mlsanityData to 7 Oct 2026

Multi-domain Clinical Natural Language Processing with MedCAT: the Medical Concept Annotation Toolkit

arXiv 2010.01165 ↗First posted 2 Oct 2020cs.CL cs.AI cs.LGcited by 66

Not on the map. Why?

Abstract (arXiv)

Electronic health records (EHR) contain large volumes of unstructured text, requiring the application of Information Extraction (IE) technologies to enable clinical analysis. We present the open-source Medical Concept Annotation Toolkit (MedCAT) that provides: a) a novel self-supervised machine learning algorithm for extracting concepts using any concept vocabulary including UMLS/SNOMED-CT; b) a feature-rich annotation interface for customising and training IE models; and c) integrations to the broader CogStack ecosystem for vendor-agnostic health system deployment. We show improved performance in extracting UMLS concepts from open datasets (F1:0.448-0.738 vs 0.429-0.650). Further real-world validation demonstrates SNOMED-CT extraction at 3 large London hospitals with self-supervised training over ~8.8B words from ~17M clinical records and further fine-tuning with ~6K clinician annotated examples. We show strong transferability (F1 > 0.94) between hospitals, datasets, and concept types indicating cross-domain EHR-agnostic utility for accelerated clinical and research use cases.

Key facts. Cited by 66 papers in the map (data through 7 Oct 2026). First posted on arXiv 2 Oct 2020.

Builds on

No reference list yet.

Built on by

Cited by year (2026 to 7 Oct)

Citing papers per year: 2021: 5; 2022: 12; 2023: 9; 2024: 15; 2025: 15; 2026: 10.

66 papers.

Sort:

By area:

  1. 2022MONAI: An open-source framework for deep learning in healthcarecited by 438
  2. 2021Does BERT Pretrained on Clinical Notes Reveal Sensitive Data?cited by 91
  3. 2024ROCOv2: Radiology Objects in COntext Version 2, an Updated Multimodal Image Datasetcited by 54
  4. 2025Harnessing the Universal Geometry of Embeddingscited by 54
  5. 2021What's in a Summary? Laying the Groundwork for Advances in Hospital-Course Summarizationcited by 35
  6. 2021RATCHET: Medical Transformer for Chest X-ray Diagnosis and Reportingcited by 34
  7. 2022Automated Clinical Coding: What, Why, and Where We Are?cited by 33
  8. 2022A Unified Review of Deep Learning for Automated Medical Codingcited by 26
  9. 2021MedGPT: Medical Concept Prediction from Clinical Narrativescited by 24
  10. 2022Medical Image Captioning via Generative Pretrained Transformerscited by 20
  11. 2022MedJEx: A Medical Jargon Extraction Model with Wiki's Hyperlink Span and Contextualized Masked Language Model Scorecited by 20
  12. 2022Discharge Summary Hospital Course Summarisation of In Patient Electronic Health Record Text with Clinical Concept Guided Deep Pre-Trained Transformer Modelscited by 17
38 more
  1. 2022Foresight -- Generative Pretrained Transformer (GPT) for Modelling of Patient Timelines using EHRscited by 11
  2. 2021Estimating Redundancy in Clinical Textcited by 10
  3. 2023An Investigation of Evaluation Metrics for Automated Medical Note Generationcited by 10
  4. 2024HunFlair2 in a cross-corpus evaluation of biomedical named entity recognition and normalization toolscited by 8
  5. 2022Ontology-Driven and Weakly Supervised Rare Disease Identification from Clinical Notescited by 7
  6. 2022Effective Few-Shot Named Entity Linking by Meta-Learningcited by 6
  7. 2023The Potential and Pitfalls of using a Large Language Model such as ChatGPT or GPT-4 as a Clinical Assistantcited by 6
  8. 2024A Data-Centric Approach To Generate Faithful and High Quality Patient Summaries with Large Language Modelscited by 6
  9. 2024Large Language Models for Medical Forecasting -- Foresight 2cited by 5
  10. 2023Validating transformers for redaction of text from electronic health records in real-world healthcarecited by 4
  11. 2022Review of Natural Language Processing in Pharmacologycited by 3
  12. 2023Progress Note Understanding -- Assessment and Plan Reasoning: Overview of the 2022 N2C2 Track 3 Shared Taskcited by 3
  13. 2025Integration of Large Language Models and Traditional Deep Learning for Social Determinants of Health Predictioncited by 3
  14. 2025Evaluating LLMs Across Multi-Cognitive Levels: From Medical Knowledge Mastery to Scenario-Based Problem Solvingcited by 3
  15. 2023Identifying Mentions of Pain in Mental Health Records Text: A Natural Language Processing Approachcited by 2
  16. 2023MedMine: Examining Pre-trained Language Models on Medication Miningcited by 2
  17. 2023Exploring the Consistency, Quality and Challenges in Manual and Automated Coding of Free-text Diagnoses from Hospital Outpatient Letterscited by 2
  18. 2024I-SIRch: AI-Powered Concept Annotation Tool For Equitable Extraction And Analysis Of Safety Insights From Maternity Investigationscited by 2
  19. 2025Automated SNOMED CT Concept Annotation in Clinical Text Using Bi-GRU Neural Networkscited by 2
  20. 2025Semantic Analysis of SNOMED CT Concept Co-occurrences in Clinical Documentation using MIMIC-IVcited by 2
  21. 2025Count-Based Approaches Remain Strong: A Benchmark Against Transformer and LLM Pipelines on Structured EHRcited by 2
  22. 2022Predicting Clinical Intent from Free Text Electronic Health Recordscited by 1
  23. 2022Negation detection in Dutch clinical texts: an evaluation of rule-based and machine learning methodscited by 1
  24. 2024Bespoke Large Language Models for Digital Triage Assistance in Mental Health Carecited by 1
  25. 2024Towards Efficient Patient Recruitment for Clinical Trials: Application of a Prompt-Based Learning Modelcited by 1
  26. 2024Biomedical Entity Linking for Dutch: Fine-tuning a Self-alignment BERT Model on an Automatically Generated Wikipedia Corpuscited by 1
  27. 2024Enhancing Biomedical Knowledge Discovery for Diseases: An Open-Source Framework Applied on Rett Syndrome and Alzheimer's Diseasecited by 1
  28. 2025Proactive Reasoning-with-Retrieval Framework for Medical Multimodal Large Language Modelscited by 1
  29. 2026MedLayBench-V: A Large-Scale Benchmark for Expert-Lay Semantic Alignment in Medical Vision Language Modelscited by 1
  30. 2026Hallucination Detection-Guided Preference Optimization for Clinical Summarizationcited by 1
  31. 2023Automatic Coding at Scale: Design and Deployment of a Nationwide System for Normalizing Referrals in the Chilean Public Healthcare Systemcited by 0
  32. 2023Development of a Knowledge Graph Embeddings Model for Paincited by 0
  33. 2024Diagnosis extraction from unstructured Dutch echocardiogram reports using span- and document-level characteristic classificationcited by 0
  34. 2024Improving Extraction of Clinical Event Contextual Properties from Electronic Health Records: A Comparative Studycited by 0
  35. 2024Facilitating phenotyping from clinical texts: the medkit librarycited by 0
  36. 2024Detecci'on Autom'atica de Patolog'ias en Notas Cl'inicas en Espa~nol Combinando Modelos de Lenguaje y Ontolog'ias M'edicoscited by 0
  37. 2024Generative Language Models Potential for Requirement Engineering Applications: Insights into Current Strengths and Limitationscited by 0
  38. 2024Automatic detection of diseases in Spanish clinical notes combining medical language models and ontologiescited by 0

50 most cited of 66 All 66 (JSON)