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    97 repositories

    • hypergraph-wavelets

      Public
      Hyperedge Representations with Hypergraph Wavelets: Applications to Spatial Transcriptomics
      graphsignal-processinghypergraph
      graphsignal-processinghypergraphhypergraphswaveletsspatial-transcriptomicswavelets-on-graphs
      Jupyter Notebook
      •
      Other
      •3•7•0•1•Updated Mar 31, 2026Mar 31, 2026

    • MIOFlow

      Public
      Jupyter Notebook
      •
      Other
      •6•36•3•0•Updated Mar 30, 2026Mar 30, 2026

    • HiPoNet

      Public
      Jupyter Notebook
      •
      Other
      •2•8•0•0•Updated Mar 27, 2026Mar 27, 2026

    • GraphWaveletEncoder

      Public
      Graph wavelet encoder
      Python
      •
      Other
      •0•1•0•0•Updated Mar 18, 2026Mar 18, 2026

    • omics_toolbox

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Mar 12, 2026Mar 12, 2026

    • RiTINI

      Public
      Regulatory Temporal Interaction Network Inference
      Jupyter Notebook
      •
      Other
      •2•14•1•0•Updated Mar 11, 2026Mar 11, 2026

    • ImmunoStruct

      Public
      [Nature Machine Intelligence] ImmunoStruct enables multimodal deep learning for immunogenicity prediction
      deep-learningcomputational-biologyprediction
      deep-learningcomputational-biologypredictionimmunologyinfectious-diseasesmultimodal-learningmultimodalmultimodal-deep-learningself-supervised-learningimmunogenicity
      Python
      •
      Other
      •16•44•1•0•Updated Mar 5, 2026Mar 5, 2026

    • ProtSCAPE-Net

      Public
      Python
      •0•0•0•0•Updated Mar 4, 2026Mar 4, 2026

    • PHATE

      Public
      PHATE (Potential of Heat-diffusion for Affinity-based Transition Embedding) is a tool for visualizing high dimensional data.
      data-visualizationdimensionality-reductionunsupervised-learning
      data-visualizationdimensionality-reductionunsupervised-learningsingle-cellmanifold-learning
      Python
      •
      Other
      •79•542•32•2•Updated Mar 4, 2026Mar 4, 2026

    • CellSpliceNet

      Public
      PyTorch implementation of CellSpliceNet, Afrasiyabi et al., 2025.
      Jupyter Notebook
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      Other
      •0•2•0•0•Updated Feb 24, 2026Feb 24, 2026

    • GRASSY-Net

      Public
      Jupyter Notebook
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      Other
      •4•1•0•0•Updated Feb 19, 2026Feb 19, 2026

    • CUTS

      Public
      [MICCAI 2024] CUTS: A Deep Learning and Topological Framework for Multigranular Unsupervised Medical Image Segmentation
      Python
      •
      Other
      •1•21•0•0•Updated Feb 14, 2026Feb 14, 2026

    • ImageFlowNet

      Public
      [ICASSP 2025 Oral] ImageFlowNet: Forecasting Multiscale Image-Level Trajectories of Disease Progression with Irregularly-Sampled Longitudinal Medical Images
      time-seriespytorchunet
      time-seriespytorchuneticassptrajectory-predictionmedical-image-analysisimage-predictiontime-series-forecastingspatial-temporalneural-ode
      Python
      •
      Other
      •3•26•0•0•Updated Feb 14, 2026Feb 14, 2026

    • Template

      Public
      Lab repository template.
      Other
      •0•2•0•0•Updated Jan 30, 2026Jan 30, 2026

    • Beta-Cell-Driven-PDAC

      Public
      Codebase for "Beta cells are essential drivers of pancreatic ductal adenocarcinoma development"
      Jupyter Notebook
      •
      Other
      •2•1•0•0•Updated Jan 20, 2026Jan 20, 2026

    • graphtools

      Public
      Tools for building and manipulating graphs in Python
      Python
      •
      GNU General Public License v3.0
      •17•46•14•3•Updated Dec 18, 2025Dec 18, 2025

    • cflows

      Public
      Jupyter Notebook
      •0•1•0•0•Updated Dec 13, 2025Dec 13, 2025

    • TPHATE

      Public
      Python
      •
      Other
      •7•37•1•0•Updated Nov 11, 2025Nov 11, 2025

    • HeatGeo

      Public
      Embedding with the Heat-geodesic dissimilarity
      data-visualizationdimensionality-reductionunsupervised-learning
      data-visualizationdimensionality-reductionunsupervised-learningmanifold-learning
      Jupyter Notebook
      •
      Other
      •2•6•0•0•Updated Oct 30, 2025Oct 30, 2025

    • HEIST

      Public
      Python
      •0•0•0•0•Updated Sep 30, 2025Sep 30, 2025

    • CellSpliceNet-dataset

      Public
      dataset for CellSpliceNet: Interpretable Multimodal Modeling of Alternative Splicing Across Neurons in C. elegans
      0•0•0•0•Updated Sep 25, 2025Sep 25, 2025

    • scprep

      Public
      A collection of scripts and tools for loading, processing, and handling single cell data.
      Python
      •
      MIT License
      •21•77•28•2•Updated Sep 22, 2025Sep 22, 2025

    • NeuroMuse

      Public
      Jupyter Notebook
      •1•0•0•0•Updated Sep 12, 2025Sep 12, 2025

    • OrganDonationTTDPrediction

      Public
      Deep learning unlocks the true potential of organ donation after circulatory death with accurate prediction of time-to-death
      Python
      •0•1•0•0•Updated Sep 2, 2025Sep 2, 2025

    • PECAN

      Public
      PECAN: Persistent Condensation
      Jupyter Notebook
      •
      Other
      •3•10•1•0•Updated Aug 9, 2025Aug 9, 2025

    • DYMAG

      Public
      Graph Differential Equation Neural Network
      Jupyter Notebook
      •2•1•0•1•Updated Aug 6, 2025Aug 6, 2025

    • Gene-Signal-Pattern-Analysis

      Public
      Learning meaningful representations of genes
      Jupyter Notebook
      •
      Other
      •1•21•0•0•Updated Jul 7, 2025Jul 7, 2025

    • GeometryAwareGenerativeAutoencoder

      Public
      [AISTATS 2025] Geometry-Aware Generative Autoencoders for Warped Riemannian Metric Learning and Generative Modeling on Data Manifolds
      Jupyter Notebook
      •2•5•0•0•Updated Jun 11, 2025Jun 11, 2025

    • MIOFlow_conditional

      Public
      Jupyter Notebook
      •
      Other
      •6•0•0•0•Updated Jun 4, 2025Jun 4, 2025

    • scRNA-seq-simulations

      Public
      Code for running SERGIO and scVelo simulations for training RITINI, BEMIOFlow, etc.
      0•0•0•0•Updated Jun 1, 2025Jun 1, 2025
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