Welcome

What follows is the documentation for using the code and data from the manuscript "A serious flaw in the design of pLM-based protein-protein interaction models".

The code, as well as the documentation, is divided into a few sections:

Section	Description
autofigures	Generates all the experimental figures present in the manuscript.
experiments	Code to conduct the experiments in the manuscript.
data	Data used for the experiments in the manuscript.

Installation & Requirements

This code base contains many small experiments, as well as the autofigures programme, which each have their own requirements. All these code bases are written in Python v3. Specific instructions for installing the required dependencies is present in each folder.

Install time for the various experiments in this repository vary greatly and depend on hardware (e.g., disk I/O), but typically will take less than 15 minutes for each code base.

Demo

To see a demo of how to regenerate all the figures in the manuscript, see our demo.

License

Code

All code files in this repository are licensed under the GNU AGPLv3 License.

Code for "A serious flaw in the design of pLM-based protein-protein interactions"

Copyright (C) 2025 Joseph Szymborski

This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.

You should have received a copy of the GNU Affero General Public License along with this program. If not, see https://www.gnu.org/licenses/.

Data

Data for "A serious flaw in the design of pLM-based protein-protein interactions" by Joseph Szymborski is licensed under CC BY-NC-SA 4.0