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Learnable Filters for Geometric Scattering Modules
Alex Tong, Frederik Wenkel, Dhananjay Bhaskar, Kincaid Macdonald, Jackson Grady, Michael Perlmutter, Smita Krishnaswamy, Guy Wolf
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Trellis tree-based analysis 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 tree-based analysis reveals stromal regulation of patient-derived organoid drug responses
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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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
Immune Cells and Their Inflammatory Mediators Modify Beta Cells and Cause Checkpoint Inhibitor-Induced Diabetes
Checkpoint inhibitors (CPIs) targeting programmed death 1 (PD-1)/programmed death ligand 1 (PD-L1) and cytotoxic T lymphocyte antigen 4 …
Ana Luisa Perdigoto, Songyan Deng, Katherine C. Du, Manik Kuchroo, Daniel B. Burkhardt, Alex Tong, Gary Israel, Marie E. Robert, Stuart P. Weisberg, Nancy Kirkiles-Smith, Angeliki M. Stamatouli, Harriet M. Kluger, Zoe Quandt, Arabella Young, Mei-Ling Yang, Mark J. Mamula, Jordan S. Pober, Mark S. Anderson, Smita Krishnaswamy, Kevan C. Herold
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Topological Analysis of Single-Cell Hierarchy Reveals Inflammatory Glial Landscape of Macular Degeneration
Brian Palmer Hafler, Manik Kuchroo, Marcello DiStasio, Eric Song, Le Zhang, Maryam Ige, Amar Sheth, Madhvi Menon, Alex Tong, Yu Xing, Scott Gigante, Jessie Huang, George Mourgkos, Smita Krishnaswamy, Rahul Dhodapkar, Guy Wolf
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Multiscale PHATE identifies multimodal signatures of COVID-19
As the biomedical community produces datasets that are increasingly complex and high dimensional, there is a need for more …
Manik Kuchroo, Jessie Huang, Patrick Wong, Jean-Christophe Grenier, Dennis Shung, Alex Tong, Carolina Lucas, Jon Klein, Daniel Burkhardt, Scott Gigante, Abhinav Godavarthi, Benjamin Israelow, Tianyang Mao, Ji Eun Oh, Julio Silva, Takehiro Takahashi, Camila D. Odio, Arnau Casanovas-Massana, John Fournier, Yale IMPACT Team, Shelli Farhadian, Charles S. Dela Cruz, Albert I. Ko, F. Perry Wilson, Julie Hussin, Guy Wolf, Akiko Iwasaki, 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. Extended from IEEE MLSP (2020) version.
Alex Tong, Guy Wolf, Smita Krishnaswamy
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Fixing Bias in Reconstruction-based Anomaly Detection with Lipschitz Discriminators
POT: Python Optimal Transport
Optimal transport has recently been reintroduced to the machine learning community thanks in part to novel efficient optimization …
Remi Flamary, Nicolas Courty, Alexandre Gramfort, Mokhtar Z Alaya, Aurelie Boisbunon, Stanislas Chambon, Laetitia Chapel, Adrien Corenflos, Kilian Fatras, Nemo Fournier, Leo Gautheron, Nathalie T H Gayraud, Hicham Janati, Alain Rakotomamonjy, Ievgen Redko, Antoine Rolet, Antony Schutz, Vivien Seguy, Danica J Sutherland, Romain Tavenard, Alex Tong, Titouan Vayer
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