Repositories list

• ASTRO

  Public
  Python

  •3•6•0•1•Updated Aug 8, 2025Aug 8, 2025

• medagents-benchmark

  Public
  MedAgentsBench: Benchmarking Thinking Models and Agent Frameworks for Complex Medical Reasoning https://arxiv.org/abs/2503.07459

  Jupyter Notebook

  •

  MIT License

  •5•51•6•0•Updated Aug 7, 2025Aug 7, 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

  •5•54•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

  •12•46•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

  •10•64•2•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

  Python

  •

  MIT License

  •9•302•0•0•Updated Jul 31, 2025Jul 31, 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-structurecomputational-biologyprotein+ 2protein-surfaceinverse-design

  Python

  •

  Apache License 2.0

  •0•16•1•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

• brainPgene

  Public
  0•0•0•0•Updated Jul 17, 2025Jul 17, 2025

• CellForge

  Public
  Python

  •2•20•0•0•Updated Jul 17, 2025Jul 17, 2025

• HEPRS

  Public
  Go

  •

  MIT License

  •1•0•0•0•Updated Jul 13, 2025Jul 13, 2025

• chronODE

  Public
  Python

  •0•3•0•0•Updated Jun 2, 2025Jun 2, 2025

• cbb752b25

  Public
  CSS

  •0•0•0•0•Updated May 19, 2025May 19, 2025

• LocAgent

  Public
  [ACL 2025] Graph-guided agentic framework for code localization https://arxiv.org/abs/2503.09089

  Python

  •

  Apache License 2.0

  •63•491•8•0•Updated May 1, 2025May 1, 2025

• QVAE

  Public
  Python

  •

  MIT License

  •0•0•0•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•1•0•0•Updated Feb 11, 2025Feb 11, 2025

• cbb752b23

  Public
  CSS

  •0•0•0•0•Updated Jan 13, 2025Jan 13, 2025

• Bay2Ctrls

  Public
  R

  •

  Other

  •0•0•0•0•Updated Dec 27, 2024Dec 27, 2024

• MOBI

  Public
  Shell

  •

  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•0•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

  moleculeproteindrug-discovery+ 1genai

  6•89•0•0•Updated Nov 30, 2024Nov 30, 2024

• MIMIR

  Public
  [EMNLP 2024] MIMIR: A Streamlined Platform for Personalized Agent Tuning in Domain Expertise https://arxiv.org/abs/2404.04285

  Python

  •0•3•0•0•Updated Nov 10, 2024Nov 10, 2024

• ProteinGraph_construction

  Public
  Python

  •

  MIT License

  •0•1•0•0•Updated Nov 5, 2024Nov 5, 2024

• PPT

  Public
  Jupyter Notebook

  •0•2•1•0•Updated Sep 16, 2024Sep 16, 2024

• GraphPartition_SBGNN

  Public
  Python

  •

  MIT License

  •0•3•0•0•Updated Aug 20, 2024Aug 20, 2024

• entexBERT-paper

  Public
  Python

  •0•1•0•0•Updated Aug 17, 2024Aug 17, 2024