NLM/NCBI BioNLP Research Group (PI: Zhiyong Lu)

Repositories

• TeamTat

  Text annotation tool for team collaboration
  JavaScript MIT 2 6 1 4 Updated Jul 9, 2020

• DeepRel

  A convolutional neural network model for relation extraction.

  nlp deep-neural-networks deep-learning nlp-machine-learning relation-extraction
  Python 2 9 2 1 Updated Jul 7, 2020

• Ab3P

  Abbreviation definition dection library trained on PubMed abstracts
  C 7 20 3 1 Updated Jul 6, 2020

• ezTag

  Web interface that allows users to perform computer-assisted text annotation
  JavaScript 5 8 1 3 Updated Jun 24, 2020

• COVID-19-CT-CXR

  COVID-19-CT-CXR, a public database of COVID-19 CXR and CT images
  Python 1 3 1 0 Updated Jun 12, 2020

• bluebert

  BlueBERT, pre-trained on PubMed abstracts and clinical notes (MIMIC-III).

  natural-language-processing pubmed mimic-iii language-model bert pubmed-abstracts bert-model
  Python 20 178 4 0 Updated Jun 9, 2020

• PubTator-Covid19

  natural-language-processing text-mining pubmed bionlp covid-19 covid19
  1 1 1 0 Updated May 6, 2020

• BLUE_Benchmark

  BLUE benchmark consists of five different biomedicine text-mining tasks with ten corpora.

  benchmark natural-language-understanding bionlp
  Python 21 121 2 1 Updated Apr 14, 2020

• NegBio

  📰 High-performance tool for negation and uncertainty detection in radiology reports

  nlp reports clinical-notes clinical-research clincal clincal-nlp
  Python 20 70 5 2 Updated Apr 5, 2020

• BioConceptVec

  text-mining deep-learning word-embeddings protein-protein-interaction biomedical-text-mining biomedical-concept-embeddings
  Jupyter Notebook 7 17 0 0 Updated Feb 25, 2020

• BioSentVec

  BioWordVec & BioSentVec: pre-trained embeddings for biomedical words and sentences

  natural-language-processing word-embeddings pubmed fasttext mimic-iii bionlp sentence-similarity
  Jupyter Notebook 36 236 5 0 Updated Feb 26, 2020

• ML_Net

  ML-Net is a novel end-to-end deep learning framework for multi-label classification of biomedical tasks. ML-Net combines the label prediction network with a label count prediction network, which can determine the output labels based on both label confidence scores and document context in an end-to-end manner.
  Python 5 19 0 0 Updated Dec 23, 2019

• DeepSeeNet

  👀 DeepSeeNet is a deep learning framework for classifying patient-based age-related macular degeneration severity in retinal color fundus photographs.
  Python 13 29 0 0 Updated Oct 2, 2019

• BioWordVec
  Python 15 44 1 0 Updated Jul 29, 2019

• NCBITextLib

  Software library for building a large-scale data infrastructure for text mining
  C++ 2 2 0 0 Updated Apr 15, 2019

• VarTriage
  Python 0 4 0 0 Updated May 29, 2018

• PubMed-Best-Match

  Machine-learning based pipeline relying on LambdaMART currently used in PubMed for relevance (Best Match) searches

  machine-learning text-mining feature-engineering biomedical-data-science
  Python 6 17 0 0 Updated Apr 30, 2018

• NQAC
  Python 1 15 0 0 Updated Apr 17, 2018

• BC6PM

  Evaluation scripts for BioCreative VI Precision Medicine Track
  Python 0 4 0 0 Updated Feb 14, 2018

• TaggerOne

  General-purpose tagger for joint named entity recognition and normalization. Includes models for both diseases and chemicals (drugs) in biomedical publications.
  0 2 1 0 Updated Oct 13, 2017

• BioC-JSON

  Tool that converts between BioC XML files and BioC JSON files
  Python 0 4 1 0 Updated Jan 10, 2017