def __init__(self, data_dictionary, model_target, kernel=LINEAR, cv_segments=10, **args):
#Create an SVM model object
#Check to see if a threshold has been specified in the function's arguments
try: self.threshold = args['threshold']
except KeyError: self.threshold=2.3711 # if there is no 'threshold' key, then use the default (2.3711)
#Store some object data
model_dict = deepcopy(data_dictionary)
self.model_target = model_target
self.folds = cv_segments
#Label the exceedances in the training set.
model_dict[model_target] = self.Assign_Labels(model_dict[model_target])
#Extract the training labels and training set
self.training_labels = model_dict.pop(model_target)
self.training_set = np.transpose(model_dict.values())
self.headers = model_dict.keys()
#Scale the covariates to [-1,1]
self.Scale_Covariates()
#Generate an SVM model.
self.svm_problem = svm.svm_problem(self.training_labels, self.training_set)
self.svm_params = {'kernel_type' : kernel, 'weight_label' : [0,1], 'weight' : [10,1]}
self.model=svm.svm_model(self.svm_problem, svm.svm_parameter(**self.svm_params))
#Use cross-validation to find the best number of components in the model.
self.Select_Linear_Model(-5, 10)
#Rebuild the model, calculating the probabilities of class membership
self.svm_params['probability']=1
self.model=svm.svm_model(self.svm_problem, svm.svm_parameter(**self.svm_params))
def lib_svm(self, train_file, test_file, digit0, digit1):
features, labels = self.get_data(train_file, digit0, digit1)
training_data = svm_problem(labels, features)
if (self.kernel == 'gaussian'):
params = svm_parameter('-s 0 -t 2 -c 1 -g 0.05')
else:
params = svm_parameter('-s 0 -t 2 -c 1 -g 0.001275')
model = svm_train(training_data, params)
test_features, test_labels = self.get_data(test_file, digit0, digit1)
p_labels, p_acc, p_vals = svm_predict(test_labels, test_features,
model)
def train(self, c, g, probability=True, compensation=True,
path=None, filename=None, save=True):
if filename is None:
filename = os.path.splitext(self.getOption('strArffFileName'))[0]
filename += '.model'
if path is None:
path = self.dctEnvPaths['data']
param = svm.svm_parameter(kernel_type=svm.RBF,
C=c, gamma=g,
probability=1 if probability else 0)
labels, samples = self.getData(normalize=True)
# because we train the SVM with dict we need to redefine the zero-insert
self.hasZeroInsert = False
if not self.oClassifier is None:
self.oClassifier.setOption('hasZeroInsert', True)
if compensation:
weight, weight_label = self._calculateCompensation(labels)
param.weight = weight
param.weight_label = weight_label
param.nr_weight = len(weight)
problem = svm.svm_problem(labels, samples)
model = svm.svm_model(problem, param)
if save:
model.save(os.path.join(path, filename))
return problem, model
def train(self, search=False, **kwargs):
""" Train the SVM on the dataset. For RBF kernels (the default), an optional meta-parameter search can be performed.
@param search: optional name of grid search class to use for RBF kernels: 'GridSearch' or 'GridSearchDOE'
@param log2g: base 2 log of the RBF width parameter
@param log2C: base 2 log of the slack parameter
@param searchlog: filename into which to dump the search log
@param others: ...are passed through to the grid search and/or libsvm
"""
self.setParams(**kwargs)
problem = svm_problem(self.ds['target'].flatten(),
self.ds['input'].tolist())
if search:
# this is a bit of a hack...
model = eval(
search +
"(problem, self.svmtarget, cmin=[0,-7],cmax=[25,1], cstep=[0.5,0.2],plotflag=self.plot,searchlog=self.searchlog,**self.params)"
)
else:
param = svm_parameter(**self.params)
model = svm_model(problem, param)
logging.info("Training completed with parameters:")
logging.info(repr(param))
self.svm.setModel(model)
def train(self, examples, parameters=None):
self.isBinary = self.isBinaryProblem(examples)
examples = self.filterTrainingSet(examples)
ExampleUtils.writeExamples(examples, self.tempDir + "/train.dat")
#prepare parameters:
if parameters.has_key("c"):
assert (not parameters.has_key("C"))
parameters["C"] = parameters["c"]
del parameters["c"]
totalExamples = float(sum(self.classes.values()))
weight_label = self.classes.keys()
weight_label.sort()
weight = []
for k in weight_label:
weight.append(1.0 - self.classes[k] / totalExamples)
libSVMparam = svm.svm_parameter(nr_weight=len(self.classes),
weight_label=weight_label,
weight=weight,
**parameters)
labels = []
samples = []
for example in examples:
labels.append(example[1])
samples.append(example[2])
problem = svm.svm_problem(labels, samples)
self.model = svm.svm_model(problem, libSVMparam)
def svm(y,K,**param_kw):
"""
Solve the SVM problem. Return ``(alpha, b)``
`y`
labels
`K`
precopmuted kernel matrix
Additional keyword arguments are passed on as svm parameters to
the model.
The wrapper is needed to precondition the precomputed matrix for
use with libsvm, and to extract the model parameters and convert
them into the canonical weight vector plus scalar offset. Normally
libsvm hides these model paramters, preferring instead to provide
a high-level model object that can be queried for results.
"""
i = arange(1,len(K)+1).reshape((-1,1))
X = hstack((i, K))
y = asarray(y,dtype=double)
X = asarray(X,dtype=double)
prob = svm_problem(y,X)
param = svm_parameter(kernel_type=PRECOMPUTED,**param_kw)
model = svm_model(prob, param)
return get_alpha_b(model)
def __init__(self,
input_dim=None,
output_dim=None,
params=None,
dtype='float64'):
""" Initializes the SVM.
params -- class of type svm_parameter with all parameters
see libsvm documentation
"""
super(BinarySVMNode, self).__init__(input_dim, output_dim, dtype)
if not params:
# make a linear SVM with C = 10
params = svm.svm_parameter(kernel_type=svm.LINEAR, C=10)
self.parameters = params
# variables for training
self.X = numpy.zeros((0, self._input_dim), dtype=self._dtype)
self.Y = numpy.zeros((0, self._output_dim), dtype=self._dtype)
# list with models, parameters and labels for each output
self.problems = []
self.models = []
self.labels = []
def train(self, labels, data):
'''
Train the classifier.
@param labels: A list of class labels.
@param data: A 2D array or list of feature vectors. One feature vector per row.
'''
# Check the types and convert to np arrays
if isinstance(data, list) or isinstance(data, tuple):
data = np.array(data, dtype=np.double)
labels = np.array(labels, dtype=np.double)
# Preprocess the data
labels, data = self._preprocessor.train(labels, data)
labels, data = self._label_scale.train(labels, data)
# Create the svm parameter data and problem description
param = svm.svm_parameter(svm_type=svm.EPSILON_SVR,
kernel_type=svm.RBF,
p=self._epsilon,
gamma=self._gamma)
prob = svm.svm_problem(labels.tolist(), data.tolist())
# train the svm
self._model = svm.svm_model(prob, param)
def _test_prob_model(self, param1, param2):
probability_param = '-b 1'
df = self.df
param_str = ' '.join(
[self.base_param, param1, param2, probability_param])
param = svm_parameter(param_str)
model = svm_train(self.prob, param)
# Get predictions with probabilities as dictionaries
(df['prediction'], _,
probability_lists) = svm_predict(self.y, self.x, model,
probability_param + ' -q')
probability_dicts = [
dict(zip([1, 2], cur_vals)) for cur_vals in probability_lists
]
df['probabilities'] = probability_dicts
spec = libsvm.convert(model, self.column_names, 'target',
'probabilities')
if macos_version() >= (10, 13):
metrics = evaluate_classifier_with_probabilities(spec,
df,
verbose=False)
self.assertEquals(metrics['num_key_mismatch'], 0)
self.assertLess(metrics['max_probability_error'], 0.00001)
def test_multi_class_without_probability(self):
# Generate some random data.
# This unit test should not rely on scikit learn for test data.
x, y = [], []
for _ in range(50):
x.append([
random.gauss(200, 30),
random.gauss(-100, 22),
random.gauss(100, 42)
])
y.append(random.choice([1, 2, 10, 12]))
y[0], y[1], y[2], y[3] = 1, 2, 10, 12
column_names = ['x1', 'x2', 'x3']
prob = svmutil.svm_problem(y, x)
df = pd.DataFrame(x, columns=column_names)
for param1 in self.non_kernel_parameters:
for param2 in self.kernel_parameters:
param_str = ' '.join([self.base_param, param1, param2])
param = svm_parameter(param_str)
model = svm_train(prob, param)
# Get predictions with probabilities as dictionaries
(df['prediction'], _, _) = svm_predict(y, x, model, ' -q')
spec = libsvm.convert(model, column_names, 'target')
metrics = evaluate_classifier(spec, df, verbose=False)
self.assertEquals(metrics['num_errors'], 0)
def constructSVMModels(self, db_250k, arrays_to_form_model, array_id2median_intensity,\
minPercUnCoveredByLerContig=0.6, cnv_method_id=6, kernel_type=None, C=10, gamma=0., \
eps=1e-2, deletedFractionType=1):
"""
2010-7-25
add argument deletedFractionType
1: CNVCall.percUnCoveredByLerContig
2: CNVCall.fractionDeletedInPECoverageData
2010-7-1
"""
sys.stderr.write("Constructing SVM models for %s arrays ...\n"%(len(arrays_to_form_model)))
from svm import svm_problem, svm_parameter, svm_model, cross_validation, LINEAR, POLY, RBF
if kernel_type is None:
kernel_type = RBF
param = svm_parameter(C = C, eps=eps, probability = 1, gamma=gamma, kernel_type = kernel_type)
array_id2model = {}
for array_id in arrays_to_form_model:
if array_id not in array_id2median_intensity: #model array has to be in array_id2median_intensity
continue
cnvFeatureData = self.getCNVFeatureData(db_250k, array_id=array_id, \
minPercUnCoveredByLerContig=minPercUnCoveredByLerContig, cnv_method_id=cnv_method_id, \
replaceAmpWithMedianIntensity=False, deletedFractionType=deletedFractionType)
problem = svm_problem(cnvFeatureData.class_label_ls, cnvFeatureData.feature_data)
model = svm_model(problem, param)
array_id2model[array_id] = model
sys.stderr.write("%s models.\n"%(len(array_id2model)))
return array_id2model
def _evaluation_test_helper_with_probability(self, labels, allow_slow):
import copy
df = pd.DataFrame(self.x, columns=self.column_names)
y = copy.copy(self.y)
for i, val in enumerate(labels):
y[i] = val
probability_param = '-b 1'
for param1 in self.non_kernel_parameters:
for param2 in self.kernel_parameters:
param_str = ' '.join([self.base_param, param1, param2, probability_param])
# print("PARAMS: ", param_str)
param = svm_parameter(param_str)
model = svm_train(self.prob, param)
# Get predictions with probabilities as dictionaries
(df['prediction'], _, probability_lists) = svm_predict(y, self.x, model, probability_param + ' -q')
probability_dicts = [dict(zip([1, 2], cur_vals)) for cur_vals in probability_lists]
df['probabilities'] = probability_dicts
spec = libsvm.convert(model, self.column_names, 'target', 'probabilities')
if macos_version() >= (10, 13):
metrics = evaluate_classifier_with_probabilities(spec, df, verbose=False)
self.assertEquals(metrics['num_key_mismatch'], 0)
self.assertLess(metrics['max_probability_error'], 0.00001)
if not allow_slow:
break
if not allow_slow:
break
def iqr_model_train(matrix_kernel_train, labels_train, idx2clipid,
svm_para = '-w1 50 -t 4 -b 1 -c 1'):
"""
Light-weighted SVM learning module for online IQR
@param matrix_kernel_train: n-by-n square numpy array with kernel values
between training data
@param labels_train: row-wise labels of training data (1 or True indicates
positive, 0 or False otherwise
@param idx2clipid: idx2clipid(row_idx) returns the clipid for the 0-base row
in matrix
@param svm_para: (optional) SVM learning parameter
@rtype: dictionary with 'clipids_SV': list of clipids for support vectors
@return: output as a dictionary with 'clipids_SV'
"""
log = logging.getLogger('iqr_model_train')
# set training inputs
matrix_kernel_train = np.vstack((np.arange(1, len(matrix_kernel_train)+1),
matrix_kernel_train)).T
log.debug("Done matrix_kernel_train")
problem = svm.svm_problem(labels_train.tolist(), matrix_kernel_train.tolist(), isKernel=True)
log.debug("Done problem")
svm_param = svm.svm_parameter(svm_para)
log.debug("Done svm_param")
# train model
model = svmutil.svm_train(problem, svm_param)
log.debug("Done train model")
# release memory
del problem
del svm_param
log.debug("Done release memory")
# check learning failure
if model.l == 0:
raise Exception('svm model learning failure')
log.debug("Done checking learning failure (no failure)")
n_SVs = model.l
clipids_SVs = []
idxs_train_SVs = svmtools.get_SV_idxs_nonlinear_svm(model)
for i in range(n_SVs):
_idx_1base = idxs_train_SVs[i]
_idx_0base = _idx_1base - 1
clipids_SVs.append(idx2clipid[_idx_0base])
model.SV[i][0].value = i+1 # within SVM model, index needs to be 1-base
log.debug("Done collecting support vector IDs")
#svmutil.svm_save_model(filepath_model, model)
output = dict()
output['model'] = model
output['clipids_SVs'] = clipids_SVs
return output
def set_svm_params(self, param_dict):
param_str = ' '.join(k for k in param_dict.keys())
Params = namedtuple('Params', param_str)
self.params = Params(**param_dict)
self._svm_parameter = svm.svm_parameter(
**{k: getattr(self.params, k)
for k in self.params._fields})
def train(self, c, g, probability=True, compensation=True,
path=None, filename=None, save=True):
if filename is None:
filename = splitext(self.arff_file)[0]
filename += '.model'
if path is None:
path = self.data_dir
param = svm.svm_parameter(kernel_type=svm.RBF,
C=c, gamma=g,
probability=1 if probability else 0)
labels, samples = self.getData(normalize=True)
# because we train the SVM with dict we need to redefine the zero-insert
self.has_zero_insert = False
if not self.classifier is None:
self.classifier.setOption('hasZeroInsert', True)
if compensation:
weight, weight_label = self._calculateCompensation(labels)
param.weight = weight
param.weight_label = weight_label
param.nr_weight = len(weight)
problem = svm.svm_problem(labels, samples)
model = svm.svm_model(problem, param)
if save:
model.save(os.path.join(path, filename))
return problem, model
def train(self,labels,data):
'''
Train the classifier.
@param labels: A list of class labels.
@param data: A 2D array or list of feature vectors. One feature vector per row.
'''
# Check the types and convert to np arrays
if isinstance(data,list) or isinstance(data,tuple):
data = np.array(data,dtype=np.double)
labels = np.array(labels,dtype=np.double)
# Preprocess the data
labels,data = self._preprocessor.train(labels,data)
labels,data = self._label_scale.train(labels,data)
# Create the svm parameter data and problem description
param = svm.svm_parameter(svm_type=svm.EPSILON_SVR,kernel_type = svm.RBF, p = self._epsilon, gamma=self._gamma)
prob = svm.svm_problem(labels.tolist(),data.tolist())
# train the svm
self._model = svm.svm_model(prob, param)
def construct_svm_anytime(type="linear",C=2.,gamma=0.1,datatype='float64'):
""" SVM anytime model.
"""
inputs = 14
outputs = 1
# Parameters
svm_C = C
svm_gamma = gamma
# construct model
if(type=='linear'):
# using a L2-loss primal SVM with eps = 0.01
# (faster if we have many timesteps)
model = BinaryLinearSVMNode(inputs,outputs,C=svm_C,solver_type=2,eps=0.01)
else:
params = svm.svm_parameter(kernel_type=svm.RBF, C=svm_C, gamma=svm_gamma)
model = BinarySVMNode(inputs,outputs,params)
# additional properties
model.dtype = datatype
model.randrange = 0
model.type = 'SVM_any'
return model
def do_one_cv_classify_predeffolds_multi(theinput):
c = theinput[0]
gamma = theinput[1]
nf = theinput[2]
output = theinput[3]
input = theinput[4]
useprob = theinput[5]
fold_start = theinput[6]
param = svm.svm_parameter('-c %g -g %g -b %d' % (c,gamma,int(useprob)))
prob = svm.svm_problem(output, input)
target = (c_double * prob.l)()
posclass = output[0]
fold_start_p = (c_int *len(fold_start))()
for i in xrange(len(fold_start)):
fold_start_p[i] = fold_start[i]
libsvm.svm_cross_validation_labeltargets(prob, fold_start_p,param, nf, target)
acc = len([i for i in xrange(len(output)) if output[i] == target[i]])*1.0/prob.l
del target
del fold_start_p
return acc
def n_gram_svm(class_size, take_size):
cost = np.array([2.0, 2.0, 2.0, 2.0, 2.0])
gamma = np.array([0.0078125, 0.0078125, 0.0078125, 0.0078125, 0.0078125])
tst = time()
preset = np.load(get_feature_file('small'))
vocab_size = int(np.max(preset[:, :-class_size])) + 1
np.random.shuffle(preset)
train_set = preset[take_size:]
train_txt = train_set[:, :-class_size].astype(np.int64)
train_cls = train_set[:, -class_size:].astype(np.float32)
train_dict = [{
gram: 1 if gram in txt else 0
for gram in np.arange(1, vocab_size)
} for txt in train_txt]
train_major: List[Set[int]] = [set() for _ in np.arange(class_size)]
for i, cls in enumerate(train_cls):
for k in np.nonzero(np.abs(cls - np.max(cls)) < 1e-4)[0]:
train_major[k].add(i)
models = []
for k in np.arange(class_size):
problem = svm_problem([
1 if i in train_major[k] else -1 for i in np.arange(len(train_cls))
], train_dict)
param = svm_parameter('-t 0 -c %f -g %f -b 1 -q' % (cost[k], gamma[k]))
models.append(svm_train(problem, param))
train_time = time() - tst
tst = time()
test_set = preset[:take_size]
test_txt = test_set[:, :-5].astype(np.int64)
test_cls = test_set[:, -5:].astype(np.float32)
res = np.array([])
test_dict = [{
gram: 1 if gram in txt else 0
for gram in np.arange(1, vocab_size)
} for txt in test_txt]
for dic, cls in zip(test_dict, test_cls):
prob = np.zeros(class_size)
for k in np.arange(class_size):
_, _, p = svm_predict([], [dic], models[k], '-b 1 -q')
prob[k] = p[0][0]
prob /= np.sum(prob)
res = np.append(
res, cls @ prob / (np.linalg.norm(cls) * np.linalg.norm(prob)))
test_time = time() - tst
test_acc = np.mean(res)
return train_time, test_time, test_acc
def do_one_cv_classify(theinput):
c = theinput[0]
gamma = theinput[1]
nf = theinput[2]
output = theinput[3]
input = theinput[4]
useprob = theinput[5]
perfmetric = theinput[6]
param = svm.svm_parameter('-c %g -g %g -b %d' % (c,gamma,int(useprob)))
prob = svm.svm_problem(output, input)
target = (c_double * prob.l)()
posclass = output[0]
fold_start = (c_int *1)();
fold_start[0] = -1;
libsvm.svm_cross_validation(prob, fold_start, param, nf, target)
ys = prob.y[:prob.l]
db = array([[ys[i],target[i]] for i in range(prob.l)])
del target
neg = len([x for x in ys if x != posclass])
pos = prob.l-neg
[topacc,topphi,minfpfnratio,topf1,auc,optbias] = optimize_results(db,neg,pos,posval,perfmetric)
return topacc,topphi,minfpfnratio,topf1,auc,optbias
def train_test():
train_subdir = "data/train/"
test_subdir = "data/test/"
img_kinds = ["happy", "anger", "neutral", "surprise"]
models = {}
params = "-t 0 -c 3"
svm_params = { "happy": params,
"anger": params,
"neutral": params,
"surprise": params}
#train the models
print 'BUILDING TRAIN MODELS'
for img_kind in img_kinds:
print "\t" + img_kind
problem = build_problem(img_kind, train_subdir)
param = svm.svm_parameter(svm_params[img_kind])
models[img_kind] = svmutil.svm_train(problem, param)
print '================================'
#for each image in test set let's see what is the answe
total_count = 0
correct_count = 0
wrong_count = 0
print 'TESTING MODELS'
for img_kind in img_kinds:
images = glob.glob(test_subdir + "f_" + img_kind + "*.jpg")
for image in images:
print "\t" + image
image_data = cv.LoadImage(image)
# Let's see what are the results from the models
results = {}
for kind in img_kinds:
test_data = get_image_features(image_data, True, kind)
predict_input_data = []
predict_input_data.append(test_data)
# do svm query
(val, val_2, label) = svmutil.svm_predict([1] ,predict_input_data, models[kind])
results[kind] = label[0][0]
sorted_results = sorted(results.iteritems(), key=operator.itemgetter(1))
result = sorted_results[len(sorted_results)-1][0]
total_count += 1
if result == img_kind:
print 'YES :' + result
correct_count += 1
else:
print 'NO :' + result
print sorted_results
wrong_count += 1
print '-----------------------'
print '================================'
print "Total Pictures: " + str(total_count)
print "Correct: " + str(correct_count)
print "Wrong: " + str(wrong_count)
print "Accuracy: " + str(correct_count/float(total_count) * 100)
class svm_classifier:
"""Support Vector Machine Classifier"""
m_name = "svm"
feature_scaling = True
m_params = svm.svm_parameter()
m_prob = None
def convert_raw_training_data(self, raw_data):
t_data = ""
for line in raw_data.split('\n'):
if line == "":
break
x = [l.strip() for l in line.split(':')]
t_data += x[0] + " "
i = 1
for feature in x[1].split():
t_data += str(i) + ":" + feature + " "
i += 1
t_data += "\n"
return t_data
def scale_features(self, variant_name, models_folder):
command = "svm-scale -s %s %s > %s" % (models_folder + variant_name + ".range",\
variant_name + ".t",\
variant_name + ".t.scale")
try:
result = subprocess.check_output(command, shell=True)
except subprocess.CalledProcessError as e:
print_error("Scaling Command Failed")
quit()
def generate_model(self, variant_name, models_folder):
training_file = variant_name + ".t"
if self.feature_scaling:
self.scale_features(variant_name, models_folder)
training_file += ".scale"
(y, x) = svm_read_problem(training_file)
self.m_prob = svm.svm_problem(y, x,
self.m_params.kernel_type == PRECOMPUTED)
libsvm_path = os.environ['LIBSVM_PATH']
scaled_filename = os.path.abspath(training_file)
cp = "python grid.py " + scaled_filename
curdir = os.getcwd()
os.chdir(libsvm_path + "/tools/")
result = call_process(cp)
os.chdir(curdir)
C, g, rate = [float(l) for l in result.split("\n")[-2].split(" ")]
print "C: %.8f, gamma: %.8f\n" % (C, g)
self.m_params.C = C
self.m_params.gamma = g
print "\n-----------------------------"
model = svm.svm_train(self.m_prob, self.m_params)
print "-----------------------------\n"
svm_save_model(models_folder + variant_name + ".model", model)
def _test_evaluation(self, allow_slow):
"""
Test that the same predictions are made
"""
from svm import svm_parameter, svm_problem
from svmutil import svm_train, svm_predict
# Generate some smallish (poly kernels take too long on anything else) random data
x, y = [], []
for _ in range(50):
cur_x1, cur_x2 = random.gauss(2, 3), random.gauss(-1, 2)
x.append([cur_x1, cur_x2])
y.append(1 + 2 * cur_x1 + 3 * cur_x2)
input_names = ["x1", "x2"]
df = pd.DataFrame(x, columns=input_names)
prob = svm_problem(y, x)
# Parameters
base_param = "-s 3" # model type is epsilon SVR
non_kernel_parameters = [
"", "-c 1.5 -p 0.5 -h 1", "-c 0.5 -p 0.5 -h 0"
]
kernel_parameters = [
"",
"-t 2 -g 1.2", # rbf kernel
"-t 0", # linear kernel
"-t 1",
"-t 1 -d 2",
"-t 1 -g 0.75",
"-t 1 -d 0 -g 0.9 -r 2", # poly kernel
"-t 3",
"-t 3 -g 1.3",
"-t 3 -r 0.8",
"-t 3 -r 0.8 -g 0.5", # sigmoid kernel
]
for param1 in non_kernel_parameters:
for param2 in kernel_parameters:
param_str = " ".join([base_param, param1, param2])
print(param_str)
param = svm_parameter(param_str)
model = svm_train(prob, param)
(df["prediction"], _, _) = svm_predict(y, x, model)
spec = libsvm.convert(model,
input_names=input_names,
target_name="target")
if _is_macos() and _macos_version() >= (10, 13):
metrics = evaluate_regressor(spec, df)
self.assertAlmostEqual(metrics["max_error"], 0)
if not allow_slow:
break
if not allow_slow:
break
def trainSVM(kernel, labels):
#need to add an id number as the first column of the list
svmKernel = column_stack((arange(1, len(kernel.tolist()) + 1), kernel))
prob = svm_problem(labels.tolist(), svmKernel.tolist(), isKernel=True)
param = svm_parameter('-t 4')
model = svm_train(prob, param)
return model
def lib_svm(train_file, test_file, kernel):
print("inside libsvm")
features, labels = get_data_from_csv(train_file)
print(features)
training_data = svm_problem(labels, features)
if (kernel == 'gaussian'):
params = svm_parameter('-s 0 -t 2 -c 1 -g 0.05')
else:
params = svm_parameter('-s 0 -t 2 -c 1 -g 0.001275')
model = svm_train(training_data, params)
test_features, test_labels = get_data_from_csv(test_file)
p_labels, p_acc, p_vals = svm_predict(test_labels, test_features, model)
return p_labels, p_acc, p_vals
def _test_evaluation(self, allow_slow):
"""
Test that the same predictions are made
"""
from svm import svm_parameter, svm_problem
from svmutil import svm_train, svm_predict
# Generate some smallish (poly kernels take too long on anything else) random data
x, y = [], []
for _ in range(50):
cur_x1, cur_x2 = random.gauss(2, 3), random.gauss(-1, 2)
x.append([cur_x1, cur_x2])
y.append(1 + 2 * cur_x1 + 3 * cur_x2)
input_names = ['x1', 'x2']
df = pd.DataFrame(x, columns=input_names)
prob = svm_problem(y, x)
# Parameters
base_param = '-s 3' # model type is epsilon SVR
non_kernel_parameters = [
'', '-c 1.5 -p 0.5 -h 1', '-c 0.5 -p 0.5 -h 0'
]
kernel_parameters = [
'',
'-t 2 -g 1.2', # rbf kernel
'-t 0', # linear kernel
'-t 1',
'-t 1 -d 2',
'-t 1 -g 0.75',
'-t 1 -d 0 -g 0.9 -r 2', # poly kernel
'-t 3',
'-t 3 -g 1.3',
'-t 3 -r 0.8',
'-t 3 -r 0.8 -g 0.5' # sigmoid kernel
]
for param1 in non_kernel_parameters:
for param2 in kernel_parameters:
param_str = ' '.join([base_param, param1, param2])
print(param_str)
param = svm_parameter(param_str)
model = svm_train(prob, param)
(df['prediction'], _, _) = svm_predict(y, x, model)
spec = libsvm.convert(model,
input_names=input_names,
target_name='target')
metrics = evaluate_regressor(spec, df)
self.assertAlmostEquals(metrics['max_error'], 0)
if not allow_slow:
break
if not allow_slow:
break
def Select_Linear_Model(self, C_min=-10, C_steps=11):
#Search for the model parameters that give the smallest CV error
C = self.__Linear_Search__(C_min, C_steps, 1)
C = self.__Linear_Search__(np.log2(C)-2, 50, 0.08)
C = self.__Linear_Search__(np.log2(C)-0.5, 50, 0.02)
self.svm_params['C'] = C
self.model = svm.svm_model(self.svm_problem, svm.svm_parameter(**self.svm_params))
def train(self, dataset):
"""
Trains the svm classifier. Converts words to real numbers for training
as SVM expects only numbers.
"""
super(SvmLearner, self).train(dataset)
prob = svm.svm_problem(self.results, self.observations)
param = svm.svm_parameter(kernel_type=svm.LINEAR, C=10, probability=1)
self.model = svm.svm_model(prob, param)
def train(self,trainset):
"""
Trains the SVM.
"""
self.n_classes = len(trainset.metadata['targets'])
# Set LIBSVM parameters
kernel_types = {'linear':libsvm.LINEAR,'polynomial':libsvm.POLY,
'rbf':libsvm.RBF,'sigmoid':libsvm.SIGMOID}
if self.kernel not in kernel_types:
raise ValueError('Invalid kernel: '+self.kernel+'. Should be either \'linear\', \'polynomial\', \'rbf\' or \'sigmoid\'')
if self.label_weights != None:
class_to_id = trainset.metadata['class_to_id']
nr_weight = self.n_classes
weight_label = range(self.n_classes)
weight = [1]*self.n_classes
for k,v in self.label_weights.iteritems():
weight[class_to_id[k]] = v
else:
nr_weight = 0
weight_label = []
weight = []
libsvm_params = libsvm.svm_parameter(svm_type = libsvm.C_SVC,
kernel_type = kernel_types[self.kernel],
degree=self.degree,
gamma=self.gamma,
coef0=self.coef0,
C=self.C,
probability=int(self.output_probabilities),
cache_size=self.cache_size,
eps=self.tolerance,
shrinking=int(self.shrinking),
nr_weight = nr_weight,
weight_label = weight_label,
weight = weight)
# Put training set in the appropriate format:
# if is sparse (i.e. a pair), inputs are converted to dictionaries
# if not, inputs are assumed to be sequences and are kept intact
libsvm_inputs = []
libsvm_targets = []
for input,target in trainset:
if type(input) == tuple:
libsvm_inputs += [dict(zip(input[1],input[0]))]
else:
libsvm_inputs += [input]
libsvm_targets += [float(target)] # LIBSVM requires double-valued targets
libsvm_problem = libsvm.svm_problem(libsvm_targets,libsvm_inputs)
# Train SVM
self.svm = libsvm.svm_model(libsvm_problem,libsvm_params)
def iterGridSearchSVM(self,
c_info=None,
g_info=None,
fold=5,
probability=False,
compensation=True):
swap = lambda a, b: (b, a)
if not c_info is None and len(c_info) >= 3:
c_begin, c_end, c_step = c_info[:3]
else:
c_begin, c_end, c_step = -5, 15, 2
if c_end < c_begin:
c_begin, c_end = swap(c_begin, c_end)
c_step = abs(c_step)
if not g_info is None and len(g_info) >= 3:
g_begin, g_end, g_step = g_info[:3]
else:
g_begin, g_end, g_step = -15, 3, 2
if g_end < g_begin:
g_begin, g_end = swap(g_begin, g_end)
g_step = abs(g_step)
labels, samples = self.getData(normalize=True)
problem = svm.svm_problem(labels, samples)
if compensation:
weight, weight_label = self._calculateCompensation(labels)
n = (c_end - c_begin) / c_step + 1
n *= (g_end - g_begin) / g_step + 1
l2c = c_begin
while l2c <= c_end:
l2g = g_begin
while l2g <= g_end:
param = svm.svm_parameter(kernel_type=svm.RBF,
C=2.**l2c,
gamma=2.**l2g,
probability=1 if probability else 0)
if compensation:
param.weight = weight
param.weight_label = weight_label
param.nr_weight = len(weight)
predictions = svm.cross_validation(problem, param, fold)
predictions = map(int, predictions)
conf = ConfusionMatrix.from_lists(labels, predictions,
self.class_names.keys())
yield n, l2c, l2g, conf
l2g += g_step
l2c += c_step
def Select_Model(self, C_min=-10, C_steps=11, gamma_min=-15, gamma_steps=16):
#Search for the model parameters that give the smallest CV error
(C, gamma) = self.__Search__(C_min, C_steps, gamma_min, gamma_steps, 1, 1)
#(C, gamma) = self.__Search__(np.log2(C)-5, 100, np.log2(gamma)-5, 100, 0.1, 0.1)
(C, gamma) = self.__Search__(np.log2(C)-1, 100, np.log2(gamma)-1, 100, 0.02, 0.02)
#(C, gamma) = self.__Search__(np.log2(C)-0.5, 100, np.log2(gamma)-0.5, 100, 0.01, 0.01)
self.svm_params['C'] = C
self.svm_params['gamma'] = gamma
self.model = svm.svm_model(self.svm_problem, svm.svm_parameter(**self.svm_params))
def search(self):
""" iterate successive parameter grid refinement and evaluation; adapted from LIBSVM grid search tool """
jobs = self.calculate_jobs()
scores = []
for line in jobs:
for (c, g) in line:
# run cross-validation for this point
self.setParams(C=2 ** c, gamma=2 ** g)
param = svm_parameter(**self.params)
cvresult = array(cross_validation(self.problem, param, self.crossval))
corr, = where(cvresult == self.targets)
res = (c, g, float(corr.size) / self.targets.size)
scores.append(res)
self._save_points(res)
self._redraw(scores)
scores = array(scores)
best = scores[scores[:, 0].argmax(), 1:]
self.setParams(C=2 ** best[0], gamma=2 ** best[1])
logging.info("best log2C=%12.7g, log2g=%11.7g " % (best[0], best[1]))
param = svm_parameter(**self.params)
return param
def go_train(self):
#输入训练参数
parameter = self.param.toPlainText()
#读取新数据
y, x = svm_read_problem("./1_scale.txt")
prob = svm_problem(y, x)
#传递训练参数
param = svm.svm_parameter(parameter)
#训练、生成模型并保存
model = svm_train(prob, param)
svm_save_model("./mode.txt", model)
self.label_5.setText("训练完成，创建分类器完成。")
def testMultiClass(self, level=1):
""" Multiclass classification test with BinarySVM Node.
"""
params = svm.svm_parameter(kernel_type=svm.RBF, C=10)
node = BinarySVMNode(2, 4, params)
node.train(self.mc_samples, self.mc_labels)
node.stop_training()
testresult = node(self.mc_samples)
# test if labels are the same as the test output
assert_array_almost_equal(self.mc_labels, testresult, 2)
def trainmodel(self,train,cv,test,modelsavepath):
y,x = svmutil.svm_read_problem(train)#读入训练数据
# ycv,xcv = svm_read_problem(cv)#读入验证集
# ytest,xtest=svm_read_problem(test)#读入测试集
prob = svm.svm_problem(y, x)
param = svm.svm_parameter('-t 2 -c 0.5 -g 0.125 -b 1')
model = svmutil.svm_train(prob, param)
yt,xt = svmutil.svm_read_problem(train)#???????????
p_labs, p_acc, p_vals = svmutil.svm_predict(yt, xt, model,'-b 1')
svmutil.svm_save_model(modelsavepath, model)#save model
# model = svmutil.svm_load_model('model_file')#读取model
pass
def search(self):
""" iterate successive parameter grid refinement and evaluation; adapted from LIBSVM grid search tool """
jobs = self.calculate_jobs()
scores = []
for line in jobs:
for (c, g) in line:
# run cross-validation for this point
self.setParams(C=2 ** c, gamma=2 ** g)
param = svm_parameter(**self.params)
cvresult = array(cross_validation(self.problem, param, self.crossval))
corr, = where(cvresult == self.targets)
res = (c, g, float(corr.size) / self.targets.size)
scores.append(res)
self._save_points(res)
self._redraw(scores)
scores = array(scores)
best = scores[scores[:, 0].argmax(), 1:]
self.setParams(C=2 ** best[0], gamma=2 ** best[1])
logging.info("best log2C=%12.7g, log2g=%11.7g " % (best[0], best[1]))
param = svm_parameter(**self.params)
return param
def iterGridSearchSVM(self, c_info=None, g_info=None, fold=5,
probability=False, compensation=True):
swap = lambda a,b: (b,a)
if not c_info is None and len(c_info) >= 3:
c_begin, c_end, c_step = c_info[:3]
else:
c_begin, c_end, c_step = -5, 15, 2
if c_end < c_begin:
c_begin, c_end = swap(c_begin, c_end)
c_step = abs(c_step)
if not g_info is None and len(g_info) >= 3:
g_begin, g_end, g_step = g_info[:3]
else:
g_begin, g_end, g_step = -15, 3, 2
if g_end < g_begin:
g_begin, g_end = swap(g_begin, g_end)
g_step = abs(g_step)
labels, samples = self.getData(normalize=True)
#print len(labels), len(samples)
problem = svm.svm_problem(labels, samples)
if compensation:
weight, weight_label = self._calculateCompensation(labels)
n = (c_end - c_begin) / c_step + 1
n *= (g_end - g_begin) / g_step + 1
l2c = c_begin
while l2c <= c_end:
l2g = g_begin
while l2g <= g_end:
param = svm.svm_parameter(kernel_type=svm.RBF,
C=2.**l2c, gamma=2.**l2g,
probability=1 if probability else 0)
if compensation:
param.weight = weight
param.weight_label = weight_label
param.nr_weight = len(weight)
predictions = svm.cross_validation(problem, param, fold)
predictions = map(int, predictions)
#print n,c,g
conf = ConfusionMatrix.from_lists(labels, predictions,
self.l2nl)
yield n,l2c,l2g,conf
l2g += g_step
l2c += c_step
def example_make_model(img_kind, svm_params): subdir = "data/" problem = build_problem(img_kind) print "Prob built" param = svm.svm_parameter(svm_params) print "Params Set" problem_model = svmutil.svm_train(problem, param) print "Model built" svmutil.svm_save_model(subdir + img_kind + '.model', problem_model) print "Done"
def learnModel(self, train_y, train_X):
# scale train data
svmScaler = preprocessing.MinMaxScaler(feature_range = (-1, 1))
train_X_scaledArr = svmScaler.fit_transform(train_X)
# learn and save svm model
X = train_X_scaledArr.tolist()
problem = svm_problem(train_y, X)
paramStr = '-c ' + str(self._param_c) + ' -g ' + str(self._param_g) + ' -q'
param = svm_parameter(paramStr)
self._model = svm_train(problem, param)
self._scaler = svmScaler
def __init__(self):
super(LIBSVMRunner, self).__init__()
self.c_range = -5, 15, 2
self.gamma_range = 3, -15, -2
self.kernel_type = 'LINEAR'
self.svmparam = svm.svm_parameter('-b 1')
self._optparser.add_option('-k', '--kernel', dest='kernel_type')
self.cvfunc = svmfun.leave_one_out
self.n_cv = None
pass
def do_one_cv_classify_predeffolds_valid(theinput):
c = theinput[0]
gamma = theinput[1]
nf = theinput[2]
output = theinput[3]
input = theinput[4]
output_valid = theinput[5]
input_valid = theinput[6]
useprob = theinput[7]
fold_start = theinput[8]
fold_start_valid = theinput[9]
perfmetric = theinput[10]
param = svm.svm_parameter('-c %g -g %g -b %d' % (c,gamma,int(useprob)))
prob = svm.svm_problem(output, input)
fold_start_p = (c_int *len(fold_start))()
for i in xrange(len(fold_start)):
fold_start_p[i] = fold_start[i]
prob_valid = svm.svm_problem(output_valid, input_valid)
fold_start_p_valid = (c_int *len(fold_start_valid))()
for i in xrange(len(fold_start_valid)):
fold_start_p_valid[i] = fold_start_valid[i]
target = (c_double * prob_valid.l)()
posclass = output[0]
# print prob
libsvm.svm_cross_validation_sepsets(prob, prob_valid,fold_start_p, fold_start_p_valid,param, nf, target)
ys = prob.y[:prob_valid.l]
db = array([[ys[i],target[i]] for i in range(prob_valid.l)])
# print db
del target
del fold_start_p
del fold_start_p_valid
neg = len([x for x in ys if x != posclass])
# print neg
pos = prob_valid.l-neg
# print pos
# print fb,neg,pos,posclass,perfmetric
[topacc,topphi,minfpfnratio,topf1,auc,optbias] = optimize_results(db,neg,pos,posclass,perfmetric)
return topacc,topphi,minfpfnratio,topf1,auc,optbias
def testSingleClass(self, level=1):
""" Single class classification test with BinarySVMNode.
"""
params = svm.svm_parameter(kernel_type=svm.RBF, C=10)
node = BinarySVMNode(2, 1, params)
node.train(self.sc_samples, self.sc_labels)
node.stop_training()
testresult = node(self.sc_samples)
# rescale from SVM output [-1,1] to [0,1]
testresult = (testresult + 1) / 2.
# test if labels are the same as the test output
assert_array_almost_equal(self.sc_labels, testresult, 2)
def test(word, documents):
import svm, random
docs = [d.copy() for d in documents if d[reverse_map[word]]]
nondocs = [d.copy() for d in documents if not d[reverse_map[word]]]
nondocs = random.sample(nondocs, min(5 * len(docs), len(nondocs)))
print float(len(nondocs)) / (len(docs) + len(nondocs))
cats = [1 for i in docs] + [0 for i in nondocs]
obs = docs + nondocs
for i in xrange(len(obs)):
obs[i][reverse_map[word]] = 0.
zobs = zip(obs, cats)
random.shuffle(zobs)
obs, cats = zip(*zobs)
params = svm.svm_parameter(C=1, kernel_type=svm.LINEAR)
problem = svm.svm_problem(cats, obs)
target = svm.cross_validation(problem, params, 20)
return sum(target[i] == cats[i] for i in cats) / float(len(cats))
def test(word, documents):
import svm,random
docs = [d.copy() for d in documents if d[reverse_map[word]]]
nondocs = [d.copy() for d in documents if not d[reverse_map[word]]]
nondocs = random.sample(nondocs,min(5*len(docs),len(nondocs)))
print float(len(nondocs))/(len(docs)+len(nondocs))
cats = [1 for i in docs] + [0 for i in nondocs]
obs = docs + nondocs
for i in xrange(len(obs)):
obs[i][reverse_map[word]] = 0.
zobs = zip(obs,cats)
random.shuffle(zobs)
obs,cats = zip(*zobs)
params = svm.svm_parameter(C=1, kernel_type=svm.LINEAR)
problem = svm.svm_problem(cats,obs)
target = svm.cross_validation(problem,params,20)
return sum(target[i] == cats[i] for i in cats)/float(len(cats))
def __Linear_Search__(self, C_min, C_steps, C_step_by=1.):
#Utility function used by Parameter_Search() to find the best parameters
param_grid = np.array( [ C for C in 2**(np.arange(C_steps, dtype=float)*C_step_by+C_min) ] )
error_grid = np.zeros( len(param_grid) )
for i in range( len(param_grid) ):
self.svm_params['C'] = float( param_grid[i] )
CV_predictions = svm.cross_validation(self.svm_problem, svm.svm_parameter(**self.svm_params), self.folds)
error = sum(abs(CV_predictions-self.training_labels))/len(self.training_labels)
error_grid[i] = error
best = mlab.find(error_grid == error_grid.flatten().min())
C = param_grid[best][0]
return C
def do_one_cv(theinput):
nu = theinput[0]
c = theinput[1]
gamma = theinput[2]
nf = theinput[3]
output = theinput[4]
input = theinput[5]
bins = theinput[6]
param = svm.svm_parameter('-s %d -t %d -n %g -c %g -g %g' % (svm.NU_SVR,svm.RBF,nu,c,gamma))
prob = svm.svm_problem(output, input)
target = (c_double * prob.l)()
fold_start = (c_int *1)();
fold_start[0] = -1;
libsvm.svm_cross_validation_labeltargets(prob, fold_start,param, nf, target)
MSE,SCC = evaluations(prob.y[:prob.l],target[:prob.l],bins)
del target
return MSE,SCC
def train(self, search=False, **kwargs):
""" Train the SVM on the dataset. For RBF kernels (the default), an optional meta-parameter search can be performed.
:key search: optional name of grid search class to use for RBF kernels: 'GridSearch' or 'GridSearchDOE'
:key log2g: base 2 log of the RBF width parameter
:key log2C: base 2 log of the slack parameter
:key searchlog: filename into which to dump the search log
:key others: ...are passed through to the grid search and/or libsvm
"""
self.setParams(**kwargs)
problem = svm_problem(self.ds['target'].flatten(), self.ds['input'].tolist())
if search:
# this is a bit of a hack...
model = eval(search + "(problem, self.svmtarget, cmin=[0,-7],cmax=[25,1], cstep=[0.5,0.2],plotflag=self.plot,searchlog=self.searchlog,**self.params)")
else:
param = svm_parameter(**self.params)
model = svm_model(problem, param)
logging.info("Training completed with parameters:")
logging.info(repr(param))
self.svm.setModel(model)
def bench_svm(X, Y, T):
"""
bench with swig-generated wrappers that come with libsvm
"""
import svm
X1 = X.tolist()
Y1 = Y.tolist()
T1 = T.tolist()
gc.collect()
# start time
tstart = datetime.now()
problem = svm.svm_problem(Y1, X1)
param = svm.svm_parameter(svm_type=0, kernel_type=0)
model = svm.svm_model(problem, param)
for i in T.tolist():
model.predict(i)
delta = (datetime.now() - tstart)
# stop time
svm_results.append(delta.seconds + delta.microseconds/mu_second)
def __Search__(self, C_min, C_steps, gamma_min, gamma_steps, C_step_by=1., gamma_step_by=1.):
#Utility function used by Parameter_Search() to find the best parameters
param_grid = np.array( [[ (C,gamma) for C in 2**(np.arange(C_steps, dtype=float)*C_step_by+C_min)] for gamma in 2**(np.arange(gamma_steps, dtype=float)*gamma_step_by+gamma_min)] )
error_grid = np.zeros( shape=param_grid.shape[0:2] )
for row in range( param_grid.shape[0] ):
for col in range( param_grid.shape[1] ):
self.svm_params['C'] = float( param_grid[row,col,0] )
self.svm_params['gamma'] = float( param_grid[row,col,1] )
CV_predictions = svm.cross_validation(self.svm_problem, svm.svm_parameter(**self.svm_params), self.folds)
error = sum(abs(CV_predictions-self.training_labels))/len(self.training_labels)
error_grid[row,col] = error
best = mlab.find(error_grid == error_grid.flatten().min())
row = best // C_steps
col = best % C_steps
(C, gamma) = param_grid[row, col][0].flatten()
return (C, gamma)
def train(self, examples, parameters=None):
self.isBinary = self.isBinaryProblem(examples)
examples = self.filterTrainingSet(examples)
ExampleUtils.writeExamples(examples, self.tempDir+"/train.dat")
#prepare parameters:
if parameters.has_key("c"):
assert(not parameters.has_key("C"))
parameters["C"] = parameters["c"]
del parameters["c"]
totalExamples = float(sum(self.classes.values()))
weight_label = self.classes.keys()
weight_label.sort()
weight = []
for k in weight_label:
weight.append(1.0-self.classes[k]/totalExamples)
libSVMparam = svm.svm_parameter(nr_weight = len(self.classes), weight_label=weight_label, weight=weight, **parameters)
labels = []
samples = []
for example in examples:
labels.append(example[1])
samples.append(example[2])
problem = svm.svm_problem(labels, samples)
self.model = svm.svm_model(problem, libSVMparam)
def train(request):
points = models.Point2d.objects.all()
# Storing the information to be presented to SVM
labels = []
inputs = []
# For each point, store the information into arrays
for p in points:
labels.append( p.label )
inputs.append([p.x, p.y])
prob = svm.svm_problem(labels, inputs)
param = svm.svm_parameter('-t 2 -c 100')
model = svmutil.svm_train(prob, param)
try:
svmutil.svm_save_model('libsvm.model', model)
except Exception as e:
print "error: ", e, "\n"
data = {"status": "trained"}
return json(data)
for i, fileName in enumerate( ['./dataset2/avon.csv', './dataset2/brian_merge.csv', './dataset2/mon_merge.csv', './dataset2/nofar_merge.csv'] ):
tmp = readDataset(fileName) # array of Instance
dataSet = dataSet + tmp
print 'size:', len(tmp)
label = label + [i]*len(tmp)
dataSet, label = shuffle(dataSet, label, random_state=0)
cutIndex = int(TRAIN_SET_RATIO*len(dataSet))
## use accel_abs and alpha_abs as input for encoding respectively
print 'learning dictionary'
data_accel = [I.accel_abs() for I in dataSet]
data_alpha = [I.alpha_abs() for I in dataSet]
RPDictionary_accel = Dictionary(PATCH_SIZE, data_accel[:cutIndex])
RPDictionary_alpha = Dictionary(PATCH_SIZE, data_alpha[:cutIndex])
aggregate_feature = [ f[0]+f[1] for f in zip( RPDictionary_accel.encoding(data_accel), RPDictionary_alpha.encoding(data_alpha) ) ]
#aggregate_feature = preprocessing.scale(aggregate_feature) ## scale columns independently to have zero mean and unit variance
writeFeature('./svm_train', aggregate_feature[:cutIndex], label[:cutIndex])
writeFeature('./svm_test', aggregate_feature[cutIndex:], label[cutIndex:])
## SVM training
X_train, Y_train = readFeature('./svm_train',PATCH_SIZE*2)
prob = svm_problem(Y_train, X_train)
param = svm_parameter('-t 1 -q -d 2')
model = svm_train(prob, param)
## SVM predicting
X_test, Y_test = readFeature('./svm_test',PATCH_SIZE*2)
p_labels, p_acc, p_vals = svm_predict(Y_test, X_test, model)
print p_acc
print confusion_matrix(Y_test, p_labels)
'meeting':2,
'selfStudy':3,
}
if __name__=='__main__':
argparser = argparse.ArgumentParser()
argparser.add_argument('topicFilePath', type=str, help='hdp_topic file')
argparser.add_argument('labelFilePath', type=str, help='hdp_topic file')
args = argparser.parse_args()
args = vars(args)
# with open(args.filePath, 'r') as fr:
# for SVM (LDA) input format
#topicNum, X_train = svm_read_problem(args['topicFilePath'])
with open(args['topicFilePath'],'r') as fr:
X_train = fr.readlines()
X_train = [[float(num) for num in e.split()] for e in X_train]
X_train = X_train[1:] # abandon the first instance
#print X_train
Y_train = []
with open(args['labelFilePath'], 'r') as fw:
for line in fw:
line = line.rstrip().split(';')
Y_train.append(label[ line[1] ])
#print Y_train
prob = svm_problem(Y_train, X_train)
param = svm_parameter('-v 5 -q')
model = svm_train(prob, param)
#print model
#svm_save_model('{}/svm_model'.format(args['outputDir']),model)
def train_SVR_Linear(self,labels,vectors,verbose, C_range, callback=None):
'''Private use only'''
# combine the labels and vectors into one set.
data = []
for i in range(len(labels)):
data.append([labels[i],vectors[i]])
#shuffle the data
rng = random.Random()
if self.random_seed != None:
rng.seed(self.random_seed)
rng.shuffle(data)
# partition into validation and training
if type(self.validation_size) == float and self.validation_size > 0.0 and self.validation_size < 1.0:
training_cutoff = int(len(data)*(1.0-self.validation_size))
elif type(self.validation_size) == int and self.validation_size < len(labels):
training_cutoff = len(labels)-self.validation_size
else:
raise NotImplementedError("Cannot determine validation set from %s"%self.validation_size)
if verbose: print "Training Cutoff:",len(labels),training_cutoff
training_data = data[:training_cutoff]
validation_data = data[training_cutoff:]
tmp_labels = []
tmp_vectors = []
for each in training_data:
tmp_labels.append(each[0])
tmp_vectors.append(each[1])
prob = svm.svm_problem(tmp_labels,tmp_vectors)
training_info = []
training_svm = []
training_table = Table()
self.training_table = training_table
i=0
for C in C_range:
param = svm.svm_parameter(svm_type=self.svm_type,kernel_type = svm.LINEAR, C = C, p=self.epsilon,nu=self.nu)
test_svm = svm.svm_model(prob, param)
mse = 0.0
total = len(validation_data)
for label,vector in validation_data:
pred = test_svm.predict(vector)
error = label - pred
mse += error*error
mse = mse/total
training_svm.append(test_svm)
training_info.append([C,mse])
training_table.setElement(i,'C',C)
training_table.setElement(i,'mse',mse)
i+=1
if callback != None:
callback(int(100*float(i)/len(C_range)))
if verbose: print
if verbose: print "------------------------------"
if verbose: print " Tuning Information:"
if verbose: print " C error"
if verbose: print "------------------------------"
best = training_info[0]
best_svm = training_svm[0]
for i in range(len(training_info)):
each = training_info[i]
if verbose: print " %8.3e %0.8f"%(each[0],each[1])
if best[-1] > each[-1]:
best = each
best_svm = training_svm[i]
if verbose: print "------------------------------"
if verbose: print
if verbose: print "------------------------------"
if verbose: print " Best Tuning:"
if verbose: print " C error"
if verbose: print "------------------------------"
if verbose: print " %8.3e %0.8f"%(best[0],best[1])
if verbose: print "------------------------------"
if verbose: print
self.training_info = training_info
self.C = best[0]
self.error = best[1]
self.svm = best_svm
