clinical-data

There are 7 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 1076
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 828
ehrbase / ehrbase
An open source openEHR server
openehr ehr clinical-data clinical cdr
Language:Java 290
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 273
NYUMedML / DeepEHR
Chronic Disease Prediction Using Medical Notes
clinical-data deep-learning embeddings medical nlp-machine-learning open-datasets open-source
Language:Python 268
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 185
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 151
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 148
genular / pandora
PANDORA :computer:
bioinformatics biomarkers clinical-data clustering data-integration data-mining data-science data-visualization drug-discovery genomic-data-analysis machine-learning microbiome pandora predictive-analytics systems-biology transcriptomics tsne umap unsupervised-machine-learning
Language:Vue 136
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.
benchmark benchmark-datasets clinical-data clinical-research clinical-research-data-warehouse clinical-trials dataset dataset-generation deep-learning drug-design drug-development graph-neural-networks life-sciences machine-learning therapeutics
Language:Python 114
VectorInstitute / cyclops
A toolkit for evaluating and monitoring AI models in clinical settings
clinical-data clinical-decision-support clinical-research data-drift deep-learning drift-detection eicu-crd electronic-health-record electronic-medical-record evaluation healthcare machine-learning mimic-iii mimic-iv model-monitoring omop-cdm physionet
Language:Python 81
imedslab / 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 80
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 64
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 46
rfhb / ctrdata
Aggregate and analyse information on clinical trials from public registers
clinical-data clinical-research clinical-studies clinical-trials cran ctgov database duckdb mongodb nodbi postgresql r r-package register rstats sqlite studies trial
Language:HTML 45
yao8839836 / CEMRClass
Traditional Chinese Medicine Clinical Records Classification. In BIBM 2016
clinical-data text-classification traditional-chinese-medicine
Language:Java 39
CogStack / MedCATtutorials
General tutorials for the setup and use of MedCAT.
clinical-data natural-language-processing electronic-health-records
Language:HTML 37
berkanlafci / oadat
OADAT: Experimental and Synthetic Clinical Optoacoustic Data for Standardized Image Processing
deep-learning optoacoustics clinical-data photoacoustics multispectral-images
Language:Python 33
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 32
AI-in-Health / Patient-Instructions
[NeurIPS 2022] Code for "Retrieve, Reason, and Refine: Generating Accurate and Faithful Discharge/Patient Instructions"
clinical-data clinical-nlp knowledge-graph machine-learning neurips neurips-2022 retrieve
Language:Jupyter Notebook 30
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 29
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
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 22
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 15
acampillos / sepsis-prediction
Early prediction of sepsis with gradient boosting (XGBoost) and deep learning (LSTM and GRU) using MIMIC-III data.
clinical-data gru lstm mimic-iii sepsis time-series-classification xgboost
Language:Jupyter Notebook 14
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 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 12
curedao / health-reference-data
Standard health reference databases including units of measurement, biomarkers, medical codes, medications, side-effects, supplements, foods, ingredients, and more.
health healthcare clinical-trials clinical-data-warehouse clinical-research clinical-data sql database
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
AnnoDash
justin13601 / AnnoDash
[JAMIA Open] A clinical terminology annotation dashboard created using Plotly Dash & the MIMIC-IV database.
annotation clinical-data dashboard nlp-machine-learning python data-visualization
Language:Python 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 8
NCATS-Tangerine / tranql
A Translator Query Language
knowledge-graph semantic-web clinical-data webgl indexeddb ncats-translator
Language:Python 8
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
8
SwanseaUniversityMedical / concept-library
Concept Library - a system for storing, managing, sharing and documenting clinical code lists in health research through Phenotypes.
clinical-coding clinical-data clinical-research health-research medical medical-coding medical-data
Language:Python 8

clinical-data

sunlabuiuc / PyHealth

YerevaNN / mimic3-benchmarks

ehrbase / ehrbase

cqframework / clinical_quality_language

NYUMedML / DeepEHR

ppazos / cabolabs-ehrserver

NYUMedML / CNN_design_for_AD

clips / clicr

genular / pandora

futianfan / clinical-trial-outcome-prediction

VectorInstitute / cyclops

imedslab / OAProgression

rvandewater / YAIB

aphp / Cohort360-FrontEnd

rfhb / ctrdata

yao8839836 / CEMRClass

CogStack / MedCATtutorials

berkanlafci / oadat

yahskapar / PPSNet

AI-in-Health / Patient-Instructions

XanderJC / medkit-learn

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

justin13601 / AnnoDash

lindvalllab / MLSym

NCATS-Tangerine / tranql

pchandiwal-livongo / datascience_books

SwanseaUniversityMedical / concept-library