clinical-data

There are 5 repositories under clinical-data topic.

PyHealth
sunlabuiuc / PyHealth
A Deep Learning Python Toolkit for Healthcare Applications.
clinical-data clinical-research data-mining deep-learning electronic-health-record electronic-medical-record healthcare medical-code preprocessing
Language:Python 876
YerevaNN / mimic3-benchmarks
Python suite to construct benchmark machine learning datasets from the MIMIC-III 💊 clinical database.
benchmark clinical-data deep-learning machine-learning
Language:Python 766
NYUMedML / DeepEHR
Chronic Disease Prediction Using Medical Notes
medical nlp-machine-learning deep-learning clinical-data embeddings open-source open-datasets
Language:Python 257
cqframework / clinical_quality_language
Clinical Quality Language (CQL) is an HL7 specification for the expression of clinical knowledge that can be used within both the Clinical Decision Support (CDS) and Clinical Quality Measurement (CQM) domains. This repository contains complementary tooling in support of that specification.
cql clinical-quality-language cds java cqm fhir fhir-path clinical-decision-support clinical-quality-measurement clinical-data clinical-trials clinical-research clinical-reasoning dqm ecqm hl7
Language:Java 243
ehrbase / ehrbase
An open source openEHR server
openehr ehr clinical-data clinical cdr
Language:Java 208
ppazos / cabolabs-ehrserver
Open platform to manage and share standardized clinical data, designed by @ppazos at CaboLabs Health Informatics.
clinical-data openehr-standard ehr cdr openehr cabolabs ehrserver
Language:Groovy 167
clips / clicr
Machine reading comprehension on clinical case reports
machine-reading question-answering clinical-data medical-dataset natural-language-processing neural-networks reading-comprehension
Language:Python 144
genular / pandora
PANDORA - Predictive Analytics aNd Data Oriented Research Applications :computer:
machine-learning systems-biology data-science data-visualization data-mining pandora bioinformatics biomarkers clinical-data clustering data-integration drug-discovery genomic-data-analysis microbiome predictive-analytics transcriptomics tsne umap unsupervised-machine-learning
Language:Vue 132
NYUMedML / CNN_design_for_AD
Code for "Generalizable deep learning model for early Alzheimer’s disease detection from structural MRIs"
convolutional-neural-networks alzheimer-disease clinical-data medical-imaging mri deep-learning artificial-intelligence dementia mild-cognitive-impairment brain-mri
Language:Jupyter Notebook 125
futianfan / clinical-trial-outcome-prediction
benchmark dataset and Deep learning method (Hierarchical Interaction Network, HINT) for clinical trial approval probability prediction, published in Cell Patterns 2022.
clinical-trials clinical-data graph-neural-networks benchmark-datasets dataset-generation benchmark drug-design drug-development life-sciences dataset therapeutics clinical-research-data-warehouse clinical-research machine-learning deep-learning
Language:Python 84
Oulu-IMEDS / OAProgression
Multimodal Machine Learning-based Knee Osteoarthritis Progression Prediction from Plain Radiographs and Clinical Data
clinical-data clinical-decision-support deep-learning disease-progression medicine osteoarthritis pytorch radiology reproducible-research
Language:Python 71
VectorInstitute / cyclops
Toolkit for health AI implementation
clinical-data drift-detection mimic-iv omop-cdm clinical-decision-support healthcare mimic-iii physionet model-monitoring data-drift machine-learning deep-learning evaluation eicu-crd clinical-research electronic-health-record electronic-medical-record
Language:Python 65
rfhb / ctrdata
Aggregate and analyse information on clinical trials from public registers
clinical-trials trial register database r studies ctgov nodbi cran duckdb mongodb postgresql r-package rstats sqlite clinical-data clinical-research clinical-studies
Language:R 39
aphp / Cohort360
A web application to find patients, build cohorts and visualize health records
cohorts clinical-data visualize-data find-patients query medical cohort-analysis cohort-studies cohort-selection cohort-data data-visualization medtech fhir-api fhir omop omop-cdm
Language:TypeScript 37
yao8839836 / CEMRClass
Traditional Chinese Medicine Clinical Records Classification. In BIBM 2016
clinical-data text-classification traditional-chinese-medicine
Language:Java 37
rvandewater / YAIB
🧪Yet Another ICU Benchmark: a holistic framework for the standardization of clinical prediction model experiments. Provide custom datasets, cohorts, prediction tasks, endpoints, preprocessing, and models. Paper: https://arxiv.org/abs/2306.05109
amsterdamumcdb benchmark clinical-data clinical-ml deep-learning ehr eicu-crd framework hirid-dataset icu machine-learning mimic-iii mimic-iv patient-monitoring time-series
Language:Python 30
berkanlafci / oadat
OADAT: Experimental and Synthetic Clinical Optoacoustic Data for Standardized Image Processing
deep-learning optoacoustics clinical-data photoacoustics multispectral-images
Language:Python 29
AI-in-Health / Patient-Instructions
Code for "Retrieve, Reason, and Refine: Generating Accurate and Faithful Patient Instructions" (NeurIPS 2022)
clinical-data clinical-nlp knowledge-graph machine-learning neurips neurips-2022 retrieve
Language:Jupyter Notebook 26
TeamHeka / medkit
This repository is now archived. Further development has been moved to https://github.com/medkit-lib/medkit.
annotations clinical-data machine-learning medicine nlp pipelines provenance speech-to-text
Language:Python 23
XanderJC / medkit-learn
The Medkit-Learn(ing) Environment: Medical Decision Modelling through Simulation (NeurIPS 2021) by Alex J. Chan, Ioana Bica, Alihan Huyuk, Daniel Jarrett, and Mihaela van der Schaar.
benchmark clinical-data imitation-learning machine-learning medicine offline-rl python reinforcement-learning synthetic-data
Language:Python 23
CogStack / MedCATtutorials
General tutorials for the setup and use of MedCAT.
clinical-data electronic-health-records natural-language-processing
Language:HTML 21
ICD_GEMs.jl
JuliaHealth / ICD_GEMs.jl
ICD_GEMs.jl is a Julia package that allows to translate ICD-9 codes in ICD-10 and viceversa via the General Equivalence Mappings (GEMs) of the International Classification of Diseases (ICD).
julia julia-language julia-package clinical-data death-certificates health-data icd-10 icd-10-cm icd-9 icd-codes cdc clinical-research who data epidemiology public-health mortality-data
Language:Julia 15
thbuerg / MetabolomicsCommonDiseases
⛑ Code for "Metabolomic profiles predict individual multi-disease outcomes" ⛑
cardiovascular-diseases clinical-data common-diseases deep-learning metabolomics nmr-metabolomics risk-modelling survival-analysis
Language:Jupyter Notebook 13
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.
diagnosis extraction natural-language-processing machine-learning clinical-data machine-learning-algorithms big-data classification-algorithm ehr-data electronic-health-records text-processing notebook-diagnosis emr text-classification python
Language:Jupyter Notebook 11
curedao / health-reference-data
Standard health reference databases including units of measurement, biomarkers, medical codes, medications, side-effects, supplements, foods, ingredients, and more.
clinical-data clinical-data-warehouse clinical-research clinical-trials database health healthcare sql
Language:HTML 9
fr4j4 / ClinicaRamis
Plataforma web clínica dental
clinical-data management-system platform laravel
Language:PHP 9
acampillos / sepsis-prediction
Early prediction of sepsis with gradient boosting (XGBoost) and deep learning (LSTM and GRU) using MIMIC-III data.
lstm clinical-data gru mimic-iii sepsis xgboost time-series-classification
Language:Jupyter Notebook 8
joanacmbarros / analysis-results-data-model
Data analysis produces data in the form of results. Although integrating and putting findings into context is a cornerstone of scientific work, data of this type is often neglected. The analysis results data model is a proposed solution to this issue that combines analysis standards with a common data model.
data-model data-analysis analysis-results data-management data-stewardship clinical-data clinical-data-management automation data-standards
Language:R 8
lindvalllab / MLSym
Deep learning for cancer symptoms monitoring on the basis of EHR unstructured clinical notes
nlp nlp-parsing clinical-notes clinical-data deep-learning ner ehr
Language:Python 7
NCATS-Tangerine / tranql
A Translator Query Language
knowledge-graph semantic-web clinical-data webgl indexeddb ncats-translator
Language:Python 7
arsenij-ust / cbpManager
Generate, manage and edit data and metadata files suitable for the import in cBioPortal for Cancer Genomics.
cancer-genomics clinical-data patient-data mutation-data cbioportal filegenerator
Language:Python 6
csinva / clinical-rule-analysis
Analyzing clinical decision instruments through the lens of data and large language models.
algorithmic-bias artificial-intelligence clinical-data clinical-data-warehouse clinical-decision-support large-language-models machine-learning natural-language-processing openai-api web-scraping deep-learning healthcare-ai healthcare-data huggingface-transformers python3 imodelsx
Language:Jupyter Notebook 6
derekmma / DICE
[ACL'23 main] DICE: Data-Efficient Clinical Event Extraction with Generative Models
clinical-data clinical-information-extraction clinical-research event-extraction generative-model information-extraction pytorch structure-prediction
6
HL7 / fhir-qi-core
Quality Improvement Core FHIR Profiles
quality-improvement fhir-profiles fhir profile clinical-data clinical-quality-measurement clinical-decision-support fhir-ig
Language:HTML 6
linhaowei1 / GDCurer
❤️ GDCurer: An AI-assisted Drug Dosage Prediction System for Graves' Disease
ai4medicine clinical-data lifelong-learning weak-supervision ai4sci
Language:JavaScript 6
vincenzorusso3 / mimic-iv-benchmarks
FDSML Course Project 2020/21
benchmark-datasets clinical-data clinical-prediction-tasks keras machine-learning mortality-prediction numpy pandas sklearn
Language:Python 6

clinical-data

sunlabuiuc / PyHealth

YerevaNN / mimic3-benchmarks

NYUMedML / DeepEHR

cqframework / clinical_quality_language

ehrbase / ehrbase

ppazos / cabolabs-ehrserver

clips / clicr

genular / pandora

NYUMedML / CNN_design_for_AD

futianfan / clinical-trial-outcome-prediction

Oulu-IMEDS / OAProgression

VectorInstitute / cyclops

rfhb / ctrdata

aphp / Cohort360

yao8839836 / CEMRClass

rvandewater / YAIB

berkanlafci / oadat

AI-in-Health / Patient-Instructions

TeamHeka / medkit

XanderJC / medkit-learn

CogStack / MedCATtutorials

JuliaHealth / ICD_GEMs.jl

thbuerg / MetabolomicsCommonDiseases

levrex / DiagnosisExtraction_ML

curedao / health-reference-data

fr4j4 / ClinicaRamis

acampillos / sepsis-prediction

joanacmbarros / analysis-results-data-model

lindvalllab / MLSym

NCATS-Tangerine / tranql

arsenij-ust / cbpManager

csinva / clinical-rule-analysis

derekmma / DICE

HL7 / fhir-qi-core

linhaowei1 / GDCurer

vincenzorusso3 / mimic-iv-benchmarks