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    29 repositories

    • cnlp_transformers

      Public
      Transformers for Clinical NLP
      Python
      •
      Apache License 2.0
      •17•24•25•4•Updated Apr 23, 2025Apr 23, 2025

    • source-free-domain-adaptation

      Public
      Scripts to manipulate data sources for the upcoming shared task on clinical negation detection and time expression parsing
      Python
      •
      Apache License 2.0
      •3•8•6•0•Updated Apr 22, 2025Apr 22, 2025

    • long-clinical-doc

      Public
      Python
      •2•7•1•0•Updated Feb 21, 2025Feb 21, 2025

    • MDR-Benchmark

      Public
      Benchmark Corpus for Medical Device Adverse Event Detection (MDR corpus)
      0•0•0•0•Updated Feb 6, 2025Feb 6, 2025

    • anaforatools

      Public
      Python
      •
      Apache License 2.0
      •5•0•0•0•Updated Nov 19, 2024Nov 19, 2024

    • thyme_gnns

      Public
      Python
      •0•1•0•0•Updated Sep 30, 2024Sep 30, 2024

    • ctakes-client-py

      Public
      Python
      •
      Apache License 2.0
      •1•4•8•2•Updated Jul 10, 2024Jul 10, 2024

    • ctakes-covid-container

      Public
      Bluespec
      •
      Apache License 2.0
      •2•5•4•0•Updated May 9, 2024May 9, 2024

    • ctakes-rest-package

      Public
      Quick repo to get setup running cTAKES REST server and making calls
      Python
      •4•6•1•0•Updated Apr 6, 2024Apr 6, 2024

    • lm-evaluation-harness

      Public
      A framework for few-shot evaluation of autoregressive language models.
      Python
      •
      MIT License
      •2.3k•0•0•0•Updated Jan 8, 2024Jan 8, 2024

    • machine-learning-for-medical-language-public.github.io

      Public
      Jekyll page for MLML lab webpage (forked from Kording lab repo)
      HTML
      •
      MIT License
      •163•1•0•1•Updated Dec 11, 2023Dec 11, 2023

    • curate-mimic

      Public
      Python
      •0•0•0•0•Updated Sep 25, 2023Sep 25, 2023

    • psychosis-sentiment-data-augmentation

      Public
      Python
      •
      MIT License
      •0•1•0•0•Updated Aug 24, 2023Aug 24, 2023

    • generative-philter-surrogates

      Public
      Philter with surrogates
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Jun 13, 2023Jun 13, 2023

    • radiotherapy_end2end

      Public
      End to End System for Extracting Radiotherapy Events, Based on Transformers for Clinical NLP v0.3.0
      Python
      •
      Apache License 2.0
      •17•1•0•0•Updated Apr 3, 2023Apr 3, 2023

    • philter-ucsf

      Public
      Open source clinical text de-identification
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •53•0•0•0•Updated Feb 23, 2023Feb 23, 2023

    • ctakes-examples

      Public
      Example physician notes for testing cTAKES
      Python
      •
      Apache License 2.0
      •0•1•0•0•Updated Oct 7, 2022Oct 7, 2022

    • ctakes-allbch-container

      Public
      Bluespec
      •
      Apache License 2.0
      •2•0•0•0•Updated Aug 24, 2022Aug 24, 2022

    • mimic3-benchmarks

      Public
      Python suite to construct benchmark machine learning datasets from the MIMIC-III 💊 clinical database.
      Python
      •
      MIT License
      •339•0•0•0•Updated Apr 28, 2022Apr 28, 2022

    • NLP_to_FHIR

      Public
      Python
      •1•0•0•0•Updated Mar 7, 2022Mar 7, 2022

    • SMMH-Medication-Detection

      Public
      Social media drug name extration and normalization sharetask, first place in SMMH21 | Paper: https://arxiv.org/abs/2111.13726
      Python
      •0•1•0•0•Updated Dec 8, 2021Dec 8, 2021

    • MIMICIII-to-FHIR

      Public
      Repository to transform the MIMIC-III dataset into a flat hierarchy FHIR format
      Jupyter Notebook
      •3•0•0•0•Updated Nov 10, 2021Nov 10, 2021

    • medspacy-covid-container

      Public
      Python
      •0•1•0•0•Updated Oct 22, 2021Oct 22, 2021

    • Concept_Norm

      Public
      Concept Normalization using Context Information
      Python
      •1•1•0•0•Updated Sep 7, 2021Sep 7, 2021

    • Tweets-Medication-Tagger

      Public
      0•0•0•0•Updated Mar 26, 2021Mar 26, 2021

    • anafora

      Public
      Anafora is a web-based raw text annotation tool
      JavaScript
      •54•0•0•0•Updated Feb 26, 2021Feb 26, 2021

    • eConsult

      Public
      Python
      •0•0•0•0•Updated Jan 30, 2021Jan 30, 2021

    • transformers

      Public
      🤗Transformers: State-of-the-art Natural Language Processing for Pytorch and TensorFlow 2.0.
      Python
      •
      Apache License 2.0
      •29k•0•0•0•Updated Nov 11, 2020Nov 11, 2020

    • PERL

      Public
      Official code for the paper "PERL: Pivot-based Domain Adaptation for Pre-trained Deep Contextualized Embedding Models".
      Python
      •9•0•0•0•Updated Oct 28, 2020Oct 28, 2020