arXiv AI

mRNA Design and Optimization with Deep Knowledge-Infused Approach

arXiv Machine Learning

Aug 31

RIBOSPAN: A Long-Context RNA Foundation Model for Versatile RNA Modeling

arXiv:2608.22849v2 Announce Type: replace Abstract: Full-length RNAs, particularly messenger RNAs, often exceed the context lengths used to pretrain existing RNA foundation models, limiting complete-...

By Ziyuan Wang, Bohao Tang, Fei Zhang, Shuo Han, Pengfei Liu

diffusion nlp benchmarks

arXiv AI

Jul 24

Generative Artificial Intelligence in Bioinformatics: A Systematic Review of Models, Applications, and Methodological Advances

arXiv:2511. 03354v2 Announce Type: replace-cross Abstract: Generative artificial intelligence (GenAI) is transforming bioinformatics by advancing genomics, proteomics, transcriptomics, structural biology, and drug discovery.

By Wasimul Karim, Riasad Alvi, Sayeem Been Zaman, Arefin Ittesafun Abian, Mohaimenul Azam Khan Raiaan, Saddam Mukta, Md Rafi Ur Rashid, Md Rafiqul Islam, Yakub Sebastian, Sami Azam

benchmarks safety

arXiv Machine Learning

Aug 4

Refine Drugs, Don't Complete Them: Uniform-Source Discrete Flows for Fragment-Based Drug Discovery

arXiv:2509. 26405v2 Announce Type: replace Abstract: We introduce InVirtuoGen, a discrete flow generative model for fragmented SMILES for de novo and fragment-constrained generation, and target-property/lead optimization of small molecules.

By Benno Kaech, Luis Wyss, Karsten Borgwardt, Gianvito Grasso

fine-tuning benchmarks

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 AI

1d ago

Pepti-drift: Scalable Safe-Active Peptide Generation Without Inference-Time Guidance

arXiv:2606.27824v3 Announce Type: replace-cross Abstract: Therapeutic peptides are a promising drug modality, but their generation must satisfy multiple therapeutic constraints. We introduce BindSafe...

By Takashi Fujiwara, Hikaru Shindo, Kaushalya Madhawa, Jun Jin Choong, Shuan Chen, Yuna Oikawa, Yiming Zhang, Gyubok Lee, Keisuke Ozawa

efficiency 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 Machine Learning

1d ago

RiboUnmix: Learning Shared Translational Dynamics from Biased and Noisy Ribo-seq Measurements

arXiv:2609.39644v2 Announce Type: new Abstract: Ribosome profiling (Ribo-seq) measures ribosome distributions along mRNAs, but observed occupancy profiles also contain experiment-specific distortions...

By Gabriele Martino, Denis Skibinski, Ivo L. Hofacker, Sebastian Tschiatschek

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

Sep 16

LLM-Guided Dynamic Action Spaces for Synthesizable Molecular Optimization

arXiv:2604.07669v3 Announce Type: replace-cross Abstract: Synthesizable molecular optimization seeks to improve target properties while ensuring that molecular modifications follow feasible synthetic...

By Tao Li, Kaiyuan Hou, Tuan Vinh, Fanglei Xue, Monika Raj, Zhichun Guo, Carl Yang

llms

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 Machine Learning

Jul 13

Variable-Length Generative Protein Design via Generalized Poisson Flow

arXiv:2607. 09039v1 Announce Type: new Abstract: The ability to generate variable-length proteins is crucial in protein design, where the optimal length is often unknown and tightly coupled to designability.

By Chaoran Cheng, Zhanghan Ni, Yanru Qu, Yuxin Chen, Ruihan Guo, Jiajun Fan, Ge Liu

diffusion multimodal

arXiv AI

Jun 17

Agentic Discovery of Non-Canonical Antimicrobial Peptides with AMPGAN v3

arXiv:2606. 17127v1 Announce Type: cross Abstract: Antimicrobial resistance causes to over a million deaths annually.

By Jay Jung, Xiaohan Zhang, Shenghan Song, Mahmoud Sayedahmed, Chijian Xiang, Yunong Xu, Ahmed AbdelKhalek, Severin T. Schneebeli, Matthew J. Wargo, Jianing Li, Safwan Wshah

agents diffusion safety

Related stories