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 57 clinical note analysis tools tracked. 2 score above 50 (established tier). The highest-rated is medspacy/medspacy at 60/100 with 637 stars.

Get all 57 projects as JSON

curl "https://pt-edge.onrender.com/api/v1/datasets/quality?domain=nlp&subcategory=clinical-note-analysis&limit=20"

Open to everyone — 100 requests/day, no key needed. Get a free key for 1,000/day.

#	Tool	Score	Tier	Stars	Language
1	medspacy/medspacy Library for clinical NLP with spaCy.	60	Established	637	Jupyter Notebook
2	jamesmullenbach/caml-mimic multilabel classification of EHR notes	51	Established	302	Python
3	ncbi-nlp/NegBio :newspaper: High-performance tool for negation and uncertainty detection in...	47	Emerging	165	Python
4	bionlplab/radtext Python Radiology Text Analysis System	47	Emerging	16	Python
5	ClarityNLP/ClarityNLP An NLP framework for clinical phenotyping. Docker \| Python \| Solr \| OMOP....	46	Emerging	109	Jupyter Notebook
6	salgadev/medical-nlp Dataset for Natural Language Processing using a corpus of medical...	45	Emerging	98	—
7	3778/icd-prediction-mimic Predicting ICD Codes from Clinical Notes	44	Emerging	64	Jupyter Notebook
8	jorgemf/kaggle_redefining_cancer_treatment Personalized Medicine: Redefining Cancer Treatment with deep learning	40	Emerging	24	Python
9	uclh-criu/miade A set of tools for extracting formattable data from clinical notes stored in...	40	Emerging	10	Python
10	kavgan/clinical-concepts Discovering Related Clinical Concepts using Large Amounts of Clinical Notes....	40	Emerging	25	—
11	levrex/DiagnosisExtraction_ML Pipeline for building Machine Learning Classifiers for the diagnosis of EHR...	37	Emerging	12	Jupyter Notebook
12	databricks-industry-solutions/oncology Generate oncology insights from real-world data using NLP. Once extracted,...	37	Emerging	12	Python
13	plandes/mednlp Medical natural language parsing and utility library	37	Emerging	14	Python
14	lindvalllab/MLSym Deep learning for cancer symptoms monitoring on the basis of EHR...	36	Emerging	8	Python
15	databricks-industry-solutions/jsl-kg-cohorts Building Patient Cohorts with NLP and Knowledge Graphs	36	Emerging	5	Python
16	01pooja10/MedGen Official submission to MIC's ResCon 1.0: Generate a detailed medical report...	35	Emerging	5	Jupyter Notebook
17	cltl/a-proof-zonmw Detecting the functioning level of a patient from a free-text clinical note in Dutch.	35	Emerging	8	Jupyter Notebook
18	DanielhCarranza/MedSearch MedSearch is a Medical Knowledge Extraction System that incorporates Neural...	35	Emerging	14	Jupyter Notebook
19	lemuria-wchen/imcs21 Code and dataset for our Bioinformatics 2022 paper: "A Benchmark for ...	34	Emerging	63	Python
20	nhsx/txt-ray-align Exploring contrastive alignment of image and text encoders for image-based...	34	Emerging	4	Python
21	databricks-industry-solutions/jsl-medical-risk-factors Automated Extraction of Medical Risk Factors For Life Insurance Underwriting	34	Emerging	5	Python
22	lindvalllab/MedSlice A sectioning tool for clinical notes using fine-tuned LLMs	32	Emerging	3	Python
23	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	32	Emerging	41	Python
24	Aliarcher/Medical-Analysis This repository contains Medical Analysis projects	31	Emerging	2	Jupyter Notebook
25	fensorechase/LLMs_SDOH_Integration Supplemental code: Large Language Models for Integrating Social Determinant...	31	Emerging	3	Python
26	JINHXu/Early-Sepsis-Prediction-using-TSF Early Prediction of Sepsis using Time Seiries Forecasting (Published at 2023...	31	Emerging	2	Python
27	Abhinand-p/Project_Medical-INLPT-WS2023 A medical NLP project developed for the WS2023 course, focusing on...	30	Emerging	2	Jupyter Notebook
28	omarsar/clinical_nlp_elastic Clinical NLP Analysis with Elasticsearch and Kibana	26	Experimental	35	Jupyter Notebook
29	omarsar/midas_api MIDAS API	25	Experimental	11	Jupyter Notebook
30	llnl/al_nlp Active Learning framework for Natural Language Processing of pathology reports.	25	Experimental	11	Jupyter Notebook
31	BoulderDS/value-of-medical-notes This repository is the implementation of Characterizing the Value of...	24	Experimental	5	Jupyter Notebook
32	uic-nlp-lab/medsecid COLING 2022: Baseline model and annotations for MedSecId, Landes et al.	24	Experimental	4	HTML
33	matthew-mcateer/NIPS2017competition Data & Scripts for the Memorial Sloan Kettering Cancer Center's (MSKCC)...	22	Experimental	6	Jupyter Notebook
34	plandes/mimic MIMIC III Corpus Parsing	21	Experimental	4	Python
35	plandes/mimicsid MIMIC-III corpus parsing and section prediction with MedSecId (COLING paper)	21	Experimental	4	Python
36	NHSE-NDRS/HSMA-Congenital-Condition-NLP This repo is for the HSMA Inception Project: 'Applying Natural Language...	20	Experimental	1	HTML
37	liyakhathshaik/MediSeven.jl this is julia repo for using the med7 python package	20	Experimental	3	Julia
38	mathworks/HospitalReadmission_MIMIC_TextAnalytics_MATLAB Predict Hospital Readmissions using Text Analytics in MATLAB	20	Experimental	5	—
39	drci-foch/BTB_extraction Transbronchial Biopsy Document restructuration. Work in progress.	19	Experimental	—	Python
40	windisch-paul/oncology_pipeline Data and code associated with the manuscript "A Pipeline for the Automatic...	19	Experimental	1	Jupyter Notebook
41	anaconda121/NeuraHealth Code for NeuraHealth: An Automated Screening Pipeline to Detect Undiagnosed...	19	Experimental	3	Jupyter Notebook
42	li-ruijie/diabetes-stories Processed oral history interviews from the Diabetes Stories project (OCDEM, Oxford)	19	Experimental	—	—
43	uwrit/mush Clinical Note Processing Pipeline Driver and Framework	19	Experimental	3	Go
44	AbdulWahabRaza123/Report-generation-work This is the data preprocessing, cleaning, and model training code for a...	18	Experimental	2	Jupyter Notebook
45	sakshamarora97/instruction-tuned-clinical-notes-scoring Instruction Tuned Scoring using Clinical Notes \| Course Project for CS 7641	18	Experimental	2	Jupyter Notebook
46	avijit-thawani/RadiologyQA MSR Cambridge Internship Summer 2023	17	Experimental	1	Vue
47	AnjaliDharmik/Skin-Disease-Text-Classification Skin Disease Text Classification uses NLP to categorize dermatology texts...	17	Experimental	1	Jupyter Notebook
48	plandes/dsprov Provenience of discharge summaries Pythonic access (BioNLP paper)	17	Experimental	1	Python
49	janayee-c/MIMIC-CXR A predictive model for pneumonia severity using multimodal radiomics,...	15	Experimental	1	Jupyter Notebook
50	KannanSA/NLPK NHS Digital Data Science Internship Project November 2019	14	Experimental	1	Python
51	poteminr/agrocode2021 MultiLabel classification of cow diseases by text and symptoms recognition (NER)	13	Experimental	12	Jupyter Notebook
52	yeahshow/word2vec_medical_record Using NLP and RNN to build a clinical decision support model, taking input...	13	Experimental	9	Jupyter Notebook
53	lchaloupsky/Medical-Reports-Generator GPT-2 based medical reports generator for X-ray images in Czech.	12	Experimental	6	TeX
54	sAndreotti/MedicalMeadow MedicalMeadow is an open-source project focused on training large language...	11	Experimental	3	Jupyter Notebook
55	SemiXQ/Identify-Key-Information-in-Patient-Notes NLP course project. A solution to a Kaggle competition...	11	Experimental	4	Python
56	HS1CMU/MediQA-Model 2022 May-Aug, NLP Summer Research Assistant at CS & AI Lab, UNNC. Explored...	11	Experimental	3	Python
57	rohithaug/sepsis-prediction Predict sepsis using structured data of patients who were admitted to the...	11	Experimental	4	Jupyter Notebook

Comparisons in this category

medspacy and mednlp (60 vs 37) caml-mimic and icd-prediction-mimic (51 vs 44)