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    52 repositories

    • BioReason

      Public
      BioReason: Incentivizing Multimodal Biological Reasoning within a DNA-LLM Model
      0•0•0•0•Updated May 30, 2025May 30, 2025

    • MedRAX

      Public
      MedRAX: Medical Reasoning Agent for Chest X-ray - ICML '25
      agentmedicalhealthcaremedical-imagingchest-xraychest-xraysreasoning-agentlangchainagentic-frameworkagentic-ai
      Python
      •
      Apache License 2.0
      •120•611•4•1•Updated May 29, 2025May 29, 2025

    • Ctrl-DNA

      Public
      Ctrl-DNA: Controllable Cell-Type-Specific Regulatory DNA Design via Constrained RL
      Python
      •
      Apache License 2.0
      •0•6•0•0•Updated May 28, 2025May 28, 2025

    • IntegrAO

      Public
      Integrate Any Omics: Towards genome-wide data integration for patient stratification
      Jupyter Notebook
      •
      MIT License
      •12•53•0•0•Updated May 19, 2025May 19, 2025

    • AGILE

      Public
      AGILE Platform: A Deep Learning-Powered Approach to Accelerate LNP Development for mRNA Delivery
      Jupyter Notebook
      •
      MIT License
      •5•39•2•0•Updated May 16, 2025May 16, 2025

    • MedSAM2

      Public
      MedSAM2: Segment Anything in 3D Medical Images and Videos
      Jupyter Notebook
      •
      Apache License 2.0
      •34•179•0•1•Updated May 9, 2025May 9, 2025

    • ECG-FM

      Public
      An electrocardiogram analysis foundation model.
      machine-learninghealthcaretransformerelectrocardiogramfoundation-modelsmimic-iv-ecgphysionet2021
      Python
      •
      MIT License
      •10•151•0•0•Updated May 7, 2025May 7, 2025

    • MedSAM

      Public
      Segment Anything in Medical Images
      Jupyter Notebook
      •
      Apache License 2.0
      •496•3.5k•5•1•Updated May 7, 2025May 7, 2025

    • genomic-FM

      Public
      genomicsgenetic-variantsfoundation-models
      Python
      •3•25•1•0•Updated Apr 28, 2025Apr 28, 2025

    • MedSAMSlicer

      Public
      3D Slicer Plugin for Segment anything in medical images
      3d-slicer-extension
      Python
      •26•233•5•2•Updated Apr 7, 2025Apr 7, 2025

    • scGPT

      Public
      gptsingle-cellfoundation-model
      Jupyter Notebook
      •
      MIT License
      •259•1.2k•140•8•Updated Mar 31, 2025Mar 31, 2025

    • AMOS-MM-Solution

      Public
      Solution to the AMOS-MM challenge
      Python
      •
      MIT License
      •0•6•1•0•Updated Mar 29, 2025Mar 29, 2025

    • MorphoDiff

      Public
      MorphoDiff is a diffusion based generative pipeline to predict high-resolution cell morphological responses under different conditions based on perturbation encoding.
      Python
      •
      Apache License 2.0
      •2•18•0•0•Updated Mar 10, 2025Mar 10, 2025

    • scGPT-spatial

      Public
      Jupyter Notebook
      •
      MIT License
      •11•96•6•0•Updated Feb 13, 2025Feb 13, 2025

    • AgentTutorial

      Public
      Jupyter Notebook
      •
      Apache License 2.0
      •0•7•0•0•Updated Feb 3, 2025Feb 3, 2025

    • Orthrus

      Public
      Orthrus is a mature RNA model for RNA property prediction. It uses a mamba encoder backbone, a variant of state-space models specifically designed for long-sequence data, such as RNA.
      Python
      •
      MIT License
      •9•64•3•0•Updated Jan 21, 2025Jan 21, 2025

    • PANORAMA

      Public
      0•1•0•0•Updated Dec 10, 2024Dec 10, 2024

    • csc413-2024

      Public
      Jupyter Notebook
      •
      MIT License
      •2•1•0•0•Updated Nov 22, 2024Nov 22, 2024

    • OCAT

      Public
      Python
      •
      GNU General Public License v3.0
      •3•18•2•0•Updated Oct 22, 2024Oct 22, 2024

    • BLEEP

      Public
      Spatially Resolved Gene Expression Prediction from H&E Histology Images via Bi-modal Contrastive Learning
      Python
      •
      Apache License 2.0
      •13•76•1•0•Updated Oct 22, 2024Oct 22, 2024

    • evlp_xray_vision

      Public
      Computer vision models for EVLP lung X-ray images.
      Python
      •
      MIT License
      •0•0•0•0•Updated Jul 2, 2024Jul 2, 2024

    • CellSeg-Transformers

      Public
      Python
      •
      Apache License 2.0
      •1•13•0•0•Updated May 7, 2024May 7, 2024

    • U-Mamba

      Public
      U-Mamba: Enhancing Long-range Dependency for Biomedical Image Segmentation
      Python
      •
      Apache License 2.0
      •81•810•37•0•Updated Apr 4, 2024Apr 4, 2024

    • DeepVelo

      Public
      Python
      •
      MIT License
      •9•47•6•3•Updated Feb 7, 2024Feb 7, 2024

    • Graph-Mamba

      Public
      Graph-Mamba: Towards Long-Range Graph Sequence Modelling with Selective State Spaces
      Python
      •35•283•5•0•Updated Feb 2, 2024Feb 2, 2024

    • BIONIC

      Public
      Biological Network Integration using Convolutions
      Python
      •
      MIT License
      •5•62•1•8•Updated Jan 17, 2024Jan 17, 2024

    • ViST-Echo

      Public
      PD's thesis work towards a Video Swin Transformer for echocardiographic data.
      Python
      •0•1•0•0•Updated Oct 20, 2023Oct 20, 2023

    • DPM-MedImgEnhance

      Public
      Pre-trained Diffusion Models for Plug-and-Play Medical Image Enhancement
      Python
      •3•25•2•0•Updated Oct 3, 2023Oct 3, 2023

    • MAESTER

      Public
      Masked Autoencoder Guided Segmentation at Pixel Resolution
      Python
      •
      MIT License
      •6•15•1•1•Updated Oct 3, 2023Oct 3, 2023

    • CongFu

      Public
      CongFu: Conditional Graph Fusion for Drug Synergy Prediction
      Python
      •3•7•3•0•Updated Sep 11, 2023Sep 11, 2023