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Trellis Single-Cell Screening Reveals Stromal Regulation of Patient-Derived Organoid Drug Responses
Trellis is a tree-based earth mover’s distance method for understanding estimating treatment effects from single cell data. In this work we apply it to colorectal cancer PDOS and investigate the chemoprotection induced by cancer-associated fibroblasts.
María Ramos Zapatero, Alex Tong, Jahangir Sufi, Petra Vlckova, Ferran Cardoso Rodriguez, Callum Nattress, Xiao Qin, Daniel Hochhauser, Smita Krishnaswamy, Christopher J. Tape
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Trellis Single-Cell Screening Reveals Stromal Regulation of Patient-Derived Organoid Drug Responses
A Heat Diffusion Perspective on Geodesic Preserving Dimensionality Reduction
Guillaume Huguet, Alex Tong, Edward De Brouwer, Yanlei Zhang, Guy Wolf, Ian Adelstein, Smita Krishnaswamy
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DynGFN: Bayesian Dynamic Causal Discovery Using Generative Flow Networks
One of the grand challenges of cell biology is inferring the gene regulatory network (GRN) which describes interactions between genes …
Lazar Atanackovic, Alex Tong, Jason Hartford, Leo J. Lee, Bo Wang, Yoshua Bengio
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DynGFN: Bayesian Dynamic Causal Discovery Using Generative Flow Networks
Understanding Graph Neural Networks with Generalized Geometric Scattering Transforms
The scattering transform is a multilayered wavelet-based deep learning architecture that acts as a model of convolutional neural …
Michael Perlmutter, Alex Tong, Feng Gao, Guy Wolf, Matthew Hirn
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Geodesic Sinkhorn for Fast and Accurate Optimal Transport on Manifolds
Efficient computation of optimal transport distance between distributions is of growing importance in data science. Sinkhorn-based …
Guillaume Huguet, Alex Tong, María Ramos Zapatero, Christpher J. Tape, Guy Wolf, Smita Krishnaswamy
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Neural FIM for Learning Fisher Information Metrics from Point Cloud Data
Oluwadamilola Fasina, Guillaume Huguet, Alex Tong, Yanlei Zhang, Guy Wolf, Maximilian Nickel, Ian Adelstein, Smita Krishnaswamy
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Time-Inhomogeneous Diffusion Geometry and Topology
Diffusion condensation is a dynamic process that yields a sequence of multiscale data representations that aim to encode meaningful …
Guillaume Huguet, Alex Tong, Bastian Rieck, Jessie Huang, Manik Kuchroo, Matthew Hirn, Guy Wolf, Smita Krishnaswamy
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Single-Cell Analysis Reveals Inflammatory Interactions Driving Macular Degeneration
Due to commonalities in pathophysiology, age-related macular degeneration (AMD) represents a uniquely accessible model to investigate …
Manik Kuchroo, Marcello DiStasio, Eric Song, Eda Calapkulu, Le Zhang, Maryam Ige, Amar H. Sheth, Abdelilah Majdoubi, Madhvi Menon, Alex Tong, Abhinav Godavarthi, Yu Xing, Scott Gigante, Holly Steach, Jessie Huang, Guillaume Huguet, Janhavi Narain, Kisung You, George Mourgkos, Rahul M. Dhodapkar, Matthew J. Hirn, Bastian Rieck, Guy Wolf, Smita Krishnaswamy, Brian P. Hafler
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Single-Cell Analysis Reveals Inflammatory Interactions Driving Macular Degeneration
Graph Fourier MMD for signals on data graphs
While numerous methods have been proposed for computing distances between probability distributions in Euclidean space, relatively …
Sam Leone, Alex Tong, Guillaume Huguet, Guy Wolf, Smita Krishnaswamy
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Manifold Interpolating Optimal-Transport Flows for Trajectory Inference
We present a method called Manifold Interpolating Optimal-Transport Flow (MIOFlow) that learns stochastic, continuous population …
Guillaume Huguet, D. S. Magruder, Alex Tong, Oluwadamilola Fasina, Manik Kuchroo, Guy Wolf, Smita Krishnaswamy
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Manifold Interpolating Optimal-Transport Flows for Trajectory Inference