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The applications of large language models (LLMs) in various biological domains have been explored recently, but their reasoning ability in complex biological systems, such as pathways, remains underexplored, which is crucial for predicting biological phenomena, formulating hypotheses, and designing experiments.
Kegg: kyoto encyclopedia of genes and genomes
Minoru Kanehisa and Susumu Goto · 2000
Earlier work this paper cites.
Pubmed and beyond: a survey of web tools for searching biomedical literature
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Earlier work this paper cites.
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Earlier work this paper cites.
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Earlier work this paper cites.
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Earlier work this paper cites.
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Earlier work this paper cites.
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Ali Madani, Bryan McCann, Nikhil Naik, Nitish Shirish Keskar, Namrata Anand, Raphael R Eguchi, Po-Ssu Huang, and Richard Socher · 2020
Earlier work this paper cites.
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Di Jin, Eileen Pan, Nassim Oufattole, Wei-Hung Weng, Hanyi Fang, and Peter Szolovits · 2021
Earlier work this paper cites.
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Earlier work this paper cites.
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Earlier work this paper cites.
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Earlier work this paper cites.
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Jason Wei, Xuezhi Wang, Dale Schuurmans, Maarten Bosma, Fei Xia, Ed Chi, Quoc V Le, Denny Zhou, et al · 2022
Earlier work this paper cites.
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Zhaocheng Zhu, Chence Shi, Zuobai Zhang, Shengchao Liu, Minghao Xu, Xinyu Yuan, Yangtian Zhang, Junkun Chen, Huiyu Cai, Jiarui Lu, et al · 2022
Earlier work this paper cites.
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Earlier work this paper cites.
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Earlier work this paper cites.
Xiaoxin He, Xavier Bresson, Thomas Laurent, Adam Perold, Yann LeCun, and Bryan Hooi · 2023
Earlier work this paper cites.
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Matching patients to clinical trials with large language models
Qiao Jin, Zifeng Wang, Charalampos S Floudas, Fangyuan Chen, Changlin Gong, Dara Bracken-Clarke, Elisabetta Xue, Yifan Yang, Jimeng Sun, and Zhiyong Lu · 2023
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Chatpathway: Conversational large language models for biology pathway detection
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Retrieved sequence augmentation for protein representation learning
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Maciej Besta, Nils Blach, Ales Kubicek, Robert Gerstenberger, Michal Podstawski, Lukas Gianinazzi, Joanna Gajda, Tomasz Lehmann, Hubert Niewiadomski, Piotr Nyczyk, et al · 2024
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Call me when necessary: Llms can efficiently and faithfully reason over structured environments
Sitao Cheng, Ziyuan Zhuang, Yong Xu, Fangkai Yang, Chaoyun Zhang, Xiaoting Qin, Xiang Huang, Ling Chen, Qingwei Lin, Dongmei Zhang, et al · 2024
Later among the works it cites.
Abhimanyu Dubey, Abhinav Jauhri, Abhinav Pandey, Abhishek Kadian, Ahmad Al-Dahle, Aiesha Letman, Akhil Mathur, Alan Schelten, Amy Yang, Angela Fan, et al · 2024
Later among the works it cites.
From local to global: A graph rag approach to query-focused summarization
Darren Edge, Ha Trinh, Newman Cheng, Joshua Bradley, Alex Chao, Apurva Mody, Steven Truitt, and Jonathan Larson · 2024
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alphaXiv searches the wider corpus for related work and actual follow-ups.
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Noah Shinn, Federico Cassano, Ashwin Gopinath, Karthik R Narasimhan, and Shunyu Yao · 2023
Cited alongside, same era.
Large language models encode clinical knowledge
Karan Singhal, Shekoofeh Azizi, Tao Tu, S Sara Mahdavi, Jason Wei, Hyung Won Chung, Nathan Scales, Ajay Tanwani, Heather Cole-Lewis, Stephen Pfohl, et al · 2023
Cited alongside, same era.
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Jiashuo Sun, Chengjin Xu, Lumingyuan Tang, Saizhuo Wang, Chen Lin, Yeyun Gong, Lionel Ni, Heung-Yeung Shum, and Jian Guo · 2023
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The promises of large language models for protein design and modeling
Giorgio Valentini, Dario Malchiodi, Jessica Gliozzo, Marco Mesiti, Mauricio Soto-Gomez, Alberto Cabri, Justin Reese, Elena Casiraghi, and Peter N Robinson · 2023
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React: Synergizing reasoning and acting in language models, 2023
Shunyu Yao, Jeffrey Zhao, Dian Yu, Nan Du, Izhak Shafran, Karthik Narasimhan, and Yuan Cao · 2023
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Ruosong Ye, Caiqi Zhang, Runhui Wang, Shuyuan Xu, Yongfeng Zhang, et al · 2023
Cited alongside, same era.
Simulating 500 million years of evolution with a language model
Tomas Hayes, Roshan Rao, Halil Akin, Nicholas J Sofroniew, Deniz Oktay, Zeming Lin, Robert Verkuil, Vincent Q Tran, Jonathan Deaton, Marius Wiggert, et al · 2024
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G-retriever: Retrieval-augmented generation for textual graph understanding and question answering
Xiaoxin He, Yijun Tian, Yifei Sun, Nitesh V Chawla, Thomas Laurent, Yann LeCun, Xavier Bresson, and Bryan Hooi · 2024
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Unigraph: Learning a cross-domain graph foundation model from natural language
Yufei He and Bryan Hooi · 2024
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Text2protein: A generative model for designated protein design on given description
Ramtin Hosseini, Siyang Zhang, and Pengtao Xie · 2024
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Graph chain-of-thought: Augmenting large language models by reasoning on graphs
Bowen Jin, Chulin Xie, Jiawei Zhang, Kashob Kumar Roy, Yu Zhang, Suhang Wang, Yu Meng, and Jiawei Han · 2024
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Shilong Li, Yancheng He, Hangyu Guo, Xingyuan Bu, Ge Bai, Jie Liu, Jiaheng Liu, Xingwei Qu, Yangguang Li, Wanli Ouyang, et al · 2024
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Augmenting large language models with chemistry tools
Andres M. Bran, Sam Cox, Oliver Schilter, Carlo Baldassari, Andrew D White, and Philippe Schwaller · 2024
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Multi-modal conditioning for metal-organic frameworks generation using 3d modeling techniques
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Jiabin Tang, Yuhao Yang, Wei Wei, Lei Shi, Lixin Su, Suqi Cheng, Dawei Yin, and Chao Huang · 2024
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