LLMs are not Zero-Shot Reasoners for Biomedical Information Extraction

Meddialog: A large-scale medical dialogue dataset

Original

Shu Chen, Zeqian Ju, Xiangyu Dong, Hongchao Fang, Sicheng Wang, Yue Yang, Jiaqi Zeng, Ruisi Zhang, Ruoyu Zhang, Meng Zhou, Penghui Zhu, and Pengtao Xie. 2020 · 2004

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GENETAG: a tagged corpus for gene/protein named entity recognition

Lorraine Tanabe, Natalie Xie, Lynne H Thom, Wayne Matten, and W John Wilbur. 2005 · 2005

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Beyond surface characteristics: a new health text-specific readability measurement

Hyeoneui Kim, Sergey Goryachev, Graciela Rosemblat, Allen Browne, Alla Keselman, and Qing Zeng-Treitler. 2007 · 2007

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Bioinfer: a corpus for information extraction in the biomedical domain

Sampo Pyysalo, Filip Ginter, Juho Heimonen, Jari Bj"orne, Jorma Boberg, Jouni J"arvinen, and Tapio Salakoski. 2007 · 2007

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Overview of BioNLP’09 shared task on event extraction

Jin-Dong Kim, Tomoko Ohta, Sampo Pyysalo, Yoshinobu Kano, and Jun’ichi Tsujii. 2009 · 2009

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Static relations: a piece in the biomedical information extraction puzzle

Sampo Pyysalo, Tomoko Ohta, Jin-Dong Kim, and Jun’ichi Tsujii. 2009 · 2009

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Applying ontology design patterns to the implementation of relations in genia

Robert Hoehndorf, Axel cyrille Ngonga Ngomo, Sampo Pyysalo, Tomoko Ohta, Anika Oellrich, and Dietrich Rebholz-schuhmann. 2010 · 2010

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A reevaluation of biomedical named entity - term relations

Tomoko Ohta, Sampo Pyysalo, Jin-Dong Kim, and Jun’ichi Tsujii. 2010 · 2010

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Overview of the entity relations (rel) supporting task of bionlp shared task 2011

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Open-domain anatomical entity mention detection

Tomoko Ohta, Sampo Pyysalo, Jun’ichi Tsujii, and Sophia Ananiadou. 2012 · 2012

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Event extraction across multiple levels of biological organization

Sampo Pyysalo, Tomoko Ohta, Makoto Miwa, Han-Cheol Cho, Jun’ichi Tsujii, and Sophia Ananiadou. 2012 · 2012

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Clinical corpus annotation: challenges and strategies

Fei Xia and Meliha Yetisgen-Yildiz. 2012 · 2012

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Effects of time constraints on clinician–computer interaction: a study on information synthesis from ehr clinical notes

Oladimeji Farri, Karen A Monsen, Serguei V Pakhomov, David S Pieczkiewicz, Stuart M Speedie, and Genevieve B Melton. 2013 · 2013

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GRO task: Populating the gene regulation ontology with events and relations

Jung-jae Kim, Xu Han, Vivian Lee, and Dietrich Rebholz-Schuhmann. 2013 · 2013

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Overview of the pathway curation (PC) task of BioNLP shared task 2013

Tomoko Ohta, Sampo Pyysalo, Rafal Rak, Andrew Rowley, Hong-Woo Chun, Sung-Jae Jung, Sung-Pil Choi, Sophia Ananiadou, and Jun’ichi Tsujii. 2013 · 2013

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Overview of the cancer genetics (CG) task of BioNLP shared task 2013

Sampo Pyysalo, Tomoko Ohta, and Sophia Ananiadou. 2013 · 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 · 2014

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Attribute-based classification for zero-shot visual object categorization

Christoph H. Lampert, Hannes Nickisch, and Stefan Harmeling. 2014 · 2014

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Extraction of relations between genes and diseases from text and large-scale data analysis: implications for translational research

Àlex Bravo, Janet Piñero, Núria Queralt-Rosinach, Michael Rautschka, and Laura I Furlong. 2015 · 2015

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Chemdner: The drugs and chemical names extraction challenge

Martin Krallinger, Florian Leitner, Obdulia Rabal, Miguel Vazquez, Julen Oyarzabal, and Alfonso Valencia. 2015 · 2015

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Ntcir13 medweb task: multi-label classification of tweets using an ensemble of neural networks

Hayate Iso, Camille Ruiz, Taichi Murayama, Katsuya Taguchi, Ryo Takeuchi, Hideya Yamamoto, Shoko Wakamiya, and Eiji Aramaki. 2017 · 2017

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CAS: French corpus with clinical cases

Natalia Grabar, Vincent Claveau, and Cl’ement Dalloux. 2018 · 2018

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A corpus with multi-level annotations of patients, interventions and outcomes to support language processing for medical literature

Benjamin Nye, Junyi Jessy Li, Roma Patel, Yinfei Yang, Iain Marshall, Ani Nenkova, and Byron Wallace. 2018 · 2018

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Assessing the readability of medical documents: a ranking approach

Jiaping Zheng, Hong Yu, et al. 2018 · 2018

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Structural scaffolds for citation intent classification in scientific publications

Arman Cohan, Waleed Ammar, Madeleine van Zuylen, and Field Cady. 2019 · 2019

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Billion-scale similarity search with GPUs

Jeff Johnson, Matthijs Douze, and Hervé Jégou. 2019 · 2019

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Sentence-bert: Sentence embeddings using siamese bert-networks

Nils Reimers and Iryna Gurevych. 2019 · 2019

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A systematic approach for developing a corpus of patient reported adverse drug events: A case study for SSRI and SNRI medications

Maryam Zolnoori, Kin Wah Fung, Timothy B. Patrick, Paul Fontelo, Hadi Kharrazi, Anthony Faiola, Yi Shuan Shirley Wu, Christina E. Eldredge, Jake Luo, Mike Conway, Jiaxi Zhu, Soo Kyung Park, Kelly Xu, Hamideh Moayyed, and Somaieh Goudarzvand. 2019 · 2019

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Retrieval-augmented generation for knowledge-intensive nlp tasks

Patrick Lewis, Ethan Perez, Aleksandra Piktus, Fabio Petroni, Vladimir Karpukhin, Naman Goyal, Heinrich Küttler, Mike Lewis, Wen-tau Yih, Tim Rocktäschel, et al. 2020 · 2020

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Overview of the biocreative vii litcovid track: multi-label topic classification for covid-19 literature annotation

Qingyu Chen, Alexis Allot, Robert Leaman, Rezarta Islamaj Doğan, and Zhiyong Lu. 2021 · 2021

Cited alongside, same era.

Medtag: a portable and customizable annotation tool for biomedical documents

Fabio Giachelle, Ornella Irrera, and Gianmaria Silvello. 2021 · 2021

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Biomedical named entity recognition at scale

Veysel Kocaman and David Talby. 2021 · 2021

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A review of author name disambiguation techniques for the pubmed bibliographic database

Debarshi Kumar Sanyal, Plaban Kumar Bhowmick, and Partha Pratim Das. 2021 · 2021

Cited alongside, same era.

Locate and label: A two-stage identifier for nested named entity recognition

Original

Yongliang Shen, Xinyin Ma, Zeqi Tan, Shuai Zhang, Wen Wang, and Weiming Lu. 2021 · 2021

Cited alongside, same era.

Retrieval-augmented few-shot text classification

Guoxin Yu, Lemao Liu, Haiyun Jiang, Shuming Shi, and Xiang Ao. 2023 · 2023

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Universalner: Targeted distillation from large language models for open named entity recognition

Original

Wenxuan Zhou, Sheng Zhang, Yu Gu, Muhao Chen, and Hoifung Poon. 2023 · 2023

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What drives performance in multilingual language models?

Sina Bagheri Nezhad and Ameeta Agrawal. 2024 · 2024

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Biomedlm: A 2.7 b parameter language model trained on biomedical text

Original

Elliot Bolton, Abhinav Venigalla, Michihiro Yasunaga, David Hall, Betty Xiong, Tony Lee, Roxana Daneshjou, Jonathan Frankle, Percy Liang, Michael Carbin, et al. 2024 · 2024

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How important is domain specificity in language models and instruction finetuning for biomedical relation extraction?

Original