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BioSentVec: creating sentence embeddings for biomedical texts

22 October 2018

Qingyu Chen

Yifan Peng

Zhiyong Lu

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Papers citing "BioSentVec: creating sentence embeddings for biomedical texts"

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Title
AI-Powered Detection of Inappropriate Language in Medical School Curricula Chiman Salavati Shannon Song Scott A. Hale Roberto E. Montenegro Shiri Dori-Hacohen Fabricio Murai ELM 48 0 0 27 Aug 2025
The Next Phase of Scientific Fact-Checking: Advanced Evidence Retrieval from Complex Structured Academic PapersInternational Conference on the Theory of Information Retrieval (ICTIR), 2025 Xingyu Deng Xi Wang Mark Stevenson 244 1 0 25 Jun 2025
PRISM: A Framework for Producing Interpretable Political Bias Embeddings with Political-Aware Cross-EncoderAnnual Meeting of the Association for Computational Linguistics (ACL), 2025 Yiqun Sun Qiang Huang Anthony K. H. Tung Jun Yu 134 0 0 30 May 2025
FinMTEB: Finance Massive Text Embedding Benchmark Yixuan Tang Yi Yang AIFin 332 9 0 16 Feb 2025
BioBridge: Unified Bio-Embedding with Bridging Modality in Code-Switched EMRIEEE Access (IEEE Access), 2024 Jangyeong Jeon Sangyeon Cho Dongjoon Lee Changhee Lee Junyeong Kim 171 0 0 16 Dec 2024
SciGisPy: a Novel Metric for Biomedical Text Simplification via Gist Inference Score Chen Lyu Gabriele Pergola 158 6 0 12 Oct 2024
Do We Need Domain-Specific Embedding Models? An Empirical Investigation Yixuan Tang Yi Yang AIFin 436 11 0 27 Sep 2024
A Survey of Deep Learning-based Radiology Report Generation Using Multimodal Data Xinyi Wang Grazziela Figueredo Ruizhe Li Wei Emma Zhang L. Yao Xin Chen MedIm ViT 327 6 0 21 May 2024
Health Text Simplification: An Annotated Corpus for Digestive Cancer Education and Novel Strategies for Reinforcement LearningJournal of Biomedical Informatics (JBI), 2024 Md Mushfiqur Rahman Mohammad Sabik Irbaz Kai North Michelle S. Williams Marcos Zampieri Kevin Lybarger 214 10 0 26 Jan 2024
An Information Retrieval and Extraction Tool for Covid-19 Related Papers Marcos V. L. Pivetta 150 0 0 20 Jan 2024
Tracing the Genealogies of Ideas with Large Language Model Embeddings Lucian Li AI4CE 53 1 0 13 Jan 2024
WellFactor: Patient Profiling using Integrative Embedding of Healthcare Data Dongjin Choi Andy Xiang Ozgur Ozturk Deep Shrestha Barry L. Drake Hamid Haidarian Faizan Javed Haesun Park 101 2 0 21 Dec 2023
Benchmarking and Analyzing In-context Learning, Fine-tuning and Supervised Learning for Biomedical Knowledge Curation: a focused study on chemical entities of biological interest Emily Groves Minhong Wang Yusuf Abdulle Holger Kunz J. Hoelscher-Obermaier Ronin Wu Honghan Wu 124 2 0 20 Dec 2023
Ascle: A Python Natural Language Processing Toolkit for Medical Text Generation Rui Yang Qingcheng Zeng Keen You Yujie Qiao Lucas Huang ... Dragomir R. Radev Zhiyong Lu Hua Xu Qingyu Chen Irene Li ELM LM&MA 188 3 0 28 Nov 2023
Screening of Pneumonia and Urinary Tract Infection at Triage using TriNet Stephen Z. Lu 58 0 0 05 Sep 2023
Patient Clustering via Integrated Profiling of Clinical and Digital DataInternational Conference on Information and Knowledge Management (CIKM), 2023 Dongjin Choi Andy Xiang Ozgur Ozturk Deep Shrestha Barry L. Drake Hamid Haidarian F. Javed Haesun Park 74 2 0 22 Aug 2023
MedCPT: Contrastive Pre-trained Transformers with Large-scale PubMed Search Logs for Zero-shot Biomedical Information Retrieval Qiao Jin Won Kim Qingyu Chen Donald C. Comeau Lana Yeganova John Wilbur Zhiyong Lu LM&MA MedIm 286 187 0 02 Jul 2023
Scientific Fact-Checking: A Survey of Resources and ApproachesAnnual Meeting of the Association for Computational Linguistics (ACL), 2023 Juraj Vladika Florian Matthes HILM 219 65 0 26 May 2023
Zero-Shot Multi-Label Topic Inference with Sentence EncodersConference on Empirical Methods in Natural Language Processing (EMNLP), 2023 Souvik Sarkar Dongji Feng Shubhra (Santu) Karmaker BDL 229 6 0 14 Apr 2023
Bioformer: an efficient transformer language model for biomedical text mining Li Fang Qingyu Chen Chih-Hsuan Wei Zhiyong Lu Kai Wang MedIm AI4CE 143 32 0 03 Feb 2023
The effects of gender bias in word embeddings on depression prediction Gizem Sogancioglu Heysem Kaya 106 3 0 15 Dec 2022
MED-SE: Medical Entity Definition-based Sentence Embedding Hyeonbin Hwang Haanju Yoo Yera Choi MedIm 247 0 0 09 Dec 2022
Automated Identification of Eviction Status from Electronic Health Record Notes Zonghai Yao J. Tsai Weisong Liu David Levy Emily Druhl J. Reisman Hongfeng Yu 293 12 0 06 Dec 2022
An Automatic SOAP Classification System Using Weakly Supervision And Transfer Learning Sunjae Kwon Zhichao Yang Hong-ye Yu 178 2 0 26 Nov 2022
Hardness-guided domain adaptation to recognise biomedical named entities under low-resource scenariosConference on Empirical Methods in Natural Language Processing (EMNLP), 2022 Ngoc Dang Nguyen Lan Du Wray Buntine Changyou Chen Richard Beare 127 8 0 11 Nov 2022
Using Bottleneck Adapters to Identify Cancer in Clinical Notes under Low-Resource ConstraintsWorkshop on Biomedical Natural Language Processing (BioNLP), 2022 Omid Rohanian Hannah Jauncey Mohammadmahdi Nouriborji Vinod Kumar Chauhan Bronner P. Gonccalves Christiana Kartsonaki Isaric Clinical Characterisation Group L. Merson David Clifton 142 8 0 17 Oct 2022
Detailed Annotations of Chest X-Rays via CT Projection for Report UnderstandingBritish Machine Vision Conference (BMVC), 2022 C. Seibold Simon Reiß Saquib Sarfraz M. Fink Victoria L. Mayer Jan Sellner Moon S. Kim Klaus H. Maier-Hein Jens Kleesiek Rainer Stiefelhagen 193 22 0 07 Oct 2022
Gender bias in (non)-contextual clinical word embeddings for stereotypical medical categories Gizem Sogancioglu Fabian Mijsters Amar van Uden Jelle Peperzak 121 3 0 02 Aug 2022
A reproducible experimental survey on biomedical sentence similarity: a string-based method sets the state of the artPLoS ONE (PLoS ONE), 2022 Alicia Lara-Clares Juan J. Lastra-Díaz A. García-Serrano 122 0 0 18 May 2022
Learning to Revise References for Faithful SummarizationConference on Empirical Methods in Natural Language Processing (EMNLP), 2022 Griffin Adams Han-Chin Shing Q. Sun C. Winestock Kathleen McKeown Noémie Elhadad 206 36 0 13 Apr 2022
Filter Drug-induced Liver Injury Literature with Natural Language Processing and Ensemble LearningIEEE journal of biomedical and health informatics (IEEE JBHI), 2022 Xianghao Zhan Fanjin Wang Olivier Gevaert 110 13 0 09 Mar 2022
How Can Graph Neural Networks Help Document Retrieval: A Case Study on CORD19 with Concept Map GenerationEuropean Conference on Information Retrieval (ECIR), 2022 Hejie Cui Jiaying Lu Yao Ge Carl Yang 162 24 0 12 Jan 2022
Pre-trained Language Models in Biomedical Domain: A Systematic SurveyACM Computing Surveys (CSUR), 2021 Benyou Wang Qianqian Xie Jiahuan Pei Zhihong Chen Prayag Tiwari Zhao Li Jie Fu LM&MA AI4CE 362 200 0 11 Oct 2021
Automated Fact-Checking: A SurveyLanguage and Linguistics Compass (LLC), 2021 Xia Zeng Amani S. Abumansour A. Zubiaga HILM 306 105 0 23 Sep 2021
Scope resolution of predicted negation cues: A two-step neural network-based approach D. D. Jong 81 1 0 15 Sep 2021
Abstract, Rationale, Stance: A Joint Model for Scientific Claim Verification Zhiwei Zhang Jiyi Li Fumiyo Fukumoto Yanming Ye 168 31 0 13 Sep 2021
Overview and Insights from the SciVer Shared Task on Scientific Claim Verification Aman Rangapur Kyle Lo 184 15 0 17 Jul 2021
Trust It or Not: Confidence-Guided Automatic Radiology Report Generation Yixin Wang Zihao Lin Zhe Xu Haoyu Dong Jiang Tian Jie Luo Peng Wang Yang Zhang Jianping Fan Zhiqiang He UQCV MedIm 221 15 0 21 Jun 2021
CLIP: A Dataset for Extracting Action Items for Physicians from Hospital Discharge NotesAnnual Meeting of the Association for Computational Linguistics (ACL), 2021 J. Mullenbach Yada Pruksachatkun Sean Adler Jennifer Seale Jordan Swartz T. McKelvey Hui Dai Yi Yang David Sontag 104 18 0 04 Jun 2021
QMUL-SDS at SCIVER: Step-by-Step Binary Classification for Scientific Claim Verification Xia Zeng A. Zubiaga 114 9 0 23 Apr 2021
Extracting Adverse Drug Events from Clinical Notes D. Mahendran Bridget T. McInnes 136 33 0 21 Apr 2021
Semantic maps and metrics for science Semantic maps and metrics for science using deep transformer encoders Brendan Chambers James A. Evans MedIm 127 0 0 13 Apr 2021
EFloat: Entropy-coded Floating Point Format for Compressing Vector Embedding Models R. Bordawekar B. Abali Ming-Hung Chen MQ 127 3 0 04 Feb 2021
A Paragraph-level Multi-task Learning Model for Scientific Fact-Verification Xiangci Li Gully A. Burns Nanyun Peng MU 280 40 0 28 Dec 2020
Ensemble model for pre-discharge icd10 coding prediction Yassien Shaalan Alexander Dokumentov Piyapong Khumrin K. Khwanngern Anawat Wisetborisu ... Nattapat Karaket Witthawin Achariyaviriya S. Auephanwiriyakul N. Theera-Umpon Terence Siganakis 65 2 0 16 Dec 2020
Biomedical Concept Relatedness -- A large EHR-based benchmarkInternational Conference on Computational Linguistics (COLING), 2020 Claudia Schulz Josh Levy-Kramer C. V. Assel Miklos Kepes Nils Y. Hammerla 98 8 0 30 Oct 2020
TweetBERT: A Pretrained Language Representation Model for Twitter Text Analysis Mohiuddin Md Abdul Qudar Vijay K. Mago SSeg 138 40 0 17 Oct 2020
Multi-label Few/Zero-shot Learning with Knowledge Aggregated from Multiple Label Graphs Jueqing Lu Lan Du Ming-Yuan Liu Joanna Dipnall 143 44 0 15 Oct 2020
Artificial Intelligence (AI) in Action: Addressing the COVID-19 Pandemic with Natural Language Processing (NLP)Annual Review of Biomedical Data Science (ARBDS), 2020 Qingyu Chen Robert Leaman Alexis Allot Ling Luo Chih-Hsuan Wei Shankai Yan Zhiyong Lu 201 40 0 09 Oct 2020
Unsupervised Pre-training for Biomedical Question AnsweringConference and Labs of the Evaluation Forum (CLEF), 2020 Vaishnavi Kommaraju K. Gunasekaran Kun Li Trapit Bansal Andrew McCallum Ivana Williams Ana-Maria Istrate SSL MedIm 111 18 0 27 Sep 2020