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Machine learning for neural decoding

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arXiv 2017年

作者： Glaser, Joshua I. Chowdhury, Raeed H. Perich, Matthew G. Miller, Lee E. Kording, Konrad P. Interdepartmental Neuroscience Program Northwestern University ChicagoIL United States Department of Physical Medicine and Rehabilitation Northwestern University and Shirley Ryan Ability Lab ChicagoIL United States Department of Physiology Northwestern University ChicagoIL United States Department of Biomedical Engineering Northwestern University ChicagoIL United States Department of Applied Mathematics Northwestern University ChicagoIL United States Department of Neuroscience University of Pennsylvania PhiladelphiaIL United States Department of Bioengineering University of Pennsylvania PhiladelphiaIL United States

Despite rapid advances in machine learning tools, the majority of neural decoding approaches still use traditional methods. Improving the performance of neural decoding algorithms allows us to better understand the information contained in a neural population, and can help advance engineering applications such as brain machine interfaces. Here, we apply modern machine learning techniques, including neural networks and gradient boosting, to decode from spiking activity in 1) motor cortex, 2) somatosensory cortex, and 3) hippocampus. We compare the predictive ability of these modern methods with traditional decoding methods such as Wiener and Kalman filters. Modern methods, in particular neural networks and ensembles, significantly outperformed the traditional approaches. For instance, for all of the three brain areas, an LSTM decoder explained over 40% of the unexplained variance from a Wiener filter. These results suggest that modern machine learning techniques should become the standard methodology for neural decoding. We provide a tutorial and code to facilitate wider implementation of these methods. Copyright © 2017, The Authors. All rights reserved.

关键词： Brain computer interface

A hybrid symbolic-numeric approach to exceptional sets of generically zero-dimensional systems

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A hybrid symbolic-numeric approach to exceptional sets of ge...

2015 International Workshop on Parallel Symbolic Computation, PASCO 2015

作者： Hauenstein, Jonathan D. Liddell, Alan C. Department of Applied and Computational Mathematics and Statistics University of Notre Dame United States

ISBN: (纸本)9781450335997

Exceptional sets are the sets where the dimension of the fiber of a map is larger than the generic fiber dimension, which we assume is zero. Such situations naturally arise in kinematics, for example, when designing a mechanism that moves when the generic case is rigid. In 2008, Sommese and Wampler showed that one can use fiber products to promote such sets to become irreducible components. We propose an alternative approach using rank constraints on Macaulay matrices. Symbolic computations are used to construct the proper Macaulay matrices, while numerical computations are used to solve the rank-constraint problem. Various exceptional sets are computed, including exceptional RR dyads, lines on surfaces in C3, and exceptional planar pentads. © 2015 ACM.

关键词： Matrix algebra

Inverse problem for the Helmholtz equation with Cauchy data: reconstruction with conditional well-posedness driven iterative regularization

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arXiv 2017年

作者： Alessandrini, Giovanni de Hoop, Maarten V. Faucher, Florian Gaburro, Romina Sincich, Eva Dipartimento di Matematica e Geoscienze Università di Trieste Italy Department of Computational and Applied Mathematics Department of Earth Science Rice University HoustonTX77005 United States Project-Team Magique-3D Inria Bordeaux Sud-Ouest Research Center Laboratoire de Mathématiques et de leurs Applications Université de Pau et des Pays de l’Adour UMR CNRS 5142 France University of Limerick Limerick Ireland

In this paper, we study the performance of Full Waveform Inversion (FWI) from time-harmonic Cauchy data via conditional well-posedness driven iterative regularization. The Cauchy data can be obtained with dual sensors measuring the pressure and the normal velocity. We define a novel misfit functional which, adapted to the Cauchy data, allows the independent location of experimental and computational sources. The conditional well-posedness is obtained for a hierarchy of subspaces in which the inverse problem with partial data is Lipschitz stable. Here, these subspaces yield piecewise linear representations of the wave speed on given domain partitions. Domain partitions can be adaptively obtained through segmentation of the gradient. The domain partitions can be taken as a coarsening of an unstructured tetrahedral mesh associated with a finite element discretization of the Helmholtz equation. We illustrate the effectiveness of the iterative regularization through computational experiments with data in dimension three. In comparison with earlier work, the Cauchy data do not suffer from eigenfrequencies in the configurations.35R30, 86A22, 65N12, 35J25, 35Q86 Copyright © 2017, The Authors. All rights reserved.

关键词： Inverse problems

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3rd International Conference on Mining Intelligence and Knowledge Exploration, MIKE 2015

作者： Latha, R. Nadarajan, R. Department of Applied Mathematics and Computational Sciences PSG College of Technology Coimbatore India

ISBN: (纸本)9783319268316

Recommender systems are becoming more and more attractive in both research and commercial communities due to Information overload problem and the popularity of the Internet applications. Collaborative Filtering, a popular branch of recommendation approaches, makes predictions based on historical data available in the system. In particular, user based Collaborative Filtering largely depends on how users rate various items of the database and the success of such a system largely relies on pair wise similarity between users. However popular items may give a negative effect on choosing similar users of the target user. The proposed work namely User Similarity Adjustment based on Item Diversity (USA_ID) is designed to achieve personalized recommendations by modifying user similarity scores, for the purpose of reducing the negative effects of popular items in user based Collaborative Filtering framework. A Recommender system is focusing exclusively on achieving accurate recommendations i.e., providing the most relevant items for the needs of a user. From user’s perspective, they would not be interested when they are facing monotonous recommendations even if they are accurate. Whilst much research effort is spent on improving accuracy of recommendations, less effort is taken on analyzing usefulness of recommendations. Novelty and Diversity have been identified as key dimensions of recommendation utility. It has been made clear that greater accuracy leads to lower diversity which results in accuracy-diversity trade off in personalized recommender systems. The proposed work provides an approach to increase the utility of a Recommender system by improving accuracy as well as diversity. Experiments are conducted on the bench mark data set MovieLens and the results show efficiency of the proposed approach in improving quality of predictions. © Springer International Publishing Switzerland 2015.

关键词： Collaborative filtering

Constraints on Cosmic Strings Using Data from the Third Advanced LIGO–Virgo Observing Run

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Physical Review Letters 2021年第24期126卷 241102-241102页

作者： R. Abbott T. D. Abbott S. Abraham F. Acernese K. Ackley A. Adams C. Adams R. X. Adhikari V. B. Adya C. Affeldt D. Agarwal M. Agathos K. Agatsuma N. Aggarwal O. D. Aguiar L. Aiello A. Ain P. Ajith T. Akutsu K. M. Aleman G. Allen A. Allocca P. A. Altin A. Amato S. Anand A. Ananyeva S. B. Anderson W. G. Anderson M. Ando S. V. Angelova S. Ansoldi J. M. Antelis S. Antier S. Appert Koya Arai Koji Arai Y. Arai S. Araki A. Araya M. C. Araya J. S. Areeda M. Arène N. Aritomi N. Arnaud S. M. Aronson H. Asada Y. Asali G. Ashton Y. Aso S. M. Aston P. Astone F. Aubin P. Auclair P. Aufmuth K. AultONeal C. Austin S. Babak F. Badaracco M. K. M. Bader S. Bae Y. Bae A. M. Baer S. Bagnasco Y. Bai L. Baiotti J. Baird R. Bajpai M. Ball G. Ballardin S. W. Ballmer M. Bals A. Balsamo G. Baltus S. Banagiri D. Bankar R. S. Bankar J. C. Barayoga C. Barbieri B. C. Barish D. Barker P. Barneo S. Barnum F. Barone B. Barr L. Barsotti M. Barsuglia D. Barta J. Bartlett M. A. Barton I. Bartos R. Bassiri A. Basti M. Bawaj J. C. Bayley A. C. Baylor M. Bazzan B. Bécsy V. M. Bedakihale M. Bejger I. Belahcene V. Benedetto D. Beniwal M. G. Benjamin T. F. Bennett J. D. Bentley M. BenYaala F. Bergamin B. K. Berger S. Bernuzzi D. Bersanetti A. Bertolini J. Betzwieser R. Bhandare A. V. Bhandari D. Bhattacharjee S. Bhaumik J. Bidler I. A. Bilenko G. Billingsley R. Birney O. Birnholtz S. Biscans M. Bischi S. Biscoveanu A. Bisht B. Biswas M. Bitossi M.-A. Bizouard J. K. Blackburn J. Blackman C. D. Blair D. G. Blair R. M. Blair F. Bobba N. Bode M. Boer G. Bogaert M. Boldrini F. Bondu E. Bonilla R. Bonnand P. Booker B. A. Boom R. Bork V. Boschi N. Bose S. Bose V. Bossilkov V. Boudart Y. Bouffanais A. Bozzi C. Bradaschia P. R. Brady A. Bramley A. Branch M. Branchesi M. Breschi T. Briant J. H. Briggs A. Brillet M. Brinkmann P. Brockill A. F. Brooks J. Brooks D. D. Brown S. Brunett G. Bruno R. Bruntz J. Bryant A. Buikema T. Bulik H. J. Bulten A. Buonanno R. Buscicchio D. Buskulic L. Cadonati M. Caesar G. Cagnoli C. Cahillane H. W. Cain, III J. Calderón Bustillo J. D LIGO Laboratory California Institute of Technology Pasadena California 91125 USA Louisiana State University Baton Rouge Louisiana 70803 USA Inter-University Centre for Astronomy and Astrophysics Pune 411007 India Dipartimento di Farmacia Università di Salerno I-84084 Fisciano Salerno Italy INFN Sezione di Napoli Complesso Universitario di Monte S.Angelo I-80126 Napoli Italy OzGrav School of Physics and Astronomy Monash University Clayton 3800 Victoria Australia Christopher Newport University Newport News Virginia 23606 USA LIGO Livingston Observatory Livingston Louisiana 70754 USA OzGrav Australian National University Canberra Australian Capital Territory 0200 Australia Max Planck Institute for Gravitational Physics (Albert Einstein Institute) D-30167 Hannover Germany Leibniz Universität Hannover D-30167 Hannover Germany University of Cambridge Cambridge CB2 1TN United Kingdom Theoretisch-Physikalisches Institut Friedrich-Schiller-Universität Jena D-07743 Jena Germany University of Birmingham Birmingham B15 2TT United Kingdom Center for Interdisciplinary Exploration and Research in Astrophysics (CIERA) Northwestern University Evanston Illinois 60208 USA Instituto Nacional de Pesquisas Espaciais 12227-010 São José dos Campos São Paulo Brazil Gravity Exploration Institute Cardiff University Cardiff CF24 3AA United Kingdom Gran Sasso Science Institute (GSSI) I-67100 L’Aquila Italy INFN Laboratori Nazionali del Gran Sasso I-67100 Assergi Italy INFN Sezione di Pisa I-56127 Pisa Italy Università di Pisa I-56127 Pisa Italy International Centre for Theoretical Sciences Tata Institute of Fundamental Research Bengaluru 560089 India Gravitational Wave Science Project National Astronomical Observatory of Japan (NAOJ) Mitaka City Tokyo 181-8588 Japan Advanced Technology Center National Astronomical Observatory of Japan (NAOJ) Mitaka City Tokyo 181-8588 Japan California State University Fullerton Fullerton California 92831 USA NCSA University of Illi

We search for gravitational-wave signals produced by cosmic strings in the Advanced LIGO and Virgo full O3 dataset. Search results are presented for gravitational waves produced by cosmic string loop features such as cusps, kinks, and, for the first time, kink-kink collisions. A template-based search for short-duration transient signals does not yield a detection. We also use the stochastic gravitational-wave background energy density upper limits derived from the O3 data to constrain the cosmic string tension Gμ as a function of the number of kinks, or the number of cusps, for two cosmic string loop distribution models. Additionally, we develop and test a third model that interpolates between these two models. Our results improve upon the previous LIGO–Virgo constraints on Gμ by 1 to 2 orders of magnitude depending on the model that is tested. In particular, for the one-loop distribution model, we set the most competitive constraints to date: Gμ≲4×10−15. In the case of cosmic strings formed at the end of inflation in the context of grand unified theories, these results challenge simple inflationary models.

关键词： Cosmic strings & domain walls Gravitational waves

A switched linear system approach to the modeling of the air path of diesel engines

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AIP Conference Proceedings 2018年第1期2040卷

作者： Zsolt Horváth Petra Csomós 1School of Postgraduate Studies of Multidisciplinary Technical Sciences Faculty of Technical Sciences Széchenyi István University Egyetem tér 1. H-9026 Győr Hungary 2Department of Applied Analysis and Computational Mathematics Faculty of Science Eötvös Loránd University Pázmány Péter sétány 1/C H-1117 Budapest Hungary

This paper discusses the designing of switched linear system to the modeling of the air path of diesel engines for purpose of fault detection. The main goal for further investigation is to extend our proposed H-infinity robust filtering procedure for the entire engine operational range. For this reason, an appropriate modelling approach are needed to handle the nonlinear engine model. Our idea is to design a switched system being reasonable for approximation of the main attribute of the nonlinear system, moreover, it can be handled as a linear system. This is done by creating linear time-invariant systems for various operating points of a nonlinear plant and, based on a pre-defined switching rule, we switch between them. After a short introduction of mathematical results how to derive a switched system, we explain the steps of the designed ***, the applicability is demonstrated based on the model of air path of diesel engines via MATLAB simulations.

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Robust camera location estimation by convex programming

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Robust camera location estimation by convex programming

IEEE Conference on Computer Vision and Pattern Recognition, CVPR 2015

作者： Özyeşil, Onur Singer, Amit Program in Applied and Computational Mathematics Princeton University PrincetonNJ08544-1000 United States Department of Mathematics Princeton University PrincetonNJ08544-1000 United States

ISBN: (纸本)9781467369640

3D structure recovery from a collection of 2D images requires the estimation of the camera locations and orientations, i.e. the camera motion. For large, irregular collections of images, existing methods for the location estimation part, which can be formulated as the inverse problem of estimating n locations t1, t2,..., tn in 3 from noisy measurements of a subset of the pairwise directions ti-tj/||ti-tj||, are sensitive to outliers in direction measurements. In this paper, we firstly provide a complete characterization of well-posed instances of the location estimation problem, by presenting its relation to the existing theory of parallel rigidity. For robust estimation of camera locations, we introduce a two-step approach, comprised of a pairwise direction estimation method robust to outliers in point correspondences between image pairs, and a convex program to maintain robustness to outlier directions. In the presence of partially corrupted measurements, we empirically demonstrate that our convex formulation can even recover the locations exactly. Lastly, we demonstrate the utility of our formulations through experiments on Internet photo collections. © 2015 IEEE.

关键词： Convex optimization

Multi-configuration Dirac-Hartree-Fock calculations of forbidden transitions within the 3dk ground configurations of highly charged ions (Z = 72 − 83)

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arXiv 2017年

作者： Zhao, Z.L. Wang, K. Li, S. Si, R. Chen, C.Y. Chen, Z.B. Yan, J. Ralchenko, Yu. Hebei Key Lab of Optic-electronic Information and Materials College of Physics Science and Technology Hebei University Baoding071002 China Institute of Applied Physics and Computational Mathematics Beijing100088 China Shanghai EBIT Lab Institute of Modern Physics Department of Nuclear Science and Technology Fudan University Shanghai200433 China College of Science National University of Defense Technology Changsha410073 China National Institute of Standards and Technology GaithersburgMD20899-8422 United States

Extensive self-consistent multi-configuration Dirac-Hartree-Fock (MCDHF) calculations are performed for the 3s23p63dk (k = 1 − 9) ground configurations of highly charged ions (Z = 72 − 83). Complete and consistent data sets of excitation energies, wavelengths, line strengths, oscillator strengths, and magnetic dipole (M1) and electric quadrupole (E2) transition rates among all these levels are given. We have compared our results with the results available in the literature and the accuracy of the data is assessed. We predict new energy levels and transition probabilities where no other experimental or theoretical results are available, which will form the basis for future experimental work. Copyright © 2017, The Authors. All rights reserved.

关键词： Electric lines

An Algorithm for Cellular Reprogramming

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arXiv 2017年

作者： Ronquist, Scott Patterson, Geoff Brown, Markus Lindsly, Stephen Chen, Haiming Muir, Lindsey A. Wicha, Max Bloch, Anthony Brockett, Roger Rajapakse, Indika Department of Computational Medicine and Bioinformatics Medical School University of Michigan Ann ArborMI48109 United States IXL Learning RaleighNC27560 United States Department of Biological Sciences University of Maryland College Park United States Department of Pediatrics and Communicable Diseases University of Michigan Ann ArborMI48109 United States Department of Hematology/Oncology University of Michigan Ann ArborMI48109 United States Department of Mathematics University of Michigan Ann ArborMI48109 United States Harvard School of Engineering and Applied Sciences CambridgeMA02138 United States

The day we understand the time evolution of subcellular elements at a level of detail comparable to physical systems governed by Newton’s laws of motion seems far away. Even so, quantitative approaches to cellular dynamics add to our understanding of cell biology, providing data-guided frameworks that allow us to develop better predictions about, and methods for, control over specific biological processes and system-wide cell behavior. In this paper, we describe an approach to optimizing the use of transcription factors (TFs) in the context of cellular reprogramming. We construct an approximate model for the natural evolution of a cell cycle synchronized population of human fibroblasts, based on data obtained by sampling the expression of 22,083 genes at several time points along the cell cycle. In order to arrive at a model of moderate complexity, we cluster gene expression based on the division of the genome into topologically associating domains (TADs) and then model the dynamics of the TAD expression levels. Based on this dynamical model and known bioinformatics, such as transcription factor binding sites (TFBS) and functions, we develop a methodology for identifying the top transcription factor candidates for a specific cellular reprogramming task. The approach used is based on a device commonly used in optimal control. Our data-guided methodology identifies a number of transcription factors previously validated for reprogramming and/or natural differentiation. Our findings highlight the immense potential of dynamical models, mathematics, and data-guided methodologies for improving strategies for control over biological processes. Copyright © 2017, The Authors. All rights reserved.

关键词： Transcription factors