NLM/NCBI BioNLP Research Group (PI: Zhiyong Lu) (@ncbi-nlp)
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ncbi-nlp

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Top repositories

1

BioSentVec

BioWordVec & BioSentVec: pre-trained embeddings for biomedical words and sentences
Jupyter Notebook
567
star
2

bluebert

BlueBERT, pre-trained on PubMed abstracts and clinical notes (MIMIC-III).
Python
545
star
3

BLUE_Benchmark

BLUE benchmark consists of five different biomedicine text-mining tasks with ten corpora.
Python
283
star
4

NegBio

📰 High-performance tool for negation and uncertainty detection in radiology reports
Python
155
star
5

BioWordVec

Python
142
star
6

DeepSeeNet

👀 DeepSeeNet is a deep learning framework for classifying patient-based age-related macular degeneration severity in retinal color fundus photographs.
Python
57
star
7

PhenoTagger

PhenoTagger
GAP
50
star
8

Ab3P

Abbreviation definition dection library trained on PubMed abstracts
C
45
star
9

PubMed-Best-Match

Machine-learning based pipeline relying on LambdaMART currently used in PubMed for relevance (Best Match) searches
Python
39
star
10

TeamTat

Text annotation tool for team collaboration
JavaScript
35
star
11

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
33
star
12

TrialGPT

Code and data for TrialGPT.
Python
23
star
13

COVID-19-CT-CXR

COVID-19-CT-CXR, a public database of COVID-19 CXR and CT images
Python
20
star
14

MedCalc-Bench

Benchmarking the medical calculation capabilities of large language models.
Python
17
star
15

ezTag

Web interface that allows users to perform computer-assisted text annotation
JavaScript
15
star
16

BioC-JSON

Tool that converts between BioC XML files and BioC JSON files
Python
15
star
17

NQAC

Python
15
star
18

pubtator-gpt

13
star
19

DeepRel

A convolutional neural network model for relation extraction.
Python
12
star
20

NCBITextLib

Software library for building a large-scale data infrastructure for text mining
C++
7
star
21

BC6PM

Evaluation scripts for BioCreative VI Precision Medicine Track
Python
6
star
22

VarTriage

Python
5
star
23

PubTator-Covid19

4
star
24

CovidTermVar

Python
2
star
25

TaggerOne

General-purpose tagger for joint named entity recognition and normalization. Includes models for both diseases and chemicals (drugs) in biomedical publications.
2
star
26

Medical-Imaging-Causal-Fairness

Python
2
star
27

Unmasking-GPT-Bias

Jupyter Notebook
1
star
28

PhenoRerank

Python
1
star