MUTational and Embedding Data Processing Library for Python (mutedpy)

mutedpy is a python library that implements tools and machine learning models able to analyze mutational datasets of protein sequences and/or structures. We implement numerous shallow models targeted for datasets of sizes $10^2 - 10^6$. The models we implement:

1. Neural Networks (feed-forward, convolutional, graph)
2. linear models
3. Gaussian processes

• utilizing different similarirty metrics
• amino-acid embeddings
• esm embeddings, data-driven embeddings
• geometric features

A significant part of the package is devolted to:

1. simulation of directed evolution campaigns
2. manipulation of sequence datasets:

• conversion between different formats
• scanning, enumeration seach
• data splitting train/test

Installation

First clone the repository:

git clone https://github.com/Mojusko/mutedpy

Inside the project directory, run

pip install -e .

The -e option installs the package in "editable" mode, where pip links to your local copy of the repository, instead of copying the files to the your site-packages directory. That way, a simple git pull will update the package. The project requires Python 3.6, and the dependencies should be installed with the package (let me know if it doesn't work for you).

Structure

Updates

• 21/05/2024 - initial commit

Requires

• Classical: pytorch, cvxpy, numpy, scipy, sklearn, pymanopt, mosek, pandas

• Special: 1. pytorch-minimize https://github.com/rfeinman/pytorch-minimize 2. stpy https://github.com/mojusko/pytorch-minimize

Contributions

Mojmir Mutny