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

Ab3P

Abbreviation definition dection library trained on PubMed abstracts

BioSentVec

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

BioWordVec

BLUE_Benchmark

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

bluebert

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

DeepSeeNet

:eyes: DeepSeeNet is a deep learning framework for classifying patient-based age-related macular degeneration severity in retinal color fundus photographs.

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.

NegBio

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

PhenoTagger

PhenoTagger

PubMed-Best-Match

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

ncbi-nlp/BioSentVec

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

ncbi-nlp/bluebert

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

ncbi-nlp/BLUE_Benchmark

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

ncbi-nlp/NegBio

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

ncbi-nlp/BioWordVec

ncbi-nlp/DeepSeeNet

:eyes: DeepSeeNet is a deep learning framework for classifying patient-based age-related macular degeneration severity in retinal color fundus photographs.

ncbi-nlp/PhenoTagger

PhenoTagger

ncbi-nlp/Ab3P

Abbreviation definition dection library trained on PubMed abstracts

ncbi-nlp/PubMed-Best-Match

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

ncbi-nlp/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.

ncbi-nlp/TeamTat

Text annotation tool for team collaboration

ncbi-nlp/COVID-19-CT-CXR

COVID-19-CT-CXR, a public database of COVID-19 CXR and CT images

ncbi-nlp/BioC-JSON

Tool that converts between BioC XML files and BioC JSON files

ncbi-nlp/ezTag

Web interface that allows users to perform computer-assisted text annotation

ncbi-nlp/NQAC

ncbi-nlp/DeepRel

A convolutional neural network model for relation extraction.

ncbi-nlp/pubtator-gpt

ncbi-nlp/TrialGPT

Code and data for TrialGPT.

ncbi-nlp/NCBITextLib

Software library for building a large-scale data infrastructure for text mining

ncbi-nlp/BC6PM

Evaluation scripts for BioCreative VI Precision Medicine Track

ncbi-nlp/VarTriage

ncbi-nlp/PubTator-Covid19

ncbi-nlp/CovidTermVar

ncbi-nlp/TaggerOne

General-purpose tagger for joint named entity recognition and normalization. Includes models for both diseases and chemicals (drugs) in biomedical publications.

ncbi-nlp/Medical-Imaging-Causal-Fairness

ncbi-nlp/PhenoRerank