def SciKits(featureValues, classLabels):
# TODO: check how non-convergence is reported
(ns, nf) = featureValues.shape
assert classLabels.shape == (ns, )
#NOTE: There is a version issue
try:
from scikits.learn.linear_model import LogisticRegression
except:
#scikits version >= 0.9
from sklearn.linear_model import LogisticRegression
RegularisationParameter = 1.0e+30 # For us, higher is better (no regularisation!)
Tolerance = 1.0e-30 # Smaller is better
# From the documentation page at
#
# http://scikit-learn.sourceforge.net/modules/generated/scikits.learn.linear_model.LogisticRegression.html
#
# "The underlying C implementation uses a random number generator to select features when fitting the model.
# It is thus not uncommon, to have slightly different results for the same input data.
# If that happens, try with a smaller tol parameter."
classifier = LogisticRegression(penalty = 'l1', C = RegularisationParameter, tol = Tolerance)
classifier.fit(featureValues, classLabels)
beta = -classifier.raw_coef_[0,:]
beta = numpy.append(beta[-1], beta[:-1])
if not all(numpy.isfinite(beta)):
return None
return beta
def train_readout_logit_onevsall(stimset, samples):
(train_data, test_data, index_to_sym) = get_np_dataset(stimset, samples)
models = {}
for sym_index,sym in index_to_sym.iteritems():
#train a logistic regression model on just this stim class vs. the rest
mdata = copy.deepcopy(data)
data[data[:, -1] != sym_index, -1] = 0
data[data[:, -1] == sym_index, -1] = 1
print ''
print list(data)
print ''
N = data.shape[1]-1
logr = LogisticRegression(penalty='l2', dual=False, tol=0.0001, C=1.0, fit_intercept=True, intercept_scaling=1)
logr.fit(train_data[:, :N], train_data[:, -1])
test_pred = logr.predict(test_data[:, 0:N])
pred_diff = np.abs(test_pred - test_data[:, -1])
zero_one_loss = pred_diff.sum() / test_data.shape[0]
print 'Stim class %s loss: %0.3f' % (sym, zero_one_loss)
models[sym] = logr
def train_readout_logit(stimset, samples):
(train_data, test_data, index_to_sym) = get_np_dataset(stimset, samples)
N = train_data.shape[1]-1
logr = LogisticRegression(penalty='l2', dual=False, tol=0.0001, C=1.0, fit_intercept=True, intercept_scaling=1)
logr.fit(train_data[:, :N], train_data[:, -1])
test_pred = logr.predict(test_data[:, 0:N])
pred_diff = test_pred - test_data[:, -1]
percent_correct = len((pred_diff == 0).nonzero()[0]) / float(len(test_pred))
print 'Logit Percent correct: %0.3f' % percent_correct
return percent_correct
def train_lrpipe(trainX, trainY, params):
""" trains LogisiticRegression model with params
logreg_C specified by params
"""
lrpipe = Pipeline([('logreg', LogisticRegression(penalty="l1", C=1))])
lrpipe = lrpipe.fit(trainX, trainY, **params)
return lrpipe
def pairwise_regress( thetas,cats, ii, jj , reg_type, reg_param):
en_cats = enumerate( cats )
set0 = [idx for (idx,cat) in en_cats if cat==ii]
en_cats = enumerate( cats )
set1 = [idx for (idx,cat) in en_cats if cat==jj]
X0 = thetas[set0,:]
Y0 = np.zeros(X0.shape[0])
X1 = thetas[set1,:]
Y1 = np.ones(X1.shape[0])
X = np.vstack( [X0,X1] )
Y = np.concatenate( [Y0, Y1] )
lr = LogisticRegression(penalty=reg_type, tol=0.00000000001, C=reg_param)
lr.fit( X, Y)
return lr
def pairwise_regress(thetas, cats, ii, jj, reg_type, reg_param):
en_cats = enumerate(cats)
set0 = [idx for (idx, cat) in en_cats if cat == ii]
en_cats = enumerate(cats)
set1 = [idx for (idx, cat) in en_cats if cat == jj]
X0 = thetas[set0, :]
Y0 = np.zeros(X0.shape[0])
X1 = thetas[set1, :]
Y1 = np.ones(X1.shape[0])
X = np.vstack([X0, X1])
Y = np.concatenate([Y0, Y1])
lr = LogisticRegression(penalty=reg_type,
tol=0.00000000001,
C=reg_param)
lr.fit(X, Y)
return lr
def main():
notes, min_pitch = get_notes()
duration, n_pitches = notes.shape
data = np.zeros((n_pitches, duration, n_pitches))
classes = np.zeros((n_pitches, duration))
state = np.zeros((n_pitches))
for t, pitches in enumerate(notes):
for i, on in enumerate(pitches):
data[i, t] = state
classes[i, t] = on
for i, on in enumerate(pitches):
state[i] = activation(state[i], on)
models = []
for i in xrange(n_pitches):
model = LogisticRegression('l2', tol=0.1)
train_data, target = repeat_classes(data[i, :], classes[i, :], 10, 10)
model.fit(train_data, target)
models.append(model)
duration *= 3
predicted = np.zeros((n_pitches, duration))
state = np.zeros((n_pitches))
state[21] = 1
for t in xrange(1, duration):
sys.stdout.write('%d\r' % t)
sys.stdout.flush()
current_state = state.reshape((1, state.shape[0]))
for i in xrange(n_pitches):
on = models[i].predict(current_state)[0]
predicted[i, t] = on
state[i] = activation(state[i], on)
state += (np.random.random((n_pitches)) - .5) * .1
write(predicted, min_pitch)
def do_grid_search(X, Y, gs_params):
""" Given data (X,Y) will perform a grid search on g_params
for a LogisticRegression called logreg
"""
lrpipe = Pipeline([('logreg', LogisticRegression())])
gs = GridSearchCV(lrpipe, gs_params, n_jobs=-1)
#print gs
gs = gs.fit(X, Y)
best_parameters, score = max(gs.grid_scores_, key=lambda x: x[1])
logger.info("best_parameters: " + str(best_parameters))
logger.info("expected score: " + str(score))
return best_parameters
def test_auto_weight():
"""Test class weights for imbalanced data"""
from scikits.learn.linear_model import LogisticRegression
# we take as dataset a the two-dimensional projection of iris so
# that it is not separable and remove half of predictors from
# class 1
from scikits.learn.svm.base import _get_class_weight
X, y = iris.data[:, :2], iris.target
unbalanced = np.delete(np.arange(y.size), np.where(y > 1)[0][::2])
assert np.argmax(_get_class_weight('auto', y[unbalanced])[0]) == 2
for clf in (svm.SVC(kernel='linear'), svm.LinearSVC(), LogisticRegression()):
# check that score is better when class='auto' is set.
y_pred = clf.fit(X[unbalanced], y[unbalanced],
class_weight={}).predict(X)
y_pred_balanced = clf.fit(X[unbalanced], y[unbalanced],
class_weight='auto').predict(X)
assert metrics.f1_score(y, y_pred) <= metrics.f1_score(y, y_pred_balanced)
def _fit_logistic_regression(X, y, C=0.1):
classifier = LogisticRegression(C=C)
classifier.fit(X, y)
return classifier
def logistic_regression(state_matrix, teacher_matrix):
for i in range(state_matrix.shape[1]):
clf = LogisticRegression(tol=0.05)
clf.fit(state_matrix, teacher_matrix[:, i])
self.output_weights[i, :] = clf.coef_
print i
dstask[ds][t] = ctr
ctr = ctr + 1
Y = N.zeros(len(copedata))
for x in range(len(copedata)):
Y[x] = dstask[copedata[x, 0]][copedata[x, 1]]
X = melodic_mix[usedata == 1, :]
loo = LeaveOneOut(len(Y))
predclass = N.zeros(len(Y))
for train, test in loo:
X_train, X_test, y_train, y_test = X[train], X[test], Y[train], Y[test]
clf = LogisticRegression(C=0.1, penalty='l1')
clf.fit(X_train, y_train)
predclass[test] = clf.predict(X_test)
print 'Mean accuracy=%0.3f' % N.mean(predclass == Y)
# randomize labels 1000 times and store accuracy
nruns = 500
randacc = N.zeros(nruns)
for r in range(nruns):
N.random.shuffle(Y)
for train, test in loo:
X_train, X_test, y_train, y_test = X[train], X[test], Y[train], Y[test]
clf = LogisticRegression(C=1, penalty='l2')
clf.fit(X_train, y_train)
import json
import matplotlib.pyplot as plt
import numpy as np
from scikits.learn.linear_model import LogisticRegression
from src.data_interface import d, L_clean, L
from src.utils import get_path, bool_to_color, sigmoid
path = get_path(__file__) + '/..'
L = list(L)
X = d.view()[:,3:]
y = d.view()[:,2]
# Learning rate when estimating parameters
C = 0.1
classifier = LogisticRegression(C=C, penalty='l2')
training_rows = range(int(1e5))
classifier.fit(X[training_rows,:], y[training_rows,:])
coef_dict = dict(zip(L[3:], list(classifier.coef_[0])))
coef_dict['intercept'] = classifier.intercept_[0]
with open('{0}/data/coefs_train_0-1e5.json'.format(path), 'w') as f:
json.dump(coef_dict, f, indent=4, sort_keys=True)
def logistic_regression(state_matrix, teacher_matrix):
for i in range(state_matrix.shape[1]):
clf = LogisticRegression(tol=0.05)
clf.fit(state_matrix, teacher_matrix[:, i])
self.output_weights[i, :] = clf.coef_
print i
# Author: Alexandre Gramfort <*****@*****.**> # License: BSD Style. import numpy as np from scikits.learn.linear_model import LogisticRegression from scikits.learn import datasets iris = datasets.load_iris() X = iris.data y = iris.target # Set regularization parameter C = 0.1 classifier_l1_LR = LogisticRegression(C=C, penalty='l1') classifier_l2_LR = LogisticRegression(C=C, penalty='l2') classifier_l1_LR.fit(X, y) classifier_l2_LR.fit(X, y) hyperplane_coefficients_l1_LR = classifier_l1_LR.coef_[:] hyperplane_coefficients_l2_LR = classifier_l2_LR.coef_[:] # hyperplane_coefficients_l1_LR contains zeros due to the # L1 sparsity inducing norm pct_non_zeros_l1_LR = np.mean(hyperplane_coefficients_l1_LR != 0) * 100 pct_non_zeros_l2_LR = np.mean(hyperplane_coefficients_l2_LR != 0) * 100 print "Percentage of non zeros coefficients (L1) : %f" % pct_non_zeros_l1_LR print "Percentage of non zeros coefficients (L2) : %f" % pct_non_zeros_l2_LR
ctr=ctr+1
Y=N.zeros(len(copedata))
for x in range(len(copedata)):
Y[x]=dstask[copedata[x,0]][copedata[x,1]]
X=melodic_mix[usedata==1,:]
loo = LeaveOneOut(len(Y))
predclass=N.zeros(len(Y))
for train, test in loo:
X_train, X_test, y_train, y_test = X[train], X[test], Y[train], Y[test]
clf=LogisticRegression(C=0.1,penalty='l1')
clf.fit(X_train,y_train)
predclass[test]=clf.predict(X_test)
print 'Mean accuracy=%0.3f'%N.mean(predclass==Y)
# randomize labels 1000 times and store accuracy
nruns=500
randacc=N.zeros(nruns)
for r in range(nruns):
N.random.shuffle(Y)
for train, test in loo:
X_train, X_test, y_train, y_test = X[train], X[test], Y[train], Y[test]
clf=LogisticRegression(C=1,penalty='l2')
clf.fit(X_train,y_train)
from rpy2.robjects import FloatVector as rfloat
import numpy as np
iris = datasets.load_iris()
def test_algorithm(algorithm, results, train_data, train_target, test_data):
algorithm.fit(train_data, train_target)
y_pred = algorithm.predict(test_data)
results.append(precision(y_pred))
def precision(y_pred):
prec = sum(y_pred == test_target)
return float(prec) / len(test_target)
svmclf = svm.SVC()
logisticclf = LogisticRegression()
nnclf= neighbors.Neighbors()
svmli = []
logli = []
nnli = []
cv = StratifiedKFold(iris.target, 20)
for train_index, test_index in cv:
train_data = iris.data[train_index]
train_target = iris.target[train_index]
test_data = iris.data[test_index]
test_target = iris.target[test_index]
#svm
test_algorithm(svmclf, svmli, train_data, train_target, test_data)
from scikits.learn.linear_model import LogisticRegression
from scikits.learn.svm import SVC
from scikits.learn import datasets
iris = datasets.load_iris()
X = iris.data[:, :2] # we only take the first two features for visualization
y = iris.target
n_features = X.shape[1]
C = 1.0
# Create different classifiers. The logistic regression cannot do
# multiclass out of the box.
classifiers = {
'L1 logistic': LogisticRegression(C=C, penalty='l1'),
'L2 logistic': LogisticRegression(C=C, penalty='l2'),
'Linear SVC': SVC(kernel='linear', C=C, probability=True),
}
n_classifiers = len(classifiers)
pl.figure(figsize=(3*2, n_classifiers*2))
pl.subplots_adjust(bottom=.2, top=.95)
for index, (name, classifier) in enumerate(classifiers.iteritems()):
classifier.fit(X, y)
y_pred = classifier.predict(X)
classif_rate = np.mean(y_pred.ravel() == y.ravel()) * 100
print "classif_rate for %s : %f " % (name, classif_rate)
# Mathieu Blondel <*****@*****.**>
# License: BSD Style.
import numpy as np
from scikits.learn.linear_model import LogisticRegression
from scikits.learn import datasets
# FIXME: the iris dataset has only 4 features!
iris = datasets.load_iris()
X = iris.data
y = iris.target
# Set regularization parameter
for C in (0.1, 1, 10):
clf_l1_LR = LogisticRegression(C=C, penalty='l1')
clf_l2_LR = LogisticRegression(C=C, penalty='l2')
clf_l1_LR.fit(X, y)
clf_l2_LR.fit(X, y)
coef_l1_LR = clf_l1_LR.coef_[:]
coef_l2_LR = clf_l2_LR.coef_[:]
# coef_l1_LR contains zeros due to the
# L1 sparsity inducing norm
sparsity_l1_LR = np.mean(coef_l1_LR == 0) * 100
sparsity_l2_LR = np.mean(coef_l2_LR == 0) * 100
print "C=%f" % C
print "Sparsity with L1 penalty: %f" % sparsity_l1_LR