arXiv:2608. 02684v1 Announce Type: cross Abstract: Large Language Models (LLMs) are accelerating biological research, yet this same capability poses a critical biosecurity threat: models that assist in protein engineering can equally be prompted to generate predicted toxin-like sequences, potentially lowering the barrier to biological misuse.
By Shu Quan, Tianfang Hao, Sitong Fang, He Geng, Jiayi Zhou, Boyuan Chen, Kaile Wang, Donghai Hong, Juntao Dai, Yaodong Yang, Jiaming Ji
arXiv:2609.16213v1 Announce Type: new
Abstract: Artificial intelligence is reshaping biological research across an increasingly connected digital-to-physical workflow. General-purpose large language...
By Candace S. Y. Chan, Aris Karatzikos, Ilias Georgakopoulos-Soares
arXiv:2608. 06779v1 Announce Type: cross Abstract: Large Language Models (LLMs) have accelerated drug discovery, particularly in the automated design of antimicrobial peptides (AMPs).
By Doniyorkhon Obidov, Xiaolong Guo, Yonghui Li, Kaichen Yang
arXiv:2606. 12429v1 Announce Type: cross Abstract: Muse Spark is the latest large language model developed by Meta.
By Cristina Menghini (Sail), Peter Ney (Sail), Hamza Kwisaba (Sail), Zifan (Sail), Wang, Miles Turpin, Felix Binder, Jean-Christophe Testud, Aidan Boyd, Nathaniel Li, Ivan Evtimov, Klaudia Krawiecka, Arman Zharmagambetov, Jeremy Kritz, Alexander R. Fabbri, Daniel Song, Jinpeng Miao, Joonas Hjelt, Meghna Ramani, Leona Lan, Reza Aghajani, Joanna Bitton, Mahesh Pasupuleti, Devin Norder, Khalid El-Arini, Paridhi Singh, V\'itor Albiero, Sahana CB, Rashnil Chaturvedi, Elahe Dabir, Edoardo Debenedetti, Jim Gust, Ziwen Han, Kat He, Sean Hendryx, Lifeng Jin, Polina Kirichenko, Sandra Lefdal, Kenneth Li, Asad Liaqat, Inna Lin, Despoina Magka, Neal Mangaokar, Ishita Mediratta, Zach Miller, Smitha Milli, Niloofar Mireshghallah, Saba Nazir, Hung Nguyen, Maximilian Nickel, Kelvin Niu, Kerem Oktar, Bhargavi Paranjape, Parth Pathak, Maya Pavlova, Emmanuel Ramirez, David Renardy, Candace Ross, Yasha Sheynin, Claudia Shi, Shivam Singhal, Evangelia Spiliopoulou, Rakshith Sharma Srinivasa, Jamelle Watson-Daniels, Spencer Whitman, Adina Williams, Chen Xing, Andy Zou, Tommy Ma, Siqi Deng, James Beldock, Prashant Ratanchandani, Kate Plawiak, Taesung Lee, Ryan Victory, Lindsay Hundley, Rachad Alao, Himaghna Bhattacharjee, Jianfeng Chi, Gary Frost, Pegah Ghahremani, Niki Howe, Yuheng Huang, Saeed Jahed, Hannah Korevaar, Trang Le, Zhe Liu, Jinghong Luo, Qin Lyu, Nina Mehrabi, Abraham Montilla, Chirag Nagpal, Cyrus Nikolaidis, Rajvardhan Oak, Manoj Ravi, Vidya Sarma, Aman Shankar, Alana Shine, Eric Michael Smith, Mariana Tandon, Michael Tontchev, Caoyu Wang, Zihan Wang, Corinne Wong, Zheng Wu, Hongyuan Zhan, Justin Zhao, Zexuan Zhong, Chengxu Zhuang, Tristan Goodman, Ayaz Minhas, Harrison Rudolph, Victoria Jeffries, Ingrid Dickinson, Alex Vaughan, Lauren Deason, Kamalika Chaudhuri, Julian Michael, Shengjia Zhao, Summer Yue
arXiv:2607. 00464v1 Announce Type: new Abstract: Current molecular generation benchmarks emphasize task complexity, molecule novelty, and property alignment; they largely overlook a critical concern: the potential safety risks of AI-generated molecules.
By Tong Xu, Xinzhe Cao, Zhihui Zhu, Keyan Ding, Huajun Chen
arXiv:2607. 05462v2 Announce Type: replace-cross Abstract: As AI agents are incorporated into life science workflows, the capabilities that speed discovery might also enable misuse.
By Edwin H. Wintermute, Harmon Bhasin, Christina M. Agapakis, Dianzhuo Wang, Evan Seeyave, Arjun Banerjee, Daniel Fulop, Matthew C. Watson, Adam J. Meyer, Sandrine Boissel, Jens H. Kuhn, Rishi Jain, Noah D. Taylor, Helena Shomar, Patrick M. Boyle, Kenny Workman
arXiv:2606. 11150v1 Announce Type: new Abstract: Large language models (LLMs) are rapidly acquiring capabilities relevant to biological research, from literature synthesis to interpretation of experimental data.
By Andrew Bo Liu, Samira Nedungadi, Bryce Cai, Alex Kleinman, Harmon Bhasin, Seth Donoughe
arXiv:2607. 05462v1 Announce Type: cross Abstract: As AI agents are incorporated into life science workflows, the capabilities that speed discovery might also enable misuse.
By Edwin H. Wintermute, Harmon Bhasin, Christina M. Agapakis, Dianzhuo Wang, Evan Seeyave, Arjun Banerjee, Daniel Fulop, Matthew C. Watson, Adam J. Meyer, Sandrine Boissel, Jens H. Kuhn, Rishi Jain, Noah D. Taylor, Helena Shomar, Patrick M. Boyle, Kenny Workman
Safety evaluation is critical for assessing whether aligned Large Language Models (LLMs) remain robust against jailbreak attacks. Existing automated testing methods, however, largely rely on response-...
arXiv:2602. 16835v2 Announce Type: replace-cross Abstract: Safety alignment is essential for the responsible deployment of Large Language Models (LLMs).
By Sasha Behrouzi, Lichao Wu, Mohamadreza Rostami, Ahmad-Reza Sadeghi
PFArena is a new benchmark for evaluating language models in protein modification tasks, featuring four controlled interfaces that span single‑mutant generation and multi‑mutant ranking. It incorporates varying levels of mutation fitness data to represent four research scenarios with different amounts of prior experimental context. The benchmark tests six protein language models, six large language models, and five LLM‑based agents, finding that PLMs excel at open‑ended single‑mutant generation while LLMs and agents perform best in multi‑mutant ranking when target‑specific data are available, yet all struggle as search space and mutation depth grow.
By Yawen Ouyang, Xinbo Zhang, Ziyuan Ma, Yixin Wu, Wenbin Liao, Feiran Zhang, Wenjie Li, Lihao Wang, Hao Wang, Xiaoqing Zheng, Xuefeng Yan, Lei Bai, Ya-Qin Zhang, Shuyi Zhang, Wei-Ying Ma, Dahua Lin, Bowen Zhou, Hao Zhou
arXiv:2606. 28332v1 Announce Type: cross Abstract: Large language models (LLMs) are increasingly used for medical and health-related questions, yet their safety in high-risk medical scenarios remains poorly understood.
By Yige Li, Jun Sun, Wei Zhao, Zhe Li, Yutao Wu, Hanxun Huang, Xiang Zheng, Xingjun Ma