knockpy 1.3.5

Knockoffs for variable selection

Knockpy

A python implementation of the knockoffs framework for variable selection. See https://amspector100.github.io/knockpy/ for detailed documentation and tutorials.

Installation

To install and begin using knockpy, simply enter:

pip install knockpy[fast]

To use the (optional) kpytorch submodule, you will need to install pytorch.

What if installation fails?

knockpy relies on heavy-duty linear algebra routines which sometimes fail on non-Linux environments.

1. To start, install a lightweight version of knockpy using pip install knockpy. This should install correctly on all devices, and contains nearly all of the functionality of the prior installation. However, the algorithms for computing optimal distributions for Gaussian knockoffs, such as minimum reconstructability knockoffs and SDP knockoffs, may be an order of magnitude slower.

2. [Optional] To speed up computation for minimum reconstructability knockoffs (the default knockoff type):

   (a) Run

   pip install cython>=0.29.14`
   

   If the installation fails, likely due to the incorrect configuration of a C compiler, you have three options. First, the Anaconda package manager includes a compiler, so the command

   install cython
   

   should work on all platforms. Second, on Windows, you can install precompiled binaries for cython here. Lastly, on all platforms, the documentation here describes how to properly configure a C compiler during installation.

   (b) Run

   pip install git+https://github.com/jcrudy/choldate.git
   

3. [Optional] To speed up computation for (non-default) SDP knockoffs, you will need to install scikit-dsdp. This can be challenging on non-Linux environments. We hope to provide more explicit instructions for installation of this package in the future.

Quickstart

Given a data-matrix X and a response vector y, knockpy makes it easy to use knockoffs to perform variable selection using a wide variety of machine learning algorithms (also known as "feature statistic") and types of knockoffs. One quick example is shown below, where we use the cross-validated lasso to assign variable importances to the features and knockoffs.

import knockpy as kpy
from knockpy.knockoff_filter import KnockoffFilter

# Generate synthetic data from a Gaussian linear model
data_gen_process = kpy.dgp.DGP()
data_gen_process.sample_data(
    n=1500, # Number of datapoints
    p=500, # Dimensionality
    sparsity=0.1,
    x_dist='gaussian',
)
X = data_gen_process.X
y = data_gen_process.y
Sigma=data_gen_process.Sigma

# Run model-X knockoffs
kfilter = KnockoffFilter(
    fstat='lasso',
    ksampler='gaussian',
)
rejections = kfilter.forward(X=X, y=y, Sigma=Sigma)

Most importantly, knockpy is built to be modular, so researchers and analysts can easily layer functionality on top of it.

Development

To install knockpy for development, you must first install uv.

git clone https://github.com/amspector100/knockpy.git
cd knockpy
make install-pre-commit

The Makefile makes it easy to perform the most common operations:

• make check-all runs linting and uv.lock checks
• make check-lint checks for linting issues
• make check-lock verifies the uv.lock is aligned to pyproject.toml
• make clean cleans the virtual environment and caches
• make default runs a default set of checks on the code
• make fix-all formats the code, fixes lint errors and runs locks uv.lock to pyproject.toml
• make fix-format formats the code
• make fix-lint fixes linting issues
• make fix-lint-unsafe fixes linting issues potentially adding inadvertant bugs
• make help outputs the different make options
• make install build install the distribution
• make install-pre-commit installs pre-commit hooks
• make lock locks uv.lock to pyproject.toml
• make install-pre-commit installs pre-commit hooks
• make run-tests runs the unit tests
• make sync syncs the python environment with uv.lock

.vscode/settings.json is set so that unit tests can be run without further configuration.

Releasing to pypi

If you are an owner of the knockpy repo, you can publish a new version to pypi by:

1. Selecting the Bump Version and Start New Release workflow
2. Selecting Run workflow
3. Ensure that the main branch is selected
4. Pressing Run workflow
5. This should trigger a new build and release in the Make a New Release workflow page. This will publish to pypi.org.
6. Select the new release in the Releases page
7. Add release notes and publish the release.

Reference

If you use knockpy in an academic publication, please consider citing Spector and Janson (2020). The bibtex entry is below:

@article{AS-LJ:2020,
  title={Powerful Knockoffs via Minimizing Reconstructability},
  author={Spector, Asher and Janson, Lucas},
  journal={Annals of Statistics},
  year={2021+},
  note={To Appear}
}