E598 KrishnaswamyLab repositories · GitHub

Krishnaswamy Lab

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96 repositories

hypergraph-wavelets
Public
Hyperedge Representations with Hypergraph Wavelets: Applications to Spatial Transcriptomics
graph signal-processing hypergraph
graph signal-processing hypergraph hypergraphs wavelets spatial-transcriptomics wavelets-on-graphs
Jupyter Notebook
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Other
•3•7•0•0•Updated Mar 12, 2026Mar 12, 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
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Other
•2•12•1•0•Updated Mar 11, 2026Mar 11, 2026
MIOFlow
Public
Jupyter Notebook
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Other
•6•35•3•0•Updated Mar 5, 2026Mar 5, 2026
ImmunoStruct
Public
[Nature Machine Intelligence] ImmunoStruct enables multimodal deep learning for immunogenicity prediction
deep-learning computational-biology prediction
deep-learning computational-biology prediction immunology infectious-diseases multimodal-learning multimodal multimodal-deep-learning self-supervised-learning immunogenicity
Python
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Other
•15•43•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-visualization dimensionality-reduction unsupervised-learning
data-visualization dimensionality-reduction unsupervised-learning single-cell manifold-learning
Python
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Other
•79•538•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
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Other
•1•20•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-series pytorch unet
time-series pytorch unet icassp trajectory-prediction medical-image-analysis image-prediction time-series-forecasting spatial-temporal neural-ode
Python
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Other
•3•25•0•0•Updated Feb 14, 2026Feb 14, 2026
HiPoNet
Public
Jupyter Notebook
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Other
•2•8•0•0•Updated Feb 6, 2026Feb 6, 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
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Other
•2•1•0•0•Updated Jan 20, 2026Jan 20, 2026
graphtools
Public
Tools for building and manipulating graphs in Python
Python
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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
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Other
•7•36•1•0•Updated Nov 11, 2025Nov 11, 2025
HeatGeo
Public
Embedding with the Heat-geodesic dissimilarity
data-visualization dimensionality-reduction unsupervised-learning
data-visualization dimensionality-reduction unsupervised-learning manifold-learning
Jupyter Notebook
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Other
•1•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
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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
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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
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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
•1•5•0•0•Updated Jun 11, 2025Jun 11, 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
SlepNet
Public
Spectral Subgraph Representation Learning
Jupyter Notebook
•0•0•0•0•Updated May 16, 2025May 16, 2025

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