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arXiv 2020年

作者： Jaffe, Ariel Amsel, Noah Nadler, Boaz Chang, Joseph T. Kluger, Yuval Program in Applied Mathematics Yale University New HavenCT06511 United States Department of Computer Science Weizmann Institute of Science Rehovot76100 Israel Department of Statistics Yale University New HavenCT06520 United States Interdepartmental Program in Computational Biology and Bioinformatics New HavenCT06511 Singapore Department of Pathology New HavenCT06511 United States

A key assumption in multiple scientific applications is that the distribution of observed data can be modeled by a latent tree graphical model. An important example is phylogenetics, where the tree models the evolutionary lineages of various organisms. Given a set of independent realizations of the random variables at the leaves of the tree, a common task is to infer the underlying tree topology. In this work we develop Spectral Neighbor Joining (SNJ), a novel method to recover latent tree graphical models. In contrast to distance based methods, SNJ is based on a spectral measure of similarity between all pairs of observed variables. We prove that SNJ is consistent, and derive a sufficient condition for correct tree recovery from an estimated similarity matrix. Combining this condition with a concentration of measure result on the similarity matrix, we bound the number of samples required to recover the tree with high probability. We illustrate via extensive simulations that SNJ requires fewer samples to accurately recover trees in regimes where the tree contains a large number of leaves or long edges. We provide theoretical support for this observation by analyzing the model of a perfect binary tree. Copyright © 2020, The Authors. All rights reserved.

关键词： Recovery

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Linearity assessment between lower limb joint angles and angular accelerations at standard maximum vertical jumps with long-short and no countermovement

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Gait & Posture 2023年 106卷 S174-S175页

作者： Rodrigues, Carlos Correia, Miguel Abrantes, João Benedetti, Marco Nadal, Jurandir Faculty of Engineering- University of Porto Biomedical Engineering Program Porto Portugal INESC TEC - Institute for Systems and Computer Engineering- Technology and Science C-BER - Centre for Biomedical Engineering Research Porto Portugal Faculty of Engineering- University of Porto Department of Electrical and Computer Engineering Porto Portugal CICANT - Centre for Research in Applied Communication- Culture and New Technologies MovLab - Laboratory of Technologies for Interactions and Interfaces Lisbon Portugal Federal University of Pernambuco Department of Electronic and Systems Recife Brazil Federal University of Rio de Janeiro Biomedical Engineering Program Rio de Janeiro Brazil

IntroductionStandard maximum vertical jump (MVJ) has been applied to assess lower limb long countermovement (CM) on countermovement jump (CMJ) and short CM on drop jump (DJ) for comparison to squat jump (SJ) without CM [1,2]. Research questionNevertheless, the ability for lower limb joint accelerations depending on lower limb joint angles at long, short and no CM remains an open issue [3,4], in particular linearity assessment of these relations at long, short and no CM in association with MVJ whole-body impulsion. MethodsFor this reason, we applied piecewise linear detection of segmented subphases on lower limb joint angles ( θ)-angular acceleration ( α) diagrams for the hip (H), knee (K) and ankle (A) during impulse phases on CMJ, DJ and SJ. Selected sample corresponds to best MVJ trials based on higher flight-time of 3 CMJ, DJ and SJ repetitions for six healthy untrained subjects with ages (21.5±1.4) years, (76.7±9.3)kg mass and (1.79±0.06)m height. Adhesive reflective markers were applied at lower limb and torso, with sagittal hip, knee, and ankle θ, α obtained by inverse kinematics. H,K,A ( θ, α) diagrams were plotted and impulsion subphases segmented at selected instants of ∂ a/∂ q phase reversal with linear fit by the least-squares method, Fig. 1. Fig. 1. Hip, knee, ankle joint ( θ, α) diagrams at CMJ, DJ, SJ with segmented subphases time span(Δt), |∂α/∂θ| slope magnitudes and R² linear fit regression. ResultsSJ presented larger number of ( θ, α) subphases than DJ, both larger than CMJ with higher |∂ α/∂ θ| variation at DJ and SJ than CMJ, pointing to higher complexity of neuromuscular control and contributing to explain reduced SJ, DJ performance without CM (0.33±0.05)m and with short CM (0.27±0.03)m in relation to CMJ with long CM (0.36±0.04)m for untrained selected subjects, Fig. 1. Thus, despite the larger total time span Δt at CMJ (0.76±0.10)s in relation to SJ (0.36±0.08)s and DJ (0.23±0.05)s, CMJ presented lower number of subphases with longer time span

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Muscle coactivation analysis for neuromuscular control assessment of lower limb stretch-shortening cycle

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Gait & Posture 2023年 106卷 S175-S176页

IntroductionMuscle stretch-shortening cycle (SSC) is a central mechanism with lower limb muscle contraction immediately preceded by muscle stretch for efficient submaximal activities such as gait and powerful maximal activities such as running and jumping [1,2]. Research questionAlthough muscle SSC can be observed at gait and running its higher expression and accessibility is performed on standard maximum vertical jump (MVJ) with an open issue on neuromuscular control assessment of lower limb muscle SSC [3]. MethodsFor this purpose, we present and applied noninvasive subject specific analysis of lower limb muscle coactivation for selected muscles with higher contribution during MVJ impulse based on corresponding conditioned surface electromyographic signals (sEMG). Selected muscles correspond to lower limb muscles vastus medialis (VM), rectus femoris (RF), vastus lateralis (VL), lateral gastrocnemius (LG) and medial gastrocnemius (MG). Twenty-seven trials were assessed corresponding for each subject to the highest MVJ based on larger flight time with long SSC at countermovement jump (CMJ), short SSC at drop jump (DJ) and squat jump (SJ) with no SSC. Trial sample is composed by a group of six young adult volunteers’ students on sports and physical education degree with the ages (21.5 ± 1.4) years, (76.7 ± 9.3) kg mass and (1.79 ± 0.06) m height. Surface skin was prepared and Aqua-Wet gel Skintact F55 electrodes were applied at bipolar configuration as indicated by SENIAN. VM, RF, VL, LG and MG sEMG linear envelopes were paired plotted with the area under the curves computed as well as the coactivation pairs defined as the common area under the curves normalized to the sum of the corresponding pair individual areas under the curves. Coactivations were compared at CMJ, DJ and SJ as well as among CMJ, DJ and SJ, Fig. 1. ResultsStrongest coactivations with decreasing intensity were detected between VM-RF and LG-MG muscles at CMJ and SJ, whereas at DJ the strongest coacti

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Explaining heterogeneity in medial entorhinal cortex with task-driven neural networks 21

Explaining heterogeneity in medial entorhinal cortex with ta...

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Proceedings of the 35th International Conference on Neural Information Processing Systems

作者： Aran Nayebi Alexander Attinger Malcolm G. Campbell Kiah Hardcastle Isabel I.C. Low Caitlin S. Mallory Gabriel C. Mel Ben Sorscher Alex H. Williams Surya Ganguli Lisa M. Giocomo Daniel L.K. Yamins Neurosciences Ph.D. Program Stanford University Department of Neurobiology Stanford University Neurosciences Ph.D. Program Stanford University and Department of Neurobiology Stanford University and Wu Tsai Neurosciences Institute Stanford University Department of Applied Physics Stanford University Department of Statistics Stanford University and Wu Tsai Neurosciences Institute Stanford University Department of Applied Physics Stanford University and Wu Tsai Neurosciences Institute Stanford University and Facebook AI Research Facebook Inc. Department of Neurobiology Stanford University and Wu Tsai Neurosciences Institute Stanford University Department of Computer Science Stanford University and Department of Psychology Stanford University and Wu Tsai Neurosciences Institute Stanford University

ISBN: (纸本)9781713845393

Medial entorhinal cortex (MEC) supports a wide range of navigational and memory related behaviors. Well-known experimental results have revealed specialized cell types in MEC — e.g. grid, border, and head-direction cells — whose highly stereotypical response profiles are suggestive of the role they might play in supporting MEC functionality. However, the majority of MEC neurons do not exhibit stereotypical firing patterns. How should the response profiles of these more "heterogeneous" cells be described, and how do they contribute to behavior? In this work, we took a computational approach to addressing these questions. We first performed a statistical analysis that shows that heterogeneous MEC cells are just as reliable in their response patterns as the more stereotypical cell types, suggesting that they have a coherent functional role. Next, we evaluated a spectrum of candidate models in terms of their ability to describe the response profiles of both stereotypical and heterogeneous MEC cells. We found that recently developed task-optimized neural network models are substantially better than traditional grid cell-centric models at matching most MEC neuronal response profiles — including those of grid cells themselves — despite not being explicitly trained for this purpose. Specific choices of network architecture (such as gated nonlinearities and an explicit intermediate place cell representation) have an important effect on the ability of the model to generalize to novel scenarios, with the best of these models closely approaching the noise ceiling of the data itself. We then performed in silico experiments on this model to address questions involving the relative functional relevance of various cell types, finding that heterogeneous cells are likely to be just as involved in downstream functional outcomes (such as path integration) as grid and border cells. Finally, inspired by recent data showing that, going beyond their spatial response selectivity, MEC cells

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Localization transition in three-dimensional stealthy hyperuniform disordered systems

arXiv

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arXiv 2021年

作者： Sgrignuoli, F. Torquato, S. Dal Negro, L. Department of Electrical and Computer Engineering & Photonics Center Boston University 8 Saint Mary’s Street BostonMA02215 United States Department of Chemistry Department of Physics Princeton Institute for the Science and Technology of Materials Program in Applied and Computational Mathematics Princeton University PrincetonNJ08540 United States Division of Material Science and Engineering Boston University 15 Saint Mary’s Street BrooklineMA02446 United States Department of Physics Boston University 590 Commonwealth Avenue BostonMA02215 United States

The purpose of this work is to understand the fundamental connection between structural correlations and light localization in three-dimensional (3D) open scattering systems of finite size. We numerically investigate the transport of vector electromagnetic waves scattered by resonant electric dipoles spatially arranged in 3D space by stealthy hyperuniform disordered point patterns. Three-dimensional stealthy hyperuniform disordered systems (3D-SHDS) are engineered with different structural correlation properties determined by their degree of stealthiness χ. Such fine control of exotic states of amorphous matter enables the systematic design of optical media that interpolate in a tunable fashion between uncorrelated random structures and crystalline materials. By solving the electromagnetic multiple scattering problem using Green’s matrix spectral method, we establish a transport phase diagram that demonstrates a clear delocalization-localization transition beyond a critical scattering density that depends on χ. The transition is characterized by studying the Thouless number and the spectral statistics of the scattering resonances. In particular, by tuning the χ parameter, we demonstrate large spectral gaps and suppressed sub-radiant proximity resonances, facilitating light localization. Moreover, consistently with previous studies, our results show a region of the transport phase diagram where the investigated scattering systems become transparent. Our work provides a systematic description of the transport and localization properties of light in stealthy hyperuniform structures and motivates the engineering of novel photonic systems with enhanced light-matter interactions for applications to both classical and quantum devices. Copyright © 2021, The Authors. All rights reserved.

关键词： Phase diagrams

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Exponential acceleration of macroscopic quantum tunneling in a Floquet Ising model

arXiv

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arXiv 2023年

作者： Grattan, George Barton, Brandon A. Feeney, Sean Mossi, Gianni Patnaik, Pratik Sagal, Jacob C. Carr, Lincoln D. Oganesyan, Vadim Kapit, Eliot Quantum Engineering Program Colorado School of Mines 1523 Illinois St CO Golden80401 United States Department of Computer Science Colorado School of Mines 1500 Illinois St CO Golden80401 United States Department of Applied Mathematics and Statistics Colorado School of Mines 1500 Illinois St CO Golden80401 United States Department of Physics Colorado School of Mines 1523 Illinois St CO Golden80401 United States KBR Inc. 601 Jefferson St. HoustonTX77002 United States NASA Ames Research Center Moffett FieldCA94035 United States Department of Physics and Astronomy College of Staten Island CUNY Staten IslandNY10314 United States Physics program and Initiative for the Theoretical Sciences The Graduate Center CUNY New YorkNY10016 United States Center for Computational Quantum Physics Flatiron Institute 162 5th Avenue New YorkNY10010 United States

The exponential suppression of macroscopic quantum tunneling (MQT) in the number of elements to be reconfigured is an essential element of broken symmetry phases. Slow MQT is also a core bottleneck in quantum algorithms, such as traversing an energy landscape in optimization, and adiabatic state preparation more generally. In this work, we demonstrate the possibility to accelerate MQT through Floquet engineering with the application of a uniform, high frequency transverse drive field. Using the ferromagnetic phase of the transverse field Ising model in one and two dimensions as a prototypical example, we identify three qualitatively distinct regimes as a function of drive strength: (i) for weak drive, the system exhibits exponentially slow MQT alongside robust magnetic order, as expected;(ii) at intermediate drive strength, we find polynomial decay of rates alongside vanishing magnetic order consistent with critical or paramagnetic state;(iii) at very strong drive strengths both the tunnelling rate and time-averaged magnetic order remain finite with increasing system size. We support these claims with extensive full wavefunction and matrix-product state numerical simulations, and theoretical analysis. An experimental test of these results presents a technologically important and novel scientific question accessible on NISQ-era quantum computers. © 2023, CC BY.

关键词： Ising model

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Endotaxial Stabilization of 2D Charge Density Waves with Long-Range Order

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Microscopy and Microanalysis 2024年第SUPPLEMENT_1期30卷

作者： Sung, Suk Hyun Agarwal, Nishkarsh Baggari, Ismail El Kezer, Patrick Goh, Yin Min Schnitzer, Noah Shen, Jeremy M Chiang, Tony Liu, Yu Lu, Wenjian Sun, Yuping Kourkoutis, Lena F Heron, John T Sun, Kai Hovden, Robert Department of Materials Science and Engineering University of Michigan Ann Arbor MI USA Rowland Institute at Harvard University Cambridge MA USA Department of Electrical and Computer Engineering University of Michigan Ann Arbor MI USA John A. Paulson School of Engineering and Applied Science Harvard University Cambridge MA USA Department of Materials Science and Engineering Cornell University Ithaca NY USA Kavli Institute at Cornell for Nanoscale Science Ithaca NY USA Key Laboratory of Materials Physics Institute of Solid State Physics Chinese Academy of Sciences Hefei PR China Collaborative Innovation Centre of Advanced Microstructures Nanjing University Nanjing PR China High Magnetic Field Laboratory Chinese Academy of Sciences Hefei PR China School of Applied and Engineering Physics Cornell University Ithaca NY USA Applied Physics Program University of Michigan Ann Arbor MI USA Department of Physics University of Michigan Ann Arbor MI USA

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KLF2 maintains lineage fidelity and suppresses CD8 T cell exhaustion during acute LCMV infection

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science (New York, N.Y.) 2025年第6735期387卷 eadn2337页

作者： Fagerberg, Eric Attanasio, John Dien, Christine Singh, Jaiveer Kessler, Emily A. Abdullah, Leena Shen, Jian Hunt, Brian G. Connolly, Kelli A. De Brouwer, Edward He, Jiaming Iyer, Nivedita R. Buck, Jessica Borr, Emily R. Damo, Martina Foster, Gena G. Giles, Josephine R. Huang, Yina H. Tsang, John S. Krishnaswamy, Smita Cui, Weiguo Joshi, Nikhil S. Department of Immunobiology Yale University School of Medicine New Haven CT United States Program in Computational Biology & Bioinformatics Yale University New Haven CT United States Department of Microbiology and Immunology Geisel School of Medicine at Dartmouth NH United States Department of Pathology Feinberg School of Medicine at Northwestern University Chicago IL United States Department of Genetics and Computer Science Yale University School of Medicine New Haven CT United States Department of Medicine University of Chicago Chicago IL United States Section of Hematology Department of Internal Medicine Yale University School of Medicine New Haven CT United States Department of Systems Pharmacology and Translational Therapeutics University of Pennsylvania Philadelphia PA United States Institute for Immunology Perelman School of Medicine University of Pennsylvania Philadelphia PA United States Parker Institute for Cancer Immunotherapy Perelman School of Medicine University of Pennsylvania Philadelphia PA United States Yale Center for Systems and Engineering Immunology Yale University School of Medicine New Haven CT United States New Haven CT United States Department of Biomedical Engineering Yale University New Haven CT United States Computational Biology and Bioinformatics Program Yale University CT USA New Haven United States Applied Math Program Yale University New Haven CT United States

Naïve CD8 T cells have the potential to differentiate into a spectrum of functional states during an immune response. How these developmental decisions are made and what mechanisms exist to suppress differentiation toward alternative fates remains unclear. We employed in vivo CRISPR-Cas9-based perturbation sequencing to assess the role of ~40 transcription factors (TFs) and epigenetic modulators in T cell fate decisions. Unexpectedly, we found that knockout of the TF Klf2 resulted in aberrant differentiation to exhausted-like CD8 T cells during acute infection. KLF2 was required to suppress the exhaustion-promoting TF TOX and to enable the TF TBET to drive effector differentiation. KLF2 was also necessary to maintain a polyfunctional tumor-specific progenitor state. Thus, KLF2 provides effector CD8 T cell lineage fidelity and suppresses the exhaustion program.

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THE SPECTRAL UNDERPINNING OF WORD2VEC

arXiv

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arXiv 2020年

作者： Jaffe, Ariel Kluger, Yuval Lindenbaum, Ofir Patsenker, Jonathan Peterfreund, Erez Steinerberger, Stefan Program in Applied Mathematics Yale University New Haven United States Department of Pathology Yale School of Medicine New Haven United States School of Computer Science and Engineering Hebrew University Jerusalem Israel Department of Mathematics Yale University New Haven United States

Word2vec due to Mikolov et al. (2013) is a word embedding method that is widely used in natural language processing. Despite its great success and frequent use, theoretical justification is still lacking. The main contribution of our paper is to propose a rigorous analysis of the highly nonlinear functional of word2vec. Our results suggest that word2vec may be primarily driven by an underlying spectral method. This insight may open the door to obtaining provable guarantees for word2vec. We support these findings by numerical simulations. One fascinating open question is whether the nonlinear properties of word2vec that are not captured by the spectral method are beneficial and, if so, by what mechanism. Copyright © 2020, The Authors. All rights reserved.

关键词： Spectroscopy

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Field-driven metamorphoses of isolated skyrmions within the conical state of cubic helimagnets

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Physical Review B 2021年第6期104卷 064432-064432页

作者： Andrey O. Leonov C. Pappas Ivan I. Smalyukh Department of Chemistry Faculty of Science Hiroshima University Kagamiyama Higashi Hiroshima Hiroshima 739-8526 Japan Chirality Research Center Hiroshima University Higashi Hiroshima Hiroshima 739-8526 Japan IFW Dresden Postfach 270016 D-01171 Dresden Germany Faculty of Applied Sciences Delft University of Technology Mekelweg 15 2629JB Delft The Netherlands Soft Materials Research Center and Materials Science and Engineering Program University of Colorado Boulder Colorado 80309 USA Department of Physics and Department of Electrical Computer and Energy Engineering University of Colorado Boulder Colorado 80309 USA Renewable and Sustainable Energy Institute National Renewable Energy Laboratory and University of Colorado Boulder Colorado 80309 USA

Topologically stable field configurations appear in many fields of physics, from elementary particles to condensed matter and cosmology. Deep physical relations and common physical features of a large variety of very different solitonic states in these systems arise from the mathematical similarity of phenomenological equations. During the last decade, chiral liquid crystals and chiral magnets took on the role of model objects for the experimental investigation of topological solitons and the understanding of their nonsingular field configurations. This is directly related to the discovery of particle-like chiral skyrmions, which are also considered as promising ingredients for technological applications. Here we introduce a paradigm of facile skyrmionic networks with mutually orthogonal orientations of constituent isolated skyrmions. On the one hand, such networks are envisioned as a novel concept of spintronic devices based, e.g., on gapless skyrmion motion along each other, and are presumably responsible for precursor phenomena near the ordering temperatures of bulk cubic helimagnets. In particular, we demonstrate an interconversion between mutually orthogonal skyrmions: horizontal skyrmions may swirl into an intermediate spring-like state and subsequently squeeze into vertical skyrmions with both polarities. On the other hand, skyrmion tubes are considered as building blocks for particle-like states with more involved internal structure. A family of target-skyrmions, which includes a so far overlooked type with a multiple topological charge, is formed owing to the tendency to minimize the interaction energy between vertical and horizontal skyrmions. The conical phase serves as a suitable background for considered skyrmion evolution. It substantializes the attracting skyrmion-skyrmion interaction in the skyrmionic networks, shapes their internal structure, and guides the nucleation processes. Alternatively, intricate textural changes of isolated skyrmions result

关键词： Skyrmions Chiral magnets Cholesteric liquid crystals Helimagnets

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