arXiv AI

Atom-JEPA: Joint-Embedding Predictive Architecture for 3D Atomistic Systems

arXiv AI
2d ago

Zatom-2: Multitask Pretraining on Atomistic Data for Generative Modeling across Domains

Zatom-2 is a multitask generative model for atomistic data that has been pretrained on about five million structures from the OMol25 and OMat24 datasets. It uses a multiscale Transformer with conditional flow matching to support tasks such as generation, structure prediction, and energy/force prediction for both molecules and materials. The model outperforms its predecessor, Zatom-1, on molecular distribution fidelity and benchmark generation tasks, and improves protein backbone designability from 67.8% to 74.8% after finetuning on 2,000 protein domains.

By Miruna Cretu, Alex Abrudan, Antonia Panescu, Tynan Perez, Rishabh Anand, N. Benjamin Erichson, Michael W. Mahoney, Samuel Blau, Joseph Jacobson, Rafael G\'omez-Bombarelli, Rex Ying, Tuomas Knowles, Pietro Li\`o, Alex Morehead
arXiv Machine Learning
Jul 1

ElemeNet: Multiscale Molecular Machine Learning with Uncertainty Quantification Across the Periodic Table

arXiv:2606. 30961v1 Announce Type: cross 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.

By Jacob W. Toney, Samir Darouich, Yiran Wang, Aaron G. Garrison, Johannes K\"astner, Heather J. Kulik
arXiv Machine Learning
Sep 17

Robust and Efficient AI Frameworks for Scalable Material Design and Property Prediction

The thesis presents AI frameworks that accelerate crystalline materials discovery by tackling both crystal property prediction and crystal structure generation. It introduces CrysXPP, CrysGNN, and CrysMMNet for efficient, data‑sparse property prediction using graph autoencoding, self‑supervised pretraining, and multimodal learning. For generation, TGDMat is a text‑guided diffusion model that jointly learns lattice parameters, atomic types, and coordinates, enabling valid, stable, and conditionally generated periodic materials.

By Kishalay Das
arXiv Machine Learning
Jul 15

SinAE: A Single-Architecture Flow-Matching Autoencoder for Cross-Domain Atomic Systems

arXiv:2607. 12380v1 Announce Type: new Abstract: Small molecules, crystals, and proteins all reduce to atoms in 3D space, yet their generative pipelines remain fragmented across domains, each with its Small molecules, crystals, and proteins all reduce to atoms in 3D space, yet their generative pipelines remain fragmented across domains, each with its own graph, equivariant, or frame-based architecture.

By Yuxuan Ren, Fan Yang, Jianhua Yao, Yatao Bian
arXiv Machine Learning
Jul 23

OrbitAll: A Unified Quantum Mechanical Representation Deep Learning Framework for All Molecular Systems

arXiv:2507. 03853v2 Announce Type: replace Abstract: We introduce OrbitAll, a geometry- and physics-informed deep learning framework that encodes any molecular system with arbitrary charges, spins, and environmental effects using electronic structure information.

By Beom Seok Kang, Vignesh C. Bhethanabotla, Amin Tavakoli, Maurice D. Hanisch, Arimitsu Horikawa-Strakovsky, Miguel Nouman, Danish Khan, William A. Goddard III, Anima Anandkumar