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2005.00239
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Biomedical Entity Representations with Synonym Marginalization
Annual Meeting of the Association for Computational Linguistics (ACL), 2020
1 May 2020
Mujeen Sung
Hwisang Jeon
Jinhyuk Lee
Jaewoo Kang
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Papers citing
"Biomedical Entity Representations with Synonym Marginalization"
50 / 52 papers shown
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Hierarchical Indexing with Knowledge Enrichment for Multilingual Video Corpus Retrieval
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BALI: Enhancing Biomedical Language Representations through Knowledge Graph and Language Model Alignment
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Overview of BioASQ 2025: The Thirteenth BioASQ Challenge on Large-Scale Biomedical Semantic Indexing and Question Answering
Conference and Labs of the Evaluation Forum (CLEF), 2025
A. Nentidis
Georgios Katsimpras
Anastasia Krithara
Martin Krallinger
Miguel Rodríguez-Ortega
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Nicola Ferro
S. Marchesin
Marco Martinelli
Gianmaria Silvello
Georgios Paliouras
223
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AutoPCR: Automated Phenotype Concept Recognition by Prompting
Yicheng Tao
Yuanhao Huang
Jie Liu
Xin Luo
Jie Liu
199
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25 Jul 2025
Search-Optimized Quantization in Biomedical Ontology Alignment
Frontiers in Artificial Intelligence (Front. Artif. Intell.), 2025
Oussama Bouaggad
Natalia Grabar
MQ
235
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18 Jul 2025
Intercept Cancer: Cancer Pre-Screening with Large Scale Healthcare Foundation Models
Liwen Sun
Hao-Ren Yao
Gary Gao
O. Frieder
Chenyan Xiong
230
1
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30 May 2025
Distilling Closed-Source LLM's Knowledge for Locally Stable and Economic Biomedical Entity Linking
International Conference on Intelligent Computing (ICIC), 2025
Yihao Ai
Zhiyuan Ning
Weiwei Dai
P. Wang
Yi Du
Wenjuan Cui
Kunpeng Liu
Yuanchun Zhou
208
1
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26 May 2025
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
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Rodrigo Dienstmann
Remond Fijneman
Eivind Hovig
Gerrit Meijer
Macha Nikolski
267
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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
349
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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
455
2
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
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T Ian Simpson
Joram M Posma
Antoine Lain
Mujeen Sung
Jaewoo Kang
MedIm
223
2
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17 Jan 2025
Learning from Negative Samples in Biomedical Generative Entity Linking
Annual Meeting of the Association for Computational Linguistics (ACL), 2024
Chanhwi Kim
Hyunjae Kim
Sihyeon Park
Jiwoo Lee
Mujeen Sung
Jaewoo Kang
MedIm
486
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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
217
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08 Jul 2024
Boosting Biomedical Concept Extraction by Rule-Based Data Augmentation
Qiwei Shao
Fengran Mo
Jian-Yun Nie
MedIm
287
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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
385
21
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19 Feb 2024
Taec: a Manually annotated text dataset for trait and phenotype extraction and entity linking in wheat breeding literature
PLoS ONE (PLoS ONE), 2024
Claire Nédellec
Clara Sauvion
Robert Bossy
Mariya Borovikova
Louise Deléger
262
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15 Jan 2024
BELHD: Improving Biomedical Entity Linking with Homonoym Disambiguation
Bioinformatics (Bioinformatics), 2024
Samuele Garda
Ulf Leser
373
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10 Jan 2024
Improving Biomedical Entity Linking with Retrieval-enhanced Learning
IEEE International Conference on Acoustics, Speech, and Signal Processing (ICASSP), 2023
Zhenxi Lin
Ziheng Zhang
Xian Wu
Yefeng Zheng
256
4
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15 Dec 2023
BioLORD-2023: Semantic Textual Representations Fusing LLM and Clinical Knowledge Graph Insights
François Remy
Kris Demuynck
Thomas Demeester
318
11
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27 Nov 2023
xMEN: A Modular Toolkit for Cross-Lingual Medical Entity Normalization
JAMIA Open (JAMIA Open), 2023
Florian Borchert
Ignacio Llorca
Roland Roller
Bert Arnrich
M. Schapranow
185
9
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17 Oct 2023
BELB: a Biomedical Entity Linking Benchmark
Samuele Garda
Leon Weber-Genzel
Robert Martin
Ulf Leser
247
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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
International Workshop on Natural Language Processing for Social Media (SocialNLP), 2023
François Remy
Simone Scaboro
Beatrice Portelli
MedIm
190
5
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31 Jul 2023
CoSiNES: Contrastive Siamese Network for Entity Standardization
Jiaqing Yuan
Michele Merler
M. Choudhury
Raju Pavuluri
Munindar P. Singh
M. Vukovic
215
1
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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
449
1
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02 Jun 2023
Generalizing over Long Tail Concepts for Medical Term Normalization
Conference on Empirical Methods in Natural Language Processing (EMNLP), 2022
Beatrice Portelli
Simone Scaboro
Enrico Santus
Hooman Sedghamiz
Emmanuele Chersoni
Giuseppe Serra
MedIm
258
10
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21 Oct 2022
BioLORD: Learning Ontological Representations from Definitions (for Biomedical Concepts and their Textual Descriptions)
Conference on Empirical Methods in Natural Language Processing (EMNLP), 2022
François Remy
Kris Demuynck
Thomas Demeester
215
20
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21 Oct 2022
Knowledge Injected Prompt Based Fine-tuning for Multi-label Few-shot ICD Coding
Conference on Empirical Methods in Natural Language Processing (EMNLP), 2022
Zhichao Yang
Shufan Wang
Bhanu Pratap Singh Rawat
Avijit Mitra
Hong-ye Yu
358
80
0
07 Oct 2022
Generative Biomedical Entity Linking via Knowledge Base-Guided Pre-training and Synonyms-Aware Fine-tuning
North American Chapter of the Association for Computational Linguistics (NAACL), 2022
Hongyi Yuan
Zheng Yuan
Sheng Yu
MedIm
331
60
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11 Apr 2022
BioBART: Pretraining and Evaluation of A Biomedical Generative Language Model
Workshop on Biomedical Natural Language Processing (BioNLP), 2022
Hongyi Yuan
Zheng Yuan
Ruyi Gan
Jiaxing Zhang
Yutao Xie
Sheng Yu
LM&MA
387
169
0
08 Apr 2022
Code Synonyms Do Matter: Multiple Synonyms Matching Network for Automatic ICD Coding
Annual Meeting of the Association for Computational Linguistics (ACL), 2022
Zheng Yuan
Chuanqi Tan
Songfang Huang
OffRL
283
101
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
301
133
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
309
54
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
216
10
0
20 Nov 2021
GraphPrompt: Graph-Based Prompt Templates for Biomedical Synonym Prediction
AAAI Conference on Artificial Intelligence (AAAI), 2021
Hanwen Xu
Jiayou Zhang
Zhirui Wang
Shizhuo Zhang
M. Bhalerao
Yucong Liu
Dawei Zhu
Sheng Wang
347
6
0
13 Nov 2021
Coreference Resolution for the Biomedical Domain: A Survey
Pengcheng Lu
Massimo Poesio
271
17
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25 Sep 2021
Can Language Models be Biomedical Knowledge Bases?
Mujeen Sung
Jinhyuk Lee
Sean S. Yi
Minji Jeon
Sungdong Kim
Jaewoo Kang
AI4MH
457
120
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
214
33
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06 Sep 2021
Entity Linking and Discovery via Arborescence-based Supervised Clustering
Dhruv Agarwal
Rico Angell
Nicholas Monath
Andrew McCallum
343
38
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02 Sep 2021
Biomedical Interpretable Entity Representations
Findings (Findings), 2021
Diego Garcia-Olano
Yasumasa Onoe
Ioana Baldini
Joydeep Ghosh
Byron C. Wallace
Kush R. Varshney
AI4CE
295
4
0
17 Jun 2021
Biomedical Entity Linking with Contrastive Context Matching
Shogo Ujiie
Hayate Iso
Eiji Aramaki
290
6
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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
183
4
0
14 Jun 2021
Learning Domain-Specialised Representations for Cross-Lingual Biomedical Entity Linking
Annual Meeting of the Association for Computational Linguistics (ACL), 2021
Fangyu Liu
Ivan Vulić
Anna Korhonen
Nigel Collier
276
68
0
30 May 2021
End-to-end Biomedical Entity Linking with Span-based Dictionary Matching
Workshop on Biomedical Natural Language Processing (BioNLP), 2021
Shogo Ujiie
Hayate Iso
Shuntaro Yada
Shoko Wakamiya
Eiji Aramaki
MedIm
245
10
0
21 Apr 2021
Sequence tagging for biomedical extractive question answering
Wonjin Yoon
Richard Jackson
Aron Lagerberg
Jaewoo Kang
MedIm
287
31
0
15 Apr 2021
KGSynNet: A Novel Entity Synonyms Discovery Framework with Knowledge Graph
International Conference on Database Systems for Advanced Applications (DASFAA), 2021
Yiying Yang
Xi Yin
Haiqing Yang
Xingjian Fei
Hao Peng
Kaijie Zhou
Kunfeng Lai
Jianping Shen
253
18
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16 Mar 2021
Drug and Disease Interpretation Learning with Biomedical Entity Representation Transformer
European Conference on Information Retrieval (ECIR), 2021
Z. Miftahutdinov
Artur Kadurin
R. Kudrin
E. Tutubalina
MedIm
259
9
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22 Jan 2021
How Do Your Biomedical Named Entity Recognition Models Generalize to Novel Entities?
IEEE Access (IEEE Access), 2021
Hyunjae Kim
Jaewoo Kang
AI4CE
527
27
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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
299
123
0
05 Nov 2020
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