title("Fp and Fd history")
plt.plot(xrange(res.get_n_iters()), Fps, hold=True)
plt.plot(xrange(res.get_n_iters()), Fds, hold=True)
plt.subplot(222)
plt.title("w dist history")
plt.plot(xrange(res.get_n_iters()), wdists)
lambda_ = 1e1
sosvm = DualLibQPBMSOSVM(model, labels, lambda_)
sosvm.set_cleanAfter(
10
) # number of iterations that cutting plane has to be inactive for to be removed
sosvm.set_cleanICP(True) # enables inactive cutting plane removal feature
sosvm.set_TolRel(0.001) # set relative tolerance
sosvm.set_verbose(True) # enables verbosity of the solver
sosvm.set_cp_models(16) # set number of cutting plane models
sosvm.set_solver(BMRM) # select training algorithm
#sosvm.set_solver(PPBMRM)
#sosvm.set_solver(P3BMRM)
sosvm.train()
res = sosvm.get_result()
Fps = np.array(res.get_hist_Fp_vector())
Fds = np.array(res.get_hist_Fp_vector())
wdists = np.array(res.get_hist_wdist_vector())
plt.figure()
plt.subplot(221)
plt.title('Fp and Fd history')
plt.plot(xrange(res.get_n_iters()), Fps, hold=True)
plt.plot(xrange(res.get_n_iters()), Fds, hold=True)
plt.subplot(222)
plt.title('w dist history')
plt.plot(xrange(res.get_n_iters()), wdists)
def structure_multiclass_bmrm(fm_train_real=traindat,
label_train_multiclass=label_traindat):
from modshogun import MulticlassSOLabels, LabelsFactory
from modshogun import RealFeatures
from modshogun import SOSVMHelper
try:
from modshogun import BMRM, PPBMRM, P3BMRM, DualLibQPBMSOSVM
except ImportError:
print(
"At least one of BMRM, PPBMRM, P3BMRM, DualLibQPBMSOSVM not available"
)
exit(0)
from modshogun import MulticlassModel, RealNumber
labels = MulticlassSOLabels(label_train_multiclass)
features = RealFeatures(fm_train_real.T)
model = MulticlassModel(features, labels)
sosvm = DualLibQPBMSOSVM(model, labels, 1.0)
# BMRM
sosvm.set_solver(BMRM)
sosvm.set_verbose(True)
sosvm.train()
bmrm_out = LabelsFactory.to_multiclass_structured(sosvm.apply())
count = 0
for i in range(bmrm_out.get_num_labels()):
yi_pred = RealNumber.obtain_from_generic(bmrm_out.get_label(i))
if yi_pred.value == label_train_multiclass[i]:
count = count + 1
#print("BMRM: Correct classification rate: %0.2f" % ( 100.0*count/bmrm_out.get_num_labels() ))
#hp = sosvm.get_helper()
#print hp.get_primal_values()
#print hp.get_train_errors()
# PPBMRM
w = np.zeros(model.get_dim())
sosvm.set_w(w)
sosvm.set_solver(PPBMRM)
sosvm.set_verbose(True)
sosvm.train()
ppbmrm_out = LabelsFactory.to_multiclass_structured(sosvm.apply())
count = 0
for i in range(ppbmrm_out.get_num_labels()):
yi_pred = RealNumber.obtain_from_generic(ppbmrm_out.get_label(i))
if yi_pred.value == label_train_multiclass[i]:
count = count + 1
#print("PPBMRM: Correct classification rate: %0.2f" % ( 100.0*count/ppbmrm_out.get_num_labels() ))
# P3BMRM
w = np.zeros(model.get_dim())
sosvm.set_w(w)
sosvm.set_solver(P3BMRM)
sosvm.set_verbose(True)
sosvm.train()
p3bmrm_out = LabelsFactory.to_multiclass_structured(sosvm.apply())
count = 0
for i in range(p3bmrm_out.get_num_labels()):
yi_pred = RealNumber.obtain_from_generic(p3bmrm_out.get_label(i))
if yi_pred.value == label_train_multiclass[i]:
count = count + 1
#print("P3BMRM: Correct classification rate: %0.2f" % ( 100.0*count/p3bmrm_out.get_num_labels() ))
return bmrm_out, ppbmrm_out, p3bmrm_out