Article-Journal

Defining and Benchmarking Open Problems in Single-Cell Analysis
With the growing number of single-cell analysis tools, benchmarks are increasingly important to guide analysis and method development. …
Malte Luecken*, Scott Gigante*, Daniel Burkhardt*, Robrecht Cannoodt, Daniel Strobl, Nikolay Markov, Luke Zappia, Giovanni Palla, Wesley Lewis, Daniel Dimitrov, Michael Vinyard, Daniel Magruder, Alma Andersson, Emma Dann, Qian Qin, Dominik Otto, Michal Klein, Olga Botvinnik, Louise Deconinck, Kai Waldrant, Bastian Rieck, Constantin Ahlmann-Eltze, Eduardo Da Veiga Beltrame, Andrew Benz, Carmen Bravo González-Blas, Ann Chen, Benjamin DeMeo, Can Ergen, Swann Floc'hlay, Adam Gayoso, Stephanie Hicks, Yuge Ji, Vitalii Kleshchevnikov, Gioele La Manno, Maximilian Lombardo, Romain Lopez, Dario Righelli, Hirak Sarkar, Valentine Svensson, Alex Tong, Galen Xing, Chenling Xu, Jonathan Bloom, Angela Pisco, Julio Saez-Rodriguez, Drausin Wulsin, Luca Pinello, Yvan Saeys, Fabian Theis, Smita Krishnaswamy
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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