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Large Language Models (LLMs), with their remarkable task-handling capabilities and innovative outputs, have catalyzed significant advancements across a spectrum of fields.
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Gene ontology: tool for the unification of biology
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Reoptimization of MDL keys for use in drug discovery
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Bleu: a method for automatic evaluation of machine translation
Kishore Papineni, Salim Roukos, Todd Ward, and Wei-Jing Zhu · 2002
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Rouge: A package for automatic evaluation of summaries
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METEOR: an automatic metric for MT evaluation with improved correlation with human judgments
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A normalized levenshtein distance metric
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BLAST+: architecture and applications
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A novel measure for evaluating classifiers
Jin-Mao Wei, Xiao-Jie Yuan, Qinghua Hu, and Shu-Qin Wang · 2009
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Rdkit: A software suite for cheminformatics, computational chemistry, and predictive modeling
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The CHEMDNER corpus of chemicals and drugs and its annotation principles
Martin Krallinger, Obdulia Rabal, Florian Leitner, Miguel Vazquez, David Salgado, Zhiyong Lu, Robert Leaman, Yanan Lu, Donghong Ji, Daniel M. Lowe, Roger A. Sayle, Riza Theresa Batista-Navarro, Rafal Rak, Torsten Huber, Tim Rocktäschel, Sérgio Matos, David Campos, Buzhou Tang, Hua Xu, Tsendsuren Munkhdalai, Keun Ho Ryu, S. V. Ramanan, P. Senthil Nathan, Slavko Zitnik, Marko Bajec, Lutz Weber, Matthias Irmer, Saber A. Akhondi, Jan A. Kors, Shuo Xu, Xin An, Utpal Kumar Sikdar, Asif Ekbal, Masaharu Yoshioka, Thaer M. Dieb, Miji Choi, Karin Verspoor, Madian Khabsa, C. Lee Giles, Hongfang Liu, Ravikumar Komandur Elayavilli, Andre Lamurias, Francisco M. Couto, Hong-Jie Dai, Richard Tzong-Han Tsai, Caglar Ata, Tolga Can, Anabel Usie, Rui Alves, Isabel Segura-Bedmar, Paloma Martínez, Julen Oyarzabal, and Alfonso Valencia · 2015
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Get your atoms in order - an open-source implementation of a novel and robust molecular canonicalization algorithm
Nadine Schneider, Roger A. Sayle, and Gregory A. Landrum · 2015
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Biocreative V CDR task corpus: a resource for chemical disease relation extraction
Jiao Li, Yueping Sun, Robin J. Johnson, Daniela Sciaky, Chih-Hsuan Wei, Robert Leaman, Allan Peter Davis, Carolyn J. Mattingly, Thomas C. Wiegers, and Zhiyong Lu · 2016
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Overview of the biocreative vi chemical-protein interaction track
Martin Krallinger, Obdulia Rabal, Saber Ahmad Akhondi, Martín Pérez Pérez, Jesus Santamaría, Gael Pérez Rodríguez, Georgios Tsatsaronis, Ander Intxaurrondo, José Antonio Baso López, Umesh K. Nandal, Erin M. van Buel, Ambika Chandrasekhar, Marleen Rodenburg, Astrid Lægreid, Marius A. Doornenbal, Julen Oyarzábal, Anália Lourenço, and Alfonso Valencia · 2017
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Mmseqs2 enables sensitive protein sequence searching for the analysis of massive data sets
Martin Steinegger and Johannes Söding · 2017
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Moleculenet: a benchmark for molecular machine learning
Zhenqin Wu, Bharath Ramsundar, Evan N Feinberg, Joseph Gomes, Caleb Geniesse, Aneesh S Pappu, Karl Leswing, and Vijay Pande · 2018
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Pubmed 2.0
Jacob White · 2020
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Evaluating large language models trained on code
Mark Chen, Jerry Tworek, Heewoo Jun, Qiming Yuan, Henrique Pondé de Oliveira Pinto, Jared Kaplan, Harrison Edwards, Yuri Burda, Nicholas Joseph, Greg Brockman, Alex Ray, Raul Puri, Gretchen Krueger, Michael Petrov, Heidy Khlaaf, Girish Sastry, Pamela Mishkin, Brooke Chan, Scott Gray, Nick Ryder, Mikhail Pavlov, Alethea Power, Lukasz Kaiser, Mohammad Bavarian, Clemens Winter, Philippe Tillet, Felipe Petroski Such, Dave Cummings, Matthias Plappert, Fotios Chantzis, Elizabeth Barnes, Ariel Herbert-Voss, William Hebgen Guss, Alex Nichol, Alex Paino, Nikolas Tezak, Jie Tang, Igor Babuschkin, Suchir Balaji, Shantanu Jain, William Saunders, Christopher Hesse, Andrew N. Carr, Jan Leike, Joshua Achiam, Vedant Misra, Evan Morikawa, Alec Radford, Matthew Knight, Miles Brundage, Mira Murati, Katie Mayer, Peter Welinder, Bob McGrew, Dario Amodei, Sam McCandlish, Ilya Sutskever, and Wojciech Zaremba · 2021
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Measuring massive multitask language understanding
Dan Hendrycks, Collin Burns, Steven Basart, Andy Zou, Mantas Mazeika, Dawn Song, and Jacob Steinhardt · 2021
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Pubchem in 2021: new data content and improved web interfaces
Sunghwan Kim, Jie Chen, Tiejun Cheng, Asta Gindulyte, Jia He, Siqian He, Qingliang Li, Benjamin A. Shoemaker, Paul A. Thiessen, Bo Yu, Leonid Zaslavsky, Jian Zhang, and Evan Bolton · 2021
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Biological structure and function emerge from scaling unsupervised learning to 250 million protein sequences
Alexander Rives, Joshua Meier, Tom Sercu, Siddharth Goyal, Zeming Lin, Jason Liu, Demi Guo, Myle Ott, C. Lawrence Zitnick, Jerry Ma, and Rob Fergus · 2021
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Robust deep learning–based protein sequence design using proteinmpnn
Justas Dauparas, Ivan Anishchenko, Nathaniel Bennett, Hua Bai, Robert J Ragotte, Lukas F Milles, Basile IM Wicky, Alexis Courbet, Rob J de Haas, Neville Bethel, et al · 2022
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Translation between molecules and natural language
Carl Edwards, Tuan Manh Lai, Kevin Ros, Garrett Honke, Kyunghyun Cho, and Heng Ji · 2022
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Training compute-optimal large language models
Jordan Hoffmann, Sebastian Borgeaud, Arthur Mensch, Elena Buchatskaya, Trevor Cai, Eliza Rutherford, Diego de Las Casas, Lisa Anne Hendricks, Johannes Welbl, Aidan Clark, Tom Hennigan, Eric Noland, Katie Millican, George van den Driessche, Bogdan Damoc, Aurelia Guy, Simon Osindero, Karen Simonyan, Erich Elsen, Jack W. Rae, Oriol Vinyals, and Laurent Sifre · 2022
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SELFIES and the future of molecular string representations
Mario Krenn, Qianxiang Ai, Senja Barthel, Nessa Carson, Angelo Frei, Nathan C. Frey, Pascal Friederich, Théophile Gaudin, Alberto Alexander Gayle, Kevin Maik Jablonka, Rafael F. Lameiro, Dominik Lemm, Alston Lo, Seyed Mohamad Moosavi, José Manuel Nápoles-Duarte, AkshatKumar Nigam, Robert Pollice, Kohulan Rajan, Ulrich Schatzschneider, Philippe Schwaller, Marta Skreta, Berend Smit, Felix Strieth-Kalthoff, Chong Sun, Gary Tom, Guido Falk von Rudorff, Andrew Wang, Andrew D. White, Adamo Young, Rose Yu, and Alán Aspuru-Guzik · 2022
Hello dolly: Democratizing the magic of chatgpt with open models, 2023
Mike Conover, Matt Hayes, Matt Mathur, Xiangrui Meng, Jianwei Xie, Jun Wan, Ali Ghodsi, Patrick Wendell, and Patrick Zaharia · 2023
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Uniprot: the universal protein knowledgebase in 2023
The UniProt Consortium · 2023
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Enhancing chat language models by scaling high-quality instructional conversations
Ning Ding, Yulin Chen, Bokai Xu, Yujia Qin, Shengding Hu, Zhiyuan Liu, Maosong Sun, and Bowen Zhou · 2023
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Multi-modal molecule structure-text model for text-based retrieval and editing
Shengchao Liu, Weili Nie, Chengpeng Wang, Jiarui Lu, Zhuoran Qiao, Ling Liu, Jian Tang, Chaowei Xiao, and Animashree Anandkumar · 2023
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Large language models generate functional protein sequences across diverse families
Ali Madani, Ben Krause, Eric R Greene, Subu Subramanian, Benjamin P Mohr, James M Holton, Jose Luis Olmos Jr, Caiming Xiong, Zachary Z Sun, Richard Socher, et al · 2023
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alphaXiv searches the wider corpus for related work and actual follow-ups.
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Language models of protein sequences at the scale of evolution enable accurate structure prediction
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Unified deep learning model for multitask reaction predictions with explanation
Jieyu Lu and Yingkai Zhang · 2022
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Training language models to follow instructions with human feedback
Long Ouyang, Jeffrey Wu, Xu Jiang, Diogo Almeida, Carroll L. Wainwright, Pamela Mishkin, Chong Zhang, Sandhini Agarwal, Katarina Slama, Alex Ray, John Schulman, Jacob Hilton, Fraser Kelton, Luke Miller, Maddie Simens, Amanda Askell, Peter Welinder, Paul F. Christiano, Jan Leike, and Ryan Lowe · 2022
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Training language models to follow instructions with human feedback
Long Ouyang, Jeffrey Wu, Xu Jiang, Diogo Almeida, Carroll L. Wainwright, Pamela Mishkin, Chong Zhang, Sandhini Agarwal, Katarina Slama, Alex Ray, John Schulman, Jacob Hilton, Fraser Kelton, Luke Miller, Maddie Simens, Amanda Askell, Peter Welinder, Paul F. Christiano, Jan Leike, and Ryan Lowe · 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
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Multitask prompted training enables zero-shot task generalization
Victor Sanh, Albert Webson, Colin Raffel, Stephen H. Bach, Lintang Sutawika, Zaid Alyafeai, Antoine Chaffin, Arnaud Stiegler, Arun Raja, Manan Dey, M Saiful Bari, Canwen Xu, Urmish Thakker, Shanya Sharma Sharma, Eliza Szczechla, Taewoon Kim, Gunjan Chhablani, Nihal V. Nayak, Debajyoti Datta, Jonathan Chang, Mike Tian-Jian Jiang, Han Wang, Matteo Manica, Sheng Shen, Zheng Xin Yong, Harshit Pandey, Rachel Bawden, Thomas Wang, Trishala Neeraj, Jos Rozen, Abheesht Sharma, Andrea Santilli, Thibault Févry, Jason Alan Fries, Ryan Teehan, Teven Le Scao, Stella Biderman, Leo Gao, Thomas Wolf, and Alexander M. Rush · 2022
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A molecular multimodal foundation model associating molecule graphs with natural language
Bing Su, Dazhao Du, Zhao Yang, Yujie Zhou, Jiangmeng Li, Anyi Rao, Hao Sun, Zhiwu Lu, and Ji-Rong Wen · 2022
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Galactica: A large language model for science
Ross Taylor, Marcin Kardas, Guillem Cucurull, Thomas Scialom, Anthony Hartshorn, Elvis Saravia, Andrew Poulton, Viktor Kerkez, and Robert Stojnic · 2022
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Do large language models understand chemistry? A conversation with chatgpt
Cayque Monteiro Castro Nascimento and André Silva Pimentel · 2023
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Tool learning with foundation models
Yujia Qin, Shengding Hu, Yankai Lin, Weize Chen, Ning Ding, Ganqu Cui, Zheni Zeng, Yufei Huang, Chaojun Xiao, Chi Han, Yi Ren Fung, Yusheng Su, Huadong Wang, Cheng Qian, Runchu Tian, Kunlun Zhu, Shihao Liang, Xingyu Shen, Bokai Xu, Zhen Zhang, Yining Ye, Bowen Li, Ziwei Tang, Jing Yi, Yuzhang Zhu, Zhenning Dai, Lan Yan, Xin Cong, Yaxi Lu, Weilin Zhao, Yuxiang Huang, Junxi Yan, Xu Han, Xian Sun, Dahai Li, Jason Phang, Cheng Yang, Tongshuang Wu, Heng Ji, Zhiyuan Liu, and Maosong Sun · 2023
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Jonas B. Sandbrink · 2023
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Could chatbots help devise the next pandemic virus?
Robert F Service · 2023
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Stanford alpaca: An instruction-following llama model
Rohan Taori, Ishaan Gulrajani, Tianyi Zhang, Yann Dubois, Xuechen Li, Carlos Guestrin, Percy Liang, and Tatsunori B Hashimoto · 2023
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Fine-tuning large neural language models for biomedical natural language processing
Robert Tinn, Hao Cheng, Yu Gu, Naoto Usuyama, Xiaodong Liu, Tristan Naumann, Jianfeng Gao, and Hoifung Poon · 2023
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Alpaca-lora
Tloen · 2023
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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, Aurélien Rodriguez, Armand Joulin, Edouard Grave, and Guillaume Lample · 2023
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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 · 2023
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Pmc-llama: Further finetuning llama on medical papers
Chaoyi Wu, Xiaoman Zhang, Ya Zhang, Yanfeng Wang, and Weidi Xie · 2023
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Baize: An open-source chat model with parameter-efficient tuning on self-chat data
Canwen Xu, Daya Guo, Nan Duan, and Julian J. McAuley · 2023
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GLM-130B: an open bilingual pre-trained model
Aohan Zeng, Xiao Liu, Zhengxiao Du, Zihan Wang, Hanyu Lai, Ming Ding, Zhuoyi Yang, Yifan Xu, Wendi Zheng, Xiao Xia, Weng Lam Tam, Zixuan Ma, Yufei Xue, Jidong Zhai, Wenguang Chen, Zhiyuan Liu, Peng Zhang, Yuxiao Dong, and Jie Tang · 2023
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Moleculegpt: Instruction following large language models for molecular property prediction
Weitong Zhang, Xiaoyun Wang, Weili Nie, Joe Eaton, Brad Rees, and Quanquan Gu · 2023
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Domain-agnostic molecular generation with self-feedback
Yin Fang, Ningyu Zhang, Zhuo Chen, Xiaohui Fan, and Huajun Chen · 2024
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Biot5+: Towards generalized biological understanding with iupac integration and multi-task tuning
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The future of molecular studies through the lens of large language models
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