ElemeNet: Multiscale Molecular Machine Learning with Uncertainty Quantification Across the Periodic Table
Authors: Jacob W. Toney, Samir Darouich, Yiran Wang, Aaron G. Garrison, Johannes Kästner, Heather J. Kulik
Organizations: Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA · Center for Computational Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA · Institute for Theoretical Chemistry, University of Stuttgart, Germany · Institute for Artificial Intelligence, University of Stuttgart, Germany · Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
Abstract
Advances in deep learning architectures and representations have enabled ML-driven chemical property prediction, but state-of-the-art (SOTA) models have remained largely confined to independent codebases and lack support for diverse chemical species. This work introduces ElemeNet, a unified, general-purpose software package for molecular machine learning. The ElemeNet software package enables the training of advanced ML models for diverse properties and datasets with an enlarged range of elemental compositions. We define molecular representations compatible with elements 1-100, supporting diverse organometallic and biological systems in addition to organic chemistry already well-served by the Chemprop ML toolkit. As well as more common atom-, bond-, and molecule-level predictions, we introduce moiety predictions. We also natively define optional conditioning on charge and spin states. Advanced E(3)-equivariant and transformer architectures are supported, as well as classical 2D models, with all classes including built-in uncertainty quantification through deterministic and statistical measures. We benchmark our protocols for ML model training against representative datasets from organic, inorganic, coordination, and biological chemistry, achieving competitive and SOTA performance relative to literature baselines and favorable scaling to millions of molecules. The entire workflow is exposed through a concise command-line interface, lowering the barrier to entry for non-expert users. We anticipate ElemeNet will empower non-computational researchers to leverage modern deep learning methods across the chemical and physical sciences.
Atomic properties such as partial charges or multipoles encode chemically meaningful information that can inform downstream molecular property prediction, but their evaluation as machine learning targets has been complicated by the absence of a principled out-of-distribution evaluation protocol at the atomic level. In this work, we propose a held-out evaluation protocol that clusters atomic environments by SOAP descriptors and computes metrics accounting only for cluster labels unseen during training. Following this procedure, we use 5×5 cross-validation and Tukey's HSD to run a statistically rigorous comparison of E(3)-equivariant against non-equivariant, rotationally augmented models for predicting electron populations and multipoles of H, C, N, and O atoms. Building on our results, we introduce the Quantum Topological Neural Network (QT-Net), a rotationally augmented, non-equivariant graph neural network. We show that QT-Net can be used to infer properties of atoms in molecules from QM9 outside our training set, and that these inferred properties can yield improvement when used as input features for downstream molecular property prediction. To further validate the framework, molecular dipole moments computed from QT-Net's per-atom outputs recover the ground-truth values reported in QM9. We release all code and data, including a JAX implementation of QT-Net, to support the broader use of learned QTA properties as inductive biases for atomic-scale molecular machine learning.
Pablo Martínez Crespo, Stefano Ribes, Martin Rahm +6
Machine learning interatomic potentials (MLIPs) require generating computationally expensive, large-scale training datasets to accurately simulate materials and molecules. Incorporating electronic structure information using multitask learning improves sample efficiency, however, training on full Hamiltonian matrices, which scale quadratically with the number of atoms, is intractable for large datasets. In this work, we show that multitask learning utilizing orbitally resolved semiempirical charges significantly improves sample efficiency and accuracy in MLIPs. To efficiently predict orbital charges, we implement a specialized equivariant model, reducing charge prediction error compared to an invariant baseline. By augmenting training with computationally inexpensive GFN1-xTB orbital charges, which scale linearly with the number of atoms, our model achieves a 46% reduction in energy mean absolute error and requires five times less data to match the performance of energy-only models. Furthermore, our approach outperforms models trained on expensive density functional theory (DFT) atomic charges, capturing orbitally resolved electronic complexity and forcing the network to learn a physically accurate latent space that spontaneously clusters metals by shared chemical properties. Because orbital charges are only required during training, this approach preserves inference efficiency, providing a scalable recipe for developing accurate, data-efficient foundation models for complex chemical systems.
Molecular property prediction integrates quantum chemistry, cheminformatics, and deep learning to connect molecular structure with physicochemical and biological behavior. This survey traces four complementary paradigms, including Quantum, Descriptor Machine Learning, Geometric Deep Learning, and Foundation Models, and outlines a unified taxonomy linking molecular representations, model architectures, and interdisciplinary applications. Benchmark analyses integrate evidence from both widely used datasets and datasets reflecting industry perspectives, encompassing quantum, physicochemical, physiological, and biophysical domains. The survey examines current standards in data curation, splitting strategies, and evaluation protocols, highlighting challenges including inconsistent stereochemistry, heterogeneous assay sources, and reproducibility limitations under random or poorly defined splits. These observations motivate the modernization of benchmark design toward more transparent, time- and scaffold-aware methodologies. We further propose three forward-looking directions: (i) physics-aware learning embedding quantum consistency, (ii) uncertainty-calibrated foundation models for trustworthy inference, and (iii) realistic multimodal benchmark ecosystems integrating computational and experimental data. Repository: https://github.com/Zongru-Li/Survey-and-Benchmarks-of-DL-for-Molecular-Property-Prediction-in-the-Foundation-Model-Era.