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Cutting edge techniques developed in the general NLP domain are often subsequently applied to the high-value, data-rich biomedical domain.
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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Mike Lewis, Yinhan Liu, Naman Goyal, Marjan Ghazvininejad, Abdelrahman Mohamed, Omer Levy, Veselin Stoyanov, and Luke Zettlemoyer. 2019 · 1910
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Vaccine adverse event text mining system for extracting features from vaccine safety reports
Taxiarchis Botsis, Thomas Buttolph, Michael D Nguyen, Scott Winiecki, Emily Jane Woo, and Robert Ball. 2012 · 2012
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Span-based joint entity and relation extraction with transformer pre-training
Markus Eberts and Adrian Ulges. 2020 · 2013
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The ddi corpus: An annotated corpus with pharmacological substances and drug–drug interactions
María Herrero-Zazo, Isabel Segura-Bedmar, Paloma Martínez, and Thierry Declerck. 2013 · 2013
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Modeling joint entity and relation extraction with table representation
Makoto Miwa and Yutaka Sasaki. 2014 · 2014
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Mimic-iii, a freely accessible critical care database
Alistair EW Johnson, Tom J Pollard, Lu Shen, Li-wei H Lehman, Mengling Feng, Mohammad Ghassemi, Benjamin Moody, Peter Szolovits, Leo Anthony Celi, and Roger G Mark. 2016 · 2016
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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 · 2016
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Deep reinforcement learning from human preferences
Paul F Christiano, Jan Leike, Tom Brown, Miljan Martic, Shane Legg, and Dario Amodei. 2017 · 2017
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Overview of the biocreative vi chemical-protein interaction track
Martin Krallinger, Obdulia Rabal, Saber A Akhondi, Martın Pérez Pérez, Jesús Santamaría, Gael Pérez Rodríguez, Georgios Tsatsaronis, Ander Intxaurrondo, José Antonio López, Umesh Nandal, et al. 2017 · 2017
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Exploiting semantic patterns over biomedical knowledge graphs for predicting treatment and causative relations
Gokhan Bakal, Preetham Talari, Elijah V Kakani, and Ramakanth Kavuluru. 2018 · 2018
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A collaborative filtering-based approach to biomedical knowledge discovery
Jake Lever, Sitanshu Gakkhar, Michael Gottlieb, Tahereh Rashnavadi, Santina Lin, Celia Siu, Maia Smith, Martin R Jones, Martin Krzywinski, and Steven JM Jones. 2018 · 2018
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Extracting relational facts by an end-to-end neural model with copy mechanism
Xiangrong Zeng, Daojian Zeng, Shizhu He, Kang Liu, and Jun Zhao. 2018 · 2018
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Publicly available clinical BERT embeddings
Emily Alsentzer, John Murphy, William Boag, Wei-Hung Weng, Di Jindi, Tristan Naumann, and Matthew McDermott. 2019 · 2019
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BERT: Pre-training of deep bidirectional transformers for language understanding
Jacob Devlin, Ming-Wei Chang, Kenton Lee, and Kristina Toutanova. 2019 · 2019
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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. 2019 · 2019
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Towards drug safety surveillance and pharmacovigilance: current progress in detecting medication and adverse drug events from electronic health records
Feifan Liu, Abhyuday Jagannatha, and Hong Yu. 2019 · 2019
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Transfer learning in biomedical natural language processing: An evaluation of bert and elmo on ten benchmarking datasets
Yifan Peng, Shankai Yan, and Zhiyong Lu. 2019 · 2019
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Language models are unsupervised multitask learners
Alec Radford, Jeffrey Wu, Rewon Child, David Luan, Dario Amodei, Ilya Sutskever, et al. 2019 · 2019
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ELECTRA: pre-training text encoders as discriminators rather than generators
Kevin Clark, Minh-Thang Luong, Quoc V. Le, and Christopher D. Manning. 2020 · 2020
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Domain-specific language model pretraining for biomedical natural language processing
Yu Gu, Robert Tinn, Hao Cheng, Michael Lucas, Naoto Usuyama, Xiaodong Liu, Tristan Naumann, Jianfeng Gao, and Hoifung Poon. 2020 · 2020
Cited alongside, same era.
Don’t stop pretraining: Adapt language models to domains and tasks
Suchin Gururangan, Ana Marasović, Swabha Swayamdipta, Kyle Lo, Iz Beltagy, Doug Downey, and Noah A. Smith. 2020 · 2020
Cited alongside, same era.
Pretrained language models for biomedical and clinical tasks: Understanding and extending the state-of-the-art
Patrick Lewis, Myle Ott, Jingfei Du, and Veselin Stoyanov. 2020 · 2020
Cited alongside, same era.
Ro{bert}a: A robustly optimized {bert} pretraining approach
Yinhan Liu, Myle Ott, Naman Goyal, Jingfei Du, Mandar Joshi, Danqi Chen, Omer Levy, Mike Lewis, Luke Zettlemoyer, and Veselin Stoyanov. 2020 · 2020
Cited alongside, same era.
S2ORC: The semantic scholar open research corpus
Kyle Lo, Lucy Lu Wang, Mark Neumann, Rodney Kinney, and Daniel Weld. 2020 · 2020
Cited alongside, same era.
Finetuned language models are zero-shot learners
Jason Wei, Maarten Bosma, Vincent Y Zhao, Kelvin Guu, Adams Wei Yu, Brian Lester, Nan Du, Andrew M Dai, and Quoc V Le. 2021 · 2021
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Drug repurposing for covid-19 via knowledge graph completion
Rui Zhang, Dimitar Hristovski, Dalton Schutte, Andrej Kastrin, Marcelo Fiszman, and Halil Kilicoglu. 2021 · 2021
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A frustratingly easy approach for entity and relation extraction
Zexuan Zhong and Danqi Chen. 2021 · 2021
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Scaling instruction-finetuned language models
Hyung Won Chung, Le Hou, Shayne Longpre, Barret Zoph, Yi Tay, William Fedus, Eric Li, Xuezhi Wang, Mostafa Dehghani, Siddhartha Brahma, et al. 2022 · 2022
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Bigbio: A framework for data-centric biomedical natural language processing
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Effective modeling of encoder-decoder architecture for joint entity and relation extraction
Tapas Nayak and Hwee Tou Ng. 2020 · 2020
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.
BioMegatron: Larger biomedical domain language model
Hoo-Chang Shin, Yang Zhang, Evelina Bakhturina, Raul Puri, Mostofa Patwary, Mohammad Shoeybi, and Raghav Mani. 2020 · 2020
Cited alongside, same era.
Megatron-lm: Training multi-billion parameter language models using model parallelism
Mohammad Shoeybi, Mostofa Patwary, Raul Puri, Patrick LeGresley, Jared Casper, and Bryan Catanzaro. 2020 · 2020
Cited alongside, same era.
Learning to summarize with human feedback
Nisan Stiennon, Long Ouyang, Jeffrey Wu, Daniel Ziegler, Ryan Lowe, Chelsea Voss, Alec Radford, Dario Amodei, and Paul F Christiano. 2020 · 2020
Cited alongside, same era.
Copymtl: Copy mechanism for joint extraction of entities and relations with multi-task learning
Daojian Zeng, Ranran Haoran Zhang, and Qianying Liu. 2020 · 2020
Cited alongside, same era.
GPT-Neo: Large scale autoregressive language modeling with mesh-tensorflow
Sid Black, Leo Gao, Phil Wang, Connor Leahy, and Stella Biderman. 2021 · 2021
Cited alongside, same era.
Jason Alan Fries, Leon Weber, Natasha Seelam, Gabriel Altay, Debajyoti Datta, Samuele Garda, Myungsun Kang, Ruisi Su, Wojciech Kusa, Samuel Cahyawijaya, et al. 2022 · 2022
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A sequence-to-sequence approach for document-level relation extraction
John Giorgi, Gary Bader, and Bo Wang. 2022 · 2022
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Discovering drug–target interaction knowledge from biomedical literature
Yutai Hou, Yingce Xia, Lijun Wu, Shufang Xie, Yang Fan, Jinhua Zhu, Tao Qin, and Tie-Yan Liu. 2022 · 2022
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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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Training language models to follow instructions with human feedback
Long Ouyang, Jeff 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 Christiano, Jan Leike, and Ryan Lowe. 2022 · 2022
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In-BoXBART: Get instructions into biomedical multi-task learning
Mihir Parmar, Swaroop Mishra, Mirali Purohit, Man Luo, Murad Mohammad, and Chitta Baral. 2022 · 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, Teven Le Scao, Arun Raja, Manan Dey, M Saiful Bari, Canwen Xu, Urmish Thakker, Shanya Sharma Sharma, Eliza Szczechla, Taewoon Kim, Gunjan Chhablani, Nihal 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 Fevry, Jason Alan Fries, Ryan Teehan, Tali Bers, Stella Biderman, Leo Gao, Thomas Wolf, and Alexander M. Rush. 2022 · 2022
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A dataset for n-ary relation extraction of drug combinations
Aryeh Tiktinsky, Vijay Viswanathan, Danna Niezni, Dana Meron Azagury, Yosi Shamay, Hillel Taub-Tabib, Tom Hope, and Yoav Goldberg. 2022 · 2022
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Automatic multi-label prompting: Simple and interpretable few-shot classification
Han Wang, Canwen Xu, and Julian McAuley. 2022 · 2022
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Finetuned language models are zero-shot learners
Jason Wei, Maarten Bosma, Vincent Zhao, Kelvin Guu, Adams Wei Yu, Brian Lester, Nan Du, Andrew M. Dai, and Quoc V Le. 2022 · 2022
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BioBART: Pretraining and evaluation of a biomedical generative language model
Hongyi Yuan, Zheng Yuan, Ruyi Gan, Jiaxing Zhang, Yutao Xie, and Sheng Yu. 2022 · 2022
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BioMedLM
Elliot Bolton, David Hall, Michihiro Yasunaga, Tony Lee, Chris Manning, and Percy Liang. 2022 · 2023
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End-to-end n n -ary relation extraction for combination drug therapies
Yuhang Jiang and Ramakanth Kavuluru. 2023 · 2023
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Llama 2: Open foundation and fine-tuned chat models
Hugo Touvron, Louis Martin, Kevin Stone, Peter Albert, Amjad Almahairi, Yasmine Babaei, Nikolay Bashlykov, Soumya Batra, Prajjwal Bhargava, Shruti Bhosale, Dan Bikel, Lukas Blecher, Cristian Canton Ferrer, Moya Chen, Guillem Cucurull, David Esiobu, Jude Fernandes, Jeremy Fu, Wenyin Fu, Brian Fuller, Cynthia Gao, Vedanuj Goswami, Naman Goyal, Anthony Hartshorn, Saghar Hosseini, Rui Hou, Hakan Inan, Marcin Kardas, Viktor Kerkez, Madian Khabsa, Isabel Kloumann, Artem Korenev, Punit Singh Koura, Marie-Anne Lachaux, Thibaut Lavril, Jenya Lee, Diana Liskovich, Yinghai Lu, Yuning Mao, Xavier Martinet, Todor Mihaylov, Pushkar Mishra, Igor Molybog, Yixin Nie, Andrew Poulton, Jeremy Reizenstein, Rashi Rungta, Kalyan Saladi, Alan Schelten, Ruan Silva, Eric Michael Smith, Ranjan Subramanian, Xiaoqing Ellen Tan, Binh Tang, Ross Taylor, Adina Williams, Jian Xiang Kuan, Puxin Xu, Zheng Yan, Iliyan Zarov, Yuchen Zhang, Angela Fan, Melanie Kambadur, Sharan Narang, Aurelien Rodriguez, Robert Stojnic, Sergey Edunov, and Thomas Scialom. 2023 · 2023
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Revisiting relation extraction in the era of large language models
Somin Wadhwa, Silvio Amir, and Byron C. Wallace. 2023 · 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 · 2023
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