A Physics-Inspired Approach to the Understanding of Molecular Representations and Models

11 December 2023, Version 1
This content is a preprint and has not undergone peer review at the time of posting.


The story of machine learning in general, and its application to molecular design in particular, has been a tale of evolving representations of data. Understanding the implications of the use of a particular representation -- including the existence of so-called `activity cliffs' for cheminformatics models -- is the key to their successful use for molecular discovery. In this work we present a physics-inspired methodology which exploits analogies between model response surfaces and energy landscapes to richly describe the relationship between the representation and the model. From these similarities, a metric emerges which is analogous to the commonly used frustration metric from the chemical physics community. This new property shows state-of-the-art prediction of model error, whilst belonging to a novel class of roughness measure that extends beyond the known data allowing the trivial identification of activity cliffs even in the absence of related training or evaluation data.


Molecular representations
Energy landscapes
Structure-property relationships
Dataset modelability
Molecular regression
Molecular discovery


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