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Generative pre-trained Transformer (GPT) has demonstrates its great success in natural language processing and related techniques have been adapted into molecular modeling.
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, Sandhini Agarwal, Ariel Herbert-Voss, Gretchen Krueger, Tom Henighan, Rewon Child, Aditya Ramesh, Daniel Ziegler, Jeffrey Wu, Clemens Winter, Chris Hesse, Mark Chen, Eric Sigler, Mateusz Litwin, Scott Gray, Benjamin Chess, Jack Clark, Christopher Berner, Sam McCandlish, Alec Radford, Ilya Sutskever, and Dario Amodei. 2020 · 1901
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Smiles, a chemical language and information system. 1. introduction to methodology and encoding rules
David Weininger. 1988 · 1988
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Reoptimization of mdl keys for use in drug discovery
Joseph L Durant, Burton A Leland, Douglas R Henry, and James G Nourse. 2002 · 2002
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Bleu: a method for automatic evaluation of machine translation
Kishore Papineni, Salim Roukos, Todd Ward, and Wei-Jing Zhu. 2002 · 2002
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Drug-drug interactions among elderly patients hospitalized for drug toxicity
David N Juurlink, Muhammad Mamdani, Alexander Kopp, Andreas Laupacis, and Donald A Redelmeier. 2003 · 2003
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Rouge: A package for automatic evaluation of summaries
Chin-Yew Lin. 2004 · 2004
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Meteor: An automatic metric for mt evaluation with improved correlation with human judgments
Satanjeev Banerjee and Alon Lavie. 2005 · 2005
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Extended-connectivity fingerprints
David Rogers and Mathew Hahn. 2010 · 2010
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Adam: A method for stochastic optimization
Diederik P Kingma and Jimmy Ba. 2015 · 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 · 2015
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Sulfur containing scaffolds in drugs: synthesis and application in medicinal chemistry
Minghao Feng, Bingqing Tang, Steven H Liang, and Xuefeng Jiang. 2016 · 2016
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Chebi in 2016: Improved services and an expanding collection of metabolites
Janna Hastings, Gareth Owen, Adriano Dekker, Marcus Ennis, Namrata Kale, Venkatesh Muthukrishnan, Steve Turner, Neil Swainston, Pedro Mendes, and Christoph Steinbeck. 2016 · 2016
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Neural machine translation of rare words with subword units
Rico Sennrich, Barry Haddow, and Alexandra Birch. 2016 · 2016
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Frechet chemnet distance: a metric for generative models for molecules in drug discovery
Kristina Preuer, Philipp Renz, Thomas Unterthiner, Sepp Hochreiter, and Gunter Klambauer. 2018 · 2018
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“found in translation”: predicting outcomes of complex organic chemistry reactions using neural sequence-to-sequence models
Philippe Schwaller, Theophile Gaudin, David Lanyi, Costas Bekas, and Teodoro Laino. 2018 · 2018
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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 · 2018
Cited alongside, same era.
SciBERT: A pretrained language model for scientific text
Iz Beltagy, Kyle Lo, and Arman Cohan. 2019 · 2019
Cited alongside, same era.
BERT: Pre-training of deep bidirectional transformers for language understanding
Jacob Devlin, Ming-Wei Chang, Kenton Lee, and Kristina Toutanova. 2019 · 2019
Cited alongside, same era.
Language models are unsupervised multitask learners
Alec Radford, Jeffrey Wu, Rewon Child, David Luan, Dario Amodei, Ilya Sutskever, et al. 2019 · 2019
Cited alongside, same era.
Exploring the limits of transfer learning with a unified text-to-text transformer
Colin Raffel, Noam Shazeer, Adam Roberts, Katherine Lee, Sharan Narang, Michael Matena, Yanqi Zhou, Wei Li, and Peter J. Liu. 2020 · 2020
Cited alongside, same era.
Protgpt2 is a deep unsupervised language model for protein design
Noelia Ferruz, Steffen Schmidt, and Birte Höcker. 2022 · 2022
Later among the works it cites.
Neural scaling of deep chemical models
Nathan Frey, Ryan Soklaski, Simon Axelrod, Siddharth Samsi, Rafael Gomez-Bombarelli, Connor Coley, and Vijay Gadepally. 2022 · 2022
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Ppt: Pre-trained prompt tuning for few-shot learning
Yuxian Gu, Xu Han, Zhiyuan Liu, and Minlie Huang. 2022 · 2022
Later among the works it cites.
Pre-training molecular graph representation with 3d geometry
Shengchao Liu, Hanchen Wang, Weiyang Liu, Joan Lasenby, Hongyu Guo, and Jian Tang. 2022 · 2022
Later among the works it cites.
BioGPT: generative pre-trained transformer for biomedical text generation and mining
Renqian Luo, Liai Sun, Yingce Xia, Tao Qin, Sheng Zhang, Hoifung Poon, and Tie-Yan Liu. 2022 · 2022
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Chatgpt: Optimizing language models for dialogue
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Yu Rong, Yatao Bian, Tingyang Xu, Weiyang Xie, Ying Wei, Wenbing Huang, and Junzhou Huang. 2020 · 2020
Cited alongside, same era.
Text2mol: Cross-modal molecule retrieval with natural language queries
Carl Edwards, ChengXiang Zhai, and Heng Ji. 2021 · 2021
Cited alongside, same era.
Making pre-trained language models better few-shot learners
Tianyu Gao, Adam Fisch, and Danqi Chen. 2021 · 2021
Cited alongside, same era.
Generative models for de novo drug design
Xiaochu Tong, Xiaohong Liu, Xiaoqin Tan, Xutong Li, Jiaxin Jiang, Zhaoping Xiong, Tingyang Xu, Hualiang Jiang, Nan Qiao, and Mingyue Zheng. 2021 · 2021
Cited alongside, same era.
Motif-based graph self-supervised learning for molecular property prediction
Zaixi Zhang, Qi Liu, Hao Wang, Chengqiang Lu, and Chee-Kong Lee. 2021 · 2021
Cited alongside, same era.
PubMedGPT 2.7B
Elliot Bolton, David Hall, Michihiro Yasunaga, Tony Lee, Chris Manning, and Percy Liang. 2022 · 2022
Cited alongside, same era.
Adaprompt: Adaptive model training for prompt-based nlp
Yulong Chen, Yang Liu, Li Dong, Shuohang Wang, Chenguang Zhu, Michael Zeng, and Yue Zhang. 2022 · 2022
Cited alongside, same era.
OpenAI. 2022 · 2022
Later among the works it cites.
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. 2022 · 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 · 2022
Later among the works it cites.
Bern2: an advanced neural biomedical named entity recognition and normalization tool
Mujeen Sung, Minbyul Jeong, Yonghwa Choi, Donghyeon Kim, Jinhyuk Lee, and Jaewoo Kang. 2022 · 2022
Later among the works it cites.
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 · 2022
Later among the works it cites.
An explanation of in-context learning as implicit bayesian inference
Sang Michael Xie, Aditi Raghunathan, Percy Liang, and Tengyu Ma. 2022 · 2022
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A deep-learning system bridging molecule structure and biomedical text with comprehension comparable to human professionals
Zheni Zeng, Yuan Yao, Zhiyuan Liu, and Maosong Sun. 2022 · 2022
Later among the works it cites.
PubChem 2023 update
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 E Bolton. 2022 · 2023
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Molgpt: Molecular generation using a transformer-decoder model
Viraj Bagal, Rishal Aggarwal, P. K. Vinod, and U. Deva Priyakumar. 2022 · 2076
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