Clinical Note Analysis NLP Tools

Tools for extracting, classifying, and analyzing information from clinical notes and EHR text (ICD coding, diagnosis extraction, readmission prediction, symptom monitoring). Does NOT include general medical knowledge bases, clinical NLP libraries without note-specific applications, or conference listings.

There are 51 clinical note analysis tools tracked. 1 score above 50 (established tier). The highest-rated is medspacy/medspacy at 62/100 with 637 stars and 12,936 monthly downloads.

Get all 51 projects as JSON

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#	Tool	Score	Tier	Stars	Language
1	medspacy/medspacy Library for clinical NLP with spaCy.	62	Established	637	Jupyter Notebook
2	bionlplab/radtext Python Radiology Text Analysis System	44	Emerging	16	Python
3	jamesmullenbach/caml-mimic multilabel classification of EHR notes	44	Emerging	302	Python
4	ncbi-nlp/NegBio :newspaper: High-performance tool for negation and uncertainty detection in...	40	Emerging	165	Python
5	ClarityNLP/ClarityNLP An NLP framework for clinical phenotyping. Docker \| Python \| Solr \| OMOP....	39	Emerging	109	Jupyter Notebook
6	salgadev/medical-nlp Dataset for Natural Language Processing using a corpus of medical...	38	Emerging	98	—
7	3778/icd-prediction-mimic Predicting ICD Codes from Clinical Notes	37	Emerging	64	Jupyter Notebook
8	uclh-criu/miade A set of tools for extracting formattable data from clinical notes stored in...	36	Emerging	10	Python
9	kavgan/clinical-concepts Discovering Related Clinical Concepts using Large Amounts of Clinical Notes....	33	Emerging	25	—
10	jorgemf/kaggle_redefining_cancer_treatment Personalized Medicine: Redefining Cancer Treatment with deep learning	33	Emerging	24	Python
11	databricks-industry-solutions/oncology Generate oncology insights from real-world data using NLP. Once extracted,...	30	Emerging	12	Python
12	judacas/Clinical-Trial-Prompts A Python tool for structured analysis of clinical trial eligibility criteria...	30	Emerging	3	Python
13	plandes/mednlp Medical natural language parsing and utility library	30	Emerging	14	Python
14	levrex/DiagnosisExtraction_ML Pipeline for building Machine Learning Classifiers for the diagnosis of EHR...	30	Emerging	12	Jupyter Notebook
15	lindvalllab/MLSym Deep learning for cancer symptoms monitoring on the basis of EHR...	29	Experimental	8	Python
16	databricks-industry-solutions/jsl-kg-cohorts Building Patient Cohorts with NLP and Knowledge Graphs	29	Experimental	5	Python
17	cltl/a-proof-zonmw Detecting the functioning level of a patient from a free-text clinical note in Dutch.	28	Experimental	8	Jupyter Notebook
18	01pooja10/MedGen Official submission to MIC's ResCon 1.0: Generate a detailed medical report...	28	Experimental	5	Jupyter Notebook
19	DanielhCarranza/MedSearch MedSearch is a Medical Knowledge Extraction System that incorporates Neural...	28	Experimental	14	Jupyter Notebook
20	databricks-industry-solutions/jsl-medical-risk-factors Automated Extraction of Medical Risk Factors For Life Insurance Underwriting	27	Experimental	5	Python
21	nhsx/txt-ray-align Exploring contrastive alignment of image and text encoders for image-based...	27	Experimental	4	Python
22	lemuria-wchen/imcs21 Code and dataset for our Bioinformatics 2022 paper: "A Benchmark for ...	27	Experimental	63	Python
23	lindvalllab/MedSlice A sectioning tool for clinical notes using fine-tuned LLMs	25	Experimental	3	Python
24	zonghui0228/chip2019task3 第五届中国健康信息处理会议（CHIP2019）- 评测三：临床试验筛选标准短文本分类	25	Experimental	41	Python
25	fensorechase/LLMs_SDOH_Integration Supplemental code: Large Language Models for Integrating Social Determinant...	24	Experimental	3	Python
26	Aliarcher/Medical-Analysis This repository contains Medical Analysis projects	24	Experimental	2	Jupyter Notebook
27	JINHXu/Early-Sepsis-Prediction-using-TSF Early Prediction of Sepsis using Time Seiries Forecasting (Published at 2023...	24	Experimental	2	Python
28	Abhinand-p/Project_Medical-INLPT-WS2023 A medical NLP project developed for the WS2023 course, focusing on...	23	Experimental	2	Jupyter Notebook
29	drci-foch/BTB_extraction Transbronchial Biopsy Document restructuration. Work in progress.	22	Experimental	—	Python
30	Princey9/NoteNest NoteNest is a Rust CLI that privacy-reduces clinical notes and patient...	21	Experimental	—	Rust
31	NHSE-NDRS/HSMA-Congenital-Condition-NLP This repo is for the HSMA Inception Project: 'Applying Natural Language...	20	Experimental	1	HTML
32	omarsar/clinical_nlp_elastic Clinical NLP Analysis with Elasticsearch and Kibana	19	Experimental	35	Jupyter Notebook
33	li-ruijie/diabetes-stories Processed oral history interviews from the Diabetes Stories project (OCDEM, Oxford)	19	Experimental	—	—
34	omarsar/midas_api MIDAS API	18	Experimental	11	Jupyter Notebook
35	llnl/al_nlp Active Learning framework for Natural Language Processing of pathology reports.	18	Experimental	11	Jupyter Notebook
36	uic-nlp-lab/medsecid COLING 2022: Baseline model and annotations for MedSecId, Landes et al.	17	Experimental	4	HTML
37	BoulderDS/value-of-medical-notes This repository is the implementation of Characterizing the Value of...	17	Experimental	5	Jupyter Notebook
38	matthew-mcateer/NIPS2017competition Data & Scripts for the Memorial Sloan Kettering Cancer Center's (MSKCC)...	15	Experimental	6	Jupyter Notebook
39	KannanSA/NLPK NHS Digital Data Science Internship Project November 2019	14	Experimental	1	Python
40	liyakhathshaik/MediSeven.jl this is julia repo for using the med7 python package	14	Experimental	3	Julia
41	plandes/mimicsid MIMIC-III corpus parsing and section prediction with MedSecId (COLING paper)	14	Experimental	4	Python
42	plandes/mimic MIMIC III Corpus Parsing	14	Experimental	4	Python
43	mathworks/HospitalReadmission_MIMIC_TextAnalytics_MATLAB Predict Hospital Readmissions using Text Analytics in MATLAB	13	Experimental	5	—
44	windisch-paul/oncology_pipeline Data and code associated with the manuscript "A Pipeline for the Automatic...	12	Experimental	1	Jupyter Notebook
45	uwrit/mush Clinical Note Processing Pipeline Driver and Framework	12	Experimental	3	Go
46	anaconda121/NeuraHealth Code for NeuraHealth: An Automated Screening Pipeline to Detect Undiagnosed...	12	Experimental	3	Jupyter Notebook
47	sakshamarora97/instruction-tuned-clinical-notes-scoring Instruction Tuned Scoring using Clinical Notes \| Course Project for CS 7641	11	Experimental	2	Jupyter Notebook
48	AbdulWahabRaza123/Report-generation-work This is the data preprocessing, cleaning, and model training code for a...	11	Experimental	2	Jupyter Notebook
49	avijit-thawani/RadiologyQA MSR Cambridge Internship Summer 2023	10	Experimental	1	Vue
50	AnjaliDharmik/Skin-Disease-Text-Classification Skin Disease Text Classification uses NLP to categorize dermatology texts...	10	Experimental	1	Jupyter Notebook
51	plandes/dsprov Provenience of discharge summaries Pythonic access (BioNLP paper)	10	Experimental	1	Python

Comparisons in this category

medspacy and mednlp (62 vs 30) caml-mimic and icd-prediction-mimic (44 vs 37)