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Gerstein Lab

All

136 repositories

ASTRO
Public
Python
•
MIT License
•5•6•0•0•Updated Dec 24, 2025Dec 24, 2025
PathwayGAT
Public
A GAT-based framework integrating multi-layer information with a pathway network
Python
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MIT License
•0•0•0•0•Updated Dec 3, 2025Dec 3, 2025
cbb7520b26
Public
CSS
•1•0•0•0•Updated Nov 26, 2025Nov 26, 2025
BC-Design
Public
BC-Design: A Biochemistry-Aware Framework for High-Precision Inverse Protein Folding https://www.biorxiv.org/content/10.1101/2024.10.28.620755v2
protein-structure computational-biology protein protein-surface inverse-design
Python
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Apache License 2.0
•3•20•0•0•Updated Nov 24, 2025Nov 24, 2025
CellForge
Public
Python
•14•125•6•0•Updated Nov 13, 2025Nov 13, 2025
HISNUC
Public
Python
•
MIT License
•0•0•0•0•Updated Nov 11, 2025Nov 11, 2025
MedAgents-2
Public
Python
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Apache License 2.0
•1•3•1•0•Updated Oct 31, 2025Oct 31, 2025
HEPRS
Public
Go
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MIT License
•1•0•0•0•Updated Oct 30, 2025Oct 30, 2025
medagents-benchmark
Public
MedAgentsBench: Benchmarking Thinking Models and Agent Frameworks for Complex Medical Reasoning
Jupyter Notebook
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MIT License
•8•71•7•0•Updated Oct 10, 2025Oct 10, 2025
brainPgene
Public
Jupyter Notebook
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MIT License
•0•0•0•0•Updated Aug 24, 2025Aug 24, 2025
HISNUC-test
Public
Python
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BSD 3-Clause "New" or "Revised" License
•0•0•0•0•Updated Aug 20, 2025Aug 20, 2025
LocAgent
Public
[ACL 2025] Graph-guided agentic framework for code localization https://arxiv.org/abs/2503.09089
Python
•
Apache License 2.0
•87•569•13•0•Updated Aug 17, 2025Aug 17, 2025
chronODE
Public
Python
•0•5•0•0•Updated Aug 14, 2025Aug 14, 2025
Struc-Bench
Public
[NAACL 2024] Struc-Bench: Are Large Language Models Good at Generating Complex Structured Tabular Data? https://aclanthology.org/2024.naacl-short.2/
llm
Python
•7•55•7•0•Updated Jul 31, 2025Jul 31, 2025
BioCoder
Public
BioCoder: A Benchmark for Bioinformatics Code Generation with Large Language Models https://arxiv.org/abs/2308.16458
Jupyter Notebook
•15•53•0•0•Updated Jul 31, 2025Jul 31, 2025
ChemAgent
Public
[ICLR 2025]ChemAgent: Self-updating Library in Large Language Models Improves Chemical Reasoning https://arxiv.org/abs/2501.06590
Python
•11•78•3•0•Updated Jul 31, 2025Jul 31, 2025
ML-Bench
Public
ML-Bench: Evaluating Large Language Models and Agents for Machine Learning Tasks on Repository-Level Code (https://arxiv.org/abs/2311.09835)
code-generation gpt-4 llm
Python
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MIT License
•11•318•0•0•Updated Jul 31, 2025Jul 31, 2025
shiny-dim-reduction
Public
This project applies dimensionality reduction to tabular data and generates applications for visualizing the results.
R
•0•2•0•0•Updated Jul 27, 2025Jul 27, 2025
cbb752b25
Public
CSS
•1•1•0•0•Updated May 19, 2025May 19, 2025
QVAE
Public
Python
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MIT License
•0•0•1•0•Updated Mar 24, 2025Mar 24, 2025
epiPgene
Public
0•0•0•0•Updated Feb 25, 2025Feb 25, 2025
cbb752b16
Public
CBB752 (Spr. '16) - Bioinformatics: Practical Application of Data Mining & Simulation
HTML
•0•0•0•0•Updated Feb 19, 2025Feb 19, 2025
.github
Public
This is the repo for the public organization profile.
MIT License
•0•0•0•0•Updated Feb 11, 2025Feb 11, 2025
cbb752b23
Public
CSS
•0•0•0•0•Updated Jan 13, 2025Jan 13, 2025
Bay2Ctrls
Public
R
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Other
•0•0•0•0•Updated Dec 27, 2024Dec 27, 2024
MOBI
Public
Shell
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MIT License
•0•0•0•0•Updated Dec 27, 2024Dec 27, 2024
ABCD
Public
R
•0•3•0•0•Updated Dec 16, 2024Dec 16, 2024
fmgene
Public
0•1•0•0•Updated Dec 15, 2024Dec 15, 2024
cbb752b20
Public
CSS
•0•0•0•0•Updated Dec 2, 2024Dec 2, 2024
GenAI4Drug
Public
[Briefings in Bioinformatics] A Survey of Generative AI for de novo Drug Design
molecule protein drug-discovery genai
6•94•0•0•Updated Nov 30, 2024Nov 30, 2024