Paper-Conference

A sandbox for prediction and integration of DNA, RNA, and protein data in single cells
The last decade has witnessed a technological arms race to encode the molecular states of cells into DNA libraries, turning DNA …
Malte D Luecken, Daniel B Burkhardt, Robrecht Cannoodt, Christopher Lance, Aditi Agrawal, Hananeh Aliee, Ann T Chen, Louise Deconinck, Angela M Detweiler, Alejandro Granados, Shelly Huynh, Laura Isacco, Yang Joon Kim, Sunil Kuppasani, Heiko Lickert, Aaron McGeever, Honey Mekonen, Joaquin Caceres, Maurizio Morri, Michaela Mueller, Norma F Neff, Sheryl Paul, Kaylie Schneider, Scott Steelman, Michael Sterr, Dan J Treacy, Alex Tong, Alexandra-Chloé Villani, Guilin Wang, Jia Yan, Ce Zhang, Angela O Pisco, Smita Krishnaswamy, Fabian J Theis, Jonathan M Bloom
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Data-Driven Learning of Geometric Scattering Networks
A geometric scattering based network with learnable scale parameters
Alex Tong*, Frederik Wenkel*, Kincaid MacDonald, Smita Krishnaswamy, Guy Wolf
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Data-Driven Learning of Geometric Scattering Networks
Multimodal data visualization and denoising with integrated diffusion
We propose a method called integrated diffusion for combining multimodal data, gathered via different sensors on the same system, to …
Manik Kuchroo*, Abhinav Godavarthi*, Alex Tong, Smita Krishnaswamy, Guy Wolf
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Diffusion Earth Mover's Distance and Distribution Embeddings
A fast diffusion-based earth mover’s distance
Alex Tong*, Guillaume Huguet*, Amine Natik*, Kincaid MacDonald, Manik Kuchroo, Ronald Coifman, Guy Wolf, Smita Krishnaswamy
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Diffusion Earth Mover's Distance and Distribution Embeddings
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
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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
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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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