GitHub topics: ehr-data
cumc-dbmi/cehrbert
CEHR-BERT: Incorporating temporal information from structured EHR data to improve prediction tasks
Language: Python - Size: 17.4 MB - Last synced at: about 10 hours ago - Pushed at: about 11 hours ago - Stars: 35 - Forks: 11
Blacksujit/Health-Summerize-AI
HealthSummarizeAI is an innovative NLP-based tool designed to transform the way healthcare professionals interact with electronic health records (EHR). By leveraging advanced entity recognition and text summarization techniques, HealthSummarize efficiently extracts and condenses critical information .
Language: Jupyter Notebook - Size: 102 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 0 - Forks: 0
ai4biomedicine/surgVAE
JAMIA: A Novel Generative Multi-Task Representation Learning Approach for Predicting Postoperative Complications in Cardiac Surgery Patients
Language: Python - Size: 113 KB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 3 - Forks: 0
CNAG-Biomedical-Informatics/convert-pheno
A software toolkit for the interconversion of standard data models for phenotypic data
Language: Perl - Size: 121 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 13 - Forks: 1
ehrtools/codelist-tools
This is a set of useful tools for using, creating, validating and generally working with Codelists in Health Research. The tools are in Rust with Python and R bindings so they can be used in any of the 3 languages.
Language: Rust - Size: 190 KB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 3 - Forks: 0
jordandeklerk/EHR-BERT
BERT style transformer model on CMS synthetic EHR data for diagnosis and procedure prediction in PyTorch
Language: Python - Size: 50.7 MB - Last synced at: 7 days ago - Pushed at: 8 days ago - Stars: 1 - Forks: 0
etnc/synmed-ehr-generator
The SynMed EHR Generator is a tool for creating synthetic Electronic Health Records (EHRs) represented as Knowledge Graphs in RDF and FHIR formats.
Language: Python - Size: 8.63 MB - Last synced at: 13 days ago - Pushed at: 13 days ago - Stars: 1 - Forks: 0
sadidan12/synthea_data-analysis
Synthea Data Analysis
Language: Jupyter Notebook - Size: 17 MB - Last synced at: 13 days ago - Pushed at: 13 days ago - Stars: 0 - Forks: 0
Simonlee711/Clinical_ModernBERT
[arXiv 2025] Pre-training script for Clinical ModernBERT
Language: Python - Size: 1 MB - Last synced at: 13 days ago - Pushed at: 13 days ago - Stars: 4 - Forks: 2
Simonlee711/MEME
[arXiv] Multiple Embedding Model for EHR (MEME) used for strong prediction on Emergency Department tasks
Language: Python - Size: 19.6 MB - Last synced at: 13 days ago - Pushed at: 13 days ago - Stars: 11 - Forks: 3
Penky-pra/RP14
This repository presents the early phase of a research project focused on clinical pathway discovery for melanoma patients using Electronic Health Record (EHR) data. The research leverages stochastic modeling, deep learning, and process mining techniques to model patient trajectories and support clinical decision-making
Language: Python - Size: 3.56 MB - Last synced at: 19 days ago - Pushed at: 19 days ago - Stars: 0 - Forks: 0
SAFEHR-data/omopcept
omopcept : an R package to access OMOP conCEPTs (no cons!) and flexible tidyverse compatible R functions for querying and visualising.
Language: R - Size: 17.2 MB - Last synced at: 20 days ago - Pushed at: 20 days ago - Stars: 13 - Forks: 2
MuhangTian/TimeDiff
Code to generate realistic synthetic healthcare data with diffusion models
Language: Jupyter Notebook - Size: 13.9 MB - Last synced at: 22 days ago - Pushed at: 22 days ago - Stars: 16 - Forks: 4
yaacoo/graphRagSqlator
LLM graph-RAG SQL generator for large databases with poor documentation
Language: Python - Size: 23.4 KB - Last synced at: 23 days ago - Pushed at: 8 months ago - Stars: 7 - Forks: 1
aim-rsf/cprd-data-wrangle
Introduction to CPRD using synthetic datasets
Language: Jupyter Notebook - Size: 25.7 MB - Last synced at: about 1 month ago - Pushed at: 2 months ago - Stars: 6 - Forks: 0
jameszhou-gl/HiSGT
Code for "Generating Clinically Realistic EHR Data via a Hierarchy- and Semantics-Guided Transformer"
Language: Python - Size: 80.6 MB - Last synced at: 15 days ago - Pushed at: 15 days ago - Stars: 3 - Forks: 1
zimolzak/healthcare-data-quality
Lecture slides on Electronic Health Record Data Quality
Language: Makefile - Size: 1.71 MB - Last synced at: about 1 month ago - Pushed at: 5 months ago - Stars: 1 - Forks: 0
carriedaymont/growthcleanr
R package for cleaning anthropometric (height and weight) data from electronic health record systems.
Language: R - Size: 14.7 MB - Last synced at: 16 days ago - Pushed at: 2 months ago - Stars: 14 - Forks: 9
mims-harvard/CLEF
Controllable Sequence Editing for Counterfactual Generation
Language: Python - Size: 630 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 1 - Forks: 0
cdcai/premier_analysis
A deep learning project predicting hyperinflammatory syndrome among COVID-19 patients using EHR data.
Language: Jupyter Notebook - Size: 23.3 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 5 - Forks: 11
yhzhu99/pyehr
COVID-19 EHR data analysis pipeline
Language: Python - Size: 178 KB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 17 - Forks: 1
N3ha-Rao/Synthea-COVID19-EDA
Exploratory Data Analysis of synthetic COVID-19 patient data generated by Synthea, focusing on patient demographics, healthcare encounters, and prevalent conditions.
Language: Python - Size: 12.7 KB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0
ehsan-ashik/smart-on-fhir-vuejs-client-portal
Smart-on-FHIR Client Portal, authorizes with Logica Sandbox server and fetches EHR data, and with fallback to local FHIR server capability.
Language: Vue - Size: 219 KB - Last synced at: about 2 months ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0
karimosman89/health-risk-assessment
Predict health risks based on patient data.Create a machine learning model that predicts health risks (like diabetes or heart disease) based on patient data.Help healthcare providers identify at-risk patients for early intervention.
Language: Jupyter Notebook - Size: 545 KB - Last synced at: 2 months ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0
Baltruschat-L/Capstone-plspm-analysis-additional-material
The code is used for my capstone which is about the user acceptability of blockchain technology to exchange EHR. For the survey analysis I used PLS SEM
Language: Jupyter Notebook - Size: 704 KB - Last synced at: 3 months ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0
EternityYW/FairEHR-CLP
Official implementation of "FairEHR-CLP: Towards Fairness-Aware Clinical Predictions with Contrastive Learning in Multimodal Electronic Health Records" (MLHC 2024)
Language: Python - Size: 150 KB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 2 - Forks: 0
PericlesHat/TACCO
Official implementation of TACCO (Task-guided Co-clustering).
Language: Python - Size: 766 KB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 2 - Forks: 1
brunof99/Data-Driven-Healthcare-Insights-and-Outcomes
Discovering healthcare insights through data-driven analysis of EHRs. This project comprises three subprojects: data cleaning & preparation, exploratory data analysis and lastly, predictive modeling for in-hospital mortality and clinical risk stratification.
Language: Jupyter Notebook - Size: 3.98 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 0 - Forks: 0
yhzhu99/pyehr-playground
COVID-19 EHR Benchmark - Online Platform
Language: Vue - Size: 735 KB - Last synced at: 12 months ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0
aaryapatel007/Patient-Selection-for-Diabetes-Drug-Testing
Built a regression model that predicts the expected days of hospitalization time and an uncertainty range estimation.
Language: Jupyter Notebook - Size: 3.73 MB - Last synced at: 12 months ago - Pushed at: almost 5 years ago - Stars: 12 - Forks: 6
Ashutosh27ind/MIMIC_EHR_Predictor
This is implementation of my Masters thesis work and aims at predicting the patient mortality from the MIMIC-III v1.4 Database
Language: Jupyter Notebook - Size: 8.42 MB - Last synced at: about 1 year ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 0
vgees/AI-in-EHR-Data
Regression Model to predict the estimated hospitalisation for a patient to test a new drug for Diabetes using EHR data
Language: HTML - Size: 874 KB - Last synced at: about 1 year ago - Pushed at: almost 5 years ago - Stars: 1 - Forks: 0
premchand9985/Predicting_Incident_HeartFailure_Disease_Based-on-Transformers
This repository hosts a cutting-edge deep learning model developed to predict 6-month incident heart failure utilizing electronic health records (EHRs). Heart failure is a multifaceted medical condition characterized by its significant impact on patients' well-being and healthcare systems.
Language: Python - Size: 302 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 0
Simonlee711/ABP_Imputation-With-EHR
ABP Imputation with EHR medication data is the second version of the ABP Imputer model.
Language: Jupyter Notebook - Size: 85.5 MB - Last synced at: about 1 year ago - Pushed at: almost 3 years ago - Stars: 0 - Forks: 0
CarlosUziel/diabetes-drug-testing
Identifying which patients to include or exclude from the clinical trials of a new diabetes drug based on predicted hospitalization time given by a machine learning regression model
Language: Jupyter Notebook - Size: 11.3 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 0
CornellMHILab/AI-Driven-Suicide-Risk-Prediction-in-Post-Hospitalized-Men Fork of rnt4002/AI-Driven-Suicide-Risk-Prediction-in-Post-Hospitalized-Men
This research uncovers the increased suicide risk in men with mental illness post-hospitalization, analyzing 1.4M+ cases. It highlights the importance of targeted interventions based on identified risk factors.
Language: Python - Size: 63.5 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0
bsn-si/IPEHR-gateway
IPEHR-gateway is a solution to provide benefits of decentralized architecture to common HMS apps using standard APIs. IPEHR gateway is used to encrypt and decrypt passing data, support AQL queries of encrypted data and manage user’s cryptographic keys.
Language: Go - Size: 3.35 MB - Last synced at: 6 months ago - Pushed at: over 1 year ago - Stars: 8 - Forks: 4
Endava/endava-hl7fhir-openapi
This repo contains demonstration code to illustrate the use of the FIHR standard for healthcare data, developed by the HL7 organisation.
Language: C# - Size: 697 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 6 - Forks: 5
Osilaja78/HealthDatum
HealthDatum is an electronic health record system that provides easy means of managing clinical data.
Language: Python - Size: 68.4 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0
MaitreeVaria/Federated-Learning-Rare-Genetic-Disorder-Classification
Welcome to the Federated Learning for Rare Genetic Disorder Classification project! This repository demonstrates the application of Federated Learning (FL) techniques to classify rare genetic disorders using Electronic Health Record (EHR) data while addressing two critical challenges: privacy and limited data availability.
Language: Jupyter Notebook - Size: 3.05 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0
PBarnaghi/medtimeline Fork of gosh-dre/medtimeline
The MedTimeline library aims to provide a standardised process for pre-processing and generating patient journey timelines for the cardiology EHR dataset. Developed by Louise Rigny (Great Ormond Street Hospital for Children)
Language: Jupyter Notebook - Size: 67.4 KB - Last synced at: about 15 hours ago - Pushed at: about 16 hours ago - Stars: 0 - Forks: 0
luoyuanlab/3dmice
Missing data imputation for longitudinal multi-variable EHR data. Paper in JAMIA.
Language: R - Size: 10.7 KB - Last synced at: over 1 year ago - Pushed at: almost 7 years ago - Stars: 6 - Forks: 0
yinchangchang/TAME
KDD2020 paper; Identifying Sepsis Subphenotypes via Time-Aware Multi-Modal Auto-Encoder
Language: Python - Size: 1.1 MB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 14 - Forks: 6
janschneida/Clinical-SimSpace-Explorer
Tool for EHR & mutation profile based patient clustering & visualization, developed in partial fulfillment of the requirements for the course “Medical Informatics” at the University Medical Center Göttingen.
Language: Python - Size: 18.1 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0
ptogias/dream-challenge-ehr
EHR DREAM Challenge: Patient Mortality Prediction Submission. "moore" team submission
Size: 391 KB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0
andysouth/caboodler
Eases access to Caboodle data warehouse from Epic Electronic Health Record
Language: R - Size: 20.5 KB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0
OmarAlkousa/Stroke-Prediction-Using-Electronic-Health-Records
This project aims to make predictions of stroke cases based on simple health data. Supervised machine learning algorithm was used after processing and analyzing the data. The model has predicted Stroke cases with 92.00% of sensitivity.
Language: Jupyter Notebook - Size: 1.85 MB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0
Aarhus-Psychiatry-Research/care-ml
CARE-ML: Predicting the use of restraint on psychiatric inpatients using EHRs and ML. Developed by sarakolding and signekb for their Master's Thesis.
Language: Python - Size: 13.3 MB - Last synced at: 5 months ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0
opensaucerer/attribute-based-access-control
A researched project that implements Attribute-Based Access Control in an EHR system. By encrypting EHRs using policies defined based on specific attributes, health care systems can be able to restrict how a data is accessed and what each user can do to the data being accessed.
Language: Python - Size: 13 MB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 8 - Forks: 4
Praneethkanchanakuntla/Electronic-Health-Care-System
A Electronic Health Care System is aimed digitalizing the health care by providing the hospital services in online mode.
Language: Jupyter Notebook - Size: 7.02 MB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 1
matjazbravc/Endava.Hl7.Fhir.OpenAPI.Demo
OpenAPI which maps custom EHRs into FHIR R4 Patient and Observation resources. Other resources were not implemented (yet).
Language: C# - Size: 1.94 MB - Last synced at: about 2 years ago - Pushed at: almost 3 years ago - Stars: 2 - Forks: 1
linzhenyuyuchen/kddMIMIC
Pipeline of Data Extraction, Preprocessing, Representation, and Training for MIMIC-III
Language: Python - Size: 37.3 MB - Last synced at: about 2 years ago - Pushed at: over 4 years ago - Stars: 9 - Forks: 1
sxtforreal/ehr_data_analysis
Electronic Health Record Analysis using SQLite
Language: Python - Size: 1.87 MB - Last synced at: about 2 years ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 0
luoyuanlab/autism_precision_medicine
Nature Medicine paper. A Multidimensional Precision Medicine Approach for Autism Subtype Identification.
Language: Shell - Size: 120 KB - Last synced at: about 2 years ago - Pushed at: almost 5 years ago - Stars: 9 - Forks: 6
magesh-technovator/bio-medical-clinical-ner
Collection of bio-medical and clinical ner models in spacy, stanza, flair with some utility files
Language: Python - Size: 1.02 MB - Last synced at: about 2 years ago - Pushed at: over 4 years ago - Stars: 4 - Forks: 1
levrex/DiagnosisExtraction_ML
Pipeline for building Machine Learning Classifiers for the diagnosis of EHR text-data. We used this pipeline for our study, published here: https://doi.org/10.2196/23930.
Language: Jupyter Notebook - Size: 31.3 MB - Last synced at: about 2 years ago - Pushed at: almost 3 years ago - Stars: 9 - Forks: 3
matjazbravc/Redox.Ehr.OpenApi.Demo
Due to the needs of one of our clients, I had to research Redox Engine and as a result, this demo was created. It shows how consume Redox APIs from a custom EHR WebAPI.
Language: C# - Size: 2.73 MB - Last synced at: about 2 years ago - Pushed at: over 4 years ago - Stars: 2 - Forks: 1
cesarcaraballoc/timing-of-blood-draws
We included the code to obtain the results reported in the study below:
Language: Stata - Size: 19.5 KB - Last synced at: about 2 years ago - Pushed at: almost 3 years ago - Stars: 0 - Forks: 0
jerrodanzalone/Rural-Urban-Mapping-Protocol-for-Linking-External-Sources
This pilot project deploys a supplemental OMOP table to map external measures of rurality (RUCC and RUCA).
Language: Python - Size: 20.2 MB - Last synced at: over 1 year ago - Pushed at: about 4 years ago - Stars: 1 - Forks: 0
YujiaBao/Hawkes-ADR
"Hawkes Process Modeling of Adverse Drug Reactions with Longitudinal Observational Data" MLHC 2017
Language: C++ - Size: 91.8 KB - Last synced at: about 2 years ago - Pushed at: over 6 years ago - Stars: 2 - Forks: 1
abhilampard/Hospital-Readmission-Prediction-XGBoost
Prediction of a readmission for a patient based on the Electronic Health Records (EHR) data. This project was done as part of a timed challenge with a time limit of 3 hours to work on this dataset. So, it is just a preliminary model using XGBoost algorithm with some basic data exploration for data processing.
Language: R - Size: 4.45 MB - Last synced at: about 2 years ago - Pushed at: over 5 years ago - Stars: 2 - Forks: 1
matjazbravc/HL7.FHIR.OpenAPI.Demo
OpenAPI which maps custom EHRs into FHIR R4 Patient and Observation resources. Other resources were not implemented (yet).
Language: C# - Size: 852 KB - Last synced at: about 2 years ago - Pushed at: about 4 years ago - Stars: 2 - Forks: 0
steve303/DeepLearning-XrayClassify
Deep Learning Methods for Chest X-ray Classification
Language: Jupyter Notebook - Size: 19.8 MB - Last synced at: about 2 years ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0
pranath/patient_select_diabetes
In this project, we will create a deep learning model trained on EHR data (Electronic Health Records) to find suitable patients for testing a new diabetes drug.
Language: Python - Size: 3.94 MB - Last synced at: about 2 years ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0
zacksaw/frozensection_MS_thesis
Used machine learning in R to assess individual variables involved in the intra-operative pathology consultation process.
Size: 329 KB - Last synced at: 6 months ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0
MuizMahdi/EHR-Route-Mono
The monolithic server-side repository of EHRoute, a secure Electronic Health Records (EHR) storage and sharing solution
Language: Java - Size: 1.63 MB - Last synced at: 5 months ago - Pushed at: over 5 years ago - Stars: 2 - Forks: 1
