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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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MURAL: An Unsupervised Random Forest-Based Embedding for Electronic Health Record Data
A unsupervised random tree distance for missing data in EHR
Michal Gerasimiuk*, Dennis L. Shung*, Alex Tong, Adrian J. Stanley, Machael Shultz, Jeffrey Ngu, Loren Laine, Guy Wolf, Smita Krishnaswamy
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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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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
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
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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