# Zatom-1: Towards a Multimodal Foundation Model for 3D Molecules and Materials

arXiv: https://arxiv.org/abs/2602.22251 · HTML: https://mlsanity.com/paper/2602.22251/

## Key facts

- Cited by 5 papers in the map (data through 14 Oct 2026).
- Builds on 82 of its 124 references that are in the map.
- First posted on arXiv 24 Feb 2026.

## Builds on (most cited first, 30 of 82)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [Denoising Diffusion Probabilistic Models](https://mlsanity.com/paper/2006.11239/) (2020)
- [Deep Unsupervised Learning using Nonequilibrium Thermodynamics](https://mlsanity.com/paper/1503.03585/) (2015)
- [Scaling Laws for Neural Language Models](https://mlsanity.com/paper/2001.08361/) (2020)
- [Flow Matching for Generative Modeling](https://mlsanity.com/paper/2210.02747/) (2022)
- [RoFormer: Enhanced Transformer with Rotary Position Embedding](https://mlsanity.com/paper/2104.09864/) (2021)
- [Generative Modeling by Estimating Gradients of the Data Distribution](https://mlsanity.com/paper/1907.05600/) (2019)
- [On the Opportunities and Risks of Foundation Models](https://mlsanity.com/paper/2108.07258/) (2021)
- [FlashAttention-2: Faster Attention with Better Parallelism and Work Partitioning](https://mlsanity.com/paper/2307.08691/) (2023)
- [GLU Variants Improve Transformer](https://mlsanity.com/paper/2002.05202/) (2020)
- [Group Equivariant Convolutional Networks](https://mlsanity.com/paper/1602.07576/) (2016)
- [MoleculeNet: A Benchmark for Molecular Machine Learning](https://mlsanity.com/paper/1703.00564/) (2017)
- [Building Normalizing Flows with Stochastic Interpolants](https://mlsanity.com/paper/2209.15571/) (2022)
- [E(n) Equivariant Graph Neural Networks](https://mlsanity.com/paper/2102.09844/) (2021)
- [Large Language Diffusion Models](https://mlsanity.com/paper/2502.09992/) (2025)
- [Improving and generalizing flow-based generative models with minibatch optimal transport](https://mlsanity.com/paper/2302.00482/) (2023)
- [Equivariant Diffusion for Molecule Generation in 3D](https://mlsanity.com/paper/2203.17003/) (2022)
- [Characterizing possible failure modes in physics-informed neural networks](https://mlsanity.com/paper/2109.01050/) (2021)
- [General E(2)-Equivariant Steerable CNNs](https://mlsanity.com/paper/1911.08251/) (2019)
- [Equivariant message passing for the prediction of tensorial properties and molecular spectra](https://mlsanity.com/paper/2102.03150/) (2021)
- [DoReMi: Optimizing Data Mixtures Speeds Up Language Model Pretraining](https://mlsanity.com/paper/2305.10429/) (2023)
- [Your Diffusion Model is Secretly a Zero-Shot Classifier](https://mlsanity.com/paper/2303.16203/) (2023)
- [Generative Flows on Discrete State-Spaces: Enabling Multimodal Flows with Applications to Protein Co-Design](https://mlsanity.com/paper/2402.04997/) (2024)
- [Crystal Diffusion Variational Autoencoder for Periodic Material Generation](https://mlsanity.com/paper/2110.06197/) (2021)
- [Equiformer: Equivariant Graph Attention Transformer for 3D Atomistic Graphs](https://mlsanity.com/paper/2206.11990/) (2022)
- [Fast and Uncertainty-Aware Directional Message Passing for Non-Equilibrium Molecules](https://mlsanity.com/paper/2011.14115/) (2020)
- [Pre-training Molecular Graph Representation with 3D Geometry](https://mlsanity.com/paper/2110.07728/) (2021)
- [GEOM: Energy-annotated molecular conformations for property prediction and molecular generation](https://mlsanity.com/paper/2006.05531/) (2020)
- [Geometric and Physical Quantities Improve E(3) Equivariant Message Passing](https://mlsanity.com/paper/2110.02905/) (2021)

## Built on by (most cited first, 5 of 5)

- [SMDD-Bench: Can LLMs Solve Real-World Small Molecule Drug Design Tasks?](https://mlsanity.com/paper/2605.21740/) (2026)
- [Pre-Training for Simulation-Based Science: A Study on Jet Foundation Model Training Objectives](https://mlsanity.com/paper/2606.14870/) (2026)
- [How Do Transformers Learn to Represent Symmetries?](https://mlsanity.com/paper/2610.10305/) (2026)
- [Zatom-2: Multitask Pretraining on Atomistic Data for Generative Modeling across Domains](https://mlsanity.com/paper/2610.11454/) (2026)
- [OctMole: Multiscale 3D Molecular Generation with Hierarchical Spatial Flows](https://mlsanity.com/paper/2610.16586/) (2026)

## Abstract (arXiv)

General-purpose 3D modeling in chemistry encompasses molecules and materials, requiring both generative and predictive capabilities. However, most existing AI approaches are optimized for a single domain (molecules or materials) and a single task (generation or prediction), which limits representation sharing and transfer. We introduce Zatom-1, a cross-domain, general-purpose model architecture that unifies generative and predictive learning of 3D molecules and materials. Zatom-1 is a deliberately simplified Transformer trained with a multimodal flow matching objective that jointly models discrete atom types and continuous 3D geometries. This approach supports scalable pretraining with predictable gains as model capacity increases, while enabling fast and stable sampling. We use cross-domain generative pretraining as a universal initialization for downstream multi-task prediction of properties, energies, and forces. Empirically, Zatom-1 outperforms or competes with specialized baselines on both multi-task generative and predictive benchmarks in data-controlled settings, while improving generative inference speed by more than an order of magnitude. Our experiments demonstrate positive predictive transfer between data domains from joint generative pretraining: modeling materials during generative pretraining improves molecular property prediction accuracy. Open-source code and model weights are freely available at https://github.com/Zatom-AI/zatom.