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@article{abrahamDerivingReproducibleBiomarkers2017,
title = {Deriving Reproducible Biomarkers from Multi-Site Resting-State Data: {{An Autism-based}} Example},
shorttitle = {Deriving Reproducible Biomarkers from Multi-Site Resting-State Data},
author = {Abraham, Alexandre and Milham, Michael P. and Di Martino, Adriana and Craddock, R. Cameron and Samaras, Dimitris and Thirion, Bertrand and Varoquaux, Gael},
year = {2017},
month = feb,
journal = {NeuroImage},
volume = {147},
pages = {736--745},
issn = {1053-8119},
doi = {10.1016/j.neuroimage.2016.10.045},
urldate = {2022-03-09}
}
@misc{acharyaLearningForecastAleatoric2023,
title = {Learning to {{Forecast Aleatoric}} and {{Epistemic Uncertainties}} over {{Long Horizon Trajectories}}},
author = {Acharya, Aastha and Russell, Rebecca and Ahmed, Nisar R.},
year = {2023},
month = feb,
number = {arXiv:2302.08669},
eprint = {2302.08669},
primaryclass = {cs},
publisher = {arXiv},
doi = {10.48550/arXiv.2302.08669},
urldate = {2024-03-14}
}
@article{achilleDynamicsReachabilityLearning2019,
title = {Dynamics and {{Reachability}} of {{Learning Tasks}}},
author = {Achille, Alessandro and Mbeng, Glen and Soatto, Stefano},
year = {2019},
month = may,
journal = {arXiv:1810.02440 [cs, stat]},
eprint = {1810.02440},
primaryclass = {cs, stat},
urldate = {2022-01-22}
}
@article{achilleEmergenceInvarianceDisentanglement2018,
title = {Emergence of {{Invariance}} and {{Disentanglement}} in {{Deep Representations}}},
author = {Achille, Alessandro and Soatto, Stefano},
year = {2018},
month = jun,
journal = {arXiv:1706.01350 [cs, stat]},
eprint = {1706.01350},
primaryclass = {cs, stat},
urldate = {2022-01-22}
}
@article{achilleInformationComplexityLearning2021,
title = {The Information Complexity of Learning Tasks, Their Structure and Their Distance},
author = {Achille, Alessandro and Paolini, Giovanni and Mbeng, Glen and Soatto, Stefano},
year = {2021},
month = mar,
journal = {Information and Inference: A Journal of the IMA},
volume = {10},
number = {1},
pages = {51--72},
issn = {2049-8772},
doi = {10.1093/imaiai/iaaa033},
urldate = {2022-01-22}
}
@article{achilleTask2VecTaskEmbedding2019,
title = {{{Task2Vec}}: {{Task Embedding}} for {{Meta-Learning}}},
shorttitle = {{{Task2Vec}}},
author = {Achille, Alessandro and Lam, Michael and Tewari, Rahul and Ravichandran, Avinash and Maji, Subhransu and Fowlkes, Charless and Soatto, Stefano and Perona, Pietro},
year = {2019},
month = feb,
journal = {arXiv:1902.03545 [cs, stat]},
eprint = {1902.03545},
primaryclass = {cs, stat},
urldate = {2022-01-22}
}
@article{achilleWhereInformationDeep2020,
title = {Where Is the {{Information}} in a {{Deep Neural Network}}?},
author = {Achille, Alessandro and Paolini, Giovanni and Soatto, Stefano},
year = {2020},
month = jun,
journal = {arXiv:1905.12213 [cs, math, stat]},
eprint = {1905.12213},
primaryclass = {cs, math, stat},
urldate = {2021-12-31}
}
@article{achtibatAttributionMapsHumanunderstandable2023,
title = {From Attribution Maps to Human-Understandable Explanations through {{Concept Relevance Propagation}}},
author = {Achtibat, Reduan and Dreyer, Maximilian and Eisenbraun, Ilona and Bosse, Sebastian and Wiegand, Thomas and Samek, Wojciech and Lapuschkin, Sebastian},
year = {2023},
month = sep,
journal = {Nature Machine Intelligence},
volume = {5},
number = {9},
pages = {1006--1019},
publisher = {Nature Publishing Group},
issn = {2522-5839},
doi = {10.1038/s42256-023-00711-8},
urldate = {2023-09-26},
copyright = {2023 The Author(s)}
}
@article{adesnikProbingNeuralCodes2021,
title = {Probing Neural Codes with Two-Photon Holographic Optogenetics},
author = {Adesnik, Hillel and Abdeladim, Lamiae},
year = {2021},
month = oct,
journal = {Nature Neuroscience},
volume = {24},
number = {10},
pages = {1356--1366},
issn = {1097-6256, 1546-1726},
doi = {10.1038/s41593-021-00902-9},
urldate = {2022-01-19}
}
@misc{ADNIAlzheimerDisease,
title = {{{ADNI}} {\textbar} {{Alzheimer}}'s {{Disease Neuroimaging Initiative}}},
urldate = {2022-03-01}
}
@article{agrawalMinimumDistortionEmbedding2021,
title = {Minimum-{{Distortion Embedding}}},
author = {Agrawal, Akshay and Ali, Alnur and Boyd, Stephen},
year = {2021},
month = mar,
journal = {arXiv:2103.02559 [cs, math, stat]},
eprint = {2103.02559},
primaryclass = {cs, math, stat},
urldate = {2021-07-20}
}
@article{ahlheimEstimatingFunctionalDimensionality2018,
title = {Estimating the Functional Dimensionality of Neural Representations},
author = {Ahlheim, Christiane and Love, Bradley C.},
year = {2018},
month = oct,
journal = {NeuroImage},
volume = {179},
pages = {51--62},
issn = {10538119},
doi = {10.1016/j.neuroimage.2018.06.015},
urldate = {2022-01-02}
}
@article{aitkenUnderstandingHowEncoderDecoder2021,
title = {Understanding {{How Encoder-Decoder Architectures Attend}}},
author = {Aitken, Kyle and Ramasesh, Vinay V. and Cao, Yuan and Maheswaranathan, Niru},
year = {2021},
month = oct,
journal = {arXiv:2110.15253 [cs, stat]},
eprint = {2110.15253},
primaryclass = {cs, stat},
urldate = {2022-05-06}
}
@misc{althubaitiDeepMOCCAPancancerPrognostic2021,
title = {{{DeepMOCCA}}: {{A}} Pan-Cancer Prognostic Model Identifies Personalized Prognostic Markers through Graph Attention and Multi-Omics Data Integration},
shorttitle = {{{DeepMOCCA}}},
author = {Althubaiti, Sara and Kulmanov, Maxat and Liu, Yang and Gkoutos, Georgios V. and Schofield, Paul and Hoehndorf, Robert},
year = {2021},
month = mar,
pages = {2021.03.02.433454},
institution = {Cold Spring Harbor Laboratory},
doi = {10.1101/2021.03.02.433454},
urldate = {2021-10-06},
chapter = {New Results},
copyright = {{\copyright} 2021, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution 4.0 International), CC BY 4.0, as described at http://creativecommons.org/licenses/by/4.0/}
}
@article{amannExplainabilityArtificialIntelligence2020,
title = {Explainability for Artificial Intelligence in Healthcare: A Multidisciplinary Perspective},
shorttitle = {Explainability for Artificial Intelligence in Healthcare},
author = {Amann, Julia and Blasimme, Alessandro and Vayena, Effy and Frey, Dietmar and Madai, Vince I. and {the Precise4Q consortium}},
year = {2020},
month = nov,
journal = {BMC Medical Informatics and Decision Making},
volume = {20},
number = {1},
pages = {310},
issn = {1472-6947},
doi = {10.1186/s12911-020-01332-6},
urldate = {2021-11-15}
}
@article{amiranashviliLearningShapeReconstruction2021,
title = {Learning {{Shape Reconstruction}} from {{Sparse Measurements}} with {{Neural Implicit Functions}}},
author = {Amiranashvili, Tamaz and L{\"u}dke, David and Li, Hongwei and Menze, Bjoern and Zachow, Stefan},
year = {2021},
month = dec,
urldate = {2022-01-27}
}
@inproceedings{amiranashviliLearningShapeReconstruction2022,
title = {Learning {{Shape Reconstruction}} from {{Sparse Measurements}} with {{Neural Implicit Functions}}},
booktitle = {Medical {{Imaging}} with {{Deep Learning}}},
author = {Amiranashvili, Tamaz and L{\"u}dke, David and Li, Hongwei and Menze, Bjoern and Zachow, Stefan},
year = {2022},
month = jun,
urldate = {2022-10-25}
}
@incollection{andersenDreamingVariationalAutoencoder2018,
title = {The {{Dreaming Variational Autoencoder}} for {{Reinforcement Learning Environments}}},
booktitle = {Artificial {{Intelligence XXXV}}},
author = {Andersen, Per-Arne and Goodwin, Morten and Granmo, Ole-Christoffer},
editor = {Bramer, Max and Petridis, Miltos},
year = {2018},
volume = {11311},
pages = {143--155},
publisher = {Springer International Publishing},
address = {Cham},
doi = {10.1007/978-3-030-04191-5_11},
urldate = {2021-12-30},
isbn = {978-3-030-04190-8 978-3-030-04191-5}
}
@article{anonymousInternalRepresentationDynamics2023,
title = {Internal {{Representation Dynamics}} in {{Transformers}}},
author = {Anonymous},
year = {2023},
month = oct,
urldate = {2024-03-04}
}
@article{anOverviewBiologicalComputational2021,
title = {An {{Overview}} of {{Biological}} and {{Computational Methods}} for {{Designing Mechanism-Informed Anti-biofilm Agents}}},
author = {An, Andy Y. and Choi, Ka-Yee Grace and Baghela, Arjun S. and Hancock, Robert E. W.},
year = {2021},
journal = {Frontiers in Microbiology},
volume = {12},
issn = {1664-302X},
urldate = {2023-11-24}
}
@misc{ansuiniIntrinsicDimensionData2019,
title = {Intrinsic Dimension of Data Representations in Deep Neural Networks},
author = {Ansuini, Alessio and Laio, Alessandro and Macke, Jakob H. and Zoccolan, Davide},
year = {2019},
month = oct,
number = {arXiv:1905.12784},
eprint = {1905.12784},
primaryclass = {cs, stat},
publisher = {arXiv},
urldate = {2023-05-08}
}
@article{arnatkeviciuteHubConnectivityNeuronal2018,
title = {Hub Connectivity, Neuronal Diversity, and Gene Expression in the {{Caenorhabditis}} Elegans Connectome},
author = {Arnatkevi{\u c}i{\=u}t{\.e}, Aurina and Fulcher, Ben D. and Pocock, Roger and Fornito, Alex},
year = {2018},
month = feb,
journal = {PLOS Computational Biology},
volume = {14},
number = {2},
pages = {e1005989},
publisher = {Public Library of Science},
issn = {1553-7358},
doi = {10.1371/journal.pcbi.1005989},
urldate = {2021-11-12}
}
@misc{arnatkeviciuteWhereGenomeMeets2021,
title = {Where the Genome Meets the Connectome: Understanding How Genes Shape Human Brain Connectivity},
shorttitle = {Where the Genome Meets the Connectome},
author = {Arnatkeviciute, Aurina and Fulcher, Ben and Bellgrove, Mark and Fornito, Alex},
year = {2021},
month = apr,
institution = {PsyArXiv},
doi = {10.31234/osf.io/hqgz7},
urldate = {2021-11-12}
}
@article{aronovMappingNonspatialDimension2017,
title = {Mapping of a Non-Spatial Dimension by the Hippocampal--Entorhinal Circuit},
author = {Aronov, Dmitriy and Nevers, Rhino and Tank, David W.},
year = {2017},
month = mar,
journal = {Nature},
volume = {543},
number = {7647},
pages = {719--722},
issn = {0028-0836, 1476-4687},
doi = {10.1038/nature21692},
urldate = {2022-01-21}
}
@article{arvivDeviationsCriticalDynamics2016,
title = {Deviations from {{Critical Dynamics}} in {{Interictal Epileptiform Activity}}},
author = {Arviv, Oshrit and Medvedovsky, Mordekhay and Sheintuch, Liron and Goldstein, Abraham and Shriki, Oren},
year = {2016},
month = nov,
journal = {Journal of Neuroscience},
volume = {36},
number = {48},
pages = {12276--12292},
issn = {0270-6474, 1529-2401},
doi = {10.1523/JNEUROSCI.0809-16.2016},
urldate = {2021-12-08},
copyright = {Copyright {\copyright} 2016 the authors 0270-6474/16/3612276-17\$15.00/0},
pmid = {27903734}
}
@article{atlasonSegAEUnsupervisedWhite2019,
title = {{{SegAE}}: {{Unsupervised}} White Matter Lesion Segmentation from Brain {{MRIs}} Using a {{CNN}} Autoencoder},
shorttitle = {{{SegAE}}},
author = {Atlason, Hans E. and Love, Askell and Sigurdsson, Sigurdur and Gudnason, Vilmundur and Ellingsen, Lotta M.},
year = {2019},
month = jan,
journal = {NeuroImage: Clinical},
volume = {24},
pages = {102085},
issn = {2213-1582},
doi = {10.1016/j.nicl.2019.102085},
urldate = {2021-11-04}
}
@article{averbeckNeuralCorrelationsPopulation2006,
title = {Neural Correlations, Population Coding and Computation},
author = {Averbeck, Bruno B. and Latham, Peter E. and Pouget, Alexandre},
year = {2006},
month = may,
journal = {Nature Reviews Neuroscience},
volume = {7},
number = {5},
pages = {358--366},
issn = {1471-003X, 1471-0048},
doi = {10.1038/nrn1888},
urldate = {2022-01-05}
}
@article{aziziTimeVaryingAnalysis2024,
title = {Time Varying Analysis of Dynamic Resting-State Functional Brain Network to Unfold Memory Function},
author = {Azizi, Tahmineh},
year = {2024},
month = mar,
journal = {Neuroscience Informatics},
volume = {4},
number = {1},
pages = {100148},
issn = {2772-5286},
doi = {10.1016/j.neuri.2023.100148},
urldate = {2024-02-01}
}
@article{badreddineLogicTensorNetworks2020a,
title = {Logic {{Tensor Networks}}},
author = {Badreddine, Samy and d'Avila Garcez, Artur and Serafini, Luciano and Spranger, Michael},
year = {2020},
month = dec,
doi = {10.1016/j.artint.2021.103649},
urldate = {2022-01-21}
}
@article{badreDimensionalityNeuralRepresentations2021,
title = {The Dimensionality of Neural Representations for Control},
author = {Badre, David and Bhandari, Apoorva and Keglovits, Haley and Kikumoto, Atsushi},
year = {2021},
month = apr,
journal = {Current Opinion in Behavioral Sciences},
volume = {38},
pages = {20--28},
issn = {23521546},
doi = {10.1016/j.cobeha.2020.07.002},
urldate = {2022-01-02}
}
@article{bahramiUsingLowDimensionalManifolds2019,
title = {Using {{Low-Dimensional Manifolds}} to {{Map Relationships Between Dynamic Brain Networks}}},
author = {Bahrami, Mohsen and Lyday, Robert G. and Casanova, Ramon and Burdette, Jonathan H. and Simpson, Sean L. and Laurienti, Paul J.},
year = {2019},
journal = {Frontiers in Human Neuroscience},
volume = {13},
pages = {430},
issn = {1662-5161},
doi = {10.3389/fnhum.2019.00430},
urldate = {2021-11-05}
}
@misc{balwaniDeepFeatureLearning2020,
title = {A {{Deep Feature Learning Approach}} for {{Mapping}} the {{Brain}}'s {{Microarchitecture}} and {{Organization}}},
author = {Balwani, Aishwarya H. and Dyer, Eva L.},
year = {2020},
month = may,
pages = {2020.05.26.117473},
institution = {bioRxiv},
doi = {10.1101/2020.05.26.117473},
urldate = {2022-02-18},
chapter = {New Results},
copyright = {{\copyright} 2020, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution-NonCommercial-NoDerivs 4.0 International), CC BY-NC-ND 4.0, as described at http://creativecommons.org/licenses/by-nc-nd/4.0/}
}
@misc{balwaniDeepFeatureLearning2020a,
title = {A {{Deep Feature Learning Approach}} for {{Mapping}} the {{Brain}}'s {{Microarchitecture}} and {{Organization}}},
author = {Balwani, Aishwarya H. and Dyer, Eva L.},
year = {2020},
month = may,
pages = {2020.05.26.117473},
institution = {bioRxiv},
doi = {10.1101/2020.05.26.117473},
urldate = {2022-02-18},
chapter = {New Results},
copyright = {{\copyright} 2020, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution-NonCommercial-NoDerivs 4.0 International), CC BY-NC-ND 4.0, as described at http://creativecommons.org/licenses/by-nc-nd/4.0/}
}
@article{baninoVectorbasedNavigationUsing2018,
title = {Vector-Based Navigation Using Grid-like Representations in Artificial Agents},
author = {Banino, Andrea and Barry, Caswell and Uria, Benigno and Blundell, Charles and Lillicrap, Timothy and Mirowski, Piotr and Pritzel, Alexander and Chadwick, Martin J. and Degris, Thomas and Modayil, Joseph and Wayne, Greg and Soyer, Hubert and Viola, Fabio and Zhang, Brian and Goroshin, Ross and Rabinowitz, Neil and Pascanu, Razvan and Beattie, Charlie and Petersen, Stig and Sadik, Amir and Gaffney, Stephen and King, Helen and Kavukcuoglu, Koray and Hassabis, Demis and Hadsell, Raia and Kumaran, Dharshan},
year = {2018},
month = may,
journal = {Nature},
volume = {557},
number = {7705},
pages = {429--433},
issn = {0028-0836, 1476-4687},
doi = {10.1038/s41586-018-0102-6},
urldate = {2021-11-23}
}
@article{baninoVectorbasedNavigationUsing2018a,
title = {Vector-Based Navigation Using Grid-like Representations in Artificial Agents},
author = {Banino, Andrea and Barry, Caswell and Uria, Benigno and Blundell, Charles and Lillicrap, Timothy and Mirowski, Piotr and Pritzel, Alexander and Chadwick, Martin J. and Degris, Thomas and Modayil, Joseph and Wayne, Greg and Soyer, Hubert and Viola, Fabio and Zhang, Brian and Goroshin, Ross and Rabinowitz, Neil and Pascanu, Razvan and Beattie, Charlie and Petersen, Stig and Sadik, Amir and Gaffney, Stephen and King, Helen and Kavukcuoglu, Koray and Hassabis, Demis and Hadsell, Raia and Kumaran, Dharshan},
year = {2018},
month = may,
journal = {Nature},
volume = {557},
number = {7705},
pages = {429--433},
issn = {0028-0836, 1476-4687},
doi = {10.1038/s41586-018-0102-6},
urldate = {2022-01-07}
}
@article{bar-gadInformationProcessingDimensionality2003,
title = {Information Processing, Dimensionality Reduction and Reinforcement Learning in the Basal Ganglia},
author = {{Bar-Gad}, Izhar and Morris, Genela and Bergman, Hagai},
year = {2003},
month = dec,
journal = {Progress in Neurobiology},
volume = {71},
number = {6},
pages = {439--473},
issn = {03010082},
doi = {10.1016/j.pneurobio.2003.12.001},
urldate = {2022-10-12}
}
@article{barackPublisherCorrectionTwo2021,
title = {Publisher {{Correction}}: {{Two}} Views of the Cognitive Brain},
shorttitle = {Publisher {{Correction}}},
author = {Barack, David L. and Krakauer, John W.},
year = {2021},
month = aug,
journal = {Nature Reviews Neuroscience},
volume = {22},
number = {8},
pages = {516--516},
issn = {1471-003X, 1471-0048},
doi = {10.1038/s41583-021-00487-z},
urldate = {2022-11-14}
}
@article{barackTwoViewsCognitive2021,
title = {Two Views on the Cognitive Brain},
author = {Barack, David L. and Krakauer, John W.},
year = {2021},
month = jun,
journal = {Nature Reviews Neuroscience},
volume = {22},
number = {6},
pages = {359--371},
issn = {1471-003X, 1471-0048},
doi = {10.1038/s41583-021-00448-6},
urldate = {2023-01-06}
}
@article{barackTwoViewsCognitive2021,
title = {Two Views on the Cognitive Brain},
author = {Barack, David L. and Krakauer, John W.},
year = {2021},
month = jun,
journal = {Nature Reviews Neuroscience},
volume = {22},
number = {6},
pages = {359--371},
publisher = {Nature Publishing Group},
issn = {1471-0048},
doi = {10.1038/s41583-021-00448-6},
urldate = {2022-05-30},
copyright = {2021 Springer Nature Limited}
}
@article{barakRecurrentNeuralNetworks2017,
title = {Recurrent Neural Networks as Versatile Tools of Neuroscience Research},
author = {Barak, Omri},
year = {2017},
month = oct,
journal = {Current Opinion in Neurobiology},
volume = {46},
pages = {1--6},
issn = {09594388},
doi = {10.1016/j.conb.2017.06.003},
urldate = {2022-04-26}
}
@article{barakSparsenessMixedSelectivity2013,
title = {The {{Sparseness}} of {{Mixed Selectivity Neurons Controls}} the {{Generalization-Discrimination Trade-Off}}},
author = {Barak, O. and Rigotti, M. and Fusi, S.},
year = {2013},
month = feb,
journal = {Journal of Neuroscience},
volume = {33},
number = {9},
pages = {3844--3856},
issn = {0270-6474, 1529-2401},
doi = {10.1523/JNEUROSCI.2753-12.2013},
urldate = {2022-11-22}
}
@article{bardesRevisitingFeaturePrediction,
title = {Revisiting {{Feature Prediction}} for {{Learning Visual Representations}} from {{Video}}},
author = {Bardes, Adrien and Garrido, Quentin and Ponce, Jean and Chen, Xinlei and Rabbat, Michael and LeCun, Yann and Assran, Mahmoud and Ballas, Nicolas}
}
@article{behrensWhatCognitiveMap2018,
title = {What {{Is}} a {{Cognitive Map}}? {{Organizing Knowledge}} for {{Flexible Behavior}}},
shorttitle = {What {{Is}} a {{Cognitive Map}}?},
author = {Behrens, Timothy E.J. and Muller, Timothy H. and Whittington, James C.R. and Mark, Shirley and Baram, Alon B. and Stachenfeld, Kimberly L. and {Kurth-Nelson}, Zeb},
year = {2018},
month = oct,
journal = {Neuron},
volume = {100},
number = {2},
pages = {490--509},
issn = {08966273},
doi = {10.1016/j.neuron.2018.10.002},
urldate = {2022-01-04}
}
@misc{beiranParametricControlFlexible2021,
title = {Parametric Control of Flexible Timing through Low-Dimensional Neural Manifolds},
author = {Beiran, Manuel and Meirhaeghe, Nicolas and Sohn, Hansem and Jazayeri, Mehrdad and Ostojic, Srdjan},
year = {2021},
month = nov,
pages = {2021.11.08.467806},
institution = {bioRxiv},
urldate = {2022-05-01},
copyright = {{\copyright} 2021, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution-NonCommercial-NoDerivs 4.0 International), CC BY-NC-ND 4.0, as described at http://creativecommons.org/licenses/by-nc-nd/4.0/}
}
@techreport{beiranParametricControlFlexible2021a,
type = {Preprint},
title = {Parametric Control of Flexible Timing through Low-Dimensional Neural Manifolds},
author = {Beiran, Manuel and Meirhaeghe, Nicolas and Sohn, Hansem and Jazayeri, Mehrdad and Ostojic, Srdjan},
year = {2021},
month = nov,
institution = {Neuroscience},
doi = {10.1101/2021.11.08.467806},
urldate = {2022-05-04}
}
@misc{bengioDeepGenerativeStochastic2014,
title = {Deep {{Generative Stochastic Networks Trainable}} by {{Backprop}}},
author = {Bengio, Yoshua and {Thibodeau-Laufer}, {\'E}ric and Alain, Guillaume and Yosinski, Jason},
year = {2014},
month = may,
number = {arXiv:1306.1091},
eprint = {1306.1091},
primaryclass = {cs},
publisher = {arXiv},
urldate = {2023-07-10}
}
@article{bengioRepresentationLearningReview2014,
title = {Representation {{Learning}}: {{A Review}} and {{New Perspectives}}},
shorttitle = {Representation {{Learning}}},
author = {Bengio, Yoshua and Courville, Aaron and Vincent, Pascal},
year = {2014},
month = apr,
journal = {arXiv:1206.5538 [cs]},
eprint = {1206.5538},
primaryclass = {cs},
urldate = {2021-11-17}
}
@article{benkarimConnectivityAlterationsAutism2021,
title = {Connectivity Alterations in Autism Reflect Functional Idiosyncrasy},
author = {Benkarim, Oualid and Paquola, Casey and Park, Bo-yong and Hong, Seok-Jun and Royer, Jessica and {Vos de Wael}, Reinder and Lariviere, Sara and Valk, Sofie and Bzdok, Danilo and Mottron, Laurent and C. Bernhardt, Boris},
year = {2021},
month = sep,
journal = {Communications Biology},
volume = {4},
number = {1},
pages = {1--15},
publisher = {Nature Publishing Group},
issn = {2399-3642},
doi = {10.1038/s42003-021-02572-6},
urldate = {2021-11-13},
copyright = {2021 The Author(s)}
}
@article{bernardiGeometryAbstractionHippocampus2020,
title = {The {{Geometry}} of {{Abstraction}} in the {{Hippocampus}} and {{Prefrontal Cortex}}},
author = {Bernardi, Silvia and Benna, Marcus K. and Rigotti, Mattia and Munuera, J{\'e}r{\^o}me and Fusi, Stefano and Salzman, C. Daniel},
year = {2020},
month = nov,
journal = {Cell},
volume = {183},
number = {4},
pages = {954-967.e21},
issn = {00928674},
doi = {10.1016/j.cell.2020.09.031},
urldate = {2022-01-04}
}
@article{bethlehemGradientsCorticalHierarchy2017,
title = {Gradients of Cortical Hierarchy in {{Autism}}},
author = {Bethlehem, Richard and Falkiewicz, Marcel and Freyberg, Jan and Parsons, Owen and Farahibozorg, Seyedeh-Rezvan and Pretzsch, Charlotte and Soergel, Bjoern and Margulies, Daniel},
year = {2017},
month = feb,
journal = {Research Ideas and Outcomes},
volume = {3},
pages = {e13391},
publisher = {Pensoft Publishers},
issn = {2367-7163},
doi = {10.3897/rio.3.e13391},
urldate = {2021-11-13},
copyright = {2021Richard Bethlehem, Marcel Falkiewicz, Jan Freyberg, Owen Parsons, Seyedeh-Rezvan Farahibozorg, Charlotte Pretzsch, Bjoern Soergel, Daniel Margulies}
}
@article{betzelGenerativeModelsNetwork2017,
title = {Generative Models for Network Neuroscience: Prospects and Promise},
shorttitle = {Generative Models for Network Neuroscience},
author = {Betzel, Richard F. and Bassett, Danielle S.},
year = {2017},
month = nov,
journal = {Journal of The Royal Society Interface},
volume = {14},
number = {136},
pages = {20170623},
publisher = {Royal Society},
doi = {10.1098/rsif.2017.0623},
urldate = {2021-11-12}
}
@article{bhatiaBuresWassersteinDistance2019,
title = {On the {{Bures}}--{{Wasserstein}} Distance between Positive Definite Matrices},
author = {Bhatia, Rajendra and Jain, Tanvi and Lim, Yongdo},
year = {2019},
month = jun,
journal = {Expositiones Mathematicae},
volume = {37},
number = {2},
pages = {165--191},
issn = {0723-0869},
doi = {10.1016/j.exmath.2018.01.002},
urldate = {2024-02-09}
}
@article{biUnderstandingComputationTime2020,
title = {Understanding the Computation of Time Using Neural Network Models},
author = {Bi, Zedong and Zhou, Changsong},
year = {2020},
month = may,
journal = {Proceedings of the National Academy of Sciences},
volume = {117},
number = {19},
pages = {10530--10540},
issn = {0027-8424, 1091-6490},
doi = {10.1073/pnas.1921609117},
urldate = {2022-05-01}
}
@article{bodnarWeisfeilerLehmanGo2021,
title = {Weisfeiler and {{Lehman Go Cellular}}: {{CW Networks}}},
shorttitle = {Weisfeiler and {{Lehman Go Cellular}}},
author = {Bodnar, Cristian and Frasca, Fabrizio and Otter, Nina and Wang, Yu Guang and Li{\`o}, Pietro and Mont{\'u}far, Guido and Bronstein, Michael},
year = {2021},
month = jun,
urldate = {2021-11-19}
}
@article{brahmaWhyDeepLearning2016,
title = {Why {{Deep Learning Works}}: {{A Manifold Disentanglement Perspective}}},
shorttitle = {Why {{Deep Learning Works}}},
author = {Brahma, Pratik Prabhanjan and Wu, Dapeng and She, Yiyuan},
year = {2016},
month = oct,
journal = {IEEE Transactions on Neural Networks and Learning Systems},
volume = {27},
number = {10},
pages = {1997--2008},
issn = {2162-237X, 2162-2388},
doi = {10.1109/TNNLS.2015.2496947},
urldate = {2021-11-24}
}
@article{brahmaWhyDeepLearning2016a,
title = {Why {{Deep Learning Works}}: {{A Manifold Disentanglement Perspective}}},
shorttitle = {Why {{Deep Learning Works}}},
author = {Brahma, Pratik Prabhanjan and Wu, Dapeng and She, Yiyuan},
year = {2016},
month = oct,
journal = {IEEE Transactions on Neural Networks and Learning Systems},
volume = {27},
number = {10},
pages = {1997--2008},
issn = {2162-237X, 2162-2388},
doi = {10.1109/TNNLS.2015.2496947},
urldate = {2022-01-04}
}
@article{broidoScalefreeNetworksAre2019,
title = {Scale-Free Networks Are Rare},
author = {Broido, Anna D. and Clauset, Aaron},
year = {2019},
month = mar,
journal = {Nature Communications},
volume = {10},
number = {1},
pages = {1017},
publisher = {Nature Publishing Group},
issn = {2041-1723},
doi = {10.1038/s41467-019-08746-5},
urldate = {2023-12-08},
copyright = {2019 The Author(s)}
}
@article{bronsteinGeometricDeepLearning2021,
title = {Geometric {{Deep Learning}}: {{Grids}}, {{Groups}}, {{Graphs}}, {{Geodesics}}, and {{Gauges}}},
shorttitle = {Geometric {{Deep Learning}}},
author = {Bronstein, Michael M. and Bruna, Joan and Cohen, Taco and Veli{\v c}kovi{\'c}, Petar},
year = {2021},
month = may,
journal = {arXiv:2104.13478 [cs, stat]},
eprint = {2104.13478},
primaryclass = {cs, stat},
urldate = {2021-09-08}
}
@misc{bronsteinLatentGraphNeural2021,
title = {Latent Graph Neural Networks: {{Manifold}} Learning 2.0?},
shorttitle = {Latent Graph Neural Networks},
author = {Bronstein, Michael},
year = {2021},
month = nov,
journal = {Medium},
urldate = {2021-11-12},
howpublished = {https://towardsdatascience.com/manifold-learning-2-99a25eeb677d}
}
@article{burbankMirroredSTDPImplements2015,
title = {Mirrored {{STDP Implements Autoencoder Learning}} in a {{Network}} of {{Spiking Neurons}}},
author = {Burbank, Kendra S.},
year = {2015},
month = dec,
journal = {PLOS Computational Biology},
volume = {11},
number = {12},
pages = {e1004566},
publisher = {Public Library of Science},
issn = {1553-7358},
doi = {10.1371/journal.pcbi.1004566},
urldate = {2021-11-16}
}
@article{buzsakiMemoryNavigationTheta2013,
title = {Memory, Navigation and Theta Rhythm in the Hippocampal-Entorhinal System},
author = {Buzs{\'a}ki, Gy{\"o}rgy and Moser, Edvard I},
year = {2013},
month = feb,
journal = {Nature Neuroscience},
volume = {16},
number = {2},
pages = {130--138},
issn = {1097-6256, 1546-1726},
doi = {10.1038/nn.3304},
urldate = {2022-01-21}
}
@book{cabezaHandbookFunctionalNeuroimaging2006,
title = {Handbook of {{Functional Neuroimaging}} of {{Cognition}}},
editor = {Cabeza, Roberto and Kingstone, Alan and Gazzaniga, Michael S.},
year = {2006},
month = may,
series = {Cognitive {{Neuroscience}}},
edition = {2},
publisher = {MIT Press},
address = {Cambridge, MA, USA},
isbn = {978-0-262-03344-2}
}
@article{camastraIntrinsicDimensionEstimation2016a,
title = {Intrinsic Dimension Estimation: {{Advances}} and Open Problems},
shorttitle = {Intrinsic Dimension Estimation},
author = {Camastra, Francesco and Staiano, Antonino},
year = {2016},
month = jan,
journal = {Information Sciences},
volume = {328},
pages = {26--41},
issn = {00200255},
doi = {10.1016/j.ins.2015.08.029},
urldate = {2022-01-06}
}
@article{campadelliIntrinsicDimensionEstimation2015,
title = {Intrinsic {{Dimension Estimation}}: {{Relevant Techniques}} and a {{Benchmark Framework}}},
shorttitle = {Intrinsic {{Dimension Estimation}}},
author = {Campadelli, P. and Casiraghi, E. and Ceruti, C. and Rozza, A.},
year = {2015},
month = oct,
journal = {Mathematical Problems in Engineering},
volume = {2015},
pages = {e759567},
publisher = {Hindawi},
issn = {1024-123X},
doi = {10.1155/2015/759567},
urldate = {2022-01-06}
}
@article{cantareiraExploringNeuralNetwork2020,
title = {Exploring {{Neural Network Hidden Layer Activity Using Vector Fields}}},
author = {Cantareira, Gabriel D. and Etemad, Elham and Paulovich, Fernando V.},
year = {2020},
month = aug,
journal = {Information},
volume = {11},
number = {9},
pages = {426},
issn = {2078-2489},
doi = {10.3390/info11090426},
urldate = {2022-01-11}
}
@misc{cetinHyperbolicDeepReinforcement2022,
title = {Hyperbolic {{Deep Reinforcement Learning}}},
author = {Cetin, Edoardo and Chamberlain, Benjamin and Bronstein, Michael and Hunt, Jonathan J.},
year = {2022},
month = oct,
number = {arXiv:2210.01542},
eprint = {2210.01542},
primaryclass = {cs},
publisher = {arXiv},
urldate = {2023-11-30}
}
@misc{chamberlainGraphNeuralNetworks2023,
title = {Graph {{Neural Networks}} for {{Link Prediction}} with {{Subgraph Sketching}}},
author = {Chamberlain, Benjamin Paul and Shirobokov, Sergey and Rossi, Emanuele and Frasca, Fabrizio and Markovich, Thomas and Hammerla, Nils and Bronstein, Michael M. and Hansmire, Max},
year = {2023},
month = may,
number = {arXiv:2209.15486},
eprint = {2209.15486},
primaryclass = {cs},
publisher = {arXiv},
doi = {10.48550/arXiv.2209.15486},
urldate = {2024-02-02}
}
@article{chamberlandDimensionalityReductionDiffusion2019,
title = {Dimensionality Reduction of Diffusion {{MRI}} Measures for Improved Tractometry of the Human Brain},
author = {Chamberland, Maxime and Raven, Erika P. and Genc, Sila and Duffy, Kate and Descoteaux, Maxime and Parker, Greg D. and Tax, Chantal M. W. and Jones, Derek K.},
year = {2019},
month = oct,
journal = {NeuroImage},
volume = {200},
pages = {89--100},
issn = {1053-8119},
doi = {10.1016/j.neuroimage.2019.06.020},
urldate = {2021-11-13}
}
@article{chaudhuriIntrinsicAttractorManifold2019,
title = {The Intrinsic Attractor Manifold and Population Dynamics of a Canonical Cognitive Circuit across Waking and Sleep},
author = {Chaudhuri, Rishidev and Ger{\c c}ek, Berk and Pandey, Biraj and Peyrache, Adrien and Fiete, Ila},
year = {2019},
month = sep,
journal = {Nature Neuroscience},
volume = {22},
number = {9},
pages = {1512--1520},
issn = {1546-1726},
doi = {10.1038/s41593-019-0460-x},
urldate = {2021-11-17},
copyright = {2019 The Author(s), under exclusive licence to Springer Nature America, Inc.}
}
@misc{chazalIntroductionTopologicalData2021,
title = {An Introduction to {{Topological Data Analysis}}: Fundamental and Practical Aspects for Data Scientists},
shorttitle = {An Introduction to {{Topological Data Analysis}}},
author = {Chazal, Fr{\'e}d{\'e}ric and Michel, Bertrand},
year = {2021},
month = feb,
number = {arXiv:1710.04019},
eprint = {1710.04019},
primaryclass = {cs, math, stat},
publisher = {arXiv},
urldate = {2022-10-10}
}
@article{chazalIntroductionTopologicalData2021a,
title = {An {{Introduction}} to {{Topological Data Analysis}}: {{Fundamental}} and {{Practical Aspects}} for {{Data Scientists}}},
shorttitle = {An {{Introduction}} to {{Topological Data Analysis}}},
author = {Chazal, Fr{\'e}d{\'e}ric and Michel, Bertrand},
year = {2021},
journal = {Frontiers in Artificial Intelligence},
volume = {4},
pages = {108},
issn = {2624-8212},
doi = {10.3389/frai.2021.667963},
urldate = {2021-11-12}
}
@article{chekroudIllusoryGeneralizabilityClinical2024,
title = {Illusory Generalizability of Clinical Prediction Models},
author = {Chekroud, Adam M. and Hawrilenko, Matt and Loho, Hieronimus and Bondar, Julia and Gueorguieva, Ralitza and Hasan, Alkomiet and Kambeitz, Joseph and Corlett, Philip R. and Koutsouleris, Nikolaos and Krumholz, Harlan M. and Krystal, John H. and Paulus, Martin},
year = {2024},
month = jan,
journal = {Science},
volume = {383},
number = {6679},
pages = {164--167},
publisher = {American Association for the Advancement of Science},
doi = {10.1126/science.adg8538},
urldate = {2024-01-18}
}
@article{chenInfoGANInterpretableRepresentation2016,
title = {{{InfoGAN}}: {{Interpretable Representation Learning}} by {{Information Maximizing Generative Adversarial Nets}}},
shorttitle = {{{InfoGAN}}},
author = {Chen, Xi and Duan, Yan and Houthooft, Rein and Schulman, John and Sutskever, Ilya and Abbeel, Pieter},
year = {2016},
month = jun,
journal = {arXiv:1606.03657 [cs, stat]},
eprint = {1606.03657},
primaryclass = {cs, stat},
urldate = {2022-01-04}
}
@misc{chenUnsupervisedManifoldAlignment2023,
title = {Unsupervised {{Manifold Alignment}} with {{Joint Multidimensional Scaling}}},
author = {Chen, Dexiong and Fan, Bowen and Oliver, Carlos and Borgwardt, Karsten},
year = {2023},
month = feb,
number = {arXiv:2207.02968},
eprint = {2207.02968},
primaryclass = {cs, stat},
publisher = {arXiv},
urldate = {2023-12-08}
}
@inproceedings{choNeuralLatentAligner2023,
title = {Neural {{Latent Aligner}}: {{Cross-trial Alignment}} for {{Learning Representations}} of {{Complex}}, {{Naturalistic Neural Data}}},
shorttitle = {Neural {{Latent Aligner}}},
booktitle = {Proceedings of the 40th {{International Conference}} on {{Machine Learning}}},
author = {Cho, Cheol Jun and Chang, Edward and Anumanchipalli, Gopala},
year = {2023},
month = jul,
pages = {5661--5676},
publisher = {PMLR},
issn = {2640-3498},
urldate = {2023-11-23}
}
@article{choudharyChaosBacterialStress2023,
title = {Chaos in a Bacterial Stress Response},
author = {Choudhary, Divya and Foster, Kevin R. and Uphoff, Stephan},
year = {2023},
month = dec,
journal = {Current Biology},
volume = {33},
number = {24},
pages = {5404-5414.e9},
issn = {0960-9822},
doi = {10.1016/j.cub.2023.11.002},
urldate = {2024-01-26}
}
@article{choVariationalAutoencoderProvides2023,
title = {A Variational Autoencoder Provides Novel, Data-Driven Features That Explain Functional Brain Representations in a Naturalistic Navigation Task},
author = {Cho, Cheol Jun and Zhang, Tianjiao and Gallant, Jack L.},
year = {2023},
month = aug,
journal = {Journal of Vision},
volume = {23},
number = {9},
pages = {5728},
issn = {1534-7362},
doi = {10.1167/jov.23.9.5728},
urldate = {2023-11-29}
}
@article{chowdhuryHypergraphCooptimalTransport2023,
title = {Hypergraph Co-Optimal Transport: Metric and Categorical Properties},
shorttitle = {Hypergraph Co-Optimal Transport},
author = {Chowdhury, Samir and Needham, Tom and Semrad, Ethan and Wang, Bei and Zhou, Youjia},
year = {2023},
month = sep,
journal = {Journal of Applied and Computational Topology},