Investigation of Machine Learning-based Coarse-Grained Mapping Schemes for Organic Molecules

TL;DR

This paper investigates a machine learning approach using Variational Autoencoders to develop coarse-grained mapping schemes for organic molecules, aiming to improve multiscale molecular simulations by reducing reliance on chemical intuition.

Contribution

It introduces a novel ML-based method for systematic coarse-graining of molecules, including hyperparameter analysis and physical consistency criteria, advancing beyond traditional intuition-based approaches.

Findings

ML approach can generate physically consistent mappings

Hyperparameter choices significantly affect model performance

Rotational invariance improves reconstruction accuracy

Abstract

Due to the wide range of timescales that are present in macromolecular systems, hierarchical multiscale strategies are necessary for their computational study. Coarse-graining (CG) allows to establish a link between different system resolutions and provides the backbone for the development of robust multiscale simulations and analyses. The CG mapping process is typically system- and application-specific, and it relies on chemical intuition. In this work, we explored the application of a Machine Learning strategy, based on Variational Autoencoders, for the development of suitable mapping schemes from the atomistic to the coarse-grained space of molecules with increasing chemical complexity. An extensive evaluation of the effect of the model hyperparameters on the training process and on the final output was performed, and an existing method was extended with the definition of different loss functions and the implementation of a selection criterion that ensures physical consistency of the output. The relationship between the input feature choice and the reconstruction accuracy was analyzed, supporting the need to introduce rotational invariance into the system. Strengths and limitations of the approach, both in the mapping and in the backmapping steps, are highlighted and critically discussed.