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Multiple previous studies have reported suboptimal performance of LLMs in biomedical text mining.
PubMed [Internet]
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Raul Rodriguez-Esteban · 2009
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Chih-Hsuan Wei, Hung-Yu Kao, and Zhiyong Lu · 2013
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Ncbi disease corpus: a resource for disease name recognition and concept normalization
Rezarta Islamaj Doğan, Robert Leaman, and Zhiyong Lu · 2014
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Michael J Erdman, Bruce A Doepker, Anthony T Gerlach, Gary S Phillips, Lucas Elijovich, and G Morgan Jones · 2014
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Takahiro Nunokawa, Masanobu Akazawa, Naoto Yokogawa, Kota Shimada, Kazuko Hiramatsu, Yasuhide Nishio, and Shoji Sugii · 2014
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Automatic semantic classification of scientific literature according to the hallmarks of cancer
Simon Baker, Ilona Silins, Yufan Guo, Imran Ali, Johan Högberg, Ulla Stenius, and Anna Korhonen · 2016
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Biocreative v cdr task corpus: a resource for chemical disease relation extraction
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Bert: Pre-training of deep bidirectional transformers for language understanding
Jacob Devlin · 2018
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Improving language understanding by generative pre-training, 2018
Alec Radford · 2018
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Yifan Peng, Shankai Yan, and Zhiyong Lu · 2019
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Language models are unsupervised multitask learners, 2019
Alec Radford, Jeffrey Wu, Rewon Child, David Luan, Dario Amodei, Ilya Sutskever, et al · 2019
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Keep up with the latest coronavirus research
Qingyu Chen, Alexis Allot, and Zhiyong Lu · 2020
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On the stability of fine-tuning bert: Misconceptions, explanations, and strong baselines
Marius Mosbach, Maksym Andriushchenko, and Dietrich Klakow · 2020
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Language models are few-shot learners
Tom Brown, Benjamin Mann, Nick Ryder, Melanie Subbiah, Jared D Kaplan, Prafulla Dhariwal, Arvind Neelakantan, Pranav Shyam, Girish Sastry, Amanda Askell, et al · 2020
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Biobert: a pre-trained biomedical language representation model for biomedical text mining
Jinhyuk Lee, Wonjin Yoon, Sungdong Kim, Donghyeon Kim, Sunkyu Kim, Chan Ho So, and Jaewoo Kang · 2020
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Recent advances in biomedical literature mining
Sendong Zhao, Chang Su, Zhiyong Lu, and Fei Wang · 2021
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Litcovid: an open database of covid-19 literature
Qingyu Chen, Alexis Allot, and Zhiyong Lu · 2021
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Gpt-ner: Named entity recognition via large language models
Shuhe Wang, Xiaofei Sun, Xiaoya Li, Rongbin Ouyang, Fei Wu, Tianwei Zhang, Jiwei Li, and Guoyin Wang · 2023
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Automatic prompt optimization with" gradient descent" and beam search
Reid Pryzant, Dan Iter, Jerry Li, Yin Tat Lee, Chenguang Zhu, and Michael Zeng · 2023
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Retrieval-augmented generation for large language models: A survey
Yunfan Gao, Yun Xiong, Xinyu Gao, Kangxiang Jia, Jinliu Pan, Yuxi Bi, Yi Dai, Jiawei Sun, and Haofen Wang · 2023
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Openllama: An open reproduction of llama, May 2023
Xinyang Geng and Hao Liu · 2023
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Pubtator 3.0: an ai-powered literature resource for unlocking biomedical knowledge
Chih-Hsuan Wei, Alexis Allot, Po-Ting Lai, Robert Leaman, Shubo Tian, Ling Luo, Qiao Jin, Zhizheng Wang, Qingyu Chen, and Zhiyong Lu · 2024
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Deep learning in biomedical text mining: contributions and challenges
Tanvir Alam and Sebastian Schmeier · 2021
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Multi-label classification for biomedical literature: an overview of the biocreative vii litcovid track for covid-19 literature topic annotations
Qingyu Chen, Alexis Allot, Robert Leaman, Rezarta Islamaj, Jingcheng Du, Li Fang, Kai Wang, Shuo Xu, Yuefu Zhang, Parsa Bagherzadeh, et al · 2022
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Training language models to follow instructions with human feedback
Long Ouyang, Jeffrey Wu, Xu Jiang, Diogo Almeida, Carroll Wainwright, Pamela Mishkin, Chong Zhang, Sandhini Agarwal, Katarina Slama, Alex Ray, et al · 2022
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Large language models are few-shot clinical information extractors
Monica Agrawal, Stefan Hegselmann, Hunter Lang, Yoon Kim, and David Sontag · 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
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Self-instruct: Aligning language models with self-generated instructions
Yizhong Wang, Yeganeh Kordi, Swaroop Mishra, Alisa Liu, Noah A Smith, Daniel Khashabi, and Hannaneh Hajishirzi · 2022
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Star: Bootstrapping reasoning with reasoning
Eric Zelikman, Yuhuai Wu, Jesse Mu, and Noah Goodman · 2022
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A comprehensive evaluation of large language models on benchmark biomedical text processing tasks
Israt Jahan, Md Tahmid Rahman Laskar, Chun Peng, and Jimmy Xiangji Huang · 2024
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Zhi Rui Tam, Cheng-Kuang Wu, Yi-Lin Tsai, Chieh-Yen Lin, Hung-yi Lee, and Yun-Nung Chen · 2024
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Advancing entity recognition in biomedicine via instruction tuning of large language models
Vipina K Keloth, Yan Hu, Qianqian Xie, Xueqing Peng, Yan Wang, Andrew Zheng, Melih Selek, Kalpana Raja, Chih Hsuan Wei, Qiao Jin, et al · 2024
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Fine-tuning large language models for chemical text mining
Wei Zhang, Qinggong Wang, Xiangtai Kong, Jiacheng Xiong, Shengkun Ni, Duanhua Cao, Buying Niu, Mingan Chen, Yameng Li, Runze Zhang, et al · 2024
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Opportunities and challenges for chatgpt and large language models in biomedicine and health
Shubo Tian, Qiao Jin, Lana Yeganova, Po-Ting Lai, Qingqing Zhu, Xiuying Chen, Yifan Yang, Qingyu Chen, Won Kim, Donald C Comeau, et al · 2024
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A systematic survey of prompt engineering in large language models: Techniques and applications
Pranab Sahoo, Ayush Kumar Singh, Sriparna Saha, Vinija Jain, Samrat Mondal, and Aman Chadha · 2024
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Scaling llm test-time compute optimally can be more effective than scaling model parameters
Charlie Snell, Jaehoon Lee, Kelvin Xu, and Aviral Kumar · 2024
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Openai o1 system card, 2024
Aaron Jaech, Adam Kalai, Adam Lerer, Adam Richardson, Ahmed El-Kishky, Aiden Low, Alec Helyar, Aleksander Madry, Alex Beutel, Alex Carney, et al · 2024
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Large language publishing: The scholarly publishing oligopoly’s bet on ai
Jefferson Pooley · 2024
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Has your paper been used to train an ai model? almost certainly
Elizabeth Gibney · 2024
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Publishers are selling papers to train ais—and making millions of dollars
Diana Kwon · 2024
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Datasets for large language models: A comprehensive survey
Yang Liu, Jiahuan Cao, Chongyu Liu, Kai Ding, and Lianwen Jin · 2024
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A survey on rag meeting llms: Towards retrieval-augmented large language models
Wenqi Fan, Yujuan Ding, Liangbo Ning, Shijie Wang, Hengyun Li, Dawei Yin, Tat-Seng Chua, and Qing Li · 2024
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A survey on knowledge distillation of large language models
Xiaohan Xu, Ming Li, Chongyang Tao, Tao Shen, Reynold Cheng, Jinyang Li, Can Xu, Dacheng Tao, and Tianyi Zhou · 2024
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Biomedrag: A retrieval augmented large language model for biomedicine
Mingchen Li, Halil Kilicoglu, Hua Xu, and Rui Zhang · 2024
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Awesome healthcare datasets, May 2024
geniusrise · 2024
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Task contamination: Language models may not be few-shot anymore
Changmao Li and Jeffrey Flanigan · 2024
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The best way to generate structured output from llms, 2024
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