arXiv Machine Learning By Martin Jankowiak, Yerdos Ordabayev, Rudraksh Tuwani, Henry N. Ward, Hunter Nisonoff, James M. McFarland, Gevorg Grigoryan

Flexible Kernels for Protein Property Prediction

Read the original on arXiv Machine Learning →

arXiv:2606. 11057v1 Announce Type: new Abstract: Despite its importance to applications in protein design, predicting protein properties like binding affinity and thermostability from sparse experimental data remains a significant challenge.

Summary generated by The Flow from the publisher's feed. The full article lives at arXiv Machine Learning.

arXiv AI
Jun 9

AMix-1: A Pathway to Test-Time Scalable Protein Foundation Model

arXiv:2507. 08920v4 Announce Type: replace-cross Abstract: We introduce AMix-1, a powerful protein foundation model built on Bayesian Flow Networks and empowered by a systematic training methodology, encompassing pretraining scaling laws, emergent capability analysis, in-context learning mechanism, and test-time scaling algorithm.

By Changze Lv, Jiang Zhou, Siyu Long, Lihao Wang, Jiangtao Feng, Dongyu Xue, Yu Pei, Hao Wang, Zherui Zhang, Yuchen Cai, Zhiqiang Gao, Ziyuan Ma, Jiakai Hu, Chaochen Gao, Jingjing Gong, Yuxuan Song, Shuyi Zhang, Xiaoqing Zheng, Deyi Xiong, Lei Bai, Wanli Ouyang, Ya-Qin Zhang, Wei-Ying Ma, Bowen Zhou, Hao Zhou
arXiv Machine Learning
Jun 29

PairSAE: Mechanistic Interpretability from Pair Representations in Protein Co-Folding

arXiv:2606. 27440v1 Announce Type: new Abstract: Foundation models for structural biology have achieved remarkable performance in predicting biomolecular structure and show promise for the design of proteins and small molecules.

By Giosue Migliorini, Aristofanis Rontogiannis, Grigori Guitchounts, Nicholas Franklin, Axel Elaldi, Olivia Viessmann