UW Bio-NLP

clinical-trials-gov-data

uwbionlp-parser

A container-based CLI for executing various NLP algorithms on documents, developed by @uw-bionlp.

ctbert

Clinical Trial Information Extraction with BERT (CT-BERT)

MIMIC-CXR_clinical_findings

This repo contains over 1 million medical problem findings and 31 K lesion findings extracted with our event extraction model.

annotation_guidelines

ards

A PyTorch Wrapper of Hierarchical Attention Network with Sentence Objectives Framework for ARDS Identification

Criteria2Query

[In Development] An application to parse freetext inclusion criteria and produce a structured cohort definition that can be executed against OMOP CDM

mspert

PL_Marker_Plus

CliniQG4QA

CliniQG4QA: Generating Diverse Questions for Domain Adaptation of Clinical Question Answering

decaNLP

The Natural Language Decathlon: A Multitask Challenge for NLP

PedSHAC

Dataset, annotation guideline and baseline experiments for the PedSHAC corpora.

pytorch_graph-rel

A PyTorch implementation of GraphRel

R-BERT

Pytorch re-implementation of R-BERT model

sara

StAtutory Reasoning Assessment

assertion-classifier

CAMIR

clinical-trials-gov-annotation

leaf-corpora

philter-ucsf

Open source clinical text de-identification

philter-v2

UCSF Philter for UC

PINE

Collaborative NLP annotation tool supporting enterprise authentication, inter-annotator statistics, active learning

spert

PyTorch code for SpERT: Span-based Entity and Relation Transformer

TREQS

Text-to-SQL Generation for Question Answering on Electronic Medical Records