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Large language models (LLMs) have become important tools in solving biological problems, offering improvements in accuracy and adaptability over conventional methods.
Bertscore: Evaluating text generation with bert
Tianyi Zhang, Varsha Kishore, Felix Wu, Kilian Q Weinberger, and Yoav Artzi. 2019 · 1904
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Pubmedqa: A dataset for biomedical research question answering
Qiao Jin, Bhuwan Dhingra, Zhengping Liu, William W Cohen, and Xinghua Lu. 2019 · 1909
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Language models as knowledge bases?
Fabio Petroni, Tim Rocktäschel, Patrick Lewis, Anton Bakhtin, Yuxiang Wu, Alexander H Miller, and Sebastian Riedel. 2019 · 1909
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Language models are few-shot learners
Tom B Brown. 2020 · 2005
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Blast: improvements for better sequence analysis
Jian Ye, Scott McGinnis, and Thomas L Madden. 2006 · 2006
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Infernal 1.0: inference of rna alignments
Eric P Nawrocki, Diana L Kolbe, and Sean R Eddy. 2009 · 2009
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Infernal 1.1: 100-fold faster rna homology searches
Eric P Nawrocki and Sean R Eddy. 2013 · 2013
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Lora: Low-rank adaptation of large language models
Edward J. Hu, Yelong Shen, Phillip Wallis, Zeyuan Allen-Zhu, Yuanzhi Li, Shean Wang, Lu Wang, and Weizhu Chen. 2021 · 2021
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Dnabert: pre-trained bidirectional encoder representations from transformers model for dna-language in genome
Yanrong Ji, Zhihan Zhou, Han Liu, and Ramana V Davuluri. 2021 · 2021
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What disease does this patient have? a large-scale open domain question answering dataset from medical exams
Di Jin, Eileen Pan, Nassim Oufattole, Wei-Hung Weng, Hanyi Fang, and Peter Szolovits. 2021 · 2021
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Highly accurate protein structure prediction with alphafold
John Jumper, Richard Evans, Alexander Pritzel, Tim Green, Michael Figurnov, Olaf Ronneberger, Kathryn Tunyasuvunakool, Russ Bates, Augustin Žídek, Anna Potapenko, et al. 2021 · 2021
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Prefix-tuning: Optimizing continuous prompts for generation
Xiang Lisa Li and Percy Liang. 2021 · 2021
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Pengfei Liu, Weizhe Yuan, Jinlan Fu, Zhengbao Jiang, Hiroaki Hayashi, and Graham Neubig. 2021 · 2021
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Robustness of learning from task instructions
Jiasheng Gu, Hongyu Zhao, Hanzi Xu, Liangyu Nie, Hongyuan Mei, and Wenpeng Yin. 2022 · 2022
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Medmcqa: A large-scale multi-subject multi-choice dataset for medical domain question answering
Ankit Pal, Logesh Kumar Umapathi, and Malaikannan Sankarasubbu. 2022 · 2022
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Leveraging large language models for multiple choice question answering. arxiv 2022
Joshua Robinson, Christopher Michael Rytting, and David Wingate. 2022 · 2022
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Self-consistency improves chain of thought reasoning in language models
Xuezhi Wang, Jason Wei, Dale Schuurmans, Quoc Le, Ed Chi, Sharan Narang, Aakanksha Chowdhery, and Denny Zhou. 2022 · 2022
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Chain-of-thought prompting elicits reasoning in large language models
Jason Wei, Xuezhi Wang, Dale Schuurmans, Maarten Bosma, Fei Xia, Ed Chi, Quoc V Le, Denny Zhou, et al. 2022 · 2022
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Peer: a comprehensive and multi-task benchmark for protein sequence understanding
Minghao Xu, Zuobai Zhang, Jiarui Lu, Zhaocheng Zhu, Yangtian Zhang, Ma Chang, Runcheng Liu, and Jian Tang. 2022 · 2022
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Self-rag: Learning to retrieve, generate, and critique through self-reflection
Akari Asai, Zeqiu Wu, Yizhong Wang, Avirup Sil, and Hannaneh Hajishirzi. 2023 · 2023
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Sparks of artificial general intelligence: Early experiments with gpt-4
Sébastien Bubeck, Varun Chandrasekaran, Ronen Eldan, Johannes Gehrke, Eric Horvitz, Ece Kamar, Peter Lee, Yin Tat Lee, Yuanzhi Li, Scott Lundberg, et al. 2023 · 2023
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An extensive benchmark study on biomedical text generation and mining with chatgpt
Qijie Chen, Haotong Sun, Haoyang Liu, Yinghui Jiang, Ting Ran, Xurui Jin, Xianglu Xiao, Zhimin Lin, Hongming Chen, and Zhangmin Niu. 2023 · 2023
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Synergpt: In-context learning for personalized drug synergy prediction and drug design
Carl Edwards, Aakanksha Naik, Tushar Khot, Martin Burke, Heng Ji, and Tom Hope. 2023 · 2023
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Jiyue Jiang, Sheng Wang, Qintong Li, Lingpeng Kong, and Chuan Wu. 2023 · 2023
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Mimic-iv, a freely accessible electronic health record dataset
Alistair EW Johnson, Lucas Bulgarelli, Lu Shen, Alvin Gayles, Ayad Shammout, Steven Horng, Tom J Pollard, Sicheng Hao, Benjamin Moody, Brian Gow, et al. 2023 · 2023
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Pre-train, prompt, and predict: A systematic survey of prompting methods in natural language processing
Pengfei Liu, Weizhe Yuan, Jinlan Fu, Zhengbao Jiang, Hiroaki Hayashi, and Graham Neubig. 2023 · 2023
Cited alongside, same era.
Factscore: Fine-grained atomic evaluation of factual precision in long form text generation
Sewon Min, Kalpesh Krishna, Xinxi Lyu, Mike Lewis, Wen-tau Yih, Pang Wei Koh, Mohit Iyyer, Luke Zettlemoyer, and Hannaneh Hajishirzi. 2023 · 2023
Cited alongside, same era.
Proteingym: Large-scale benchmarks for protein design and fitness prediction
Pascal Notin, Aaron W Kollasch, Daniel Ritter, Lood van Niekerk, Steffanie Paul, Hansen Spinner, Nathan Rollins, Ada Shaw, Ruben Weitzman, Jonathan Frazer, et al. 2023 · 2023
Cited alongside, same era.
Towards expert-level medical question answering with large language models
Assessing gpt-4 for cell type annotation in single-cell rna-seq analysis
Wenpin Hou and Zhicheng Ji. 2024 · 2024
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Hui Huang, Yingqi Qu, Jing Liu, Muyun Yang, and Tiejun Zhao. 2024 · 2024
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Qwen2. 5-coder technical report
Binyuan Hui, Jian Yang, Zeyu Cui, Jiaxi Yang, Dayiheng Liu, Lei Zhang, Tianyu Liu, Jiajun Zhang, Bowen Yu, Kai Dang, et al. 2024 · 2024
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Olaph: Improving factuality in biomedical long-form question answering
Minbyul Jeong, Hyeon Hwang, Chanwoong Yoon, Taewhoo Lee, and Jaewoo Kang. 2024 · 2024
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How well do llms handle cantonese? benchmarking cantonese capabilities of large language models
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Karan Singhal, Tao Tu, Juraj Gottweis, Rory Sayres, Ellery Wulczyn, Le Hou, Kevin Clark, Stephen Pfohl, Heather Cole-Lewis, Darlene Neal, et al. 2023 · 2023
Cited alongside, same era.
quehry: a question answering system to query electronic health records
Sarvesh Soni, Surabhi Datta, and Kirk Roberts. 2023 · 2023
Cited alongside, same era.
Medchatzh: a better medical adviser learns from better instructions
Yang Tan, Mingchen Li, Zijie Huang, Huiqun Yu, and Guisheng Fan. 2023 · 2023
Cited alongside, same era.
Llama: Open and efficient foundation language models
Hugo Touvron, Thibaut Lavril, Gautier Izacard, Xavier Martinet, Marie-Anne Lachaux, Timothée Lacroix, Baptiste Rozière, Naman Goyal, Eric Hambro, Faisal Azhar, et al. 2023 · 2023
Cited alongside, same era.
Judging llm-as-a-judge with mt-bench and chatbot arena
Lianmin Zheng, Wei-Lin Chiang, Ying Sheng, Siyuan Zhuang, Zhanghao Wu, Yonghao Zhuang, Zi Lin, Zhuohan Li, Dacheng Li, Eric Xing, et al. 2023 · 2023
Cited alongside, same era.
Judgelm: Fine-tuned large language models are scalable judges
Lianghui Zhu, Xinggang Wang, and Xinlong Wang. 2023 · 2023
Cited alongside, same era.
Linker-tuning: Optimizing continuous prompts for heterodimeric protein prediction
Shuxian Zou, Shentong Mo, Hui Li, Xingyi Cheng, Le Song, and Eric Xing. 2023 · 2023
Cited alongside, same era.
Hugging face inference api and endpoints
2024 · 2024
Cited alongside, same era.
Jiyue Jiang, Pengan Chen, Liheng Chen, Sheng Wang, Qinghang Bao, Lingpeng Kong, Yu Li, and Chuan Wu. 2024 · 2024
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Dual-space optimization: Improved molecule sequence design by latent prompt transformer
Deqian Kong, Yuhao Huang, Jianwen Xie, Edouardo Honig, Ming Xu, Shuanghong Xue, Pei Lin, Sanping Zhou, Sheng Zhong, Nanning Zheng, et al. 2024 · 2024
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Multistate and functional protein design using rosettafold sequence space diffusion
Sidney Lyayuga Lisanza, Jacob Merle Gershon, Samuel WK Tipps, Jeremiah Nelson Sims, Lucas Arnoldt, Samuel J Hendel, Miriam K Simma, Ge Liu, Muna Yase, Hongwei Wu, et al. 2024 · 2024
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Prollama: A protein large language model for multi-task protein language processing
Liuzhenghao Lv, Zongying Lin, Hao Li, Yuyang Liu, Jiaxi Cui, Calvin Yu-Chian Chen, Li Yuan, and Yonghong Tian. 2024 · 2024
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Inadequacies of large language model benchmarks in the era of generative artificial intelligence
Timothy R McIntosh, Teo Susnjak, Nalin Arachchilage, Tong Liu, Paul Watters, and Malka N Halgamuge. 2024 · 2024
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migtissera/Tess-3-Mistral-Large-2-123B · Hugging Face — huggingface.co
Mistral-AI. 2024 · 2024
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Sequence modeling and design from molecular to genome scale with evo
Eric Nguyen, Michael Poli, Matthew G. Durrant, Brian Kang, Dhruva Katrekar, David B. Li, Liam J. Bartie, Armin W. Thomas, Samuel H. King, Garyk Brixi, Jeremy Sullivan, Madelena Y. Ng, Ashley Lewis, Aaron Lou, Stefano Ermon, Stephen A. Baccus, Tina Hernandez-Boussard, Christopher Ré, Patrick D. Hsu, and Brian L. Hie. 2024 · 2024
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Beacon: Benchmark for comprehensive rna tasks and language models
Yuchen Ren, Zhiyuan Chen, Lifeng Qiao, Hongtai Jing, Yuchen Cai, Sheng Xu, Peng Ye, Xinzhu Ma, Siqi Sun, Hongliang Yan, et al. 2024 · 2024
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Paul Röttger, Valentin Hofmann, Valentina Pyatkin, Musashi Hinck, Hannah Rose Kirk, Hinrich Schütze, and Dirk Hovy. 2024 · 2024
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Rnabench: A comprehensive library for in silico rna modelling
Frederic Runge, Karim Farid, Jorg KH Franke, and Frank Hutter. 2024 · 2024
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Llms predict protein phases
Arunima Singh. 2024 · 2024
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Hgtdp-dta: Hybrid graph-transformer with dynamic prompt for drug-target binding affinity prediction
Xi Xiao, Wentao Wang, Jiacheng Xie, Lijing Zhu, Gaofei Chen, Zhengji Li, Tianyang Wang, and Min Xu. 2024 · 2024
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Proteinbench: A holistic evaluation of protein foundation models
Fei Ye, Zaixiang Zheng, Dongyu Xue, Yuning Shen, Lihao Wang, Yiming Ma, Yan Wang, Xinyou Wang, Xiangxin Zhou, and Quanquan Gu. 2024 · 2024
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Exploring the comprehension of chatgpt in traditional chinese medicine knowledge
Li Yizhen, Huang Shaohan, Qi Jiaxing, Quan Lei, Han Dongran, and Luan Zhongzhi. 2024 · 2024
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xfinder: Robust and pinpoint answer extraction for large language models
Qingchen Yu, Zifan Zheng, Shichao Song, Zhiyu Li, Feiyu Xiong, Bo Tang, and Ding Chen. 2024 · 2024
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Improving the robustness of large language models via consistency alignment
Zhao Yukun, Yan Lingyong, Sun Weiwei, Xing Guoliang, Wang Shuaiqiang, Meng Chong, Cheng Zhicong, Ren Zhaochun, and Yin Dawei. 2024 · 2024
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Prompt-based generation of natural language explanations of synthetic lethality for cancer drug discovery
Ke Zhang, Yimiao Feng, and Jie Zheng. 2024a · 2024
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Genome modeling and design across all domains of life with evo 2
Garyk Brixi, Matthew G Durrant, Jerome Ku, Michael Poli, Greg Brockman, Daniel Chang, Gabriel A Gonzalez, Samuel H King, David B Li, Aditi T Merchant, Mohsen Naghipourfar, Eric Nguyen, Chiara Ricci-Tam, David W Romero, Gwanggyu Sun, Ali Taghibakshi, Anton Vorontsov, Brandon Yang, Myra Deng, Liv Gorton, Nam Nguyen, Nicholas K Wang, Etowah Adams, Stephen A Baccus, Steven Dillmann, Stefano Ermon, Daniel Guo, Rajesh Ilango, Ken Janik, Amy X Lu, Reshma Mehta, Mohammad R.K. Mofrad, Madelena Y Ng, Jaspreet Pannu, Christopher Re, Jonathan C Schmok, John St. John, Jeremy Sullivan, Kevin Zhu, Greg Zynda, Daniel Balsam, Patrick Collison, Anthony B. Costa, Tina Hernandez-Boussard, Eric Ho, Ming-Yu Liu, Tom McGrath, Kimberly Powell, Dave P. Burke, Hani Goodarzi, Patrick D Hsu, and Brian Hie. 2025 · 2025
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Deepseek-r1: Incentivizing reasoning capability in llms via reinforcement learning
Daya Guo, Dejian Yang, Haowei Zhang, Junxiao Song, Ruoyu Zhang, Runxin Xu, Qihao Zhu, Shirong Ma, Peiyi Wang, Xiao Bi, et al. 2025 · 2025
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