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    89 repositories

    • omics_toolbox

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Jul 22, 2025Jul 22, 2025

    • scprep

      Public
      A collection of scripts and tools for loading, processing, and handling single cell data.
      Python
      •
      MIT License
      •19•74•26•2•Updated Jul 21, 2025Jul 21, 2025

    • hypergraph-wavelets

      Public
      Hyperedge Representations with Hypergraph Wavelets: Applications to Spatial Transcriptomics
      graphsignal-processinghypergraphhypergraphswaveletsspatial-transcriptomicswavelets-on-graphs
      Python
      •
      Other
      •2•5•0•0•Updated Jul 20, 2025Jul 20, 2025

    • MIOFlow

      Public
      Jupyter Notebook
      •
      Other
      •6•27•2•0•Updated Jul 9, 2025Jul 9, 2025

    • Gene-Signal-Pattern-Analysis

      Public
      Learning meaningful representations of genes
      Jupyter Notebook
      •
      Other
      •1•19•0•0•Updated Jul 7, 2025Jul 7, 2025

    • graphtools

      Public
      Tools for building and manipulating graphs in Python
      Python
      •
      GNU General Public License v3.0
      •16•42•12•2•Updated Jun 21, 2025Jun 21, 2025

    • ImageFlowNet

      Public
      [ICASSP 2025 Oral] ImageFlowNet: Forecasting Multiscale Image-Level Trajectories of Disease Progression with Irregularly-Sampled Longitudinal Medical Images
      time-seriespytorchuneticassptrajectory-predictionmedical-image-analysisimage-predictiontime-series-forecastingspatial-temporalneural-ode
      Python
      •
      Other
      •0•15•0•0•Updated Jun 16, 2025Jun 16, 2025

    • GeometryAwareGenerativeAutoencoder

      Public
      [AISTATS 2025] Geometry-Aware Generative Autoencoders for Warped Riemannian Metric Learning and Generative Modeling on Data Manifolds
      Jupyter Notebook
      •1•4•0•0•Updated Jun 11, 2025Jun 11, 2025

    • ImmunoStruct

      Public
      ImmunoStruct: a multimodal neural network framework for immunogenicity prediction from peptide-MHC sequence, structure, and biochemical properties
      Python
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      Other
      •5•10•1•0•Updated Jun 6, 2025Jun 6, 2025

    • MIOFlow_conditional

      Public
      Jupyter Notebook
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      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

    • CUTS

      Public
      [MICCAI 2024] CUTS: A Deep Learning and Topological Framework for Multigranular Unsupervised Medical Image Segmentation
      Python
      •
      Other
      •2•18•0•0•Updated May 19, 2025May 19, 2025

    • SlepNet

      Public
      Spectral Subgraph Representation Learning
      Jupyter Notebook
      •0•0•0•0•Updated May 16, 2025May 16, 2025

    • DYMAG

      Public
      Graph Differential Equation Neural Network
      Jupyter Notebook
      •2•0•0•1•Updated May 14, 2025May 14, 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 May 4, 2025May 4, 2025

    • Neuroscape

      Public
      Geometrical and topological representation of latent trajectories of neural data
      Jupyter Notebook
      •0•1•0•0•Updated May 4, 2025May 4, 2025

    • PHATE

      Public
      PHATE (Potential of Heat-diffusion for Affinity-based Transition Embedding) is a tool for visualizing high dimensional data.
      data-visualizationunsupervised-learningmanifold-learningdimensionality-reductionsingle-cell
      Python
      •
      Other
      •79•512•32•1•Updated Apr 16, 2025Apr 16, 2025

    • DiffKillR

      Public
      [ICASSP 2025 Oral] DiffKillR: Killing and Recreating Diffeomorphisms for Cell Annotation in Dense Microscopy Images
      pytorchdiffeomorphismimage-registrationcell-segmentationmicroscopy-imageshistological-imagesfew-shot-learningfew-shot-segmentation
      Python
      •
      Other
      •0•5•1•0•Updated Apr 7, 2025Apr 7, 2025

    • PointCloudNet

      Public
      Jupyter Notebook
      •
      Other
      •1•1•0•0•Updated Mar 28, 2025Mar 28, 2025

    • neural-PRISM

      Public
      Multimodal latent trajectories of brain dynamics
      Python
      •
      Other
      •1•0•0•0•Updated Mar 26, 2025Mar 26, 2025

    • TPHATE

      Public
      Python
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      Other
      •5•26•0•0•Updated Feb 21, 2025Feb 21, 2025

    • AAnet

      Public
      Archetypal Analysis network (AAnet)
      Jupyter Notebook
      •
      Other
      •11•36•4•1•Updated Jan 30, 2025Jan 30, 2025

    • GRASSY

      Public
      Python
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      Other
      •0•0•0•0•Updated Jan 16, 2025Jan 16, 2025

    • Beta-Cell-Driven-PDAC

      Public
      Codebase for "Beta cells are essential drivers of pancreatic ductal adenocarcinoma development"
      Jupyter Notebook
      •
      Other
      •1•1•0•0•Updated Jan 10, 2025Jan 10, 2025

    • krishnaswamy-lab-site

      Public
      Svelte
      •0•1•0•0•Updated Dec 24, 2024Dec 24, 2024

    • DiffusionEMD

      Public
      Code corresponding to the paper Diffusion Earth Mover's Distance and Distribution Embeddings
      Jupyter Notebook
      •
      Other
      •7•37•2•0•Updated Nov 29, 2024Nov 29, 2024

    • MIOFlow_growth_rate

      Public
      Jupyter Notebook
      •
      Other
      •6•0•0•0•Updated Nov 22, 2024Nov 22, 2024

    • GSPA-manuscript-analyses

      Public
      Learning meaningful representations of genes
      Jupyter Notebook
      •
      Other
      •1•9•0•0•Updated Oct 19, 2024Oct 19, 2024

    • SCONE

      Public
      Indication expansion through knowledge graph embeddings
      Other
      •0•0•0•0•Updated Oct 15, 2024Oct 15, 2024

    • LAD

      Public
      Lipschitz Anomaly Discriminator
      Python
      •
      Other
      •0•4•0•0•Updated Oct 3, 2024Oct 3, 2024