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dde969a Sep 9, 2015
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"""
Implementation of logistic ordinal regression (aka proportional odds) model
"""
from __future__ import print_function
from sklearn import metrics
from scipy import linalg, optimize, sparse
import numpy as np
import warnings
BIG = 1e10
SMALL = 1e-12
def phi(t):
"""
logistic function, returns 1 / (1 + exp(-t))
"""
idx = t > 0
out = np.empty(t.size, dtype=np.float)
out[idx] = 1. / (1 + np.exp(-t[idx]))
exp_t = np.exp(t[~idx])
out[~idx] = exp_t / (1. + exp_t)
return out
def log_logistic(t):
"""
(minus) logistic loss function, returns log(1 / (1 + exp(-t)))
"""
idx = t > 0
out = np.zeros_like(t)
out[idx] = np.log(1 + np.exp(-t[idx]))
out[~idx] = (-t[~idx] + np.log(1 + np.exp(t[~idx])))
return out
def ordinal_logistic_fit(X, y, alpha=0, l1_ratio=0, n_class=None, max_iter=10000,
verbose=False, solver='TNC', w0=None):
"""
Ordinal logistic regression or proportional odds model.
Uses scipy's optimize.fmin_slsqp solver.
Parameters
----------
X : {array, sparse matrix}, shape (n_samples, n_feaures)
Input data
y : array-like
Target values
max_iter : int
Maximum number of iterations
verbose: bool
Print convergence information
Returns
-------
w : array, shape (n_features,)
coefficients of the linear model
theta : array, shape (k,), where k is the different values of y
vector of thresholds
"""
X = np.asarray(X)
y = np.asarray(y)
w0 = None
if not X.shape[0] == y.shape[0]:
raise ValueError('Wrong shape for X and y')
# .. order input ..
idx = np.argsort(y)
idx_inv = np.zeros_like(idx)
idx_inv[idx] = np.arange(idx.size)
X = X[idx]
y = y[idx].astype(np.int)
# make them continuous and start at zero
unique_y = np.unique(y)
for i, u in enumerate(unique_y):
y[y == u] = i
unique_y = np.unique(y)
# .. utility arrays used in f_grad ..
alpha = 0.
k1 = np.sum(y == unique_y[0])
E0 = (y[:, np.newaxis] == np.unique(y)).astype(np.int)
E1 = np.roll(E0, -1, axis=-1)
E1[:, -1] = 0.
E0, E1 = map(sparse.csr_matrix, (E0.T, E1.T))
def f_obj(x0, X, y):
"""
Objective function
"""
w, theta_0 = np.split(x0, [X.shape[1]])
theta_1 = np.roll(theta_0, 1)
t0 = theta_0[y]
z = np.diff(theta_0)
Xw = X.dot(w)
a = t0 - Xw
b = t0[k1:] - X[k1:].dot(w)
c = (theta_1 - theta_0)[y][k1:]
if np.any(c > 0):
return BIG
#loss = -(c[idx] + np.log(np.exp(-c[idx]) - 1)).sum()
loss = -np.log(1 - np.exp(c)).sum()
loss += b.sum() + log_logistic(b).sum() \
+ log_logistic(a).sum() \
+ .5 * alpha * w.dot(w) - np.log(z).sum() # penalty
if np.isnan(loss):
pass
#import ipdb; ipdb.set_trace()
return loss
def f_grad(x0, X, y):
"""
Gradient of the objective function
"""
w, theta_0 = np.split(x0, [X.shape[1]])
theta_1 = np.roll(theta_0, 1)
t0 = theta_0[y]
t1 = theta_1[y]
z = np.diff(theta_0)
Xw = X.dot(w)
a = t0 - Xw
b = t0[k1:] - X[k1:].dot(w)
c = (theta_1 - theta_0)[y][k1:]
# gradient for w
phi_a = phi(a)
phi_b = phi(b)
grad_w = -X[k1:].T.dot(phi_b) + X.T.dot(1 - phi_a) + alpha * w
# gradient for theta
idx = c > 0
tmp = np.empty_like(c)
tmp[idx] = 1. / (np.exp(-c[idx]) - 1)
tmp[~idx] = np.exp(c[~idx]) / (1 - np.exp(c[~idx])) # should not need
grad_theta = (E1 - E0)[:, k1:].dot(tmp) \
+ E0[:, k1:].dot(phi_b) - E0.dot(1 - phi_a)
grad_theta[:-1] += 1. / np.diff(theta_0)
grad_theta[1:] -= 1. / np.diff(theta_0)
out = np.concatenate((grad_w, grad_theta))
return out
def f_hess(x0, s, X, y):
x0 = np.asarray(x0)
w, theta_0 = np.split(x0, [X.shape[1]])
theta_1 = np.roll(theta_0, 1)
t0 = theta_0[y]
t1 = theta_1[y]
z = np.diff(theta_0)
Xw = X.dot(w)
a = t0 - Xw
b = t0[k1:] - X[k1:].dot(w)
c = (theta_1 - theta_0)[y][k1:]
D = np.diag(phi(a) * (1 - phi(a)))
D_= np.diag(phi(b) * (1 - phi(b)))
D1 = np.diag(np.exp(-c) / (np.exp(-c) - 1) ** 2)
Ex = (E1 - E0)[:, k1:].toarray()
Ex0 = E0.toarray()
H_A = X[k1:].T.dot(D_).dot(X[k1:]) + X.T.dot(D).dot(X)
H_C = - X[k1:].T.dot(D_).dot(E0[:, k1:].T.toarray()) \
- X.T.dot(D).dot(E0.T.toarray())
H_B = Ex.dot(D1).dot(Ex.T) + Ex0[:, k1:].dot(D_).dot(Ex0[:, k1:].T) \
- Ex0.dot(D).dot(Ex0.T)
p_w = H_A.shape[0]
tmp0 = H_A.dot(s[:p_w]) + H_C.dot(s[p_w:])
tmp1 = H_C.T.dot(s[:p_w]) + H_B.dot(s[p_w:])
return np.concatenate((tmp0, tmp1))
import ipdb; ipdb.set_trace()
import pylab as pl
pl.matshow(H_B)
pl.colorbar()
pl.title('True')
import numdifftools as nd
Hess = nd.Hessian(lambda x: f_obj(x, X, y))
H = Hess(x0)
pl.matshow(H[H_A.shape[0]:, H_A.shape[0]:])
#pl.matshow()
pl.title('estimated')
pl.colorbar()
pl.show()
def grad_hess(x0, X, y):
grad = f_grad(x0, X, y)
hess = lambda x: f_hess(x0, x, X, y)
return grad, hess
x0 = np.random.randn(X.shape[1] + unique_y.size) / X.shape[1]
if w0 is not None:
x0[:X.shape[1]] = w0
else:
x0[:X.shape[1]] = 0.
x0[X.shape[1]:] = np.sort(unique_y.size * np.random.rand(unique_y.size))
#print('Check grad: %s' % optimize.check_grad(f_obj, f_grad, x0, X, y))
#print(optimize.approx_fprime(x0, f_obj, 1e-6, X, y))
#print(f_grad(x0, X, y))
#print(optimize.approx_fprime(x0, f_obj, 1e-6, X, y) - f_grad(x0, X, y))
#import ipdb; ipdb.set_trace()
def callback(x0):
x0 = np.asarray(x0)
# print('Check grad: %s' % optimize.check_grad(f_obj, f_grad, x0, X, y))
if verbose:
# check that gradient is correctly computed
print('OBJ: %s' % f_obj(x0, X, y))
if solver == 'TRON':
import pytron
out = pytron.minimize(f_obj, grad_hess, x0, args=(X, y))
else:
options = {'maxiter' : max_iter, 'disp': 0, 'maxfun':10000}
out = optimize.minimize(f_obj, x0, args=(X, y), method=solver,
jac=f_grad, hessp=f_hess, options=options, callback=callback)
if not out.success:
warnings.warn(out.message)
w, theta = np.split(out.x, [X.shape[1]])
return w, theta
def ordinal_logistic_predict(w, theta, X):
"""
Parameters
----------
w : coefficients obtained by ordinal_logistic
theta : thresholds
"""
unique_theta = np.sort(np.unique(theta))
out = X.dot(w)
unique_theta[-1] = np.inf # p(y <= max_level) = 1
tmp = out[:, None].repeat(unique_theta.size, axis=1)
return np.argmax(tmp < unique_theta, axis=1)
if __name__ == '__main__':
DOC = """
================================================================================
Compare the prediction accuracy of different models on the boston dataset
================================================================================
"""
print(DOC)
from sklearn import cross_validation, datasets
boston = datasets.load_boston()
X, y = boston.data, np.round(boston.target)
#X -= X.mean()
y -= y.min()
idx = np.argsort(y)
X = X[idx]
y = y[idx]
cv = cross_validation.ShuffleSplit(y.size, n_iter=50, test_size=.1, random_state=0)
score_logistic = []
score_ordinal_logistic = []
score_ridge = []
for i, (train, test) in enumerate(cv):
#test = train
if not np.all(np.unique(y[train]) == np.unique(y)):
# we need the train set to have all different classes
continue
assert np.all(np.unique(y[train]) == np.unique(y))
train = np.sort(train)
test = np.sort(test)
w, theta = ordinal_logistic_fit(X[train], y[train], verbose=True,
solver='TNC')
pred = ordinal_logistic_predict(w, theta, X[test])
1/0
s = metrics.mean_absolute_error(y[test], pred)
print('ERROR (ORDINAL) fold %s: %s' % (i+1, s))
score_ordinal_logistic.append(s)
from sklearn import linear_model
clf = linear_model.LogisticRegression(C=1.)
clf.fit(X[train], y[train])
pred = clf.predict(X[test])
s = metrics.mean_absolute_error(y[test], pred)
print('ERROR (LOGISTIC) fold %s: %s' % (i+1, s))
score_logistic.append(s)
from sklearn import linear_model
clf = linear_model.Ridge(alpha=1.)
clf.fit(X[train], y[train])
pred = np.round(clf.predict(X[test]))
s = metrics.mean_absolute_error(y[test], pred)
print('ERROR (RIDGE) fold %s: %s' % (i+1, s))
score_ridge.append(s)
print()
print('MEAN ABSOLUTE ERROR (ORDINAL LOGISTIC): %s' % np.mean(score_ordinal_logistic))
print('MEAN ABSOLUTE ERROR (LOGISTIC REGRESSION): %s' % np.mean(score_logistic))
print('MEAN ABSOLUTE ERROR (RIDGE REGRESSION): %s' % np.mean(score_ridge))
# print('Chance level is at %s' % (1. / np.unique(y).size))