Archival

Quantifying the effect of experimental perturbations in single-cell RNA-sequencing data using graph signal processing
Single-cell RNA-sequencing (scRNA-seq) is a powerful tool to quantify transcriptional states in thousands to millions of cells. It is …
Daniel B. Burkhardt*, Jay S. Stanley*, Alex Tong, Ana Luisa Perdigoto, Scott A. Gigante, Kevan C. Herold, Guy Wolf, Antonio J. Giraldez, David Van Dijk, Smita Krishnaswamy
Cite Code DOI BioRxiv
Uncovering the Folding Landscape of RNA Secondary Structure with Deep Graph Embeddings
Biomolecular graph analysis has recently gained much attention in the emerging field of geometric deep learning. While numerous …
Egbert Castro, Andrew Benz, Alex Tong, Guy Wolf, Smita Krishnaswamy
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Fixing Bias in Reconstruction-based Anomaly Detection with Lipschitz Discriminators
We fix unwanted biases in standard deep anomaly detection with a new architecture.
Alex Tong, Guy Wolf, Smita Krishnaswamy
PDF Cite Code Slides Video Yale Daily Article Best Paper Award
Fixing Bias in Reconstruction-based Anomaly Detection with Lipschitz Discriminators
TrajectoryNet: A Dynamic Optimal Transport Network for Modeling Cellular Dynamics
A Combination of Continuous Normalizing Flows and Dynamic Optimal Transport to model the dynamics of cells.
Alex Tong, Jessie Huang, Guy Wolf, David Van Dijk, Smita Krishnaswamy
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TrajectoryNet: A Dynamic Optimal Transport Network for Modeling Cellular Dynamics
Interpretable Neuron Structuring with Graph Spectral Regularization
While neural networks are powerful approximators used to classify or embed data into lower dimensional spaces, they are often regarded …
Alex Tong*, David Van Dijk*, Jay S. Stanley III, Matthew Amodio, Kristina Yim, Rebecca Muhle, James Noonan, Guy Wolf, Smita Krishnaswamy
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Finding Archetypal Spaces Using Neural Networks
Archetypal analysis is a data decomposition method that describes each observation in a dataset as a convex combination of …
David Van Dijk*, Daniel B. Burkhardt*, Matthew Amodio, Alex Tong, Guy Wolf, Smita Krishnaswamy
PDF Cite Code DOI Arxiv
Allocate-On-Use Space Complexity of Shared-Memory Algorithms
Many fundamental problems in shared-memory distributed computing, including mutual exclusion [8], consensus [18], and implementations …
James Aspnes*, Bernhard Haeupler, Alex Tong, Philipp Woelfel
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