Biomedical Entity Representations with Synonym Marginalization

1 May 2020

Papers citing "Biomedical Entity Representations with Synonym Marginalization"

44 / 44 papers shown

Title
TrialMatchAI: An End-to-End AI-powered Clinical Trial Recommendation System to Streamline Patient-to-Trial Matching Majd Abdallah Sigve Nakken Mariska Bierkens Johanna Galvis Alexis Groppi ... Rodrigo Dienstmann Remond Fijneman Eivind Hovig Gerrit Meijer Macha Nikolski 28 0 0 13 May 2025
CDE-Mapper: Using Retrieval-Augmented Language Models for Linking Clinical Data Elements to Controlled Vocabularies Komal Gilani Marlo Verket Christof Peters Michel Dumontier Hans-Peter Brunner-La Rocca V. Urovi 42 0 0 07 May 2025
RuCCoD: Towards Automated ICD Coding in Russian A. Nesterov Andrey Sakhovskiy Ivan Sviridov Airat Valiev Vladimir Makharev Petr Anokhin Galina Zubkova E. Tutubalina 48 0 0 28 Feb 2025
KU AIGEN ICL EDI@BC8 Track 3: Advancing Phenotype Named Entity Recognition and Normalization for Dysmorphology Physical Examination Reports Hajung Kim Chanhwi Kim Jiwoong Sohn Tim Beck Marek Rei ... T Ian Simpson Joram M Posma Antoine Lain Mujeen Sung Jaewoo Kang MedIm 33 0 0 17 Jan 2025
Learning from Negative Samples in Generative Biomedical Entity Linking Chanhwi Kim Hyunjae Kim Sihyeon Park Jiwoo Lee Mujeen Sung Jaewoo Kang MedIm 29 0 0 29 Aug 2024
Hybrid X-Linker: Automated Data Generation and Extreme Multi-label Ranking for Biomedical Entity Linking Pedro Ruas Fernando Gallego Francisco-Javier Veredas Francisco M. Couto MedIm 23 0 0 08 Jul 2024
Boosting Biomedical Concept Extraction by Rule-Based Data Augmentation Qiwei Shao Fengran Mo Jian-Yun Nie MedIm 54 0 0 03 Jul 2024
HunFlair2 in a cross-corpus evaluation of biomedical named entity recognition and normalization tools Mario Sanger Samuele Garda Xing David Wang Leon Weber-Genzel Pia Droop Benedikt Fuchs Alan Akbik Ulf Leser 43 6 0 19 Feb 2024
Taec: a Manually annotated text dataset for trait and phenotype extraction and entity linking in wheat breeding literature Claire Nédellec Clara Sauvion Robert Bossy Mariya Borovikova Louise Deléger 18 1 0 15 Jan 2024
BELHD: Improving Biomedical Entity Linking with Homonoym Disambiguation Samuele Garda Ulf Leser 30 2 0 10 Jan 2024
Improving Biomedical Entity Linking with Retrieval-enhanced Learning Zhenxi Lin Ziheng Zhang Xian Wu Yefeng Zheng 31 2 0 15 Dec 2023
BioLORD-2023: Semantic Textual Representations Fusing LLM and Clinical Knowledge Graph Insights François Remy Kris Demuynck Thomas Demeester 37 3 0 27 Nov 2023
xMEN: A Modular Toolkit for Cross-Lingual Medical Entity Normalization Florian Borchert Ignacio Llorca Roland Roller Bert Arnrich M. Schapranow 33 6 0 17 Oct 2023
BELB: a Biomedical Entity Linking Benchmark Samuele Garda Leon Weber-Genzel Robert Martin Ulf Leser 11 6 0 22 Aug 2023
Boosting Adverse Drug Event Normalization on Social Media: General-Purpose Model Initialization and Biomedical Semantic Text Similarity Benefit Zero-Shot Linking in Informal Contexts François Remy Simone Scaboro Beatrice Portelli MedIm 27 1 0 31 Jul 2023
CoSiNES: Contrastive Siamese Network for Entity Standardization Jiaqing Yuan Michele Merler M. Choudhury Raju Pavuluri Munindar P. Singh M. Vukovic 24 0 0 05 Jun 2023
Simple Data Augmentation Techniques for Chinese Disease Normalization Wenqian Cui Xiangling Fu Shao-Chen Liu Mingjun Gu Xien Liu Ji Wu Irwin King 40 0 0 02 Jun 2023
Generalizing over Long Tail Concepts for Medical Term Normalization Beatrice Portelli Simone Scaboro Enrico Santus Hooman Sedghamiz Emmanuele Chersoni Giuseppe Serra MedIm 21 8 0 21 Oct 2022
BioLORD: Learning Ontological Representations from Definitions (for Biomedical Concepts and their Textual Descriptions) François Remy Kris Demuynck Thomas Demeester 27 14 0 21 Oct 2022
Knowledge Injected Prompt Based Fine-tuning for Multi-label Few-shot ICD Coding Zhichao Yang Shufan Wang Bhanu Pratap Singh Rawat Avijit Mitra Hong-ye Yu 121 49 0 07 Oct 2022
Generative Biomedical Entity Linking via Knowledge Base-Guided Pre-training and Synonyms-Aware Fine-tuning Hongyi Yuan Zheng Yuan Sheng Yu MedIm 22 43 0 11 Apr 2022
BioBART: Pretraining and Evaluation of A Biomedical Generative Language Model Hongyi Yuan Zheng Yuan Ruyi Gan Jiaxing Zhang Yutao Xie Sheng Yu LM&MA 33 123 0 08 Apr 2022
Code Synonyms Do Matter: Multiple Synonyms Matching Network for Automatic ICD Coding Zheng Yuan Chuanqi Tan Songfang Huang OffRL 18 71 0 03 Mar 2022
BERN2: an advanced neural biomedical named entity recognition and normalization tool Mujeen Sung Minbyul Jeong Yonghwa Choi Donghyeon Kim Jinhyuk Lee Jaewoo Kang MedIm 14 99 0 06 Jan 2022
Knowledge-Rich Self-Supervision for Biomedical Entity Linking Sheng Zhang Hao Cheng Shikhar Vashishth Cliff Wong Jinfeng Xiao Xiaodong Liu Tristan Naumann Jianfeng Gao Hoifung Poon 25 41 0 15 Dec 2021
Improving Tagging Consistency and Entity Coverage for Chemical Identification in Full-text Articles Hyunjae Kim Mujeen Sung Wonjin Yoon Sungjoon Park Jaewoo Kang 32 10 0 20 Nov 2021
GraphPrompt: Graph-Based Prompt Templates for Biomedical Synonym Prediction Hanwen Xu Jiayou Zhang Zhirui Wang Shizhuo Zhang M. Bhalerao Yucong Liu Dawei Zhu Sheng Wang 24 5 0 13 Nov 2021
Coreference Resolution for the Biomedical Domain: A Survey Pengcheng Lu Massimo Poesio 34 15 0 25 Sep 2021
Can Language Models be Biomedical Knowledge Bases? Mujeen Sung Jinhyuk Lee Sean S. Yi Minji Jeon Sungdong Kim Jaewoo Kang AI4MH 128 105 0 15 Sep 2021
BERT might be Overkill: A Tiny but Effective Biomedical Entity Linker based on Residual Convolutional Neural Networks T. Lai Heng Ji ChengXiang Zhai 30 31 0 06 Sep 2021
Entity Linking and Discovery via Arborescence-based Supervised Clustering Dhruv Agarwal Rico Angell Nicholas Monath Andrew McCallum 34 33 0 02 Sep 2021
Biomedical Interpretable Entity Representations Diego Garcia-Olano Yasumasa Onoe Ioana Baldini Joydeep Ghosh Byron C. Wallace Kush R. Varshney AI4CE 11 3 0 17 Jun 2021
Biomedical Entity Linking with Contrastive Context Matching Shogo Ujiie Hayate Iso Eiji Aramaki 8 6 0 14 Jun 2021
Named Entity Normalization Model Using Edge Weight Updating Neural Network: Assimilation Between Knowledge-Driven Graph and Data-Driven Graph Sung Hwan Jeon Sungzoon Cho MedIm 6 3 0 14 Jun 2021
Learning Domain-Specialised Representations for Cross-Lingual Biomedical Entity Linking Fangyu Liu Ivan Vulić Anna Korhonen Nigel Collier 28 49 0 30 May 2021
End-to-end Biomedical Entity Linking with Span-based Dictionary Matching Shogo Ujiie Hayate Iso Shuntaro Yada Shoko Wakamiya Eiji Aramaki MedIm 14 10 0 21 Apr 2021
Sequence tagging for biomedical extractive question answering Wonjin Yoon Richard Jackson Aron Lagerberg Jaewoo Kang MedIm 18 26 0 15 Apr 2021
KGSynNet: A Novel Entity Synonyms Discovery Framework with Knowledge Graph Yiying Yang Xi Yin Haiqing Yang Xingjian Fei Hao Peng Kaijie Zhou Kunfeng Lai Jianping Shen 19 14 0 16 Mar 2021
Drug and Disease Interpretation Learning with Biomedical Entity Representation Transformer Z. Miftahutdinov Artur Kadurin R. Kudrin E. Tutubalina MedIm 41 8 0 22 Jan 2021
How Do Your Biomedical Named Entity Recognition Models Generalize to Novel Entities? Hyunjae Kim Jaewoo Kang AI4CE 91 21 0 01 Jan 2021
CODER: Knowledge infused cross-lingual medical term embedding for term normalization Zheng Yuan Zhengyun Zhao Haixia Sun Jiao Li Fei Wang Sheng Yu MedIm 26 95 0 05 Nov 2020
Answering Questions on COVID-19 in Real-Time Jinhyuk Lee Sean S. Yi Minbyul Jeong Mujeen Sung Wonjin Yoon Yonghwa Choi Miyoung Ko Jaewoo Kang 21 43 0 29 Jun 2020
Neural Entity Linking: A Survey of Models Based on Deep Learning Ozge Sevgili Artem Shelmanov Mikhail V. Arkhipov Alexander Panchenko Christian Biemann VLM 3DV AI4TS 23 118 0 31 May 2020
Google's Neural Machine Translation System: Bridging the Gap between Human and Machine Translation Yonghui Wu M. Schuster Zhehuai Chen Quoc V. Le Mohammad Norouzi ... Alex Rudnick Oriol Vinyals G. Corrado Macduff Hughes J. Dean AIMat 718 6,748 0 26 Sep 2016