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

All

39 repositories

cell-o1
Public
Code and data for Cell-o1.
Python
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Other
•2•23•0•0•Updated Sep 19, 2025Sep 19, 2025
MedCalc-Bench
Public
[NeurIPS 2024 Datasets and Benchmark Track Oral] MedCalc-Bench: Evaluating Large Language Models for Medical Calculations
Python
•13•71•0•0•Updated Sep 17, 2025Sep 17, 2025
FAIR-SMART
Public
Java
•1•1•0•0•Updated Sep 4, 2025Sep 4, 2025
BioREDirect
Public
Python
•0•10•0•0•Updated Aug 20, 2025Aug 20, 2025
LLM-Medicine-Primer
Public
Other
•2•7•0•0•Updated Aug 13, 2025Aug 13, 2025
Clinical-Tool-Learning
Public
Python
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Other
•1•10•0•0•Updated Aug 10, 2025Aug 10, 2025
GeneAgent
Public
The code for gene set analysis by accessing domain databases
Python
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Other
•13•76•3•2•Updated Aug 8, 2025Aug 8, 2025
DeepSeeNet
Public
👀 DeepSeeNet is a deep learning framework for classifying patient-based age-related macular degeneration severity in retinal color fundus photographs.
Python
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Other
•30•63•2•1•Updated Jul 25, 2025Jul 25, 2025
deepseenet-plus
Public
Python
•0•1•1•0•Updated Jul 25, 2025Jul 25, 2025
adversarial-manipulations
Public
Jupyter Notebook
•0•0•0•0•Updated Jul 24, 2025Jul 24, 2025
TrialGPT
Public
Code and data for TrialGPT.
Python
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Other
•57•124•0•2•Updated Jan 24, 2025Jan 24, 2025
Calculator-Recommendation
Public
MedQA-Calc is a benchmarking dataset designed to assess the capability of LLMs to recommend clinical calculators
Python
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Other
•0•1•0•0•Updated Oct 22, 2024Oct 22, 2024
EnzChemRED
Public
0•1•0•0•Updated Sep 17, 2024Sep 17, 2024
Unmasking-GPT-Bias
Public
Jupyter Notebook
•0•3•0•0•Updated Sep 4, 2024Sep 4, 2024
Deep-RPD-Net
Public
Python
•1•0•0•0•Updated Aug 30, 2024Aug 30, 2024
PhenoTagger
Public
PhenoTagger
hpo bionlp phenotype-concept-recognition
GAP
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MIT License
•16•59•1•0•Updated Jan 24, 2024Jan 24, 2024
TeamTat
Public
Text annotation tool for team collaboration
JavaScript
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MIT License
•12•42•8•8•Updated Jan 10, 2024Jan 10, 2024
NCBITextLib
Public
Software library for building a large-scale data infrastructure for text mining
C++
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Other
•4•10•1•1•Updated Jan 7, 2024Jan 7, 2024
Medical-Imaging-Causal-Fairness
Public
Python
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Other
•0•2•0•0•Updated Jan 4, 2024Jan 4, 2024
BioWordVec
Public
Python
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Other
•30•152•1•1•Updated Nov 30, 2023Nov 30, 2023
pubtator-gpt
Public
3•30•0•0•Updated Nov 30, 2023Nov 30, 2023
PhenoRerank
Public
Python
•2•2•2•0•Updated Aug 24, 2023Aug 24, 2023
BioSentVec
Public
BioWordVec & BioSentVec: pre-trained embeddings for biomedical words and sentences
natural-language-processing word-embeddings pubmed mimic-iii bionlp sentence-similarity fasttext sentence-embeddings sent2vec
Jupyter Notebook
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Other
•100•598•13•1•Updated Aug 15, 2023Aug 15, 2023
NegBio
Public
📰 High-performance tool for negation and uncertainty detection in radiology reports
nlp reports clinical-notes clinical-research clincal clincal-nlp
Python
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Other
•43•163•7•4•Updated Jul 16, 2023Jul 16, 2023
bluebert
Public
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
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Other
•81•578•5•1•Updated Mar 25, 2023Mar 25, 2023
COVID-19-CT-CXR
Public
COVID-19-CT-CXR, a public database of COVID-19 CXR and CT images
Python
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Other
•9•24•2•1•Updated Mar 25, 2023Mar 25, 2023
DeepRel
Public
A convolutional neural network model for relation extraction.
nlp deep-neural-networks deep-learning nlp-machine-learning relation-extraction
Python
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Other
•4•12•3•2•Updated Mar 24, 2023Mar 24, 2023
ezTag
Public
Web interface that allows users to perform computer-assisted text annotation
JavaScript
•6•15•4•10•Updated Jan 19, 2023Jan 19, 2023
BLUE_Benchmark
Public
BLUE benchmark consists of five different biomedicine text-mining tasks with ten corpora.
benchmark natural-language-understanding bionlp
Python
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Other
•41•297•2•2•Updated Jan 12, 2022Jan 12, 2022
CovidTermVar
Public
Python
•2•2•0•0•Updated Oct 8, 2020Oct 8, 2020