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@gersteinlab Gerstein Lab

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    145 repositories

    • ScRNA_processing

      Public
      Python
      •0•2•0•0•Updated Sep 8, 2026Sep 8, 2026

    • CellForge

      Public
      Agentic design of virtual cell models
      Python
      •
      MIT License
      •18•163•7•9•Updated Sep 7, 2026Sep 7, 2026

    • cbb7520b27

      Public
      Python
      •2•0•0•0•Updated Aug 31, 2026Aug 31, 2026

    • PathwayGAT

      Public
      A GAT-based framework integrating multi-layer information with a pathway network
      Python
      •
      MIT License
      •0•1•0•0•Updated Aug 21, 2026Aug 21, 2026

    • MedicalAgentsBench

      Public
      [Patterns] MedAgentsBench: Benchmarking Thinking Models and Agent Frameworks for Complex Medical Reasoning
      Jupyter Notebook
      •
      MIT License
      •9•86•7•0•Updated Aug 18, 2026Aug 18, 2026

    • pyGENIE

      Public
      Python
      •
      MIT License
      •0•1•0•0•Updated Aug 17, 2026Aug 17, 2026

    • LocAgent

      Public
      [ACL 2025] Graph-guided agentic framework for code localization https://arxiv.org/abs/2503.09089
      Python
      •
      Apache License 2.0
      •97•627•15•1•Updated Aug 12, 2026Aug 12, 2026

    • uni-id

      Public
      uni-id
      Python
      •
      Other
      •0•0•0•0•Updated Jul 30, 2026Jul 30, 2026

    • brainPgene

      Public
      R
      •
      MIT License
      •0•1•0•0•Updated Jun 29, 2026Jun 29, 2026

    • cbb7520b26

      Public
      Python
      •2•1•0•0•Updated Jun 15, 2026Jun 15, 2026

    • composite_QNN

      Public
      Python
      •
      Other
      •0•0•0•0•Updated Jun 12, 2026Jun 12, 2026

    • epiPgene

      Public
      R
      •
      MIT License
      •0•2•0•0•Updated Jun 4, 2026Jun 4, 2026

    • WAE

      Public
      Neural Topic Modeling with Wasserstein Autoencoders in Large Scale Multiomic Datasets
      Jupyter Notebook
      •0•0•0•0•Updated May 30, 2026May 30, 2026

    • entexBERT-paper

      Public
      Python
      •0•1•0•0•Updated May 28, 2026May 28, 2026

    • elign

      Public
      Python
      •
      Apache License 2.0
      •0•2•0•0•Updated May 25, 2026May 25, 2026

    • ASTRO

      Public
      Python
      •
      MIT License
      •5•9•0•0•Updated Apr 26, 2026Apr 26, 2026

    • sinkbiofilm

      Public
      Studying sink drain biofilms before and after disinfection through short and long-read metagenomic sequencing.
      HTML
      •
      The Unlicense
      •0•0•0•0•Updated Apr 23, 2026Apr 23, 2026

    • NoisyFlow

      Public
      Python
      •0•1•0•0•Updated Feb 7, 2026Feb 7, 2026

    • Vulnerability

      Public
      Python
      •0•0•0•0•Updated Feb 7, 2026Feb 7, 2026

    • cbb752b25

      Public
      CSS
      •2•1•0•0•Updated Jan 15, 2026Jan 15, 2026

    • 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-structurecomputational-biologyprotein
      protein-structurecomputational-biologyproteinprotein-surfaceinverse-design
      Python
      •
      Apache License 2.0
      •4•22•1•0•Updated Nov 24, 2025Nov 24, 2025

    • HISNUC

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Nov 11, 2025Nov 11, 2025

    • MedAgents-X

      Public
      Python
      •
      Apache License 2.0
      •2•7•1•1•Updated Oct 31, 2025Oct 31, 2025

    • HEPRS

      Public
      Go
      •
      MIT License
      •2•1•0•0•Updated Oct 30, 2025Oct 30, 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
      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
      •16•58•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
      •12•91•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-generationgpt-4llm
      code-generationgpt-4llm
      Python
      •
      MIT License
      •11•317•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
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