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
Alternatives and similar repositories for phenotyping:
Users that are interested in phenotyping are comparing it to the libraries listed below
- Public release of the DeepPhe analytic software☆30Updated 2 years ago
- Python library for hierarchy of ICD9 Codes☆104Updated 6 years ago
- Health knowledge graph for 157 diseases and 491 symptoms, learned from >270,000 patients' data☆101Updated 4 years ago
- ☆53Updated 5 years ago
- ☆30Updated 7 years ago
- Mapping the MIMIC-III database to the OMOP schema☆133Updated last year
- Implementation of Deep Patient Representation of Clinical Notes at Intensive Care Unit for Multi-Task Prediction☆32Updated 5 years ago
- Surfacing Semantic Data from Clinical Notes in Electronic Health Records for Tailored Care, Trial Recruitment and Clinical Research☆89Updated 2 years ago
- Python wraper for MetaMap☆171Updated 4 years ago
- Real time mortality prediction in the MIMIC-III database☆53Updated 7 years ago
- ☆98Updated 3 years ago
- Open or Easy Access Clinical Data Sources for Biomedical Research☆171Updated 8 years ago
- A torch package for learning diagnosis models from temporal patient data.☆115Updated 7 years ago
- Source code used to develop the OHDSI knowledge base of sources with information relevant for assessing assocations between drugs and hea…☆55Updated 6 years ago
- Predicting 30-day ICU readmissions from the MIMIC-III database☆86Updated 7 years ago
- [In Development] An application to parse freetext inclusion criteria and produce a structured cohort definition that can be executed agai…☆65Updated 9 months ago
- Source code for Medical Concept Embedding with Time-Aware Embedding☆22Updated 5 years ago
- Python package for machine learning for healthcare using a OMOP common data model☆108Updated last year
- Sample code that demonstrates the use of the NCBO REST services☆44Updated last year
- Adversarial Learning of Knowledge Embeddings for the Unified Medical Language System☆39Updated 5 years ago
- Dataset containing 7,025 discharge summary notes from the MIMIC III dataset annotated for 7 SBDHs☆14Updated 2 years ago
- A clinical BERT-based NLP tool for parsing clinical trial abstracts following the PICO framework☆45Updated 4 years ago
- A near real-time named-entity recognizer☆59Updated 11 months ago
- MedTagger is a light weight clinical NLP system built upon Apache UIMA.☆67Updated 2 weeks ago
- FlexIble Data-Driven pipeLinE – a preprocessing pipeline that transforms structured EHR data into feature vectors to be used with ML algo…☆92Updated 10 months ago
- Data and code from our "Inferring Which Medical Treatments Work from Reports of Clinical Trials", NAACL 2019. This work concerns inferrin…☆62Updated 3 years ago
- Code for the paper "Knowledge Base Completion for Constructing Problem-Oriented Medical Records" at MLHC 2020☆11Updated 3 years ago
- A simple interface to inspect, improve and add concepts to biomedical NER+L -> MedCAT.☆80Updated this week
- A fine-tuned BERT using EHR notes.☆14Updated 5 years ago
- Classes for ClinicalTrials.gov related projects☆47Updated 5 years ago