Kernel-Based Evaluation of Conditional Biological Sequence Models
Pierre Glaser, Steffanie Paul, Alissa M Hummer, Charlotte Deane, Debora Susan Marks, Alan Nawzad Amin
Abstract
We propose a set of kernel-based tools to evaluate the designs and tune the hyperparameters of conditional sequence models, with a focus on problems in computational biology. The backbone of our tools is a new measure of discrepancy between the true conditional distribution and the model's estimate, called the Augmented Conditional Maximum Mean Discrepancy (ACMMD). Provided that the model can be sampled from, the ACMMD can be estimated unbiasedly from data to quantify absolute model fit, integrated within hypothesis tests, and used to evaluate model reliability. We demonstrate the utility of our approach by analyzing a popular protein design model, ProteinMPNN. We are able to reject the hypothesis that ProteinMPNN fits its data for various protein families, and tune the model's temperature hyperparameter to achieve a better fit.
BibTeX
@inproceedings{
glaser2024kernelbased,
title={Kernel-Based Evaluation of Conditional Biological Sequence Models},
author={Pierre Glaser and Steffanie Paul and Alissa M Hummer and Charlotte Deane and Debora Susan Marks and Alan Nawzad Amin},
booktitle={Forty-first International Conference on Machine Learning},
year={2024},
url={https://openreview.net/forum?id=2dlmcTXfcY}
}