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clogistic

https://travis-ci.com/guillermo-navas-palencia/clogistic.svg?branch=master https://img.shields.io/pypi/v/clogistic?color=blue https://pepy.tech/badge/clogistic

Logistic regression with bound and linear constraints. L1, L2 and Elastic-Net regularization.

This is a Python implementation of the constrained logistic regression with a scikit-learn like API. This library uses CVXPY and scipy optimizer L-BFGS-B. Currently, only binary classification is supported.

Installation

To install the current release of clogistic from PyPI:

pip install clogistic

To install from source, download or clone the git repository

git clone https://github.com/guillermo-navas-palencia/clogistic.git
cd clogistic
python setup.py install

Dependencies

  • cvxpy>=1.0.31
  • numpy
  • scikit-learn>=0.20.0
  • scipy

Examples

clogistic can flawlessly replace the scikit-learn LogisticRegression import when bounds or linear constraints are required:

# from sklearn.linear_models import LogisticRegression
from clogistic import LogisticRegression

L1-norm / Elastic-Net

In the unconstrained problem, the L-BFGS-B solver supports both L1 and Elastic-Net regularization.

>>> from clogistic import LogisticRegression
>>> from sklearn.datasets import load_breast_cancer
>>> X, y = load_breast_cancer(return_X_y=True)
>>> clf = LogisticRegression(solver="L-BFGS-B", penalty="l1")
>>> clf.fit(X, y)
LogisticRegression(C=1.0, class_weight=None, fit_intercept=True, l1_ratio=None,
                   max_iter=100, penalty='l1', solver='L-BFGS-B', tol=0.0001,
                   verbose=False, warm_start=False)
>>> clf.predict(X[:5, :])
array([0, 0, 0, 1, 0])
>>> clf.predict_proba(X[:5, :])
array([[1.00000000e+00, 1.77635684e-14],
       [9.99999984e-01, 1.61472709e-08],
       [9.99999651e-01, 3.48756416e-07],
       [1.99686878e-01, 8.00313122e-01],
       [9.99992767e-01, 7.23307080e-06]])
>>> clf.score(X, y)
0.9384885764499121
>>> clf.coef_
array([[ 0.21636945,  0.24114984,  0.60707879, -0.02554191,  0.        ,
        -0.01089683, -0.02143886, -0.00094761,  0.        ,  0.        ,
         0.        ,  0.04741039, -0.04362739, -0.08740847,  0.        ,
         0.        ,  0.        ,  0.        ,  0.        ,  0.        ,
         0.22373333, -0.33820163, -0.30848864, -0.00795973,  0.        ,
        -0.06749937, -0.08757346, -0.01489128, -0.00660756,  0.        ]])
>>> clf.intercept_
array([0.02357148])
>>> clf = LogisticRegression(solver="L-BFGS-B", penalty="elasticnet", l1_ratio=0.5)
>>> clf.fit(X, y)
LogisticRegression(C=1.0, class_weight=None, fit_intercept=True, l1_ratio=0.5,
                   max_iter=100, penalty='elasticnet', solver='L-BFGS-B',
                   tol=0.0001, verbose=False, warm_start=False)
>>> clf.score(X, y)
0.9402460456942003

L1-norm with bounds

Add bound constraints to force all coefficients to be negative. The intercept represents the last position of the lower and upper bound arrays lb, ub, in this case, it is unconstrained.

>>> import numpy as np
>>> from scipy.optimize import Bounds
>>> lb = np.r_[np.full(X.shape[1], -1), -np.inf]
>>> ub = np.r_[np.zeros(X.shape[1]), np.inf]
>>> bounds = Bounds(lb, ub)
>>> clf = LogisticRegression(solver="ecos", penalty="l1")
>>> clf.fit(X, y, bounds=bounds)
LogisticRegression(C=1.0, class_weight=None, fit_intercept=True, l1_ratio=None,
                   max_iter=100, penalty='l1', solver='ecos', tol=0.0001,
                   verbose=False, warm_start=False)
>>> clf.score(X, y)
0.9507908611599297
>>> clf.coef_
array([[ 6.42042386e-10,  6.69614517e-10,  7.49065341e-10,
         2.47466729e-10, -7.46445480e-08, -1.66525870e-07,
        -5.07484194e-06, -9.67293096e-08, -9.94240524e-08,
        -5.10981877e-08, -6.24719977e-08, -2.53429851e-09,
        -2.07856647e-08, -5.03914527e-02, -4.44953073e-08,
        -4.26536917e-08, -4.63999149e-08, -4.53887837e-08,
        -4.58750836e-08, -4.32208857e-08, -2.25323306e-08,
        -2.32851192e-01, -1.56344127e-01,  4.11491956e-11,
        -1.82998431e-07, -9.99999982e-01, -9.99999988e-01,
        -9.99999848e-01, -9.99999947e-01, -7.78260579e-08]])
>>> clf.intercept_
array([25.93817947])

L2-norm with bounds

If we choose penalty="l2" or penalty="none", the L-BFGS-B solver can handle bound constraints.

>>> clf = LogisticRegression(solver="L-BFGS-B", penalty="l2")
>>> clf.fit(X, y, bounds=bounds)
LogisticRegression(C=1.0, class_weight=None, fit_intercept=True, l1_ratio=None,
                   max_iter=100, penalty='l2', solver='L-BFGS-B', tol=0.0001,
                   verbose=False, warm_start=False)
>>> clf.score(X, y, bounds=bounds)
0.9507908611599297
>>> clf.coef_
array([[ 0.00000000e+00,  0.00000000e+00,  0.00000000e+00,
         0.00000000e+00, -1.25630653e-01, -4.92843035e-01,
        -5.85325868e-01, -4.06870366e-01, -1.79105954e-01,
        -4.60000473e-02, -3.22302459e-01,  0.00000000e+00,
         0.00000000e+00, -4.54736330e-02, -6.33875425e-03,
        -6.32628802e-03, -2.51268348e-02, -1.17129553e-02,
        -1.71495885e-02, -5.82817365e-04, -8.19771941e-04,
        -2.44436774e-01, -1.53861432e-01,  0.00000000e+00,
        -2.47266502e-01, -1.00000000e+00, -1.00000000e+00,
        -6.42342321e-01, -5.32446169e-01, -1.41399360e-01]])
>>> clf.intercept_
array([25.96760162])

Elastic-Net with bounds and constraints

If solver="ecos" or solver="scs", linear constraints are supported. First, we solve the unconstrained problem:

>>> clf = LogisticRegression(solver="ecos", penalty="elasticnet", l1_ratio=0.5)
>>> clf.fit(X, y)
LogisticRegression(C=1.0, class_weight=None, fit_intercept=True, l1_ratio=0.5,
                   max_iter=100, penalty='elasticnet', solver='ecos',
                   tol=0.0001, verbose=False, warm_start=False)
>>> clf.coef_
array([[ 1.09515934e+00,  1.78915210e-01, -2.88199448e-01,
         2.26253000e-02, -2.38177991e-08, -3.48595366e-08,
        -1.11789210e-01, -5.41772242e-08, -4.46703080e-08,
        -3.70030911e-09, -9.23360225e-09,  1.34197557e+00,
         2.38283098e-08, -1.02639970e-01, -2.87375705e-09,
         6.99608679e-09, -4.41159130e-09, -4.39357355e-09,
        -4.51432833e-09,  1.46276767e-09,  1.75313422e-08,
        -4.39081317e-01, -9.05714045e-02, -1.32670345e-02,
        -8.77722530e-08, -4.68697190e-01, -1.91274067e+00,
        -2.41172826e-01, -5.15782954e-01, -1.16567422e-08]])
>>> clf.intercept_
array([28.2732499])
>>> clf.score(X, y)
0.9578207381370826

Now, we require to impose bounds and a linear constraint, for example, -coef_[0] + coef_[1] <= 0.5. The constraint has the general inequality form: lb <= A^Tx <= ub.

>>> from scipy.optimize import LinearConstraint
>>> lb = np.array([0.0])
>>> ub = np.array([0.5])
>>> A = np.zeros((1, X.shape[1] + 1))
>>> A[0, :2] = np.array([-1, 1])
>>> A
array([[-1.,  1.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,
         0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,  0.,
         0.,  0.,  0.,  0.,  0.]])
>>> constraints = LinearConstraint(A, lb, ub)
>>> clf = LogisticRegression(solver="ecos", penalty="elasticnet", l1_ratio=0.5)
>>> clf.fit(X, y, bounds=bounds, constraints=constraints)
>>> clf.coef_
array([[ 8.38950646e-10,  9.59874680e-10,  1.09096379e-09,
         3.71912590e-10, -4.85762520e-07, -2.64846257e-01,
        -8.30023820e-01, -2.06338097e-06, -3.66858725e-06,
        -1.79685666e-07, -2.68157291e-07, -3.73083163e-09,
        -3.11904337e-08, -5.04565568e-02, -1.39102635e-07,
        -1.24094215e-07, -1.43485412e-07, -1.43613114e-07,
        -1.46108738e-07, -1.31353775e-07, -6.01051773e-08,
        -2.33773767e-01, -1.54775716e-01, -5.94112471e-11,
        -3.88166017e-01, -9.99999970e-01, -9.99999980e-01,
        -9.99999695e-01, -9.99999911e-01, -5.33323276e-07]])
>>> clf.intercept_
array([25.95361153])
>>> clf.score(X, y)
0.9507908611599297