Patient-level Analysis

AAnet resolves a continuum of spatially-localized cell states to unveil tumor complexity
AAnet is a neural network for nonlinear archetypal analysis of single-cell data.

A Venkat*, S Youlten*,…,S Krishnaswamy, CL Chaffer. Cancer Discovery 2025.
Paper Code CSHL Systems Immunology 2021
AAnet resolves a continuum of spatially-localized cell states to unveil tumor complexity
Graph Fourier MMD for Signals on Graphs
GFMMD embeds signals defined on graphs via an optimal witness function.

S Leone, A Tong, G Huguet, A Venkat, G Wolf, S Krishnaswamy. SampTA 2023.
Paper Code SAMPTA 2023 Manuscript Published
Graph Fourier MMD for Signals on Graphs
Mapping the gene space at single-cell resolution with gene signal pattern analysis
GSPA learns gene-gene relationships from single-cell data by embedding the gene space.

A Venkat, S Leone, S Youlten, E Fagerberg, J Attanasio, NS Joshi, S Krishnaswamy. Nature Computational Science 2024.
Paper Blog Post Code ISMB 2021 Immunology 2023 Manuscript Published
Mapping the gene space at single-cell resolution with gene signal pattern analysis