fastridge 1.2.0

Fast and robust approach to ridge regression with simultaneous estimation of model parameters and hyperparameter tuning within a Bayesian framework via expectation-maximization (EM).

fastridge

Fast and Accurate Ridge Regression via Expectation Maximization

by Shu Yu Tew, Mario Boley, Daniel F. Schmidt

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The statistical performance of the ridge regression estimate for linear regression parameters fitted to a training dataset $\mathbf{X}\in\mathbb{R}^{n \times p}$, $\boldsymbol{y} \in \mathbb{R}^n$, i.e.,

$$ \hat{\boldsymbol{\beta}}\alpha = \arg\min{\boldsymbol{\beta} \in \mathbb{R}^p} \lbrace\Vert\boldsymbol{y} - \boldsymbol{X}\boldsymbol{\beta}\Vert^2 + \alpha\Vert\boldsymbol{\beta}\Vert^2\rbrace $$

strongly depends on the choice of the regularisation parameter $\alpha \in \mathbb{R}_+$. The commonly used approach to estimate the optimal value for this parameter is by leave-one-out cross-validation.

This package provides an alternative iterative algorithm based on the Bayesian formulation of ridge regression:

\begin{aligned}
\boldsymbol{y} \mid \boldsymbol{X}, \boldsymbol{\beta}, \sigma^2, \tau^2 &\sim \mathrm{N}(\boldsymbol{X}\boldsymbol{\beta}, \sigma^2 \boldsymbol{I}_n)\\
\boldsymbol{\beta} \mid \sigma^2, \tau^2 &\sim \mathrm{N}(0, \tau^{-2}\sigma^{-2}\boldsymbol{I}_p)\\
\sigma^2 &\sim \sigma^{-2}\,\mathrm{d}\sigma^2\\
\tau^2 &\sim \pi(\tau^2)\,\mathrm{d}\tau^2
\end{aligned}

In particular, the package implements an expectation maximisation (EM) approach that approximates the marginal posterior mode $\arg\max_{\sigma^2, \tau^2} p(\sigma^2, \tau^2 \mid \boldsymbol{X}, \boldsymbol{y})$ by iterating the equation

$$ \sigma^2_{t+1}, \tau^2_{t+1} = \arg\min_{\sigma^2, \tau^2} \mathbb{E}_{\boldsymbol{\beta} \mid \sigma^2_t, \tau^2_t} \left[-\log\thinspace p(\boldsymbol{\beta}, \sigma^2, \tau^2)\right] $$

until a convergence criterion is met.

Usage

import numpy as np
from fastridge import RidgeEM, RidgeLOOCV

# synthetic regression data
rng = np.random.default_rng(0)
beta = np.array([1.0, -2.0, 0.5, 3.0, -1.5, 0.0])
x_train = rng.standard_normal((20, 6))
y_train = x_train @ beta + 0.1 * rng.standard_normal(20)
x_test = rng.standard_normal((1000, 6))
y_test = x_test @ beta + 0.1 * rng.standard_normal(1000)

# fit using EM approach 
em = RidgeEM().fit(x_train, y_train)
y_train_em = em.predict(x_train)
y_test_em = em.predict(x_test)
print(f'EM   train MSE: {np.mean((y_train - y_train_em)**2):.4f}')
print(f'EM   test MSE:  {np.mean((y_test - y_test_em)**2):.4f}')
print(f'EM   coef_:         {em.coef_}')
print(f'EM   alpha_:        {em.alpha_:.4f}')
print(f'EM   sigma_square:  {em.sigma_square_:.4f}')

# fit using fast LOOCV
cv = RidgeLOOCV().fit(x_train, y_train)
y_train_cv = cv.predict(x_train)
y_test_cv = cv.predict(x_test)
print(f'CV   train MSE: {np.mean((y_train - y_train_cv)**2):.4f}')
print(f'CV   test MSE:  {np.mean((y_test - y_test_cv)**2):.4f}')
print(f'CV   coef_:    {cv.coef_}')
print(f'CV   alpha_:   {cv.alpha_:.4f}')

Package Installation

To install the package from pypi use

pip install fastridge

or to install directly from this repository use

pip install git+https://github.com/marioboley/fastridge.git

(pip or pip3 depending on the local Python setup.)

Project Setup

To alter the package or to run and modify the analysis code, run

pip3 install -r requirements.txt
pip3 install -e .

at the root of the repository after cloning.

The second step (local editable installation) is required so that import fastridge works for the analysis notebooks in subdirectories.

It is recommended to install package and dependencies into a dedicated virtual environment by running at the project root before the above steps:

python3 -m venv .venv
source .venv/bin/activate   # or: conda create/activate for Anaconda

To test the project setup, run the test suite:

pytest

Citation

Should you find this repository helpful, please consider citing the associated paper:

@article{tew2023bayes,
  title={Bayes beats cross validation: Efficient and accurate ridge regression via expectation maximization},
  author={Tew, Shu Yu and Boley, Mario and Schmidt, Daniel},
  journal={Advances in Neural Information Processing Systems},
  volume={36},
  pages={19749--19768},
  year={2023}
}