clinical-data

There are 6 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 988
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 805
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.
cds clinical-data clinical-decision-support clinical-quality-language clinical-quality-measurement clinical-reasoning clinical-research clinical-trials cql cqm dqm ecqm fhir fhir-path hl7 java
Language:Java 266
NYUMedML / DeepEHR
Chronic Disease Prediction Using Medical Notes
clinical-data deep-learning embeddings medical nlp-machine-learning open-datasets open-source
Language:Python 266
ehrbase / ehrbase
An open source openEHR server
cdr clinical clinical-data ehr openehr
Language:Java 262
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 181
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 149
NYUMedML / CNN_design_for_AD
Code for "Generalizable deep learning model for early Alzheimer’s disease detection from structural MRIs"
alzheimer-disease artificial-intelligence brain-mri clinical-data convolutional-neural-networks deep-learning dementia medical-imaging mild-cognitive-impairment mri
Language:Jupyter Notebook 140
genular / pandora
PANDORA :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 135
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 102
VectorInstitute / cyclops
Toolkit for evaluating and monitoring AI models in clinical settings
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 76
Oulu-IMEDS / OAProgression
Multimodal Machine Learning-based Knee Osteoarthritis Progression Prediction from Plain Radiographs and Clinical Data
osteoarthritis pytorch disease-progression reproducible-research deep-learning medicine radiology clinical-data clinical-decision-support
Language:Python 75
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 54
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 43
aphp / Cohort360-FrontEnd
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 42
yao8839836 / CEMRClass
Traditional Chinese Medicine Clinical Records Classification. In BIBM 2016
clinical-data text-classification traditional-chinese-medicine
Language:Java 39
berkanlafci / oadat
OADAT: Experimental and Synthetic Clinical Optoacoustic Data for Standardized Image Processing
clinical-data deep-learning multispectral-images optoacoustics photoacoustics
Language:Python 32
CogStack / MedCATtutorials
General tutorials for the setup and use of MedCAT.
clinical-data natural-language-processing electronic-health-records
Language:HTML 31
AI-in-Health / Patient-Instructions
Code for "Retrieve, Reason, and Refine: Generating Accurate and Faithful Discharge/Patient Instructions" (NeurIPS 2022)
clinical-data clinical-nlp knowledge-graph machine-learning neurips neurips-2022 retrieve
Language:Jupyter Notebook 28
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.
python machine-learning reinforcement-learning offline-rl medicine clinical-data synthetic-data imitation-learning benchmark
Language:Python 28
yahskapar / PPSNet
PPSNet: Leveraging Near-Field Lighting for Monocular Depth Estimation from Endoscopy Videos (ECCV, 2024)
clinical-data depth depth-estimation depth-refinement endoscopic-vision endoscopy endoscopy-video inverse-rendering knowledge-distillation monocular-depth-estimation near-field photometric sim2real transfer-learning
Language:Python 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 24
thbuerg / MetabolomicsCommonDiseases
⛑ Code for "Metabolomic profiles predict individual multi-disease outcomes" ⛑
nmr-metabolomics metabolomics deep-learning risk-modelling survival-analysis clinical-data common-diseases cardiovascular-diseases
Language:Jupyter Notebook 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 17
ineelhere / clintrialx
R package to fetch and explore clinical trials data from freely available registries. Fetch data in bulk, customize data and build comprehensive html reports. Currently, it supports the ClinicalTrials.gov registry and CTTI AACT (Access to Aggregate Content of ClinicalTrials.gov).
clinical-data clinical-trials data data-management r-language r-package bioinformatics medical-informatics trials aact ctti clinicaltrialsgov
Language:R 14
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 13
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 12
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
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 9
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 8
fr4j4 / ClinicaRamis
Plataforma web clínica dental
clinical-data management-system platform laravel
Language:PHP 8
NCATS-Tangerine / tranql
A Translator Query Language
clinical-data indexeddb knowledge-graph ncats-translator semantic-web webgl
Language:Python 8
AnnoDash
justin13601 / AnnoDash
A clinical terminology annotation dashboard created using Plotly Dash & the MIMIC-IV database.
annotation clinical-data dashboard data-visualization nlp-machine-learning python
Language:Python 7
lindvalllab / MLSym
Deep learning for cancer symptoms monitoring on the basis of EHR unstructured clinical notes
clinical-data clinical-notes deep-learning ehr ner nlp nlp-parsing
Language:Python 7
pchandiwal-livongo / datascience_books
Springer has released hundreds of free books on a wide range of topics to the general public.
ai algebra bayesian clinical-data data-science datascience machine-learning machine-learning-algorithms ml mlops regression-models springer springer-book statistical-analysis statistics time-series
7

clinical-data

sunlabuiuc / PyHealth

YerevaNN / mimic3-benchmarks

cqframework / clinical_quality_language

NYUMedML / DeepEHR

ehrbase / ehrbase

ppazos / cabolabs-ehrserver

clips / clicr

NYUMedML / CNN_design_for_AD

genular / pandora

futianfan / clinical-trial-outcome-prediction

VectorInstitute / cyclops

Oulu-IMEDS / OAProgression

rvandewater / YAIB

rfhb / ctrdata

aphp / Cohort360-FrontEnd

yao8839836 / CEMRClass

berkanlafci / oadat

CogStack / MedCATtutorials

AI-in-Health / Patient-Instructions

XanderJC / medkit-learn

yahskapar / PPSNet

TeamHeka / medkit

thbuerg / MetabolomicsCommonDiseases

JuliaHealth / ICD_GEMs.jl

ineelhere / clintrialx

acampillos / sepsis-prediction

vincenzorusso3 / mimic-iv-benchmarks

levrex / DiagnosisExtraction_ML

curedao / health-reference-data

joanacmbarros / analysis-results-data-model

arsenij-ust / cbpManager

fr4j4 / ClinicaRamis

NCATS-Tangerine / tranql

justin13601 / AnnoDash

lindvalllab / MLSym

pchandiwal-livongo / datascience_books