Learning on compressed molecular representations

Autor(en)

Jan Weinreich, Daniel Probst

Abstrakt

Last year, a preprint gained notoriety, proposing that a k-nearest neighbour classifier is able to outperform large-language models using compressed text as input and normalised compression distance (NCD) as a metric. In chemistry and biochemistry, molecules are often represented as strings, such as SMILES for small molecules or single-letter amino acid sequences for proteins. Here, we extend the previously introduced approach with support for regression and multitask classification and subsequently apply it to the prediction of molecular properties and protein-ligand binding affinities. We further propose converting numerical descriptors into string representations, enabling the integration of text input with domain-informed numerical descriptors. Finally, we show that the method can achieve performance competitive with chemical fingerprint- and GNN-based methodologies in general, and perform better than comparable methods on quantum chemistry and protein-ligand binding affinity prediction tasks.

Organisation(en)

Computergestützte Materialphysik

Externe Organisation(en)

École polytechnique fédérale de Lausanne

Journal

Digital Discovery

Band

4

Seiten

84-92

Anzahl der Seiten

9

ISSN

2635-098X

DOI

https://doi.org/10.1039/d4dd00162a

Publikationsdatum

11-2024

Peer-reviewed

Ja

ÖFOS 2012

102019 Machine Learning, 104027 Computational Chemistry

ASJC Scopus Sachgebiete

Chemistry (miscellaneous)

Link zum Portal

https://ucrisportal.univie.ac.at/de/publications/a22f6fbe-e3f3-4365-8384-c21453621846