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DOE OSTI2024

Active causal learning for decoding chemical complexities with targeted interventions

Abstract Predicting and enhancing inherent properties based on molecular structures is paramount to design tasks in medicine, materials science, and environmental management. Most of the current machine learning and deep learning approaches have become standard for predictions, but they face challenges when applied across different datasets due to reliance on correlations between molecular representation and target properties. These approaches typically depend on large datasets to capture the diversity within the chemical space, facilitating a more accurate approximation, interpolation, or extrapolation of the chemical behavior of molecules. In our research, we introduce an active learning approach that discerns underlying cause-effect relationships through strategic sampling with the use of a graph loss function. This method identifies the smallest subset of the dataset capable of encoding the most information representative of a much larger chemical space. The identified causal relations are then leveraged to conduct systematic interventions, optimizing the design task within a chemical space that the models have not encountered previously. While our implementation focused on the QM9 quantum-chemical dataset for a specific design task—finding molecules with a large dipole moment—our active causal learning approach, driven by intelligent sampling and interventions, holds potential for broader applications in molecular, materials design and discovery.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Factors Governing Oxygen Vacancy Formation in Oxide Perovskites

The control of oxygen vacancy (V O ) formation is critical to advancing multiple metal-oxide-perovskite-based technologies. In this work, we report the construction of a compact linear model for the neutral V O formation energy in ABO 3 perovskites that reproduces, with reasonable fidelity, Hubbard-U-corrected density functional theory calculations based on the state-of-the-art, strongly constrained and appropriately normed exchange-correlation functional. We obtain a mean absolute error of 0.45 eV for perovskites stable at 298 K, an accuracy that holds across a large, electronically diverse set of ABO 3 perovskites. Our model considers perovskites containing alkaline-earth metals (Ca, Sr, and Ba) and lanthanides (La and Ce) on the A-site and 3d transition metals (Ti, V, Cr, Mn, Fe, Co, and Ni) on the B-site in six different crystal systems (cubic, tetragonal, orthorhombic, hexagonal, rhombohedral, and monoclinic) common to perovskites. Physically intuitive metrics easily extracted from existing experimental thermochemical data or via inexpensive quantum mechanical calculations, including crystal bond dissociation energies and (solid phase) reduction potentials, are key components of the model. Beyond validation of the model against known experimental trends in materials used in solid oxide fuel cells, the model yields new candidate perovskites not contained in our training data set, such as (Bi,Y)(Fe,Co)O 3 , which we predict may have favorable thermochemical water-splitting properties. The confluence of sufficient accuracy, efficiency, and interpretability afforded by our model not only facilitates high-throughput computational screening for any application that requires the precise control of V O concentrations but also provides a clear picture of the dominant physics governing V O formation in metal-oxide perovskites.

08 HYDROGEN↗
DOE OSTI2022

Effect of disorder on thermodynamic instability of binary Rare-earth – Nickel – Palladium compounds

In this work, we have investigated the thermodynamic stability of disordered rare-earth phases SmX 2 and Sm 10 X 21 (X=Ni, Pd) using machine-learning based analytical descriptor and first-principles density functional theory methods. The absence of Laves phase compounds in R-Pd binary systems is a longstanding problem of rare earth science: even though Ni and Pd belong to the same group of the periodic table and have similar electronic structure, the Pd compound crystallizes in a monoclinic (C2/m) phase with 10:21 stoichiometry, i.e., Sm 10 Pd 21 , while the Ni compound adopts a cubic Laves phase (MgCu 2 ) structure. To understand this contrasting phase stability, we performed thermodynamic convex hull analysis of Sm x Ni 1-x and Sm x Pd 1-x binary systems, which is experimentally validated using powder X-ray diffraction (PXRD) analyzes of polycrystalline Sm(Ni x Pd 1-x ) 2 samples with x=0, 0.5, and 1. A detailed electronic-structure (band-structure, charge density, and Fermi-surface) analysis of the differences between SmNi 2 /SmPd 2 and Sm 10 Ni 21 /Sm 10 Pd 21 compounds provides the quantum mechanical origin of the unfavorable mixing of Pd with Ni in cubic Laves phase. We show that the stability of Sm-Pd in 10:21 stoichiometry arises from improved intra-/inter-layer 5d-4d bonding compared to the 1:2 stoichiometry. Our work emphasizes the importance of ab-initio methods and computationally inexpensive analytical descriptors for the detailed analysis of thermodynamic and electronic properties of hard-to-prepare rare-earth compounds.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Neural-network model for force prediction in multi-principal-element alloys

Atomistic simulations can provide useful insights into the physical properties of multi-principal-element alloys. However, classical potentials mostly fail to capture key quantum (electronic-structure) effects. Here we present a deep 3D convolutional neural network (3D CNN) based framework combined with a voxelization technique to design interatomic potentials for chemically complex alloys. We highlight the performance of the 3D CNN model and its efficacy in computing potentials using the medium-entropy alloy TaNbMo. In order to provide insights into the effect of voxel resolution, we implemented two approaches based on the inner and outer bounding boxes. An efficient 3D CNN model, which is as accurate as the density-functional theory (DFT) approach, for calculating potentials will provide a promising schema for accurate atomistic simulations of structure and dynamics of general multi-principle element alloys.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Limited-view Cone Beam CT reconstruction using 3D Patch-based Supervised and Adversarial Learning [Slides]

We present a novel machine learning CNN architecture that can learn from limited data combined appropriately with physics and statistical priors (e.g., forward models and noise models). To address the limited availability of training data we adopt a 3D patch-based approach for our models. Patch-based learning is central to several image reconstruction methods and demands fewer training data than DL approaches, as a single data volume can be broken into several millions of overlapping 3D sub-volumes or patches. This creates a very large number of training sub-volumes from a limited number of overall image volumes. A 3D Generative Adversarial Networks (GAN) is then trained to remove artifacts at the sub-volume level. The combination of a sub-volume-based approach with DL allows us to exploit the richness of the latter in extracting and representing image features, while avoiding risks associated with overfitting due to limited training data.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

Generalized Quantum Convolution for Multidimensional Data

The convolution operation plays a vital role in a wide range of critical algorithms across various domains, such as digital image processing, convolutional neural networks, and quantum machine learning. In existing implementations, particularly in quantum neural networks, convolution operations are usually approximated by the application of filters with data strides that are equal to the filter window sizes. One challenge with these implementations is preserving the spatial and temporal localities of the input features, specifically for data with higher dimensions. In addition, the deep circuits required to perform quantum convolution with a unity stride, especially for multidimensional data, increase the risk of violating decoherence constraints. In this work, we propose depth-optimized circuits for performing generalized multidimensional quantum convolution operations with unity stride targeting applications that process data with high dimensions, such as hyperspectral imagery and remote sensing. We experimentally evaluate and demonstrate the applicability of the proposed techniques by using real-world, high-resolution, multidimensional image data on a state-of-the-art quantum simulator from IBM Quantum.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Phase Equilibrium of Water with Hexagonal and Cubic Ice Using the SCAN Functional

Machine learning models are rapidly becoming widely used to simulate complex physicochemical phenomena with ab initio accuracy. Here, we use one such model as well as direct density functional theory (DFT) calculations to investigate the phase equilibrium of water, hexagonal ice (Ih), and cubic ice (Ic), with an eye toward studying ice nucleation. The machine learning model is based on deep neural networks and has been trained on DFT data obtained using the SCAN exchange and correlation functional. We use this model to drive enhanced sampling simulations aimed at calculating a number of complex properties that are out of reach of DFT-driven simulations and then employ an appropriate reweighting procedure to compute the corresponding properties for the SCAN functional. This approach allows us to calculate the melting temperature of both ice polymorphs, the driving force for nucleation, the heat of fusion, the densities at the melting temperature, the relative stability of ices Ih and Ic, and other properties. We find a correct qualitative prediction of all properties of interest. In some cases, quantitative agreement with experiment is better than for state-of-the-art semiempirical potentials for water. Furthermore, our results also show that SCAN correctly predicts that ice Ih is more stable than ice Ic.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Progress toward favorable landscapes in quantum combinatorial optimization

The performance of variational quantum algorithms relies on the success of using quantum and classical computing resources in tandem. Here, we study how these quantum and classical components interrelate. In particular, we focus on algorithms for solving the combinatorial optimization problem MaxCut, and study how the structure of the classical optimization landscape relates to the quantum circuit used to evaluate the MaxCut objective function. In order to analytically characterize the impact of quantum features on the critical points of the landscape, we consider a family of quantum circuit ansätze composed of mutually commuting elements. We identify multiqubit operations as a key resource and show that overparameterization allows for obtaining favorable landscapes. Namely, we prove that an ansatz from this family containing exponentially many variational parameters yields a landscape free of local optima for generic graphs. However, we further prove that these ansätze do not offer superpolynomial advantages over purely classical MaxCut algorithms. Here, we then present a series of numerical experiments illustrating that noncommutativity and entanglement are important features for improving algorithm performance.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Automated discovery of a robust interatomic potential for aluminum

Machine learning, trained on quantum mechanics (QM) calculations, is a powerful tool for modeling potential energy surfaces. A critical factor is the quality and diversity of the training dataset. Here we present a highly automated approach to dataset construction and demonstrate the method by building a potential for elemental aluminum (ANI-Al). In our active learning scheme, the ML potential under development is used to drive non-equilibrium molecular dynamics simulations with time-varying applied temperatures. Whenever a configuration is reached for which the ML uncertainty is large, new QM data is collected. The ML model is periodically retrained on all available QM data. The final ANI-Al potential makes very accurate predictions of radial distribution function in melt, liquid-solid coexistence curve, and crystal properties such as defect energies and barriers. We perform a 1.3M atom shock simulation and show that ANI-Al force predictions shine in their agreement with new reference DFT calculations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

A machine learning approach for efficient multi-dimensional integration

Many physics problems involve integration in multi-dimensional space whose analytic solution is not available. The integrals can be evaluated using numerical integration methods, but it requires a large computational cost in some cases, so an efficient algorithm plays an important role in solving the physics problems. We propose a novel numerical multi-dimensional integration algorithm using machine learning (ML). After training a ML regression model to mimic a target integrand, the regression model is used to evaluate an approximation of the integral. Then, the difference between the approximation and the true answer is calculated to correct the bias in the approximation of the integral induced by ML prediction errors. Because of the bias correction, the final estimate of the integral is unbiased and has a statistically correct error estimation. Three ML models of multi-layer perceptron, gradient boosting decision tree, and Gaussian process regression algorithms are investigated. The performance of the proposed algorithm is demonstrated on six different families of integrands that typically appear in physics problems at various dimensions and integrand difficulties. The results show that, for the same total number of integrand evaluations, the new algorithm provides integral estimates with more than an order of magnitude smaller uncertainties than those of the VEGAS algorithm in most of the test cases.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

Hamiltonian learning using machine-learning models trained with continuous measurements

Here, we build upon recent work on the use of machine-learning models to estimate Hamiltonian parameters using continuous weak measurement of qubits as input. We consider two settings for the training of our model: (1) supervised learning, where the weak-measurement training record can be labeled with known Hamiltonian parameters, and (2) unsupervised learning, where no labels are available. The first has the advantage of not requiring an explicit representation of the quantum state, thus potentially scaling very favorably to a larger number of qubits. The second requires the implementation of a physical model to map the Hamiltonian parameters to a measurement record, which we implement using an integrator of the physical model with a recurrent neural network to provide a model-free correction at every time step to account for small effects not captured by the physical model. We test our construction on a system of two qubits and demonstrate accurate prediction of multiple physical parameters in both the supervised context and the unsupervised context. We demonstrate that the model benefits from larger training sets, establishing that it is “learning,” and we show robustness regarding errors in the assumed physical model by achieving accurate parameter estimation in the presence of unanticipated single-particle relaxation.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Analytic continuation of noisy data using Adams Bashforth residual neural network

We propose a data-driven learning framework for the analytic continuation problem in numerical quantum many-body physics. Designing an accurate and efficient framework for the analytic continuation of imaginary time using computational data is a grand challenge that has hindered meaningful links with experimental data. The standard Maximum Entropy (MaxEnt)-based method is limited by the quality of the computational data and the availability of prior information. Also, the MaxEnt is not able to solve the inversion problem under high level of noise in the data. Here we introduce a novel learning model for the analytic continuation problem using a Adams-Bashforth residual neural network (AB-ResNet). Additionally, the advantage of this deep learning network is that it is model independent and, therefore, does not require prior information concerning the quantity of interest given by the spectral function. More importantly, the ResNet-based model achieves higher accuracy than MaxEnt for data with higher level of noise. Finally, numerical examples show that the developed AB-ResNet is able to recover the spectral function with accuracy comparable to MaxEnt where the noise level is relatively small.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Development of neural network force fields for corrosion studies

To fully understand the chemistry and physics of corrosion, novel methods of simulation must be developed. One approach is designing machine learning (ML) algorithms integrated with density functional theory to develop adaptive force fields to gain insight into corrosion behavior namely at the surface of metal oxides. Current methods of modeling corrosion are slow due to the computational cost of resolving both reaction mechanics and mass transport processes. Machine learning methods can be implemented to obtain structure-activity relationships at both the molecular and bulk scale while still retaining the accuracy of density functional theory (DFT) and significantly decreasing the time needed for simulations of complex chemical processes in the various environments of corrosion. Multiscale models are needed for corrosion studies to fully understand its processes not only at the atomic length scale (chemical bonding, energies, and forces), but also at the nano and meso length scales (solid-state physics and material science processes). Current methods of study include DFT, molecular dynamics, and Monte Carlo. The limitation of DFT is that only a small number of atoms or molecules can be simulated at that level of theory. Density functional theory is used to study the electronic structure of atoms and molecules, and calculate the force component of each atom. However, these calculations are limited to about 1000 atoms. Custom periodic boundary conditions (PBC) can be used to describe the various environments and defects that affect the atomic forces to produce a large data set from which a training set can be derived. Machine learning can be utilized to overcome the barrier of modeling macroscopic and multi-scale processes from ab initio calculations through the development of adaptive force fields. Local environments determine the atomic forces of a given system, therefore adaptive force fields must be created to produce reliable quantum mechanical calculations. This can be achieved by developing a learning algorithm that uses the mapped atomic forces or fingerprint as an input to produce energies and magnetic moments as output. A systematic approach was used to begin to build a data set in order to accurately describe the atomic forces in various environments. In Figure 4 below, a simple PBC cell of Fe{sub 2}O{sub 3} was first optimized. A surface optimization was performed next, followed by a hydroxylated surface optimization. Once this calculation has converged, the adsorption of halide species to the hydroxylated surface will be investigated. TensorFlow is an open source platform for machine learning developed by Google. Using a high level application program interface (API) such as Keras allows for building and training ML models easily in a number of different environments and languages. For this project, a neural network was developed within Anaconda in Python. Future Work: Further development of reference data set; Refining neural network and learning algorithm; Fingerprinting atomic environment to enable mapping of atomic force components; Choosing appropriate training set from reference data; Learning from training set and enabling non-linear mapping of training set fingerprints and the atomic forces; Estimation of uncertainty to identify ranges of outside applicability; Testing and analysis of molecular dynamic simulations.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Predicting Energetics Materials’ Crystalline Density from Chemical Structure by Machine Learning

To expedite new molecular compound development, a long-sought goal within the chemistry community has been to predict molecules’ bulk properties of interest a priori to synthesis from a chemical structure alone. In this work, we demonstrate that machine learning methods can indeed be used to directly learn the relationship between chemical structures and bulk crystalline properties of molecules, even in the absence of any crystal structure information or quantum mechanical calculations. We focus specifically on a class of organic compounds categorized as energetic materials called high explosives (HE) and predicting their crystalline density. An ongoing challenge within the chemistry machine learning community is deciding how best to featurize molecules as inputs into machine learning models—whether expert handcrafted features or learned molecular representations via graph-based neural network models—yield better results and why. We evaluate both types of representations in combination with a number of machine learning models to predict the crystalline densities of HE-like molecules curated from the Cambridge Structural Database, and we report the performance and pros and cons of our methods. Our message passing neural network (MPNN) based models with learned molecular representations generally perform best, outperforming current state-of-the-art methods at predicting crystalline density and performing well even when testing on a data set not representative of the training data. However, these models are traditionally considered black boxes and less easily interpretable. Here, to address this common challenge, we also provide a comparison analysis between our MPNN-based model and models with fixed feature representations that provides insights as to what features are learned by the MPNN to accurately predict density.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

A cornucopia of AdS5 vacua

We report on a systematic search for AdS 5 vacua corresponding to critical points of the potential in the five-dimensional $$ \mathcal{N} $$ N = 8 SO(6) gauged supergravity. By employing Google’s TensorFlow Machine Learning library, we find the total of 32 critical points including 5 previously known ones. All 27 new critical points are non-supersymmetric. We compute the mass spectra of scalar fluctuatons for all points and find that the non- supersymmetric AdS 5 vacua are perturbatively unstable. Many of the new critical points can be found analytically within consistent truncations of the $$ \mathcal{N} $$ N = 8 supergravity with respect to discrete subgroups of the S(O(6) × GL(2 , R)) symmetry of the potential. In par- ticular, we discuss in detail a $$ {\mathrm{\mathbb{Z}}}_2^3 $$ Z 2 3 -invariant truncation with 10 scalar fields and 15 critical points. We also compute explicitly the scalar potential in a $$ {\mathrm{\mathbb{Z}}}_2^2 $$ Z 2 2 -invariant extension of that truncation to 18 scalar fields and reproduce 17 of the 32 critical points from the numerical search. Finally, we show that the full potential as a function of 42 scalar fields can be studied analytically using the so-called solvable parametrization. In particular, we find that all critical points lie in a Z 2 -invariant subspace spanned by 22 scalar fields.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2026

Minimization of Disorder as a Key Design Principle for Natural Sizes of Light Harvesting 2 Complexes

The light harvesting 2 (LH2) complex of purple bacteria has excellent energy conversion efficiency. Clarifying the design principle behind such efficiency at the atomistic level is crucial for understanding its structure–function relationship and can be utilized for the design of artificial light harvesting systems. To this end, we conducted comprehensive computational investigation of the dynamical and statistical nature of electronic excited states of pigment molecules in a natural LH2 complex with 9-fold symmetry and its two non-natural in silico analogues with 6- and 12-fold symmetries. To ensure reliable and efficient all-atomistic molecular dynamics simulations, we combined a well established interpolation approach for the construction of the potential energy surface with a neural network machine learning approach. Outcomes of these calculations clarify that non-natural forms of LH2-type complexes have significantly larger quasistatic disorder than those for the natural one. In addition, non-natural systems have more disruptions of the hydrogen bonding, underscoring its crucial role for reducing the disorder. On the other hand, local environmental dynamics are relatively insensitive to the structural changes although there is moderate enhancement in the anharmonic or interatomic components for the synthetic ones. These findings based on all-atomistic simulations provide direct computational evidence that the structure and sizes of natural LH2 complexes are designed to minimize the energetic disorder. We analyze quantitative implications of these for the energy transferring capability of the LH2 complex.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

HydraGNN_Predictive_GFM_2026 - Ensemble of predictive graph foundation models for atomistic materials modeling

This release contains data and parameters of HydraGNN-based graph foundation models trained as a result of the work published in the pre-print "Exascale Multi-Task Graph Foundation Models for Imbalanced, Multi-Fidelity Atomistic Data" by M. Lupo Pasini et al. (https://arxiv.org/abs/2604.15380). We jointly train on 16 open first-principles datasets (544+ million structures covering 85+ elements) using a multi-task architecture with per-dataset heads and a scalable ADIOS2/DDStore data pipeline. On Frontier, we execute six large-scale DeepHyper hyperparameter optimization campaigns in FP64 and promote the top-performing message-passing models to sustained 2,048-node training, yielding a PaiNN-based lead model. The version of HydraGNN used to generate the outputs provided in this release is HydraGNN v5.0 (https://github.com/ORNL/HydraGNN/releases/tag/v5.0) The list of datasets used for the training of the graph foundation model is the following: 1) Alexandria [1] 2) ANI1x [2] 3) MPTrj [3] 4) Open Catalyst 2020 (OC20) [4] 5) Open Catalyst 2022 (OC22) [5] 6) Open Catalyst 2025 (OC25) [6] 7) Open Direct ir Capture 2023 (ODAC23) [7] 8) Open Materials 2024 (OMat24) [8] 9) Open Molecules 2025 (OMol25) [9] 10) OMol25-neutral (subset of OMol25 that contains only molecules with zero total charge) 11) OMol25-non-neutral (subset of OMol25 that contains only molecules with non-zero total charge) 12) Open Polymers 2026 (OPoly2026) [10] 13) Nabla2DFT [11] 14) QCML [12] 15) QM7X [reference 13] 16) transition1x [14] Dataset references: [1] J. Schmidt et al., “A dataset of 175k stable and metastable materials calculated with the PBEsol and SCAN functionals,” Scientific Data, vol. 9, p. 64, 2022. [2] J. S. Smith et al., “The ANI-1ccx and ANI-1x data sets, coupled-cluster and density functional theory properties for molecules,” Scientific Data, vol. 7, p. 134, 2020. [Online]. Available: https: //www.nature.com/articles/s41597-020-0473-z [3] A. Jain et al., “Commentary: The Materials Project: A materials genome approach to accelerating materials innovation,” APL Materials, vol. 1, no. 1, p. 011002, 07 2013. [Online]. Available: https://doi.org/10.1063/1.4812323 [4] L. Chanussot et al., “Open catalyst 2020 (oc20) dataset and community challenges,” ACS Catalysis, vol. 11, no. 10, pp. 6059–6072, 2021. [Online]. Available: https://doi.org/10.1021/acscatal.0c04525 [5] K. Tran et al., “Open catalyst 2022 (oc22) dataset and challenges for oxidation electrocatalysts,” ACS Catalysis, vol. 13, no. 5, pp. 3066–3084, 2023. [Online]. Available: https://doi.org/10.1021/acscatal.2c05426 [6] S. J. Sahoo et al., “The open catalyst 2025 (oc25) dataset and models for solid-liquid interfaces,” arXiv preprint arXiv:2509.17862, 2025. [Online]. Available: https://arxiv.org/abs/2509.17862 [7] A. Sriram et al., “The open DAC 2023 dataset and challenges for sorbent discovery in direct air capture,” ACS Central Science, vol. 10, no. 5, pp. 923–941, 2024. [8] L. Barroso-Luque et al., “Open materials 2024 (omat24) inorganic materials dataset and models,” 2024. [Online]. Available: https://arxiv.org/abs/2410.12771 [9] D. S. Levine et al., “The open molecules 2025 (OMol25) dataset, evaluations, and models,” 2025. [Online]. Available: https://arxiv.org/abs/2505.08762 [10] D. S. Levine et al., The open polymers 2026 (OPoly26) dataset and evaluations,” arXiv preprint arXiv:2512.23117, 2025. [Online]. Available: https://arxiv.org/abs/2512.23117 [11] K. Khrabrov et al., “Nabla2dft: A universal quantum chemistry dataset of drug-like molecules and a benchmark for neural network potentials,” in NeurIPS 2024 Datasets and Benchmarks Track, 2024. [Online]. Available: https://openreview.net/forum?id=ElUrNM9U8c [12] S. Ganscha et al., “The QCML dataset, quantum chemistry reference data from 33.5M DFT and 14.7B semi-empirical calculations,” Scientific Data, vol. 12, p. 406, 2025. [13] J. Hoja et al., “QM7-X, a comprehensive dataset of quantum-mechanical properties spanning the chemical space of small organic molecules,” Scientific Data, vol. 8, p. 43, 2021. [Online]. Available: https://www.nature.com/articles/s41597-021-00812-2 [14] M. Schreiner et al., “Transition1x - a dataset for building generalizable reactive machine learning potentials,” Scientific Data, vol. 9, p. 779, 2022. The folder "datasets_ADIOS2_format" contains the set of pre-processed datasets in Adaptable I/O System (ADIOS) format (https://www.exascaleproject.org/research-project/adios/) that have been used for the development and training of GFMs in this work. The "datasets_ADIOS2_format" directory contains 2 sub-directories, one for the version "v1" of the datasets and one for the version "v2" of the datasets. The version "v1" of the datasets provides values of the total energy as they are extracted from the original data as it was released by the respective institutions. The version "v2" of the datasets provides values of the energy that have been realigned. The realignment was performed by training a linear regression model that predicts the total energy as a function of the chemical composition of the atomistic structure, and then subtract such prediction from the original value of the total energy. Both folders "v1" and "v2" contain 16 sub-directories, each corresponding to an ADIOS2-formatted dataset The folder "DeepHyper-results" contains the configurational files and model's parameters for all the 186 HPO trials that were successfully completed by the scalable hyperparameter optimization (HPO) runs on Frontier. The content of the folder "DeepHyper-results" I structured as follows: 1) task-list.txt: list of mpnn name, jobid, and deephyper task id 2) gfm_${MPNN}_${JOBID}_0.${TASKID}: run directory with checkpoint files 3) gfm_${MPNN}: deephyper summary directory (*.csv) for each specific MPNN type 4) deephyper-experiment-${JOBID}: output and error logs for each job The file "deephyper-sorted.csv" contains the details of each HydraGNN model built and tested by HPO, obtained by merging the (*.csv) filed from each HPO run executed. Out of all the HPO trials, we selected 10 to continue the training of the respective HydraGNN models. Due to limited computational budget available in the LRN070 allocation we could not complete the training till convergence for all these 10 selected models. The folder "models" contains multiple sub-folders, one per each HydraGNN model trained. Each model sub-folder contains the parameters of each HydraGNN model, with multiple checkpoint-restarts. The list of sub-folders are as follows: 1) multidataset_hpo-BEST1-fp64 2) multidataset_hpo-BEST2-fp64 3) multidataset_hpo-BEST3-fp64 4) multidataset_hpo-BEST4-fp64 5) multidataset_hpo-BEST5-fp64 6) multidataset_hpo-BEST6-fp64 7) multidataset_hpo-BEST7-fp64 8) multidataset_hpo-BEST8-fp64 9) multidataset_hpo-BEST9-fp64 10) multidataset_hpo-BEST10-fp64 Within each one of these folders, additional auxiliary log files are provided with descriptions about how the training proceeded. The lead PaiNN-model is contained inside "multidataset_hpo-BEST6-fp64". The file "mlp_branch_weights" contains the parameters of the multi-layer perceptron (MLP) used to reconcile the predictions of the 16 output decoding heads of the HydragNN architectures. The MLP takes in input the chemical composition of the atomistic structure and predicts averaging weights to linearly mix the predictions of each output decoding head toward consolidating them into a single one. The folder "1.1billion-structure-inference" contains 1.1 billion atomistic structures randomly generated. Each structures is associated with energy and forces predicted with the lead-PaiNN model combined with the MLP model for reconciliation of the multi-branch predictions generated by the 16 output decoding heads. The folder "1.1billion-structure-inference" contains 9,300 (*.tar.gz) subdirectories, one per Frontier compute node used to execute the inference at exascale. Once uncompressed, each (*.tar.gz) subdirectory contains an ADIOS2 (*.bp) file container, where each atomistic structure is stored as a PyTorch-Geometric Data object. The file "export_dataset_environment_variables.sh" contains the environment variables that need to be set before running the HydraGNN code to reproduce the results provided in this dataset release. The code that can be used to load the ADIOS2 files, load HydraGNN models, and run inference is available at: https://github.com/ORNL/HydraGNN/releases/tag/v5.0

36 MATERIALS SCIENCE↗
DOE OSTI2021

Deep Learning Coordinate-Free Quantum Chemistry

Computing quantum chemical properties of small molecules and polymers can provide insights valuable to physicists, chemists and biologists when designing new materials, catalysts, biological probes and drugs. Deep learning can compute quantum chemical properties accurately in a fraction of the time required by commonly used methods such as density functional theory (DFT). However, many of these deep learning architectures require energy minimized molecular geometries as input, which is also computationally expensive, and decreasing the reproducibility and throughput of these methods. In this study, we demonstrate that accurate quantum chemical computations can be performed without optimized geometries by operating in the coordinate-free domain using deep learning on graph encodings. Furthermore, we also find that the choice of graph-encoding architecture substantially affects the performance of these methods. The Wave architecture outperforms graph convolution architectures, particularly on complex molecules. Furthermore, the structures of these graph encoding architectures provide an opportunity to probe an important, outstanding question in quantum mechanics: What types of quantum chemical properties can be represented by local-variable models? We find that Wave, a local-variable model, is more accurately calculates quantum chemical properties. Graph convolutional architectures require global variables, and are not as effective as as Wave. We anticipate that coordinate-free, deep-learning models of quantum chemistry will become valuable tools in chemistry and biology, enabling researchers to rapidly screen chemical databases or identify new molecules using automated, de-novo design algorithms.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗