sebastianGehrmann / phenotyping
This repository contains data and code for the paper"Comparing deep learning and concept extraction based methods for patient phenotyping".
☆21Updated 6 years ago
Related projects ⓘ
Alternatives and complementary repositories for phenotyping
- Python library for hierarchy of ICD9 Codes☆102Updated 5 years ago
- ☆30Updated 7 years ago
- Mapping the MIMIC-III database to the OMOP schema☆127Updated 7 months ago
- Public release of the DeepPhe analytic software☆30Updated last year
- Health knowledge graph for 157 diseases and 491 symptoms, learned from >270,000 patients' data☆97Updated 3 years ago
- ☆51Updated 4 years ago
- Source code for Medical Concept Embedding with Time-Aware Embedding☆20Updated 5 years ago
- init☆11Updated 2 months ago
- Surfacing Semantic Data from Clinical Notes in Electronic Health Records for Tailored Care, Trial Recruitment and Clinical Research☆89Updated last year
- Implementation of Deep Patient Representation of Clinical Notes at Intensive Care Unit for Multi-Task Prediction☆31Updated 5 years ago
- Corresponding code for experiments described in "Predicting Clinical Outcomes Across Changing Electronic Health Records." Presented at KD…☆11Updated 7 years ago
- Quick script to parse out medications from discharge summaries in MIMIC format. Not that this approach uses minimal NLP, and can be vatly…☆27Updated 6 years ago
- Unofficial Journal of American Medical Informatics Association (JAMIA) Markdown Journal Article Template☆12Updated 8 years ago
- Source code used to develop the OHDSI knowledge base of sources with information relevant for assessing assocations between drugs and hea…☆56Updated 6 years ago
- Real time mortality prediction in the MIMIC-III database☆52Updated 6 years ago
- FlexIble Data-Driven pipeLinE – a preprocessing pipeline that transforms structured EHR data into feature vectors to be used with ML algo…☆86Updated 4 months ago
- Python wraper for MetaMap☆170Updated 4 years ago
- Open or Easy Access Clinical Data Sources for Biomedical Research☆169Updated 7 years ago
- A clinical BERT-based NLP tool for parsing clinical trial abstracts following the PICO framework☆44Updated 4 years ago
- Python package for machine learning for healthcare using a OMOP common data model☆104Updated last year
- Dataset containing 7,025 discharge summary notes from the MIMIC III dataset annotated for 7 SBDHs☆12Updated 2 years ago
- An information extraction system for free-text eligibility criteria☆36Updated 5 years ago
- [In Development] An application to parse freetext inclusion criteria and produce a structured cohort definition that can be executed agai…☆64Updated 3 months ago
- source codes based on PyTorch to analyze EHR☆128Updated 9 months ago
- Predicting 30-day ICU readmissions from the MIMIC-III database☆82Updated 6 years ago
- Adversarial Learning of Knowledge Embeddings for the Unified Medical Language System☆39Updated 4 years ago
- MedTagger is a light weight clinical NLP system built upon Apache UIMA.☆63Updated last month
- A Deep Dynamic Memory Model for Predictive Medicine☆70Updated 6 years ago
- AMIA submission examining note-derived vector representations☆9Updated last year
- Readmission Prediction via Deep Contextual Embedding of Clinical Concepts☆18Updated 6 years ago