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    14 repositories

    • SCMBench

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Mar 16, 2026Mar 16, 2026

    • CRISP

      Public
      Nature Computational Science: Predicting drug responses of unseen cell types through transfer learning with foundation models
      Jupyter Notebook
      •
      MIT License
      •3•37•4•0•Updated Feb 2, 2026Feb 2, 2026

    • HMD-AMP

      Public
      Python
      •
      MIT License
      •5•8•0•0•Updated Jan 7, 2026Jan 7, 2026

    • USPNet

      Public
      Nature Computational Science: Unbiased organism-agnostic and highly sensitive signal peptide predictor with deep protein language model
      metagenomicssignal-peptide-detectionprotein-language-models
      metagenomicssignal-peptide-detectionprotein-language-models
      Python
      •
      MIT License
      •2•35•1•0•Updated Nov 10, 2025Nov 10, 2025

    • RhoFold

      Public
      Nature Methods: RhoFold+, Accurate RNA 3D structure prediction using a language model-based deep learning approach
      Python
      •
      Apache License 2.0
      •27•227•7•2•Updated May 29, 2025May 29, 2025

    • RNA-FM

      Public
      Nature Methods: RNA foundation model (together with RhoFold)
      Jupyter Notebook
      •
      MIT License
      •42•362•16•0•Updated May 27, 2025May 27, 2025

    • RiboDiffusion

      Public
      ISMB-24/Bioinformatics: Tertiary Structure-based RNA Inverse Folding with Generative Diffusion Models
      Python
      •
      MIT License
      •6•53•0•0•Updated Nov 17, 2024Nov 17, 2024

    • RhoDesign

      Public
      Nature Computational Science: RhoDesign is a structure-to-sequence model for RNA design.
      Jupyter Notebook
      •
      MIT License
      •5•61•3•0•Updated Nov 8, 2024Nov 8, 2024

    • CasAINet

      Public
      Accurate and explainable detection of Cas proteins via robust large language model and attentive network
      0•0•0•0•Updated Sep 6, 2024Sep 6, 2024

    • Dense-Homolog-Retrieval

      Public
      Nature Biotechnology: Ultra-fast, sensitive detection of protein remote homologs using deep dense retrieval
      proteinhomology-searchprotein-structure-prediction
      proteinhomology-searchprotein-structure-predictionalphafolddense-retrievalprotein-language-modelmsa-construction
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •9•122•7•1•Updated Aug 30, 2024Aug 30, 2024

    • ifDEEPre

      Public
      large protein language-based deep learning enables interpretable and fast predictions of enzyme commission numbers
      Python
      •
      MIT License
      •1•2•0•1•Updated Jul 24, 2024Jul 24, 2024

    • e2efold

      Public
      pytorch implementation for "RNA Secondary Structure Prediction By Learning Unrolled Algorithms"
      Python
      •
      MIT License
      •18•122•9•0•Updated Apr 7, 2024Apr 7, 2024

    • E2Efold-3D

      Public
      End-to-End Deep Learning Method for accurate de novo RNA 3D Structure Prediction
      0•4•1•0•Updated Jan 4, 2024Jan 4, 2024

    • CLEAR

      Public
      CLEAR: Self-supervised contrastive learning for integrative single-cell RNA-seq data analysis
      Python
      •9•34•1•0•Updated Nov 30, 2022Nov 30, 2022
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