Pinned Repositories
MAGIC
MAGIC (Markov Affinity-based Graph Imputation of Cells), is a method for imputing missing values restoring structure of large biological datasets.
MELD
Quantifying experimental perturbations at single cell resolution
Multiscale_PHATE
Creating multi-resolution embeddings and clusters from high dimensional data
PHATE
PHATE (Potential of Heat-diffusion for Affinity-based Transition Embedding) is a tool for visualizing high dimensional data.
phateR
PHATE dimensionality reduction method implemented in R
ReLSO-Guided-Generative-Protein-Design-using-Regularized-Transformers
a Transformer-based neural network for generating highly optimized protein sequences called Regularized Latent Space Optimization (RELSO)
SAUCIE
scprep
A collection of scripts and tools for loading, processing, and handling single cell data.
SingleCellWorkshop
TrajectoryNet
TrajectoryNet: A Dynamic Optimal Transport Network for Modeling Cellular Dynamics
Krishnaswamy Lab's Repositories
KrishnaswamyLab/PHATE
PHATE (Potential of Heat-diffusion for Affinity-based Transition Embedding) is a tool for visualizing high dimensional data.
KrishnaswamyLab/MAGIC
MAGIC (Markov Affinity-based Graph Imputation of Cells), is a method for imputing missing values restoring structure of large biological datasets.
KrishnaswamyLab/MELD
Quantifying experimental perturbations at single cell resolution
KrishnaswamyLab/SAUCIE
KrishnaswamyLab/DiffusionEMD
Code corresponding to the paper Diffusion Earth Mover's Distance and Distribution Embeddings
KrishnaswamyLab/AAnet
Archetypal Analysis network (AAnet)
KrishnaswamyLab/MIOFlow
KrishnaswamyLab/TPHATE
KrishnaswamyLab/CUTS
[MICCAI 2024] CUTS: A Deep Learning and Topological Framework for Multigranular Unsupervised Medical Image Segmentation
KrishnaswamyLab/Gene-Signal-Pattern-Analysis
Learning meaningful representations of genes
KrishnaswamyLab/ProtSCAPE
KrishnaswamyLab/ImageFlowNet
[ICASSP 2025] ImageFlowNet: Forecasting Multiscale Image-Level Trajectories of Disease Progression with Irregularly-Sampled Longitudinal Medical Images
KrishnaswamyLab/CATCH
Learning cellular hierarchy from scRNAseq data
KrishnaswamyLab/PECAN
PECAN: Persistent Condensation
KrishnaswamyLab/GSPA-manuscript-analyses
Learning meaningful representations of genes
KrishnaswamyLab/DiffKillR
[ICASSP 2025] DiffKillR: Killing and Recreating Diffeomorphisms for Cell Annotation in Dense Microscopy Images
KrishnaswamyLab/LAD
Lipschitz Anomaly Discriminator
KrishnaswamyLab/hypergraph-wavelets
Hyperedge Representations with Hypergraph Wavelets: Applications to Spatial Transcriptomics
KrishnaswamyLab/Beta-Cell-Driven-PDAC
Codebase for "Beta cells are essential drivers of pancreatic ductal adenocarcinoma development"
KrishnaswamyLab/krishnaswamy-lab-site
KrishnaswamyLab/PointCloudNet
KrishnaswamyLab/DYMAG
Graph Differential Equation Neural Network
KrishnaswamyLab/DEMaP
Denoised Embedding Manifold Preservation
KrishnaswamyLab/GeometryAwareGenerativeAutoencoder
KrishnaswamyLab/h_phate_demo
Demonstration of Hierarchical PHATE
KrishnaswamyLab/MIOFlow_conditional
KrishnaswamyLab/MIOFlow_growth_rate
KrishnaswamyLab/neural-PRISM
Multimodal latent trajectories of brain dynamics
KrishnaswamyLab/Neuro-SPECTRUM
Geometrical and topological representation of latent trajectories of neural data
KrishnaswamyLab/SCONE
Indication expansion through knowledge graph embeddings