Can Language Models be Biomedical Knowledge Bases?

The unified medical language system (umls): integrating biomedical terminology

Olivier Bodenreider. 2004 · 2004

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Best: next-generation biomedical entity search tool for knowledge discovery from biomedical literature

Sunwon Lee, Donghyeon Kim, Kyubum Lee, Jaehoon Choi, Seongsoon Kim, Minji Jeon, Sangrak Lim, Donghee Choi, Sunkyu Kim, Aik-Choon Tan, et al. 2016 · 2016

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Deep contextualized word representations

Matthew E. Peters, Mark Neumann, Mohit Iyyer, Matt Gardner, Christopher Clark, Kenton Lee, and Luke Zettlemoyer. 2018 · 2018

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SciBERT: A pretrained language model for scientific text

Iz Beltagy, Kyle Lo, and Arman Cohan. 2019 · 2019

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BERT: Pre-training of deep bidirectional transformers for language understanding

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Language models as knowledge bases?

Fabio Petroni, Tim Rocktäschel, Sebastian Riedel, Patrick Lewis, Anton Bakhtin, Yuxiang Wu, and Alexander Miller. 2019 · 2019

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Wikidata: A large-scale collaborative ontological medical database

Houcemeddine Turki, Thomas Shafee, Mohamed Ali Hadj Taieb, Mohamed Ben Aouicha, Denny Vrandečić, Diptanshu Das, and Helmi Hamdi. 2019 · 2019

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X-FACTR: Multilingual factual knowledge retrieval from pretrained language models

Zhengbao Jiang, Antonios Anastasopoulos, Jun Araki, Haibo Ding, and Graham Neubig. 2020a · 2020

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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. 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

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E-BERT: Efficient-yet-effective entity embeddings for BERT

Nina Poerner, Ulli Waltinger, and Hinrich Schütze. 2020 · 2020

Cited alongside, same era.

Biomedical entity representations with synonym marginalization

Mujeen Sung, Hwisang Jeon, Jinhyuk Lee, and Jaewoo Kang. 2020 · 2020

Later among the works it cites.

Science forum: Wikidata as a knowledge graph for the life sciences

Andra Waagmeester, Gregory Stupp, Sebastian Burgstaller-Muehlbacher, Benjamin M Good, Malachi Griffith, Obi L Griffith, Kristina Hanspers, Henning Hermjakob, Toby S Hudson, Kevin Hybiske, et al. 2020 · 2020

Later among the works it cites.

Knowledgeable or educated guess? revisiting language models as knowledge bases

Boxi Cao, Hongyu Lin, Xianpei Han, Le Sun, Lingyong Yan, Meng Liao, Tong Xue, and Jin Xu. 2021 · 2021

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Comparative Toxicogenomics Database (CTD): update 2021

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Factual probing is [MASK]: Learning vs. learning to recall

Zexuan Zhong, Dan Friedman, and Danqi Chen. 2021 · 2021

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