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arXiv 2023年

作者： Poldrack, Russell A. Markiewicz, Christopher J. Appelhoff, Stefan Ashar, Yoni K. Auer, Tibor Baillet, Sylvain Bansal, Shashank Beltrachini, Leandro Bénar, Christian G. Bertazzoli, Giacomo Bhogawar, Suyash Blair, Ross W. Bortoletto, Marta Boudreau, Mathieu Brooks, Teon L. Calhoun, Vince D. Castelli, Filippo Maria Clement, Patricia Cohen, Alexander L. Cohen-Adad, Julien D'Ambrosio, Sasha de Hollander, Gilles de la Iglesia-Vayá, María de la Vega, Alejandro Delorme, Arnaud Devinsky, Orrin Draschkow, Dejan Duff, Eugene Paul DuPre, Elizabeth Earl, Eric Esteban, Oscar Feingold, Franklin W. Flandin, Guillaume Galassi, Anthony Gallitto, Giuseppe Ganz, Melanie Gau, Rémi Gholam, James Ghosh, Satrajit S. Giacomel, Alessio Gillman, Ashley G. Gleeson, Padraig Gramfort, Alexandre Guay, Samuel Guidali, Giacomo Halchenko, Yaroslav O. Handwerker, Daniel A. Hardcastle, Nell Herholz, Peer Hermes, Dora Honey, Christopher J. Innis, Robert B. Ioanas, Horea-Ioan Jahn, Andrew Karakuzu, Agah Keator, David B. Kiar, Gregory Kincses, Balint Laird, Angela R. Lau, Jonathan C. Lazari, Alberto Legarreta, Jon Haitz Li, Adam Li, Xiangrui Love, Bradley C. Lu, Hanzhang Maumet, Camille Mazzamuto, Giacomo Meisler, Steven L. Mikkelsen, Mark Mutsaerts, Henk Nichols, Thomas E. Nikolaidis, Aki Nilsonne, Gustav Niso, Guiomar Norgaard, Martin Okell, Thomas W. Oostenveld, Robert Ort, Eduard Park, Patrick J. Pawlik, Mateusz Pernet, Cyril R. Pestilli, Franco Petr, Jan Phillips, Christophe Poline, Jean-Baptiste Pollonini, Luca Raamana, Pradeep Reddy Ritter, Petra Rizzo, Gaia Robbins, Kay A. Rockhill, Alexander P. Rogers, Christine Rokem, Ariel Rorden, Chris Routier, Alexandre Saborit-Torres, Jose Manuel Salo, Taylor Schirner, Michael Smith, Robert E. Spisak, Tamas Sprenger, Julia Swann, Nicole C. Szinte, Martin Takerkart, Sylvain Thirion, Bertrand Thomas, Adam G. Torabian, Sajjad Varoquaux, Gael Voytek, Bradley Welzel, Julius Wilson, Martin Yarkoni, Tal Gorgolewski, Krzysztof J. Department of Psychology Stanford University StanfordCA United States Max Planck Institute for Human Development Berlin Germany University of Colorado Anschutz Medical Campus AuroraCO United States School of Psychology University of Surrey Guildford United Kingdom McConnell Brain Imaging Centre Montréal Neurological Institute McGill University Montréal Canada Department of Bioengineering University of California San Diego La Jolla CA United States School of Physics Astronomy Cardiff University Wales United Kingdom Institut de Neurosciences des Systèmes Marseille France Neurophysiology Lab IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli Brescia Italy Center for Mind/Brain Sciences - CIMeC University of Trento TN Rovereto Italy Brigham and Women’s Hospital BostonMA United States Massachusetts General Hospital BostonMA United States Harvard Medical School BostonMA United States Rackspace Technology San AntonioTX United States NeuroPoly Lab Polytechnique Montréal MontréalQC Canada Georgia State Georgia Tech Emory AtlantaGA United States University of Florence Sesto Fiorentino Italy Bioretics srl Cesena Italy Department of Medical Imaging Ghent University Hospital Ghent Belgium Department of Diagnostic Sciences Ghent University Ghent Belgium Department of Neurology Boston Children's Hospital BostonMA United States Dipartimento di Scienze della Salute dell'Università degli Studi di Milano Milan Italy Department of Clinical and Experimental Epilepsy University College London United Kingdom Zurich Center for Neuroeconomics Department of Economics University of Zurich Zurich Switzerland UMIB-FISABIO Valencia Spain The University of Texas at Austin AustinTX United States SCCN University of California San Diego La Jolla CA United States Department of Neurology NYU Langone Medical Center New YorkNY United States Department of Experimental Psychology University of Oxford Oxford United Kingdom UK Dementia Research Ins

The brain Imaging Data Structure (BIDS) is a community-driven standard for the organization of data and metadata from a growing range of neuroscience modalities. This paper is meant as a history of how the standard has developed and grown over time. We outline the principles behind the project, the mechanisms by which it has been extended, and some of the challenges being addressed as it evolves. We also discuss the lessons learned through the project, with the aim of enabling researchers in other domains to learn from the success of BIDS. © 2023, CC BY.

关键词： Data structures

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Color naming reflects both perceptual structure and communicative need

arXiv

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arXiv 2018年

作者： Zaslavsky, Noga Kemp, Charles Tishby, Naftali Regier, Terry Edmond and Lily Safra Centre for Brain Sciences Hebrew University Jerusalem9190401 Israel Department of Psychology Carnegie Mellon University PittsburghPA15213 United States Benin School of Computer Science and Engineering Hebrew University Jerusalem9190401 Israel Department of Linguistics University of California BerkeleyCA94720 United States Cognitive Science Program University of California BerkeleyCA94720 United States

Gibson et al. (2017) argued that color naming is shaped by patterns of communicative need. In support of this claim, they showed that color naming systems across languages support more precise communication about warm colors than cool colors, and that the objects we talk about tend to be warm-colored rather than cool-colored. Here, we present new analyses that alter this picture. We show that greater communicative precision for warm than for cool colors, and greater communicative need, may both be explained by perceptual structure. However, using an information-theoretic analysis, we also show that color naming across languages bears signs of communicative need beyond what would be predicted by perceptual structure alone. We conclude that color naming is shaped both by perceptual structure, as has traditionally been argued, and by patterns of communicative need, as argued by Gibson et al. - although for reasons other than those they advanced. Copyright © 2018, The Authors. All rights reserved.

关键词： Color

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Patterns of somatic structural variation in human cancer genomes (vol 578, pg 112, 2020)

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NATURE 2023年第7948期614卷 E38-E38页

作者： Li, Yilong Roberts, Nicola D. Wala, Jeremiah A. Shapira, Ofer Schumacher, Steven E. Kumar, Kiran Khurana, Ekta Waszak, Sebastian Korbel, Jan O. Haber, James E. Imielinski, Marcin Weischenfeldt, Joachim Beroukhim, Rameen Campbell, Peter J. Cancer Genome Project Wellcome Trust Sanger Institute Hinxton UK Totient Inc Cambridge MA USA Wellcome Sanger Institute Wellcome Genome Campus Hinxton UK Department of Haematology University of Cambridge Cambridge UK Cambridge University Hospitals NHS Foundation Trust Cambridge UK Korea Advanced Institute of Science and Technology Daejeon South Korea Department of Zoology Genetics and Physical Anthropology University of Santiago de Compostela Santiago de Compostela Spain Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS) University of Santiago de Compostela Santiago de Compostela Spain The Biomedical Research Centre (CINBIO) University of Vigo Vigo Spain Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS) Universidade de Santiago de Compostela Santiago de Compostela Spain Department of Zoology Genetics and Physical Anthropology (CiMUS) Universidade de Santiago de Compostela Santiago de Compostela Spain The Biomedical Research Centre (CINBIO) Universidade de Vigo Vigo Spain The Broad Institute of Harvard and MIT Cambridge MA USA Bioinformatics and Integrative Genomics Harvard University Cambridge MA USA Department of Cancer Biology Dana-Farber Cancer Institute Boston MA USA Broad Institute of MIT and Harvard Cambridge MA USA Department of Medical Oncology Dana-Farber Cancer Institute Boston MA USA Harvard Medical School Boston MA USA Massachusetts General Hospital Center for Cancer Research Charlestown MA USA Dana-Farber Cancer Institute Boston MA USA Department of Biostatistics and Computational Biology Dana-Farber Cancer Institute and Harvard Medical School Boston MA USA Weill Cornell Medical College New York NY USA Department of Physiology and Biophysics Weill Cornell Medicine New York NY USA Institute for Computational Biomedicine Weill Cornell Medicine New York NY USA Controlled Department and Institution New York NY USA Englander Institute for Precision Medicine Weill Cornell Medicine Ne

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Genomic basis for RNA alterations in cancer (vol 578, pg 129, 2020)

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NATURE 2023年第7948期614卷 E37-E37页

作者： Calabrese, Claudia Davidson, Natalie R. Demircioglu, Deniz Fonseca, Nuno A. He, Yao Lehmann, Kjong-Van Liu, Fenglin Shiraishi, Yuichi Soulette, Cameron M. Urban, Lara Greger, Liliana Li, Siliang Liu, Dongbing Perry, Marc D. Xiang, Qian Zhang, Fan Zhang, Junjun Bailey, Peter Erkek, Serap Hoadley, Katherine A. Hou, Yong Huska, Matthew R. Kilpinen, Helena Korbel, Jan O. Marin, Maximillian G. Markowski, Julia Nandi, Tannistha Pan-Hammarstrom, Qiang Pedamallu, Chandra Sekhar Siebert, Reiner Stark, Stefan G. Su, Hong Tan, Patrick Waszak, Sebastian M. Yung, Christina Zhu, Shida Awadalla, Philip Creighton, Chad J. Meyerson, Matthew Ouellette, B. F. Francis Wu, Kui Yang, Huanming Brazma, Alvis Brooks, Angela N. Goke, Jonathan Ratsch, Gunnar Schwarz, Roland F. Stegle, Oliver Zhang, Zemin European Molecular Biology Laboratory European Bioinformatics Institute Hinxton UK European Molecular Biology Laboratory European Bioinformatics Institute (EMBL-EBI) Cambridge UK Genome Biology Unit European Molecular Biology Laboratory (EMBL) Heidelberg Germany CIBIO/InBIO - Research Center in Biodiversity and Genetic Resources Universidade do Porto Vairão Portugal Berlin Institute for Medical Systems Biology Max Delbruck Center for Molecular Medicine Berlin Germany German Cancer Consortium (DKTK) partner site Berlin Germany German Cancer Research Center (DKFZ) Heidelberg Germany Berlin Institute for Medical Systems Biology Max Delbrück Center for Molecular Medicine Berlin Germany German Cancer Consortium (DKTK) Partner site Berlin Berlin Germany European Molecular Biology Laboratory Genome Biology Unit Heidelberg Germany Division of Computational Genomics and Systems Genetics German Cancer Research Center (DKFZ) Heidelberg Germany ETH Zurich Zurich Switzerland Memorial Sloan Kettering Cancer Center New York NY USA Weill Cornell Medical College New York NY USA SIB Swiss Institute of Bioinformatics Lausanne Switzerland University Hospital Zurich Zurich Switzerland Computational Biology Center Memorial Sloan Kettering Cancer Center New York NY USA Department of Biology ETH Zurich Zürich Switzerland Department of Computer Science ETH Zurich Zurich Switzerland Korea University Seoul South Korea Computational and Systems Biology Program Memorial Sloan Kettering Cancer Center New York NY USA Department of Physiology and Biophysics Weill Cornell Medicine New York NY USA Institute for Computational Biomedicine Weill Cornell Medicine New York NY USA Controlled Department and Institution New York NY USA Englander Institute for Precision Medicine Weill Cornell Medicine New York NY USA National University of Singapore Singapore Singapore Genome Institute of Singapore Singapore Singapore Computational and Systems Biology Genome Institute of Singap

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Flexible neural representation for physics prediction

arXiv

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arXiv 2018年

作者： Mrowca, Damian Zhuang, Chengxu Wang, Elias Haber, Nick Fei-Fei, Li Tenenbaum, Joshua B. Yamins, Daniel L.K. Department of Computer Science StanfordCA94305 United States Department of Psychology StanfordCA94305 United States Department of Electrical Engineering StanfordCA94305 United States Department of Pediatrics StanfordCA94305 United States Department of Biomedical Data Science StanfordCA94305 Wu Tsai Neurosciences Institute StanfordCA94305 United States Department of Brain and Cognitive Sciences MIT CambridgeMA02139 United States Department of Computer Science and Artificial Intelligence Laboratory MIT CambridgeMA02139 United States

Humans have a remarkable capacity to understand the physical dynamics of objects in their environment, flexibly capturing complex structures and interactions at multiple levels of detail. Inspired by this ability, we propose a hierarchical particle-based object representation that covers a wide variety of types of three-dimensional objects, including both arbitrary rigid geometrical shapes and deformable materials. We then describe the Hierarchical Relation Network (HRN), an end-to-end differentiable neural network based on hierarchical graph convolution, that learns to predict physical dynamics in this representation. Compared to other neural network baselines, the HRN accurately handles complex collisions and nonrigid deformations, generating plausible dynamics predictions at long time scales in novel settings, and scaling to large scene configurations. These results demonstrate an architecture with the potential to form the basis of next-generation physics predictors for use in computer vision, robotics, and quantitative cognitive science. Copyright © 2018, The Authors. All rights reserved.

关键词： Forecasting

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Towards explaining anomalies: A deep Taylor decomposition of one-class models

arXiv

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arXiv 2018年

作者： Kauffmann, Jacob Müller, Klaus-Robert Montavon, Grégoire Department of Electrical Engineering & Computer Science Technische Universität Berlin Marchstr. 23 Berlin10587 Germany Department of Brain & Cognitive Engineering Korea University Anam-dong 5ga Seongbuk-gu Seoul136-713 Korea Republic of Max Planck Institute for Informatics Stuhlsatzenhausweg Saarbrücken66123 Germany

A common machine learning task is to discriminate between normal and anomalous data points. In practice, it is not always sufficient to reach high accuracy at this task, one also would like to understand why a given data point has been predicted in a certain way. We present a new principled approach for one-class SVMs that decomposes outlier predictions in terms of input variables. The method first recomposes the one-class model as a neural network with distance functions and min-pooling, and then performs a deep Taylor decomposition (DTD) of the model output. The proposed One-Class DTD is applicable to a number of common distance-based SVM kernels and is able to reliably explain a wide set of data anomalies. Furthermore, it outperforms baselines such as sensitivity analysis, nearest neighbor, or simple edge detection. Copyright © 2018, The Authors. All rights reserved.

关键词： Anomaly detection

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Supervising neural attention models for video captioning by human gaze data

arXiv

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arXiv 2017年

作者： Yu, Youngjae Choi, Jongwook Kim, Yeonhwa Yoo, Kyung Lee, Sang-Hun Kim, Gunhee Department of Computer Science and Engineering Department of Brain and Cognitive Sciences Seoul National University Seoul Korea Republic of

The attention mechanisms in deep neural networks are inspired by human's attention that sequentially focuses on the most relevant parts of the information over time to generate prediction output. The attention parameters in those models are implicitly trained in an end-to-end manner, yet there have been few trials to explicitly incorporate human gaze tracking to supervise the attention models. In this paper, we investigate whether attention models can benefit from explicit human gaze labels, especially for the task of video captioning. We collect a new dataset called VAS, consisting of movie clips, and corresponding multiple descriptive sentences along with human gaze tracking data. We propose a video captioning model named Gaze Encoding Attention Network (GEAN) that can leverage gaze tracking information to provide the spatial and temporal attention for sentence generation. Through evaluation of language similarity metrics and human assessment via Amazon mechanical Turk, we demonstrate that spatial attentions guided by human gaze data indeed improve the performance of multiple captioning methods. Moreover, we show that the proposed approach achieves the state-of-the-art performance for both gaze prediction and video captioning not only in our VAS dataset but also in standard datasets (e.g. LSMDC [24] and Hollywood2 [18]). Copyright © 2017, The Authors. All rights reserved.

关键词： Eye tracking

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Decoding of Visual Short-Term Memory Supports the Theory of Automatic Feature Binding: An EEG Study

Decoding of Visual Short-Term Memory Supports the Theory of ...

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2017 IEEE 国际医学影像物理和工程大会暨第八届中国医学影像物理学术年会

作者： Sizhu Han Baihan Wang Maoquan Wang Yufei Xie Zhao Lu Yixuan Ku The Key Lab of Brain Functional Genomics MOE &STCSM School of Psychology and Cognitive ScienceEast China Normal University School of Psychology and Cognitive Science East China Normal University School of Computer Science and Software Engineering East China Normal University NYU-ECNU Institute of Brain and Cognitive Science NYU Shanghai

Objective: The storage form of representations in the short-term memory is still controversial. Previous studies provided evidence from behavioral data or univariate activities from local brain areas. Instead, the present study explored this issue by decoding the neural data from the whole brain. Methods: Fifteen participants were recruited to complete a short-term memory task, where they first remembered the direction of a grating, and then after a brief delay（2 s）, they needed to recall the direction by moving and clicking a mouse to match the probe grating with their memorized one. The location of the grating changed from trial to trial. The electroencephalograph（EEG） data were recorded simultaneously, to examine the decoding accuracy of the attended feature（direction） and unattended feature（location）. EEG signals were pre-processed and timefrequency decomposed. Pattern analysis was then conducted on the time-frequency data to predict the feature of direction or location in the memorandum. Results: During the periods of memory encoding and maintenance, the accuracies of predicting the attended feature（direction） and the unattended feature（location） were both 60% ~ 80%, which were significantly higher than the guessing rate（50%） and the predication results using the permutation of the same data. Conclusion: The representation in the visual shortterm memory is stored as a form of binding features in the brain, and the binding between the direction and location may happen in the very early stage of perception that is preattentive.

关键词： visual short-term memory weak-object theory feature binding pattern identification EEG

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AudioMNIST: Exploring Explainable Artificial Intelligence for Audio Analysis on a Simple Benchmark

arXiv

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arXiv 2018年

作者： Becker, Sören Vielhaben, Johanna Ackermann, Marcel Müller, Klaus-Robert Lapuschkin, Sebastian Samek, Wojciech Department of Artificial Intelligence Fraunhofer Heinrich-Hertz-Institute Berlin Germany Department of Electrical Engineering and Computer Science Technische Universität Berlin Berlin Germany Department of Brain and Cognitive Engineering Korea University Seoul Korea Republic of Max Planck Institute for Informatics Saarbrücken Germany BIFOLD Berlin Institute for the Foundations of Learning and Data Berlin Germany

Explainable Artificial Intelligence (XAI) is targeted at understanding how models perform feature selection and derive their classification decisions. This paper explores post-hoc explanations for deep neural networks in the audio domain. Notably, we present a novel Open Source audio dataset consisting of 30,000 audio samples of English spoken digits which we use for classification tasks on spoken digits and speakers’ biological sex. We use the popular XAI technique Layer-wise Relevance Propagation (LRP) to identify relevant features for two neural network architectures that process either waveform or spectrogram representations of the data. Based on the relevance scores obtained from LRP, hypotheses about the neural networks’ feature selection are derived and subsequently tested through systematic manipulations of the input data. Further, we take a step beyond visual explanations and introduce audible heatmaps. We demonstrate the superior interpretability of audible explanations over visual ones in a human user study. Copyright © 2018, The Authors. All rights reserved.

关键词： Speech recognition

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GLEU-guided Multi-Resolution Network for Short Text Conversation

GLEU-guided Multi-Resolution Network for Short Text Conversa...

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第十四届全国人机语音通讯学术会议

作者： Xuan Liu Kai Yu Key Laboratory of Shanghai Education Commission for Intelligent Interaction and Cognitive Engineering SpeechLab Department of Computer Science and Engineering Brain Science and Technology Research Center Shanghai Jiao Tong University

With the recent development of sequence-to-sequence framework,generation approach for short text conversation becomes *** sequence-to-sequence method for short text conversation often suffers from dull response ***-resolution generation approach has been introduced to address this problem by dividing the generation process into two steps:keywords-sequence generation and response ***,this method still tends to generate short and common *** this work,a new multi-resolution generation framework is *** of using the word-level maximum likelihood criterion,we optimize the sequence-level GLEU score of the entire generated keywords-sequence using a policy gradient approach in reinforcement *** show that the proposed approach can generate longer and more diverse ***,it achieves better score in human evaluation.

关键词： short text conversation sequence-to-sequence policy gradient

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