On Recovering Higher-order Interactions from Protein Language Models

This repository contains code for the paper:

"On Recovering Higher-order Interactions from Protein Language Models", Darin Tsui, Amirali Aghazadeh

Paper: https://openreview.net/forum?id=WfA5oWpYT4

Description of folders

ESM/: Code needed to run q-sft for ESM. More information has been left in the folder.

FFT/: Code needed to run Walsh-Hadamard analysis for ESM. More information has been left in the folder.

qsft/: Functions needed to run q-sft.

Quick Start

Generate all necessary files

cd ESM/
mkdir model/
cd scripts/
sh 0_setup.sh

Run q-sft

cd ESM/scripts/
sh 1_helper.sh

Run Walsh-Hadamard Analysis

cd FFT/
python 1_sampling.py

Visualize reuslts using 2_analysis.ipynb.