From Molecules to Materials: Pre-training Large Generalizable Models for Atomic Property Prediction
Not on the map. Why?
Abstract (arXiv)
Foundation models have been transformational in machine learning fields such as natural language processing and computer vision. Similar success in atomic property prediction has been limited due to the challenges of training effective models across multiple chemical domains. To address this, we introduce Joint Multi-domain Pre-training (JMP), a supervised pre-training strategy that simultaneously trains on multiple datasets from different chemical domains, treating each dataset as a unique pre-training task within a multi-task framework. Our combined training dataset consists of ~120M systems from OC20, OC22, ANI-1x, and Transition-1x. We evaluate performance and generalization by fine-tuning over a diverse set of downstream tasks and datasets including: QM9, rMD17, MatBench, QMOF, SPICE, and MD22. JMP demonstrates an average improvement of 59% over training from scratch, and matches or sets state-of-the-art on 34 out of 40 tasks. Our work highlights the potential of pre-training strategies that utilize diverse data to advance property prediction across chemical domains, especially for low-data tasks. Please visit https://nima.sh/jmp for further information.
Key facts. Cited by 39 papers in the map (data through 7 Oct 2026). Builds on 36 of its 70 references that are in the map. First posted on arXiv 25 Oct 2023.
Builds on
36 of 70 references.
References · 36
- 2018BERT: Pre-training of Deep Bidirectional Transformers for Language Understandingcited by 40,204
- 2020Denoising Diffusion Implicit Modelscited by 9,655
- 2016SGDR: Stochastic Gradient Descent with Warm Restartscited by 4,993
- 2017Multi-Task Learning Using Uncertainty to Weigh Losses for Scene Geometry and Semanticscited by 1,345
- 2020Gradient Surgery for Multi-Task Learningcited by 1,210
- 2017MoleculeNet: A Benchmark for Molecular Machine Learningcited by 1,037
- 2019DropEdge: Towards Deep Graph Convolutional Networks on Node Classificationcited by 679
- 2017SchNet: A continuous-filter convolutional neural network for modeling quantum interactionscited by 569
- 2020Directional Message Passing for Molecular Graphscited by 556
- 2019Quantifying the Carbon Emissions of Machine Learningcited by 516
- 2022MACE: Higher Order Equivariant Message Passing Neural Networks for Fast and Accurate Force Fieldscited by 467
- 2021GemNet: Universal Directional Graph Neural Networks for Moleculescited by 342
24 more
- 2021OGB-LSC: A Large-Scale Challenge for Machine Learning on Graphscited by 328
- 2022Equiformer: Equivariant Graph Attention Transformer for 3D Atomistic Graphscited by 258
- 2022Learning Local Equivariant Representations for Large-Scale Atomistic Dynamicscited by 254
- 2021Pre-training Molecular Graph Representation with 3D Geometrycited by 248
- 2020The Open Catalyst 2020 (OC20) Dataset and Community Challengescited by 246
- 2022TorchMD-NET: Equivariant Transformers for Neural Network based Molecular Potentialscited by 179
- 2022Pre-training via Denoising for Molecular Property Predictioncited by 124
- 2022The Open Catalyst 2022 (OC22) Dataset and Challenges for Oxide Electrocatalystscited by 95
- 2022SPICE, A Dataset of Drug-like Molecules and Peptides for Training Machine Learning Potentialscited by 80
- 2022Molecular Geometry Pretraining with SE(3)-Invariant Denoising Distance Matchingcited by 67
- 2022In Defense of the Unitary Scalarization for Deep Multi-Task Learningcited by 65
- 2022GemNet-OC: Developing Graph Neural Networks for Large and Diverse Molecular Simulation Datasetscited by 61
- 2020An Introduction to Electrocatalyst Design using Machine Learning for Renewable Energy Storagecited by 45
- 2022Unified 2D and 3D Pre-Training of Molecular Representationscited by 45
- 2022Transition1x -- a Dataset for Building Generalizable Reactive Machine Learning Potentialscited by 37
- 2023Fractional Denoising for 3D Molecular Pre-trainingcited by 33
- 2021Artificial Intelligence in Drug Discovery: Applications and Techniquescited by 28
- 2022MOFormer: Self-Supervised Transformer model for Metal-Organic Framework Property Predictioncited by 28
- 2023Towards Predicting Equilibrium Distributions for Molecular Systems with Deep Learningcited by 26
- 2022Towards Training Billion Parameter Graph Neural Networks for Atomic Simulationscited by 25
- 2023Evaluation of the MACE Force Field Architecture: from Medicinal Chemistry to Materials Sciencecited by 25
- 2022Causes and Cures for Interference in Multilingual Translationcited by 23
- 2023May the Force be with You: Unified Force-Centric Pre-Training for 3D Molecular Conformationscited by 13
- 2023Connectivity Optimized Nested Graph Networks for Crystal Structurescited by 11
Built on by
Citing papers per year: 2024: 10; 2025: 20; 2026: 9.
39 papers.
Sort:
By area:
- 2025UMA: A Family of Universal Models for Atomscited by 99
- 2024A Review of Large Language Models and Autonomous Agents in Chemistrycited by 96
- 2025All-atom Diffusion Transformers: Unified generative modelling of molecules and materialscited by 75
- 2024Orb: A Fast, Scalable Neural Network Potentialcited by 63
- 2024Fully-inductive Node Classification on Arbitrary Graphscited by 36
- 2024Doob's Lagrangian: A Sample-Efficient Variational Approach to Transition Path Samplingcited by 25
- 2025A practical guide to machine learning interatomic potentials -- Status and futurecited by 24
- 2024textttMiniMol: A Parameter-Efficient Foundation Model for Molecular Learningcited by 19
- 2024AdsorbDiff: Adsorbate Placement via Conditional Denoising Diffusioncited by 8
- 2025MatLLMSearch: Crystal Structure Discovery with Evolution-Guided Large Language Modelscited by 7
- 2025MatterTune: An Integrated, User-Friendly Platform for Fine-Tuning Atomistic Foundation Models to Accelerate Materials Simulation and Discoverycited by 4
- 2025LeMat-Traj: A Scalable and Unified Dataset of Materials Trajectories for Atomistic Modelingcited by 4
27 more
- 2024Pretraining Graph Transformers with Atom-in-a-Molecule Quantum Properties for Improved ADMET Modelingcited by 3
- 2025Understanding and Mitigating Distribution Shifts For Machine Learning Force Fieldscited by 3
- 2025DEQuify your force field: More efficient simulations using deep equilibrium modelscited by 3
- 2026Towards Agentic Intelligence for Materials Sciencecited by 3
- 2026Self-Conditioned Denoising for Atomistic Representation Learningcited by 3
- 2025Enhancing Machine Learning Potentials through Transfer Learning across Chemical Elementscited by 2
- 2026Better without U: Impact of Selective Hubbard U Correction on Foundational MLIPscited by 2
- 2024Pushing the Pareto front of band gap and permittivity: ML-guided search for dielectric materialscited by 1
- 2025Pre-training Graph Neural Networks with Structural Fingerprints for Materials Discoverycited by 1
- 2025Accelerating and enhancing thermodynamic simulations of electrochemical interfacescited by 1
- 2025Optimizing Data Distribution and Kernel Performance for Efficient Training of Chemistry Foundation Models: A Case Study with MACEcited by 1
- 2025Towards Faster and More Compact Foundation Models for Molecular Property Predictioncited by 1
- 2025Multi-task parallelism for robust pre-training of graph foundation models on multi-source, multi-fidelity atomistic modeling datacited by 1
- 2025Training Dynamics of Learning 3D-Rotational Equivariancecited by 1
- 2026Mixture of experts architectures for machine learning interatomic potentialscited by 1
- 2026BaLoRA: Bayesian Low-Rank Adaptation of Large Scale Modelscited by 1
- 2024Improving Molecular Modeling with Geometric GNNs: an Empirical Studycited by 0
- 2024Implicit Delta Learning of High Fidelity Neural Network Potentialscited by 0
- 2025On the Importance of Pretraining Data Alignment for Atomic Property Predictioncited by 0
- 2025MoMa: A Modular Deep Learning Framework for Material Property Predictioncited by 0
- 2025A Materials Map Integrating Experimental and Computational Data via Graph-Based Machine Learning for Enhanced Materials Discoverycited by 0
- 2025LaMM: Semi-Supervised Pre-Training of Large-Scale Materials Modelscited by 0
- 2025Learning 3D Anisotropic Noise Distributions Improves Molecular Force Field Modelingcited by 0
- 2026Exascale Multi-Task Graph Foundation Models for Imbalanced, Multi-Fidelity Atomistic Datacited by 0
- 2026PaMM: Periodic Motif Memory for Atomistic Models with an Explicit Local-Structure Interfacecited by 0
- 2026Optimizing Expert-Designed Crystal Graph Networks for Band-Gap Prediction with an Autonomous LLM Research Loopcited by 0
- 2026A strategic roadmap for an atomistic machine-learning ecosystemcited by 0
- 2026A strategic roadmap for an atomistic machine-learning ecosystem30 Sep 2026
- 2026Optimizing Expert-Designed Crystal Graph Networks for Band-Gap Prediction with an Autonomous LLM Research Loop29 Jun 2026
- 2026PaMM: Periodic Motif Memory for Atomistic Models with an Explicit Local-Structure Interface13 May 2026
- 2026BaLoRA: Bayesian Low-Rank Adaptation of Large Scale Models27 Apr 2026
- 2026Exascale Multi-Task Graph Foundation Models for Imbalanced, Multi-Fidelity Atomistic Data15 Apr 2026
- 2026Self-Conditioned Denoising for Atomistic Representation Learning17 Mar 2026
- 2026Mixture of experts architectures for machine learning interatomic potentials9 Mar 2026
- 2026Towards Agentic Intelligence for Materials Science29 Jan 2026
- 2026Better without U: Impact of Selective Hubbard U Correction on Foundational MLIPs28 Jan 2026
- 2025Training Dynamics of Learning 3D-Rotational Equivariance2 Dec 2025
- 2025Learning 3D Anisotropic Noise Distributions Improves Molecular Force Field Modeling25 Oct 2025
- 2025DEQuify your force field: More efficient simulations using deep equilibrium models10 Sep 2025
27 more
- 2025LeMat-Traj: A Scalable and Unified Dataset of Materials Trajectories for Atomistic Modeling28 Aug 2025
- 2025UMA: A Family of Universal Models for Atoms30 Jun 2025
- 2025Multi-task parallelism for robust pre-training of graph foundation models on multi-source, multi-fidelity atomistic modeling data26 Jun 2025
- 2025LaMM: Semi-Supervised Pre-Training of Large-Scale Materials Models28 May 2025
- 2025Towards Faster and More Compact Foundation Models for Molecular Property Prediction28 Apr 2025
- 2025Optimizing Data Distribution and Kernel Performance for Efficient Training of Chemistry Foundation Models: A Case Study with MACE14 Apr 2025
- 2025MatterTune: An Integrated, User-Friendly Platform for Fine-Tuning Atomistic Foundation Models to Accelerate Materials Simulation and Discovery14 Apr 2025
- 2025Accelerating and enhancing thermodynamic simulations of electrochemical interfaces22 Mar 2025
- 2025A practical guide to machine learning interatomic potentials -- Status and future12 Mar 2025
- 2025Understanding and Mitigating Distribution Shifts For Machine Learning Force Fields11 Mar 2025
- 2025A Materials Map Integrating Experimental and Computational Data via Graph-Based Machine Learning for Enhanced Materials Discovery10 Mar 2025
- 2025All-atom Diffusion Transformers: Unified generative modelling of molecules and materials5 Mar 2025
- 2025Pre-training Graph Neural Networks with Structural Fingerprints for Materials Discovery3 Mar 2025
- 2025MatLLMSearch: Crystal Structure Discovery with Evolution-Guided Large Language Models28 Feb 2025
- 2025MoMa: A Modular Deep Learning Framework for Material Property Prediction21 Feb 2025
- 2025Enhancing Machine Learning Potentials through Transfer Learning across Chemical Elements19 Feb 2025
- 2025On the Importance of Pretraining Data Alignment for Atomic Property Prediction16 Feb 2025
- 2024Implicit Delta Learning of High Fidelity Neural Network Potentials8 Dec 2024
- 2024Orb: A Fast, Scalable Neural Network Potential29 Oct 2024
- 2024Pretraining Graph Transformers with Atom-in-a-Molecule Quantum Properties for Improved ADMET Modeling10 Oct 2024
- 2024Doob's Lagrangian: A Sample-Efficient Variational Approach to Transition Path Sampling10 Oct 2024
- 2024Improving Molecular Modeling with Geometric GNNs: an Empirical Study11 Jul 2024
- 2024A Review of Large Language Models and Autonomous Agents in Chemistry26 Jun 2024
- 2024Fully-inductive Node Classification on Arbitrary Graphs30 May 2024
- 2024AdsorbDiff: Adsorbate Placement via Conditional Denoising Diffusion7 May 2024
- 2024textttMiniMol: A Parameter-Efficient Foundation Model for Molecular Learning23 Apr 2024
- 2024Pushing the Pareto front of band gap and permittivity: ML-guided search for dielectric materials11 Jan 2024
- 2026Towards Agentic Intelligence for Materials Science29 Jan 2026
- 2024A Review of Large Language Models and Autonomous Agents in Chemistry26 Jun 2024
- 2025UMA: A Family of Universal Models for Atomscited by 99
- 2024Orb: A Fast, Scalable Neural Network Potentialcited by 63
- 2024Fully-inductive Node Classification on Arbitrary Graphscited by 36
- 2024Doob's Lagrangian: A Sample-Efficient Variational Approach to Transition Path Samplingcited by 25
- 2025A practical guide to machine learning interatomic potentials -- Status and futurecited by 24
- 2024textttMiniMol: A Parameter-Efficient Foundation Model for Molecular Learningcited by 19
- 2024AdsorbDiff: Adsorbate Placement via Conditional Denoising Diffusioncited by 8
- 2025MatLLMSearch: Crystal Structure Discovery with Evolution-Guided Large Language Modelscited by 7
- 2025MatterTune: An Integrated, User-Friendly Platform for Fine-Tuning Atomistic Foundation Models to Accelerate Materials Simulation and Discoverycited by 4
- 2025LeMat-Traj: A Scalable and Unified Dataset of Materials Trajectories for Atomistic Modelingcited by 4
- 2024Pretraining Graph Transformers with Atom-in-a-Molecule Quantum Properties for Improved ADMET Modelingcited by 3
- 2025Understanding and Mitigating Distribution Shifts For Machine Learning Force Fieldscited by 3
12 most cited of 35 All 35 (JSON)
- 2026A strategic roadmap for an atomistic machine-learning ecosystem30 Sep 2026
- 2026Optimizing Expert-Designed Crystal Graph Networks for Band-Gap Prediction with an Autonomous LLM Research Loop29 Jun 2026
- 2026PaMM: Periodic Motif Memory for Atomistic Models with an Explicit Local-Structure Interface13 May 2026
- 2026BaLoRA: Bayesian Low-Rank Adaptation of Large Scale Models27 Apr 2026
- 2026Exascale Multi-Task Graph Foundation Models for Imbalanced, Multi-Fidelity Atomistic Data15 Apr 2026
- 2026Self-Conditioned Denoising for Atomistic Representation Learning17 Mar 2026
- 2026Better without U: Impact of Selective Hubbard U Correction on Foundational MLIPs28 Jan 2026
- 2025Training Dynamics of Learning 3D-Rotational Equivariance2 Dec 2025
- 2025Learning 3D Anisotropic Noise Distributions Improves Molecular Force Field Modeling25 Oct 2025
- 2025DEQuify your force field: More efficient simulations using deep equilibrium models10 Sep 2025
- 2025LeMat-Traj: A Scalable and Unified Dataset of Materials Trajectories for Atomistic Modeling28 Aug 2025
- 2025UMA: A Family of Universal Models for Atoms30 Jun 2025
12 newest of 35 All 35 (JSON)