mlsanityData to 7 Oct 2026

BioSentVec: creating sentence embeddings for biomedical texts

arXiv 1810.09302 ↗First posted 22 Oct 2018cs.CL cs.AI cs.LGcited by 47

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Abstract (arXiv)

Sentence embeddings have become an essential part of today's natural language processing (NLP) systems, especially together advanced deep learning methods. Although pre-trained sentence encoders are available in the general domain, none exists for biomedical texts to date. In this work, we introduce BioSentVec: the first open set of sentence embeddings trained with over 30 million documents from both scholarly articles in PubMed and clinical notes in the MIMIC-III Clinical Database. We evaluate BioSentVec embeddings in two sentence pair similarity tasks in different text genres. Our benchmarking results demonstrate that the BioSentVec embeddings can better capture sentence semantics compared to the other competitive alternatives and achieve state-of-the-art performance in both tasks. We expect BioSentVec to facilitate the research and development in biomedical text mining and to complement the existing resources in biomedical word embeddings. BioSentVec is publicly available at https://github.com/ncbi-nlp/BioSentVec

Key facts. Cited by 47 papers in the map (data through 7 Oct 2026). First posted on arXiv 22 Oct 2018.

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Citing papers per year: 2021: 11; 2022: 12; 2023: 10; 2024: 7; 2025: 5; 2026: 2.

47 papers.

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  1. 2023MedCPT: Contrastive Pre-trained Transformers with Large-scale PubMed Search Logs for Zero-shot Biomedical Information Retrievalcited by 182
  2. 2021Pre-trained Language Models in Biomedical Domain: A Systematic Surveycited by 87
  3. 2023Benchmarking large language models for biomedical natural language processing applications and recommendationscited by 78
  4. 2021Automated Fact-Checking: A Surveycited by 55
  5. 2023Scientific Fact-Checking: A Survey of Resources and Approachescited by 53
  6. 2022Learning to Revise References for Faithful Summarizationcited by 28
  7. 2022Detailed Annotations of Chest X-Rays via CT Projection for Report Understandingcited by 24
  8. 2021Abstract, Rationale, Stance: A Joint Model for Scientific Claim Verificationcited by 20
  9. 2021CLIP: A Dataset for Extracting Action Items for Physicians from Hospital Discharge Notescited by 18
  10. 2025FinMTEB: Finance Massive Text Embedding Benchmarkcited by 18
  11. 2021Overview and Insights from the SciVer Shared Task on Scientific Claim Verificationcited by 17
  12. 2024Do We Need Domain-Specific Embedding Models? An Empirical Investigationcited by 12
35 more
  1. 2021Trust It or Not: Confidence-Guided Automatic Radiology Report Generationcited by 9
  2. 2023Bioformer: an efficient transformer language model for biomedical text miningcited by 9
  3. 2021Extracting Adverse Drug Events from Clinical Notescited by 7
  4. 2022How Can Graph Neural Networks Help Document Retrieval: A Case Study on CORD19 with Concept Map Generationcited by 7
  5. 2021QMUL-SDS at SCIVER: Step-by-Step Binary Classification for Scientific Claim Verificationcited by 6
  6. 2022Hardness-guided domain adaptation to recognise biomedical named entities under low-resource scenarioscited by 6
  7. 2022Automated Identification of Eviction Status from Electronic Health Record Notescited by 6
  8. 2023Zero-Shot Multi-Label Topic Inference with Sentence Encoderscited by 6
  9. 2024A Survey of Deep Learning-based Radiology Report Generation Using Multimodal Datacited by 6
  10. 2025The Next Phase of Scientific Fact-Checking: Advanced Evidence Retrieval from Complex Structured Academic Paperscited by 6
  11. 2022Using Bottleneck Adapters to Identify Cancer in Clinical Notes under Low-Resource Constraintscited by 5
  12. 2025PRISM: A Framework for Producing Interpretable Political Bias Embeddings with Political-Aware Cross-Encodercited by 5
  13. 2022Filter Drug-induced Liver Injury Literature with Natural Language Processing and Ensemble Learningcited by 4
  14. 2023Ascle: A Python Natural Language Processing Toolkit for Medical Text Generationcited by 3
  15. 2024SciGisPy: a Novel Metric for Biomedical Text Simplification via Gist Inference Scorecited by 3
  16. 2026EPPCMinerBen: A Novel Benchmark for Evaluating Large Language Models on Electronic Patient-Provider Communication via the Patient Portalcited by 3
  17. 2022Gender bias in (non)-contextual clinical word embeddings for stereotypical medical categoriescited by 2
  18. 2023Benchmarking and Analyzing In-context Learning, Fine-tuning and Supervised Learning for Biomedical Knowledge Curation: a focused study on chemical entities of biological interestcited by 2
  19. 2021EFloat: Entropy-coded Floating Point Format for Compressing Vector Embedding Modelscited by 1
  20. 2022An Automatic SOAP Classification System Using Weakly Supervision And Transfer Learningcited by 1
  21. 2022The effects of gender bias in word embeddings on depression predictioncited by 1
  22. 2023WellFactor: Patient Profiling using Integrative Embedding of Healthcare Datacited by 1
  23. 2024Health Text Simplification: An Annotated Corpus for Digestive Cancer Education and Novel Strategies for Reinforcement Learningcited by 1
  24. 2025Evaluating Causal Explanation in Medical Reports with LLM-Based and Human-Aligned Metricscited by 1
  25. 2021Semantic maps and metrics for science Semantic maps and metrics for science using deep transformer encoderscited by 0
  26. 2021Scope resolution of predicted negation cues: A two-step neural network-based approachcited by 0
  27. 2022A reproducible experimental survey on biomedical sentence similarity: a string-based method sets the state of the artcited by 0
  28. 2022MED-SE: Medical Entity Definition-based Sentence Embeddingcited by 0
  29. 2023Patient Clustering via Integrated Profiling of Clinical and Digital Datacited by 0
  30. 2023Screening of Pneumonia and Urinary Tract Infection at Triage using TriNetcited by 0
  31. 2024An Information Retrieval and Extraction Tool for Covid-19 Related Paperscited by 0
  32. 2024Tracing the Genealogies of Ideas with Large Language Model Embeddingscited by 0
  33. 2024BioBridge: Unified Bio-Embedding with Bridging Modality in Code-Switched EMRcited by 0
  34. 2025AI-Powered Detection of Inappropriate Language in Medical School Curriculacited by 0
  35. 2026BioHiCL: Hierarchical Multi-Label Contrastive Learning for Biomedical Retrieval with MeSH Labelscited by 0