arXiv Machine Learning

APO: Unsupervised Atomic Policy Optimization for 3D Structure Prediction of Atomic Systems

arXiv:2607. 28553v1 Announce Type: new Abstract: Predicting the 3D structures of atomic systems is fundamental to advancing material science and drug discovery.

arXiv Machine Learning

Jun 9

Few-step Cofolding with All-Atom Flow Maps

arXiv:2606. 08375v1 Announce Type: new Abstract: All-atom generative modeling of 3D biomolecular complexes has emerged as the dominant paradigm for predicting the structure of proteins and protein-ligand systems.

By Gianluca Scarpellini, Ron Shprints, Peter Holderrieth, Juno Nam, Pranav Murugan, Rafael G\'omez-Bombarelli, Tommi Jaakola, Maruan Al-Shedivat, Nicholas Matthew Boffi, Avishek Joey Bose

diffusion efficiency benchmarks safety

arXiv AI

Jul 1

CryoACE: An Atom-centric Framework for Accurate and Automated Model Building in Cryo-EM

arXiv:2606. 31332v1 Announce Type: new Abstract: Protein automodeling from cryo-EM density maps faces unique challenges in enforcing physicochemical validity and managing conformational heterogeneity.

By Minzhang Li, Mingrui Li, Weichen Qin, Qihe Chen, Sixian Shen, Yuan Pei, Jiakai Zhang, Jingyi Yu

multimodal benchmarks

arXiv AI

Jun 30

Beyond Drug Discovery: The Nanotechnology Molecular Optimization (NMO) Benchmark

arXiv:2606. 30170v1 Announce Type: cross Abstract: Generative molecular design is shaped by simple proxy benchmarks for drug-like properties and models pretrained on large pharmaceutical datasets.

By Matthias Blaschke, Daniel Kienzle, Zsuzsanna Koczor-Benda, Julian Lorenz, Rainer Lienhart, Fabian Pauly

benchmarks safety

arXiv AI

Jul 7

Folding, Reasoning, and Scaling with Open-source Drug Discovery Engine

arXiv:2607. 03787v1 Announce Type: new Abstract: Accurately modeling biomolecular interactions is a central bottleneck in biology and therapeutic discovery.

By Aureka AI OpenDDE project

benchmarks

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

llms diffusion benchmarks

arXiv AI

Jul 7

NextCrystal: a Symmetry-Driven Generative Framework for Crystal Structure Prediction

arXiv:2602. 17176v4 Announce Type: replace-cross Abstract: Crystal structure prediction (CSP), which aims to predict the 3D atomic arrangement of a crystal from its composition, is central to materials discovery and mechanistic understanding.

By Jinming Mu, Lixin He, Xudong Zhu, Shi Yin

llms diffusion benchmarks

arXiv Machine Learning

Jun 11

ProHiFlo: Hierarchical Flow Matching with Functional Guidance for De Novo Protein Generation

arXiv:2606. 11243v1 Announce Type: new Abstract: De novo protein generation has transformative potential in therapeutic design, enzyme engineering, and synthetic biology.

By Chuanzhen Wang, Meade Cleti, Pete Jano

diffusion

arXiv Machine Learning

Jun 9

Enhancing Spatial Reasoning in Large Language Models for Metal-Organic Frameworks Structure Prediction

arXiv:2601. 09285v2 Announce Type: replace Abstract: Metal-organic frameworks (MOFs) are porous crystalline materials with broad applications such as carbon capture and drug delivery, yet accurately predicting their 3D structures remains a significant challenge.

By Mianzhi Pan, JianFei Li, Peishuo Liu, Botian Wang, Yawen Ouyang, Yiming Rong, Hao Zhou, Jianbing Zhang

llms reinforcement-learning fine-tuning benchmarks

arXiv Machine Learning

2d ago

READ: A Retrieval-Alignment Diffusion Framework for Structure-based Drug Design

arXiv:2506. 14488v2 Announce Type: replace-cross Abstract: Structure-based drug design (SBDD) models are central to modern pharmaceutical research, enabling the rational exploration of protein-ligand interactions at atomic resolution.

By Dong Xu, Zhangfan Yang, Junchuang Cai, Sisi Yuan, Zexuan Zhu, Jianqiang Li, Junkai Ji

diffusion benchmarks safety

arXiv Machine Learning

Jul 7

FastCSP: Accelerated Molecular Crystal Structure Prediction with Universal Model for Atoms

arXiv:2508. 02641v2 Announce Type: replace-cross Abstract: Molecular crystal structure prediction (CSP) is essential for applications in pharmaceuticals and organic electronics.

By Vahe Gharakhanyan, Yi Yang, Luis Barroso-Luque, Daniel S. Levine, Sushree Jagriti Sahoo, Brandon M. Wood, Kyle Michel, Muhammed Shuaibi, Gregory J. O. Beran, Viachaslau Bernat, Misko Dzamba, Xiang Fu, Meng Gao, Xingyu Liu, Benjamin K. Miller, Keian Noori, Lafe J. Purvis, Tingling Rao, Ammar Rizvi, Matt Uyttendaele, Andrew J. Ouderkirk, Chiara Daraio, C. Lawrence Zitnick, Arman Boromand, Noa Marom, Zachary W. Ulissi, Anuroop Sriram

fine-tuning efficiency

arXiv AI

Jun 19

Emyx: Fast and efficient all-atom protein generation

arXiv:2606. 19377v1 Announce Type: cross Abstract: Computational enzyme design requires generating proteins that scaffold catalytic residues and ligands, a task that demands both geometric accuracy and structural diversity from the underlying generative model.

By Nicholas J. Williams, Ward Haddadin, Matteo P. Ferla, Constantin Schneider, Nicholas B. Woodall, Ruby Sedgwick, Christian D. Madsen, Andrew L. Hopkins, Edward O. Pyzer-Knapp

llms rag diffusion benchmarks

arXiv Machine Learning

Jun 10

Gradient-Guided Furthest Point Sampling for Robust Training Set Selection

arXiv:2510. 08906v2 Announce Type: replace-cross Abstract: Training set sampling methods are used to improve model performance and lower data costs in machine learning problems relevant to chemistry.

By Morris Trestman, Stefan Gugler, Felix A. Faber, O. A. von Lilienfeld

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