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Functional magnetic resonance imaging (fMRI) is a notoriously noisy measurement of brain activity because of the large variations between individuals, signals marred by environmental differences during collection, and spatiotemporal averaging required by the measurement resolution.
Laplacian eigenmaps for dimensionality reduction and data representation
Mikhail Belkin and Partha Niyogi · 2003
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Diffusion maps
Ronald R Coifman and Stéphane Lafon · 2006
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Metric multidimensional scaling (mds): analyzing distance matrices
Hervé Abdi · 2007
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Modeling group fmri data
Jeanette A Mumford and Russell A Poldrack · 2007
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Visualizing data using t-sne
Laurens Van der Maaten and Geoffrey Hinton · 2008
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A common, high-dimensional model of the representational space in human ventral temporal cortex
James V Haxby, J Swaroop Guntupalli, Andrew C Connolly, Yaroslav O Halchenko, Bryan R Conroy, M Ida Gobbini, Michael Hanke, and Peter J Ramadge · 2011
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Coarse-grained localized diffusion
Guy Wolf, Aviv Rotbart, Gil David, and Amir Averbuch · 2012
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Physiological noise in brainstem fmri
Jonathan Charles William Brooks, Olivia Kate Faull, Kyle TS Pattinson, and Mark Jenkinson · 2013
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Embedding with autoencoder regularization
Wenchao Yu, Guangxiang Zeng, Ping Luo, Fuzhen Zhuang, Qing He, and Zhongzhi Shi · 2013
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A high-resolution 7-tesla fmri dataset from complex natural stimulation with an audio movie
Michael Hanke, Florian J. Baumgartner, Pierre Ibe, Falko R. Kaule, Stefan Pollmann, Oliver Speck, Wolf Zinke, and Jörg Stadler · 2014
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Group-pca for very large fmri datasets
Stephen M Smith, Aapo Hyvärinen, Gaël Varoquaux, Karla L Miller, and Christian F Beckmann · 2014
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A reduced-dimension fmri shared response model
Po-Hsuan (Cameron) Chen, Janice Chen, Yaara Yeshurun, Uri Hasson, James Haxby, and Peter J Ramadge · 2015
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Laplacian auto-encoders: An explicit learning of nonlinear data manifold
Kui Jia, Lin Sun, Shenghua Gao, Zhan Song, and Bertram E Shi · 2015
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An annotation of cuts, depicted locations, and temporal progression in the motion picture "forrest gump" [version 1; peer review: 3 approved]
CO Husler and M Hanke · 2016
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A studyforrest extension, retinotopic mapping and localization of higher visual areas
Ayan Sengupta, Falko R. Kaule, J. Swaroop Guntupalli, Michael B. Hoffmann, Christian Häusler, Jörg Stadler, and Michael Hanke · 2016
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Shared memories reveal shared structure in neural activity across individuals
Janice Chen, Yuan Chang Leong, Christopher J. Honey, Chung H. Yong, Kenneth A. Norman, and Uri Hasson · 2017
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Visualizing structure and transitions in high-dimensional biological data
Kevin R. Moon, David van Dijk, Zheng Wang, Scott Gigante, Daniel B. Burkhardt, William S. Chen, Kristina Yim, Antonia van den Elzen, Matthew J. Hirn, Ronald R. Coifman, Natalia B. Ivanova, Guy Wolf, and Smita Krishnaswamy · 2019
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Measuring shared responses across subjects using intersubject correlation
Samuel A Nastase, Valeria Gazzola, Uri Hasson, and Christian Keysers · 2019
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Endocrine-exocrine signaling drives obesity-associated pancreatic ductal adenocarcinoma
Katherine Minjee Chung, Jaffarguriqbal Singh, Lauren Lawres, Kimberly Judith Dorans, Cathy Garcia, Daniel B Burkhardt, Rebecca Robbins, Arjun Bhutkar, Rebecca Cardone, Xiaojian Zhao, et al · 2020
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Extendable and invertible manifold learning with geometry regularized autoencoders
Andrés F Duque, Sacha Morin, Guy Wolf, and Kevin Moon · 2020
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Non-linear manifold learning in fmri uncovers a low-dimensional space of brain dynamics
Siyuan Gao, Gal Mishne, and Dustin Scheinost · 2020
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Leland McInnes, John Healy, and James Melville · 2018
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Mapping between fmri responses to movies and their natural language annotations
Kiran Vodrahalli, Po-Hsuan Chen, Yingyu Liang, Christopher Baldassano, Janice Chen, Esther Yong, Christopher Honey, Uri Hasson, Peter Ramadge, Kenneth A. Norman, and Sanjeev Arora · 2018
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Exploring single-cell data with deep multitasking neural networks
Matthew Amodio, David Van Dijk, Krishnan Srinivasan, William S Chen, Hussein Mohsen, Kevin R Moon, Allison Campbell, Yujiao Zhao, Xiaomei Wang, Manjunatha Venkataswamy, et al · 2019
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Coarse graining of data via inhomogeneous diffusion condensation
Nathan Brugnone, Alex Gonopolskiy, Mark W Moyle, Manik Kuchroo, David van Dijk, Kevin R Moon, Daniel Colon-Ramos, Guy Wolf, Matthew J Hirn, and Smita Krishnaswamy · 2019
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Visualizing the phate of neural networks
Scott Gigante, Adam S Charles, Smita Krishnaswamy, and Gal Mishne · 2019
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Diffusion nets
Gal Mishne, Uri Shaham, Alexander Cloninger, and Israel Cohen · 2019
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Multiscale phate exploration of sars-cov-2 data reveals multimodal signatures of disease
Manik Kuchroo, Jessie Huang, Patrick Wong, Jean-Christophe Grenier, Dennis Shung, Alexander Tong, Carolina Lucas, Jon Klein, Daniel Burkhardt, Scott Gigante, et al · 2020
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Topological autoencoders
Michael Moor, Max Horn, Bastian Rieck, and Karsten Borgwardt · 2020
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Transcriptomic and clonal characterization of t cells in the human central nervous system
Jenna L Pappalardo, Le Zhang, Maggie K Pecsok, Kelly Perlman, Chrysoula Zografou, Khadir Raddassi, Ahmad Abulaban, Smita Krishnaswamy, Jack Antel, David van Dijk, et al · 2020
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Uncovering the topology of time-varying fmri data using cubical persistence
Bastian Rieck, Tristan Yates, Christian Bock, Karsten Borgwardt, Guy Wolf, Nicholas Turk-Browne, and Smita Krishnaswamy · 2020
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Single cell immune profiling of dengue virus patients reveals intact immune responses to zika virus with enrichment of innate immune signatures
Yujiao Zhao, Matthew Amodio, Brent Vander Wyk, Bram Gerritsen, Mahesh M Kumar, David van Dijk, Kevin Moon, Xiaomei Wang, Anna Malawista, Monique M Richards, et al · 2020
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Hybrid hyperalignment: A single high-dimensional model of shared information embedded in cortical patterns of response and functional connectivity
Erica L. Busch, Lukas Slipski, Ma Feilong, J. Swaroop Guntupalli, Matteo Visconti di Oleggio Castello, Jeremy F. Huckins, Samuel A. Nastase, M. Ida Gobbini, Tor D. Wager, and James V. Haxby · 2021
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