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The biomedical field relies heavily on concept linking in various areas such as literature mining, graph alignment, information retrieval, question-answering, data, and knowledge integration.
Medical subject headings (mesh)
Carolyn E Lipscomb · 2000
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Pubmed central: The genbank of the published literature, 2001
Richard J Roberts · 2001
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Snomed clinical terms: overview of the development process and project status
Michael Q Stearns, Colin Price, Kent A Spackman, and Amy Y Wang · 2001
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The unified medical language system (umls): integrating biomedical terminology
Olivier Bodenreider · 2004
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Omim (online mendelian inheritance in man)
Victor McKusick · 2011
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Logmap: Logic-based and scalable ontology matching
Ernesto Jiménez-Ruiz and Bernardo Cuenca Grau · 2011
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Ordo: an ontology connecting rare disease, epidemiology and genetic data
Drashtti Vasant, Laetitia Chanas, James Malone, Marc Hanauer, Annie Olry, Simon Jupp, Peter N Robinson, Helen Parkinson, and Ana Rath · 2014
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Review of ontology matching approaches and challenges
Sarawat Anam, Yang Sok Kim, Byeong Ho Kang, and Qing Liu · 2015
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Quickumls: a fast, unsupervised approach for medical concept extraction
Luca Soldaini and Nazli Goharian · 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
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Systematic integration of biomedical knowledge prioritizes drugs for repurposing
Daniel Scott Himmelstein, Antoine Lizee, Christine Hessler, Leo Brueggeman, Sabrina L Chen, Dexter Hadley, Ari Green, Pouya Khankhanian, and Sergio E Baranzini · 2017
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Metamap lite: an evaluation of a new java implementation of metamap
Dina Demner-Fushman, Willie J Rogers, and Alan R Aronson · 2017
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Attention is all you need
Ashish Vaswani, Noam Shazeer, Niki Parmar, Jakob Uszkoreit, Llion Jones, Aidan N Gomez, Łukasz Kaiser, and Illia Polosukhin · 2017
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Bert: Pre-training of deep bidirectional transformers for language understanding
Jacob Devlin, Ming-Wei Chang, Kenton Lee, and Kristina Toutanova · 2018
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A survey on literature based discovery approaches in biomedical domain
Vishrawas Gopalakrishnan, Kishlay Jha, Wei Jin, and Aidong Zhang · 2019
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Fine-tuning bidirectional encoder representations from transformers (bert)–based models on large-scale electronic health record notes: an empirical study
Fei Li, Yonghao Jin, Weisong Liu, Bhanu Pratap Singh Rawat, Pengshan Cai, Hong Yu, et al · 2019
Cited alongside, same era.
Ontology mapping for semantically enabled applications
Ian Harrow, Rama Balakrishnan, Ernesto Jimenez-Ruiz, Simon Jupp, Jane Lomax, Jane Reed, Martin Romacker, Christian Senger, Andrea Splendiani, Jabe Wilson, et al · 2019
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Scispacy: fast and robust models for biomedical natural language processing
Mark Neumann, Daniel King, Iz Beltagy, and Waleed Ammar · 2019
Cited alongside, same era.
Biomedical named entity recognition and linking datasets: survey and our recent development
Ming-Siang Huang, Po-Ting Lai, Pei-Yen Lin, Yu-Ting You, Richard Tzong-Han Tsai, and Wen-Lian Hsu · 2020
Cited alongside, same era.
Bert-based ranking for biomedical entity normalization
Zongcheng Ji, Qiang Wei, and Hua Xu · 2020
Graph representation learning in bioinformatics: trends, methods and applications
Hai-Cheng Yi, Zhu-Hong You, De-Shuang Huang, and Chee Keong Kwoh · 2022
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Machine learning-friendly biomedical datasets for equivalence and subsumption ontology matching
Yuan He, Jiaoyan Chen, Hang Dong, Ernesto Jiménez-Ruiz, Ali Hadian, and Ian Horrocks · 2022
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Chain of thought prompting elicits reasoning in large language models
Jason Wei, Xuezhi Wang, Dale Schuurmans, Maarten Bosma, Ed Chi, Quoc Le, and Denny Zhou · 2022
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Self-consistency improves chain of thought reasoning in language models
Xuezhi Wang, Jason Wei, Dale Schuurmans, Quoc Le, Ed Chi, Sharan Narang, Aakanksha Chowdhery, and Denny Zhou · 2022
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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
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Cited alongside, same era.
Self-alignment pretraining for biomedical entity representations
Fangyu Liu, Ehsan Shareghi, Zaiqiao Meng, Marco Basaldella, and Nigel Collier · 2020
Cited alongside, same era.
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 · 2020
Cited alongside, same era.
Contrastive representation learning: A framework and review
Phuc H Le-Khac, Graham Healy, and Alan F Smeaton · 2020
Cited alongside, same era.
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, et al · 2020
Cited alongside, same era.
A comprehensive survey of entity alignment for knowledge graphs
Kaisheng Zeng, Chengjiang Li, Lei Hou, Juanzi Li, and Ling Feng · 2021
Cited alongside, same era.
Deep learning methods for biomedical named entity recognition: a survey and qualitative comparison
Bosheng Song, Fen Li, Yuansheng Liu, and Xiangxiang Zeng · 2021
Cited alongside, same era.
Lsmatch results for oaei 2021
Abhisek Sharma, Archana Patel, and Sarika Jain · 2021
Cited alongside, same era.
Later among the works it cites.
A comprehensive survey on pretrained foundation models: A history from bert to chatgpt
Ce Zhou, Qian Li, Chen Li, Jun Yu, Yixin Liu, Guangjing Wang, Kai Zhang, Cheng Ji, Qiben Yan, Lifang He, et al · 2023
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Chatgpt and the rise of large language models: the new ai-driven infodemic threat in public health
Luigi De Angelis, Francesco Baglivo, Guglielmo Arzilli, Gaetano Pierpaolo Privitera, Paolo Ferragina, Alberto Eugenio Tozzi, and Caterina Rizzo · 2023
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Accelerating the integration of chatgpt and other large-scale ai models into biomedical research and healthcare
Ding-Qiao Wang, Long-Yu Feng, Jin-Guo Ye, Jin-Gen Zou, and Ying-Feng Zheng · 2023
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A survey on in-context learning
Qingxiu Dong, Lei Li, Damai Dai, Ce Zheng, Zhiyong Wu, Baobao Chang, Xu Sun, Jingjing Xu, Lei Li, and Zhifang Sui · 2023
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Sparks of artificial general intelligence: Early experiments with gpt-4
Sébastien Bubeck, Varun Chandrasekaran, Ronen Eldan, Johannes Gehrke, Eric Horvitz, Ece Kamar, Peter Lee, Yin Tat Lee, Yuanzhi Li, Scott Lundberg, et al · 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, et al · 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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Generative agents: Interactive simulacra of human behavior
Joon Sung Park, Joseph C O’Brien, Carrie J Cai, Meredith Ringel Morris, Percy Liang, and Michael S Bernstein · 2023
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Qlora: Efficient finetuning of quantized llms
Tim Dettmers, Artidoro Pagnoni, Ari Holtzman, and Luke Zettlemoyer · 2023
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