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 42 clinical code embeddings tools tracked. 1 score above 50 (established tier). The highest-rated is mims-harvard/ClinVec at 50/100 with 83 stars.

Get all 42 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...	50	Established	83	Jupyter Notebook
2	NYUMedML/DeepEHR Chronic Disease Prediction Using Medical Notes	49	Emerging	272	Python
3	mims-harvard/SHEPHERD SHEPHERD: Few shot learning for phenotype-driven diagnosis of patients with...	47	Emerging	79	HTML
4	biocentral/biocentral_server Compute functionality for biocentral.	44	Emerging	4	Python
5	nomic-ai/contrastors Train Models Contrastively in Pytorch	43	Emerging	777	Python
6	hybrid-kg/clep 🤖 A Python Package for generating new patient representations driven by data...	43	Emerging	24	Python
7	biocentral/biocentral Biomedical data, from lab to paper.	41	Emerging	18	Dart
8	JohnGiorgi/DeCLUTR The corresponding code from our paper "DeCLUTR: Deep Contrastive Learning...	41	Emerging	378	Python
9	shipra25jain/ESSNet Embedding-based Scalable Segmentation Network	39	Emerging	28	Python
10	multimodal/multimodal A collection of multimodal datasets, and visual features for VQA and...	37	Emerging	84	Python
11	clips/yarn Disambiguating biomedical and clinical concepts with word embeddings	36	Emerging	14	Python
12	squaresLab/VarCLR VarCLR: Variable Semantic Representation Pre-training via Contrastive Learning	34	Emerging	40	Python
13	biocentral/biocentral_api Programmatic access to the biocentral ecosystem.	34	Emerging	2	Python
14	ratschlab/clinical-embeddings Repository for the Paper: „On the Importance of Step-wise Embeddings for...	33	Emerging	7	Python
15	bio-ontology-research-group/ontology-extension Combining lexical and context features for automatic ontology extension	32	Emerging	4	Python
16	faris-k/self-supervised-wafermaps Self-Supervised Representation Learning of Semiconductor Wafer Maps using PyTorch	31	Emerging	4	Jupyter Notebook
17	janmejaybhoi/Sequential-Sentence-Classification-in-Medical-Abstracts Implemented a Research paper "PubMed 200k RCT: a Dataset for Sequential...	31	Emerging	3	Jupyter Notebook
18	sdimi/Step2heart 🏋️ Extract generalizable physiological representations from sensor...	30	Emerging	19	Python
19	jacobdeasy/flexible-ehr Time-Sensitive Deep Learning for ICU Outcome Prediction Without Variable...	30	Emerging	19	Python
20	imonban/RadiologyReportEmbedding Intelligent Word Embeddings of Free-Text Radiology Reports	29	Experimental	24	—
21	BrahimFakri/Patient-Health-Data-Analysis-And-Feature-Extraction-For-Machine-Learning Embeddings generation from MIMIC-IV and MIMIC-CXR	28	Experimental	8	Jupyter Notebook
22	elleros/DSHealth2019_loinc_embeddings Code and Word2Vec embeddings of LOINC codes for KDD 2019 DSHealth paper...	28	Experimental	11	Jupyter Notebook
23	GanjinZero/CODER CODER: Knowledge infused cross-lingual medical term embedding for term...	27	Experimental	80	Python
24	lamalab-org/PolyBind API for getting embeddings for different polymer identifiers	25	Experimental	5	Python
25	biocentral/bio_flutter Working with biological data in flutter.	24	Experimental	2	Dart
26	dermatologist/cui-embed Gensim wrapper for the clinical (CUI) embeddings	23	Experimental	3	Python
27	przemo145235/radiology-report-triage-llm 🩻 Classify radiology reports as Normal or Abnormal with high accuracy using...	23	Experimental	—	Python
28	drgriffis/text-essence Preprocessing and analysis for training SNOMED-CT concept embeddings from...	22	Experimental	16	Python
29	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	21	Experimental	7	—
30	zenlm/jin Multimodal AI — vision, audio, 3D embeddings	21	Experimental	—	Python
31	ThalesMMS/mammography-pipelines-py Mammography experimentation repo delivering reproducible preprocessing,...	21	Experimental	—	Python
32	rezacsedu/Convolutional-embedded-networks Convolutional Embedded Networks for Population Scale Clustering and...	20	Experimental	11	Python
33	zurlog/abs-embeddings-eval Code for the paper "Abstracts Embeddings Evaluation: A Case Study of...	18	Experimental	2	Jupyter Notebook
34	SharvenRane/radiology-report-triage-llm Zero-shot radiology report triage using LLM embeddings (Sentence...	17	Experimental	—	Python
35	hunsao/embeddings-age-bias-analysis Analysis of embeddings and age biases in image generation models using CLIP,...	15	Experimental	—	HTML
36	MeghanaDarla99/medical-foundation-models-datathon Interactive visualization of Emory CXR embeddings using foundation models...	13	Experimental	—	Jupyter Notebook
37	roytalman/Deep_contrastive_embedding Deep supervised conistrastive learning for small datasets (few shot...	13	Experimental	10	Jupyter Notebook
38	Charithareddt/healthcare-nlp-embeddings-retrieval Healthcare NLP project using transformer-based embeddings for text...	13	Experimental	—	Python
39	SharvenRane/multimodal-embeddings Building and comparing multimodal embedding spaces across text, image, and...	13	Experimental	—	Python
40	tvtaerum/embedding_derived_heatmaps cGAN_diff - more than pretty faces	11	Experimental	—	Python
41	rahulvigneswaran/pix2pix-zero-directions This repo contains edit directions for 100 more classes for the paper...	11	Experimental	—	Python
42	nshen7/multimodal-cell-matching Solution to one of the problems in 2021 NeurIPS Competition: A...	10	Experimental	2	Jupyter Notebook

Comparisons in this category

biocentral_server and biocentral_api (44 vs 34)