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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
Improving and Generalizing Flow-Based Generative Models with Minibatch Optimal Transport
We present methods for learning simple flows over R^d with optimal transport conditional flow matching (OT-CFM). Training with this objective leads to imprved results on a variety of conditional and unconditional generation tasks, such as inferring single cell dynamics, unsupervised image translation, and Schrodinger bridge inference.
Alex Tong, Nikolay Malkin, Guillaume Huguet, Yanlei Zhang, Jarrid Rector-Brooks, Kilian Fatras, Guy Wolf, Yoshua Bengio
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Improving and Generalizing Flow-Based Generative Models with Minibatch Optimal Transport
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
Embedding Signals on Knowledge Graphs with Unbalanced Diffusion Earth Mover's Distance
In modern relational machine learning it is common to encounter large graphs that arise via interactions or similarities between …
Alex Tong, Guillaume Huguet, Dennis Shung, Amine Natik, Manik Kuchroo, Guillaume Lajoie, Guy Wolf, Smita Krishnaswamy
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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, Alexander 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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