# Probabilistic thermal stability prediction through sparsity promoting transformer representation

arXiv: https://arxiv.org/abs/2211.05698 · HTML: https://mlsanity.com/paper/2211.05698/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 3 of its 18 references that are in the map.
- First posted on arXiv 10 Nov 2022.

## Builds on (most cited first, 3 of 3)

- [Evaluating Protein Transfer Learning with TAPE](https://mlsanity.com/paper/1906.08230/) (2019)
- [ProtTrans: Towards Cracking the Language of Life's Code Through Self-Supervised Deep Learning and High Performance Computing](https://mlsanity.com/paper/2007.06225/) (2020)
- [BERTology Meets Biology: Interpreting Attention in Protein Language Models](https://mlsanity.com/paper/2006.15222/) (2020)

## Abstract (arXiv)

Pre-trained protein language models have demonstrated significant applicability in different protein engineering task. A general usage of these pre-trained transformer models latent representation is to use a mean pool across residue positions to reduce the feature dimensions to further downstream tasks such as predicting bio-physics properties or other functional behaviours. In this paper we provide a two-fold contribution to machine learning (ML) driven drug design. Firstly, we demonstrate the power of sparsity by promoting penalization of pre-trained transformer models to secure more robust and accurate melting temperature (Tm) prediction of single-chain variable fragments with a mean absolute error of 0.23C. Secondly, we demonstrate the power of framing our prediction problem in a probabilistic framework. Specifically, we advocate for the need of adopting probabilistic frameworks especially in the context of ML driven drug design.