Graph-Based Deep Learning Models for Thermodynamic Property Prediction: The Interplay between Target Definition, Data Distribution, Featurization, and Model Architecture

In this contribution, we examine the interplay between target definition, data distribution, featurization approaches, and model architectures on graph-based deep learning models for thermodynamic property prediction. Through consideration of five curated data sets, exhibiting diversity in elemental composition, multiplicity, charge state, and size, we examine the impact of each of these factors on model accuracy. We observe that target definition, i.e., using formation instead of atomization energy/enthalpy, is a decisive factor, and so is a careful selection of the featurization approach. Our attempts at directly modifying model architectures result in more modest, though not negligible, accuracy gains. Remarkably, we observe that molecule-level predictions tend to outperform atom-level increment predictions, in contrast to previous findings. Overall, this work paves the way toward the development of robust graph-based thermodynamic model architectures with more universal capabilities, i.e., architectures that can reach excellent accuracy across data sets and compound domains.

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Publication Details

Journal
Journal of Chemical Information and Modeling
Published
2025-01-09
DOI
https://doi.org/10.1021/acs.jcim.4c02014
Citations
2
Primary Topic
Machine Learning in Materials Science
Type
article
Field-Weighted Citation Impact
1.04

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article

Graph-Based Deep Learning Models for Thermodynamic Property Prediction: The Interplay between Target Definition, Data Distribution, Featurization, and Model Architecture

Thijs Stuyver, Bowen Deng
2 citations
Journal of Chemical Information and Modeling
Machine Learning in Materials Science
1.04
article

Graph-Based Deep Learning Models for Thermodynamic Property Prediction: The Interplay between Target Definition, Data Distribution, Featurization, and Model Architecture

Thijs Stuyver, Bowen Deng
article en
2 citations

Abstract

In this contribution, we examine the interplay between target definition, data distribution, featurization approaches, and model architectures on graph-based deep learning models for thermodynamic property prediction. Through consideration of five curated data sets, exhibiting diversity in elemental composition, multiplicity, charge state, and size, we examine the impact of each of these factors on model accuracy. We observe that target definition, i.e., using formation instead of atomization energy/enthalpy, is a decisive factor, and so is a careful selection of the featurization approach. Our attempts at directly modifying model architectures result in more modest, though not negligible, accuracy gains. Remarkably, we observe that molecule-level predictions tend to outperform atom-level increment predictions, in contrast to previous findings. Overall, this work paves the way toward the development of robust graph-based thermodynamic model architectures with more universal capabilities, i.e., architectures that can reach excellent accuracy across data sets and compound domains.

Journal of Chemical Information and ModelingVol. 65(2)
Centre National de la Recherche Scientifique (FR), Chimie ParisTech - PSL (FR), Université Paris Sciences et Lettres (FR)
Agence Nationale de la Recherche, Centre National de la Recherche Scientifique
Openalex Percentile: Top 29%
Machine Learning in Materials Science
1.04
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Graph-Based Deep Learning Models for Thermodynamic Property Prediction: The Interplay between Target Definition, Data Distribution, Featurization, and Model Architecture — Thijs Stuyver, Bowen Deng · Journal of Chemical Information and Modeling (2025) | TGRS Research Map | TGRS