mlsanityData to 13 Oct 2026

Launching into clinical space with medspaCy: a new clinical text processing toolkit in Python

arXiv 2106.07799 ↗First posted 14 Jun 2021cs.CLcited by 40

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Abstract (arXiv)

Despite impressive success of machine learning algorithms in clinical natural language processing (cNLP), rule-based approaches still have a prominent role. In this paper, we introduce medspaCy, an extensible, open-source cNLP library based on spaCy framework that allows flexible integration of rule-based and machine learning-based algorithms adapted to clinical text. MedspaCy includes a variety of components that meet common cNLP needs such as context analysis and mapping to standard terminologies. By utilizing spaCy's clear and easy-to-use conventions, medspaCy enables development of custom pipelines that integrate easily with other spaCy-based modules. Our toolkit includes several core components and facilitates rapid development of pipelines for clinical text.

Key facts. Cited by 40 papers in the map (data through 13 Oct 2026). Builds on 2 of its 41 references that are in the map. First posted on arXiv 14 Jun 2021.

Builds on

2 of 41 references.

References · 2

  1. 2019ScispaCy: Fast and Robust Models for Biomedical Natural Language Processingcited by 244
  2. 2019Natural Language Processing of Clinical Notes on Chronic Diseases: Systematic Reviewcited by 36

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Cited by year (2026 to 13 Oct)

Citing papers per year: 2021: 1; 2022: 7; 2023: 11; 2024: 7; 2025: 7; 2026: 7.

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  1. 2024RaTEScore: A Metric for Radiology Report Generationcited by 65
  2. 2023Large Language Models to Identify Social Determinants of Health in Electronic Health Recordscited by 55
  3. 2023NoteChat: A Dataset of Synthetic Doctor-Patient Conversations Conditioned on Clinical Notescited by 48
  4. 2024Data Extraction Attacks in Retrieval-Augmented Generation via Backdoorscited by 23
  5. 2021Literature-Augmented Clinical Outcome Predictioncited by 20
  6. 2023UMASS_BioNLP at MEDIQA-Chat 2023: Can LLMs generate high-quality synthetic note-oriented doctor-patient conversations?cited by 14
  7. 2023Effective Matching of Patients to Clinical Trials using Entity Extraction and Neural Re-rankingcited by 8
  8. 2024HunFlair2 in a cross-corpus evaluation of biomedical named entity recognition and normalization toolscited by 8
  9. 2022Radiology Text Analysis System (RadText): Architecture and Evaluationcited by 5
  10. 2023Natural language processing to automatically extract the presence and severity of esophagitis in notes of patients undergoing radiotherapycited by 5
  11. 2026Possible or Definite? A Benchmark for Evaluating Diagnostic Uncertainty Preservation in Clinical Textcited by 4
  12. 2023Ascle: A Python Natural Language Processing Toolkit for Medical Text Generationcited by 3
28 more
  1. 2023calamanCy: A Tagalog Natural Language Processing Toolkitcited by 2
  2. 2023Extracting periodontitis diagnosis in clinical notes with RoBERTa and regular expressioncited by 2
  3. 2025MedSlice: Fine-Tuned Large Language Models for Secure Clinical Note Sectioningcited by 2
  4. 2026EMSDialog: Synthetic Multi-person Emergency Medical Service Dialogue Generation from Electronic Patient Care Reports via Multi-LLM Agentscited by 2
  5. 2022EHRKit: A Python Natural Language Processing Toolkit for Electronic Health Record Textscited by 1
  6. 2022Assessing mortality prediction through different representation models based on concepts extracted from clinical notescited by 1
  7. 2022Negation detection in Dutch clinical texts: an evaluation of rule-based and machine learning methodscited by 1
  8. 2022An Automatic SOAP Classification System Using Weakly Supervision And Transfer Learningcited by 1
  9. 2023Cross-institution text mining to uncover clinical associations: a case study relating social factors and code status in intensive care medicinecited by 1
  10. 2024Assertion Detection Large Language Model In-context Learning LoRA Fine-tuningcited by 1
  11. 2025A Typology of Synthetic Datasets for Dialogue Processing in Clinical Contextscited by 1
  12. 2025Bias Detection in Emergency Psychiatry: Linking Negative Language to Diagnostic Disparitiescited by 1
  13. 2026MTDiag: A Multi-Turn Diagnostic Dataset Towards Clinically Meaningful LLM Evaluationcited by 1
  14. 2022Natural Language Processing Methods to Identify Oncology Patients at High Risk for Acute Care with Clinical Notescited by 0
  15. 2022Auditing Algorithmic Fairness in Machine Learning for Health with Severity-Based LOGANcited by 0
  16. 2023Clinical BioBERT Hyperparameter Optimization using Genetic Algorithmcited by 0
  17. 2023Applying unsupervised keyphrase methods on concepts extracted from discharge sheetscited by 0
  18. 2024Korean Bio-Medical Corpus (KBMC) for Medical Named Entity Recognitioncited by 0
  19. 2024LLM-Based Section Identifiers Excel on Open Source but Stumble in Real World Applicationscited by 0
  20. 2024CRTRE: Causal Rule Generation with Target Trial Emulation Frameworkcited by 0
  21. 2025Enhancing LLMs for Identifying and Prioritizing Important Medical Jargons from Electronic Health Record Notes Utilizing Data Augmentation: A Comparative Studycited by 0
  22. 2025Accelerating Clinical NLP at Scale with a Hybrid Framework with Reduced GPU Demands: A Case Study in Dementia Identificationcited by 0
  23. 2025Comparing Lexical and Semantic Vector Search Methods When Classifying Medical Documentscited by 0
  24. 2025Initial Investigation of LLM-Assisted Development of Rule-Based Clinical NLP Systemcited by 0
  25. 2026A Semi-Automated Annotation Workflow for Paediatric Histopathology Reports Using Small Language Modelscited by 0
  26. 2026Characterizing Treatment-Context Medication Evidence Across Clinic Notes and Structured EHR Medication Historycited by 0
  27. 2026A knowledge-guided agentic framework for mitigating patient-context ambiguity in health queriescited by 0
  28. 2026VERGE: Verification-Enhanced Refinement for Grounded Extraction of Early-Onset Colorectal Cancer Symptoms in Clinical Notescited by 0