Clinical Code Embeddings Embedding Tools

Tools for generating and working with embeddings of clinical concepts, medical codes (LOINC, ICD, CUI), EHR data, and clinical notes to enable knowledge-grounded AI in healthcare. Does NOT include general biomedical text embeddings, radiology report analysis as primary focus, or foundation models for non-embedding tasks.

There are 41 clinical code embeddings tools tracked. The highest-rated is mims-harvard/ClinVec at 43/100 with 83 stars.

Get all 41 projects as JSON

curl "https://pt-edge.onrender.com/api/v1/datasets/quality?domain=embeddings&subcategory=clinical-code-embeddings&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	mims-harvard/ClinVec ClinVec: Unified Embeddings of Clinical Codes Enable Knowledge-Grounded AI...	43	Emerging	83	Jupyter Notebook
2	NYUMedML/DeepEHR Chronic Disease Prediction Using Medical Notes	42	Emerging	272	Python
3	mims-harvard/SHEPHERD SHEPHERD: Few shot learning for phenotype-driven diagnosis of patients with...	40	Emerging	79	HTML
4	biocentral/biocentral_server Compute functionality for biocentral.	40	Emerging	4	Python
5	biocentral/biocentral_api Programmatic access to the biocentral ecosystem.	36	Emerging	2	Python
6	nomic-ai/contrastors Train Models Contrastively in Pytorch	36	Emerging	777	Python
7	hybrid-kg/clep 🤖 A Python Package for generating new patient representations driven by data...	36	Emerging	24	Python
8	biocentral/biocentral Biomedical data, from lab to paper.	34	Emerging	18	Dart
9	JohnGiorgi/DeCLUTR The corresponding code from our paper "DeCLUTR: Deep Contrastive Learning...	34	Emerging	378	Python
10	shipra25jain/ESSNet Embedding-based Scalable Segmentation Network	32	Emerging	28	Python
11	multimodal/multimodal A collection of multimodal datasets, and visual features for VQA and...	30	Emerging	84	Python
12	clips/yarn Disambiguating biomedical and clinical concepts with word embeddings	29	Experimental	14	Python
13	squaresLab/VarCLR VarCLR: Variable Semantic Representation Pre-training via Contrastive Learning	27	Experimental	40	Python
14	ratschlab/clinical-embeddings Repository for the Paper: „On the Importance of Step-wise Embeddings for...	26	Experimental	7	Python
15	bio-ontology-research-group/ontology-extension Combining lexical and context features for automatic ontology extension	25	Experimental	4	Python
16	przemo145235/radiology-report-triage-llm 🩻 Classify radiology reports as Normal or Abnormal with high accuracy using...	24	Experimental	—	Python
17	faris-k/self-supervised-wafermaps Self-Supervised Representation Learning of Semiconductor Wafer Maps using PyTorch	24	Experimental	4	Jupyter Notebook
18	janmejaybhoi/Sequential-Sentence-Classification-in-Medical-Abstracts Implemented a Research paper "PubMed 200k RCT: a Dataset for Sequential...	24	Experimental	3	Jupyter Notebook
19	sdimi/Step2heart 🏋️ Extract generalizable physiological representations from sensor...	23	Experimental	19	Python
20	jacobdeasy/flexible-ehr Time-Sensitive Deep Learning for ICU Outcome Prediction Without Variable...	23	Experimental	19	Python
21	imonban/RadiologyReportEmbedding Intelligent Word Embeddings of Free-Text Radiology Reports	22	Experimental	24	—
22	ThalesMMS/mammography-pipelines-py Mammography experimentation repo delivering reproducible preprocessing,...	22	Experimental	—	Python
23	elleros/DSHealth2019_loinc_embeddings Code and Word2Vec embeddings of LOINC codes for KDD 2019 DSHealth paper...	21	Experimental	11	Jupyter Notebook
24	BrahimFakri/Patient-Health-Data-Analysis-And-Feature-Extraction-For-Machine-Learning Embeddings generation from MIMIC-IV and MIMIC-CXR	21	Experimental	8	Jupyter Notebook
25	GanjinZero/CODER CODER: Knowledge infused cross-lingual medical term embedding for term...	20	Experimental	80	Python
26	zenlm/jin Multimodal AI — vision, audio, 3D embeddings	19	Experimental	—	Python
27	lamalab-org/PolyBind API for getting embeddings for different polymer identifiers	19	Experimental	5	Python
28	biocentral/bio_flutter Working with biological data in flutter.	17	Experimental	2	Dart
29	dermatologist/cui-embed Gensim wrapper for the clinical (CUI) embeddings	16	Experimental	3	Python
30	SharvenRane/radiology-report-triage-llm Zero-shot radiology report triage using LLM embeddings (Sentence...	15	Experimental	—	Python
31	HROlive/Generative-AI-with-Diffusion-Models Deep dive on diffusion models, which are a popular choice for text-to-image...	15	Experimental	2	Jupyter Notebook
32	drgriffis/text-essence Preprocessing and analysis for training SNOMED-CT concept embeddings from...	15	Experimental	16	Python
33	Yang-qwq/nahida-pt-embeddings 本项目是基于stable-diffusion-webui，通过pixiv图片训练得到的纳西妲模型	14	Experimental	7	—
34	DavePower-cloud/Diffusion_X-ray_Generator Diffusion-based generative model for synthesising chest X-ray images using a...	14	Experimental	—	Jupyter Notebook
35	rezacsedu/Convolutional-embedded-networks Convolutional Embedded Networks for Population Scale Clustering and...	13	Experimental	11	Python
36	hunsao/embeddings-age-bias-analysis Analysis of embeddings and age biases in image generation models using CLIP,...	13	Experimental	—	HTML
37	zurlog/abs-embeddings-eval Code for the paper "Abstracts Embeddings Evaluation: A Case Study of...	11	Experimental	2	Jupyter Notebook
38	harinik05/LeukoDif Denoising Diffusion Medical Model (DDMM) on PyTorch for generating datasets...	11	Experimental	2	Jupyter Notebook
39	Charithareddt/healthcare-nlp-embeddings-retrieval Healthcare NLP project using transformer-based embeddings for text...	11	Experimental	—	Python
40	MeghanaDarla99/medical-foundation-models-datathon Interactive visualization of Emory CXR embeddings using foundation models...	11	Experimental	—	Jupyter Notebook
41	SharvenRane/multimodal-embeddings Building and comparing multimodal embedding spaces across text, image, and...	11	Experimental	—	Python

Comparisons in this category

biocentral_server and biocentral_api (40 vs 36)