arXiv Machine Learning

Evolution-Aware MSA Reasoning for Subsampling via Factor Graphs

arXiv:2607. 22314v1 Announce Type: new Abstract: Multiple Sequence Alignments (MSAs) provide protein language models with explicit evolutionary context, but their large depth makes subsampling unavoidable under limited token budgets.

arXiv AI

Jul 23

SubQuad: Near-Quadratic-Free Structure Inference with Distribution-Balanced Objectives in Adaptive Receptor framework

arXiv:2602. 17330v5 Announce Type: replace-cross Abstract: Comparative analysis of adaptive immune repertoires at population scale is hampered by two practical bottlenecks: the near-quadratic cost of pairwise affinity evaluations and dataset imbalances that obscure clinically important minority clonotypes.

By Rong Fu, Zijian Zhang, Kun Liu, Jiekai Wu, Xianda Li, Simon Fong

rag efficiency multimodal safety

arXiv Machine Learning

Jul 28

Chamaileon: Cross-Context Binder Design with Contextualized Modeling and Mixed Sampling

arXiv:2607. 23518v1 Announce Type: new Abstract: The rapid evolution of generative models has unlocked new potentials in protein binder design, a pivotal task in structural biology, by facilitating end-to-end generation via joint sequence-structure modeling or hallucination.

By Hengyuan Cao, Shizhuo Cheng, Mingxuan Liu, Weicheng Huang, Yunhong Lu, Chenxi Cai, Yan Zhang, Min Zhang

benchmarks safety

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

llms safety

arXiv AI

Jun 2

AgentPLM: Agentic Protein Language Models with Reasoning-Augmented Decoding for Protein Sequence Design

arXiv:2606. 02386v1 Announce Type: new Abstract: Protein language models (PLMs) are passive oracles: they generate sequences in a single forward pass with no mechanism to consult external biophysical feedback or redirect generation when a candidate violates thermodynamic or structural constraints.

By Sahil Rahman, Maxx Richard Rahman

llms agents benchmarks

arXiv Machine Learning

Jun 26

Training-Free Generation of Protein Sequences from Small Family Alignments via Stochastic Attention

arXiv:2603. 14717v2 Announce Type: replace Abstract: Generating novel protein sequences that respect a family's statistical constraints typically requires training deep generative models on thousands to millions of examples.

By Jeffrey D. Varner

llms safety

arXiv AI

Aug 12

Proteo-R1: Reasoning Foundation Models for De Novo Protein Design

arXiv:2605. 02937v2 Announce Type: replace-cross Abstract: Deep learning in de novo protein design has achieved atomic-level fidelity.

By Fang Wu, Weihao Xuan, Heli Qi, Hanqun Cao, Heng-Jui Chang, Zeqi Zhou, Haokai Zhao, Ma Jian, Carl Ma, Yu-Chi Cheng, Kuan Pang, Xiangru Tang, Zehong Wang, Guanlue Li, Hanchen Wang, Kejun Ying, Pan Lu, Chiho Im, Seungju Han, Peng Xia, Tinson Xu, Yinxi Li, Deyao Zhu, Pheng-Ann Heng, Naoto Yokoya, Masashi Sugiyama, Li Erran Li, Jure Leskovec, Yejin Choi

llms diffusion multimodal benchmarks safety

arXiv Machine Learning

Jun 9

Constraint-Aware Optimization for Robust Protein Stability Prediction

arXiv:2606. 08100v1 Announce Type: new Abstract: Multimodal $\Delta\Delta G$ predictors integrating protein language models with inverse-folding representations achieve strong in-distribution accuracy on the Megascale dataset but exhibit limited robustness on out-of-distribution (OOD) proteins, persistent forward-reverse bias on paired-mutation benchmarks, and under-representation of rare stabilizing mutations.

By A Shivram, Aneesh S. Chivukula, Manik Gupta, Sourav Chowdhury

llms multimodal benchmarks safety

arXiv AI

Jun 26

EvoOptiGraph: Weakness-Driven Coevolution via Graph-Based Structural Generation for Optimization Modeling

arXiv:2606. 26578v1 Announce Type: new Abstract: Automating optimization modeling from natural language with large language models (LLMs) faces two key challenges.

By Qingcan Kang, Mingyang Liu, Xiaojin Fu, Shixiong Kai, Tao Zhong, Mingxuan Yuan

llms agents reinforcement-learning fine-tuning

arXiv AI

Jul 3

MKGR: Multimodal Knowledge-Graph Representation Learning for Cold-Start Protein-Protein Interaction Prediction

arXiv:2607. 01627v1 Announce Type: cross Abstract: Accurate protein-protein interaction (PPI) prediction is central to functional genomics, disease mechanism discovery, and drug development.

By Wenbo Zhang

rag multimodal benchmarks

arXiv Machine Learning

Jun 4

Towards A Generative Protein Evolution Machine with DPLM-Evo

arXiv:2605. 00182v3 Announce Type: replace Abstract: Proteins are shaped by gradual evolution under biophysical and functional constraints.

By Xinyou Wang, Liang Hong, Jiasheng Ye, Zaixiang Zheng, Yu Li, Shujian Huang, Quanquan Gu

llms diffusion benchmarks safety

arXiv AI

Jul 28

LC-SEPLM: long-range contact-supervised adaptation for sequence-only protein representation learning

arXiv:2607. 22777v1 Announce Type: cross Abstract: Protein language models learn transferable sequence representations.

By Chen Wang, Boming Kang, Qinghua Cui

llms fine-tuning benchmarks

arXiv AI

Jul 21

GRIP: In-Parameter Graph Reasoning through Fine-Tuning Large Language Models

arXiv:2511. 07457v2 Announce Type: replace-cross Abstract: Large Language Models (LLMs) have demonstrated remarkable capabilities in modeling sequential textual data and generalizing across diverse tasks.

By Jiarui Feng, Donghong Cai, Yixin Chen, Muhan Zhang

llms fine-tuning safety

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