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Deep inference of latent dynamics with spatio-temporal super-resolution using selective backpropagation through time

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arXiv 2021年

作者： Zhu, Feng Sedler, Andrew R. Grier, Harrison A. Ahad, Nauman Davenport, Mark A. Kaufman, Matthew T. Giovannucci, Andrea Pandarinath, Chethan Neuroscience Graduate Program Emory University Center for Machine Learning Georgia Tech Computational Neuroscience Graduate Program The University of Chicago School of Electrical and Computer Engineering Georgia Tech Dept. of Organismal Biology and Anatomy The University of Chicago Neuroscience Institute The University of Chicago Joint Dept. of Biomedical Engineering UNC Chapel Hill NC State University UNC Chapel Hill Neuroscience Center Coulter Dept. of Biomedical Engineering Emory University Georgia Tech Dept. of Neurosurgery Emory University

Modern neural interfaces allow access to the activity of up to a million neurons within brain circuits. However, bandwidth limits often create a trade-off between greater spatial sampling (more channels or pixels) and the temporal frequency of sampling. Here we demonstrate that it is possible to obtain spatio-temporal super-resolution in neuronal time series by exploiting relationships among neurons, embedded in latent low-dimensional population dynamics. Our novel neural network training strategy, selective backpropagation through time (SBTT), enables learning of deep generative models of latent dynamics from data in which the set of observed variables changes at each time step. The resulting models are able to infer activity for missing samples by combining observations with learned latent dynamics. We test SBTT applied to sequential autoencoders and demonstrate more efficient and higher-fidelity characterization of neural population dynamics in electrophysiological and calcium imaging data. In electrophysiology, SBTT enables accurate inference of neuronal population dynamics with lower interface bandwidths, providing an avenue to significant power savings for implanted neuroelectronic interfaces. In applications to two-photon calcium imaging, SBTT accurately uncovers high-frequency temporal structure underlying neural population activity, substantially outperforming the current state-of-the-art. Finally, we demonstrate that performance could be further improved by using limited, high-bandwidth sampling to pretrain dynamics models, and then using SBTT to adapt these models for sparsely-sampled data. © 2021, CC BY-NC-SA.

关键词： Neurons

DCFormer: Efficient 3D Vision-Language Modeling with Decomposed Convolutions

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arXiv 2025年

作者： Ates, Gorkem Can Xin, Yu Gong, Kuang Shao, Wei Department of Medicine University of Florida GainesvilleFL32611 United States Department of Electrical and Computer Engineering University of Florida GainesvilleFL32611 United States Department of Biomedical Engineering University of Florida GainesvilleFL32611 United States Intelligent Clinical Care Center University of Florida GainesvilleFL32611 United States

Vision-language models (VLMs) have been widely applied to 2D medical image analysis due to their ability to align visual and textual representations. However, extending VLMs to 3D imaging remains computationally challenging. Existing 3D VLMs often rely on Vision Transformers (ViTs), which are computationally expensive due to the quadratic complexity of self-attention, or on 3D convolutions, which require large numbers of parameters and FLOPs as kernel size increases. We introduce DCFormer, an efficient 3D image encoder that factorizes 3D convolutions into three parallel 1D convolutions along the depth, height, and width dimensions. This design preserves spatial information while significantly reducing computational cost. Integrated into a CLIP-based vision-language framework, DCFormer is trained and evaluated on CT-RATE, a dataset of 50,188 paired 3D chest CT volumes and radiology reports. In zero-shot and fine-tuned detection of 18 pathologies, as well as in image–text retrieval tasks, DCFormer consistently outperforms state-of-the-art 3D vision encoders, including CT-ViT, ViT, ConvNeXt, PoolFormer, and TransUNet. These results highlight DCFormer’s potential for scalable, clinically deployable 3D medical VLMs. Our code is available at: https://***/mirthAI/DCFormer. © 2025, CC BY-NC-SA.

关键词： Three dimensional computer graphics

Quantum simulation of an extended Dicke model with a magnetic solid

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Communications Materials

Communications Materials 2024年第1期5卷 42页

作者： Marquez Peraca, Nicolas Li, Xinwei Moya, Jaime M. Hayashida, Kenji Kim, Dasom Ma, Xiaoxuan Neubauer, Kelly J. Fallas Padilla, Diego Huang, Chien-Lung Dai, Pengcheng Nevidomskyy, Andriy H. Pu, Han Morosan, Emilia Cao, Shixun Bamba, Motoaki Kono, Junichiro Department of Physics and Astronomy Rice University HoustonTX United States Department of Physics California Institute of Technology PasadenaCA United States Applied Physics Graduate Program Smalley–Curl Institute Rice University HoustonTX United States Division of Applied Physics Graduate School of Engineering Hokkaido University Hokkaido Japan Department of Electrical and Computer Engineering Rice University HoustonTX United States Department of Physics International Center of Quantum and Molecular Structures and Materials Genome Institute Shanghai University Shanghai China Department of Physics and Center for Quantum Frontiers of Research and Technology National Cheng Kung University Tainan Taiwan Department of Chemistry Rice University HoustonTX United States Department of Physics I Kyoto University Kyoto Japan The Hakubi Center for Advanced Research Kyoto University Kyoto Japan PRESTO Japan Science and Technology Agency Saitama Japan Department of Physics Yokohama National University Yokohama Japan Department of Materials Science and NanoEngineering Rice University HoustonTX United States

The Dicke model describes the cooperative interaction of an ensemble of two-level atoms with a single-mode photonic field and exhibits a quantum phase transition as a function of light–matter coupling strength. Extending this model by incorporating short-range atom–atom interactions makes the problem intractable but is expected to produce new physical phenomena and phases. Here, we simulate such an extended Dicke model using a crystal of ErFeO3, where the role of atoms (photons) is played by Er3+ spins (Fe3+ magnons). Through terahertz spectroscopy and magnetocaloric effect measurements as a function of temperature and magnetic field, we demonstrated the existence of a novel atomically ordered phase in addition to the superradiant and normal phases that are expected from the standard Dicke model. Further, we elucidated the nature of the phase boundaries in the temperature–magnetic-field phase diagram, identifying both first-order and second-order phase transitions. These results lay the foundation for studying multiatomic quantum optics models using well-characterized many-body solid-state systems. © The Author(s) 2024.

关键词： Atoms

Consensus Statement on Brillouin Light Scattering Microscopy of Biological Materials

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arXiv 2024年

作者： Bouvet, Pierre Bevilacqua, Carlo Ambekar, Yogeshwari Antonacci, Giuseppe Au, Joshua Caponi, Silvia Chagnon-Lessard, Sophie Czarske, Juergen Dehoux, Thomas Fioretto, Daniele Fu, Yujian Guck, Jochen Hamann, Thorsten Heinemann, Dag Jähnke, Torsten Jean-Ruel, Hubert Kabakova, Irina Koski, Kristie Koukourakis, Nektarios Krause, David La Cavera, Salvatore Landes, Timm Li, Jinhao Margueritat, Jeremie Mattarelli, Maurizio Monaghan, Michael Overby, Darryl R. Perez-Cota, Fernando Pontecorvo, Emanuele Prevedel, Robert Ruocco, Giancarlo Sandercock, John Scarcelli, Giuliano Scarponi, Filippo Testi, Claudia Török, Peter Vovard, Lucie Weninger, Wolfgang Yakovlev, Vladislav Yun, Seok-Hyun Zhang, Jitao Palombo, Francesca Bilenca, Alberto Elsayad, Kareem Center for Anatomy and Cell Biology Medical University of Vienna Austria Cell Biology and Biophysics Unit European Molecular Biology Laboratory Germany Fischell Department of Bioengineering University of Maryland United States Specto Srl. Milan Italy Unità di Perugia Italy LightMachinery Inc. Canada Departement of Electronics Carleton University Canada TU Dresden Germany Cluster of Excellence Physics of Life TU Dresden Germany Competence Center for Biomedical Computational Laser Systems TU Dresden Germany Institut Lumière Matière UMR5306 Université Lyon 1 CNRS Université de Lyon France Dipartimento di Fisica e Geologia Università di Perugia Italy Max Planck Institute for the Science of Light Erlangen Germany Department of Biology Norwegian University of Science and Technology Trondheim Norway Hannover Centre for Optical Technologies Leibniz University Hannover Germany CellSense Technologies GmbH Berlin Germany School of Mathematical and Physical Sciences University of Technology Sydney Australia Department of Chemistry University of California Davis United States Optics & Photonics Group Faculty of Engineering University of Nottingham United Kingdom Discipline of Mechanical Manufacturing & Biomedical Engineering Trinity College Dublin Ireland Department of Bioengineering Imperial College London United Kingdom CREST Optics S.p.A. Rome Italy Heidelberg Germany Center for Life Nano- & Neuro-Science Istituto Italiano di Tecnologia Rome Italy The Table Stable Ltd. Mettmenstetten Switzerland School of Physical & Mathematical Sciences Nanyang Technological University Singapore Nanyang Technological University Singapore Institute for Digital Molecular Analytics & Sciences Nanyang Technological University Singapore Department of Biomedical Engineering Texas A&M University United States Department of Electrical and Computer Engineering Texas A&M University United States Department of Physics and Astronomy Texas A&M University United States Harvard Me

Brillouin Light Scattering (BLS) spectroscopy is a non-invasive, non-contact, label-free optical technique that can provide information on the mechanical properties of a material on the sub-micron scale. Over the last decade it has seen increased applications in the life sciences, driven by the observed significance of mechanical properties in biological processes, the realization of more sensitive BLS spectrometers and its extension to an imaging modality. As with other spectroscopic techniques, BLS measurements not only detect signals characteristic of the investigated sample, but also of the experimental apparatus, and can be significantly affected by measurement conditions. The aim of this consensus statement is to improve the comparability of BLS studies by providing reporting recommendations for the measured parameters and detailing common artifacts. Given that most BLS studies of biological matter are still at proof-of-concept stages and use different-often self-built-spectrometers, a consensus statement is particularly timely to assure unified advancement. © 2024, CC BY.

关键词： Brillouin scattering

A review of fluid-structure interaction: blood flow in arteries

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Biomedical Engineering Advances

biomedical engineering Advances 2025年 9卷

作者： Zubeir Allum Saib Farid Abed Mergen H. Ghayesh Marco Amabili Biomedical Engineering Graduate Program American University of Sharjah Sharjah United Arab Emirates Department of Bioengineering New York University Abu Dhabi Abu Dhabi United Arab Emirates Department of Civil Engineering American University of Sharjah Sharjah United Arab Emirates School of Electrical and Mechanical Engineering University of Adelaide South Australia Australia School of Engineering Westlake University Hangzhou Zhejiang province China

Over the past decade, Fluid-Structure Interaction studies related to blood vessels have been an active area of research, as they adequately capture the multiphysics of blood flow within the circulatory system. Despite the growing interest, only few state-of-the-art reviews have been published in the literature, each focusing individually on the coronary artery, carotid artery, aorta, heart valves and peripheral arteries. This systematic review assesses the current research and implications of Fluid-Structure Interaction implementation strategies in relation to human arteries. It is meant to comprehensively amalgamate research studies on an array of arteries coupled with cardiovascular complications such as atherosclerosis, plaque calcification, aneurysms, aortic dissections and valve dysfunction. It additionally covers computational finite element and finite volume solver demands, coupling schemes, inlet and outlet boundary conditions specifications, Newtonian and non-Newtonian blood rheological properties, laminar and turbulent flow types, as well as the modelling of the vessel wall’s hyperelastic and viscoelastic mechanical behavior. The research information is retrieved from the last ten years and summarized in a tabulated format, to help researchers in easily extracting useful information for future investigations and reviews.

关键词： Fluid-structure interaction Computational fluid dynamics Finite element analysis Blood flow Hemodynamics Biomechanics Atherosclerosis Aneurysm Calcification Artery Plaque Valve

Phase transition in magic with random quantum circuits

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arXiv 2023年

作者： Niroula, Pradeep White, Christopher David Wang, Qingfeng Johri, Sonika Zhu, Daiwei Monroe, Christopher Noel, Crystal Gullans, Michael J. Joint Center for Quantum Information and Computer Science University of Maryland and NIST College ParkMD20742 United States Joint Quantum Institute University of Maryland and NIST College ParkMD20742 United States Chemical Physics Program Institute for Physical Science and Technology University of Maryland College ParkMD20742 United States IonQ Inc. College ParkMD20740 United States Duke Quantum Center Department of Electrical & Computer Engineering Department of Physics Duke University DurhamNC27701 United States

Magic is a property of quantum states that enables universal fault-tolerant quantum computing using simple sets of gate operations. Understanding the mechanisms by which magic is created or destroyed is, therefore, a crucial step towards efficient and practical fault-tolerant computation. We observe that a random stabilizer code subject to coherent errors exhibits a phase transition in magic, which we characterize through analytic, numeric and experimental probes. Below a critical error rate, stabilizer syndrome measurements remove the accumulated magic in the circuit, effectively protecting against coherent errors;above the critical error rate syndrome measurements concentrate magic. A better understanding of such rich behavior in the resource theory of magic could shed more light on origins of quantum speedup and pave pathways for more efficient magic state generation. © 2023, CC BY.

关键词： Random errors

Dynamic Time-Over-Threshold Readout for Improved Energy Linearity in PET Detectors that Achieve 100 ps CTR

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Dynamic Time-Over-Threshold Readout for Improved Energy Line...

IEEE Symposium on Nuclear Science (NSS/MIC)

作者： Shirin Pourashraf Andrea Gonzalez-Montoro Joshua W. Cates Zhixiang Zhao Jun Yeon Won Jae Sung Lee Craig S. Levin Department of Radiology Stanford University Stanford USA Applied Nuclear Physics Program at Lawrence Berkeley National Laboratory Berkeley USA School of Biomedical Engineering Shanghai Jiao Tong University Shanghai People's Republic of China Department of Nuclear Medicine and Biomedical Sciences Seoul National University Seoul South Korea Departments of Radiology Bioengineering Physics and Electrical Engineering Molecular Imaging Program Stanford University Stanford CA 94305

ISBN: (数字)9781665421133

ISBN: (纸本)9781665421140

We have embedded a dynamic time-over-threshold (DynTOT) block in our scalable TOF-PET detector readout electronics to linearize the multiplexed energy spectra while keeping 100 ps FWHM Coincidence Time Resolution (CTR) performance. This DynTOT block is constructed by off-the-shelve components and consumes only 20 mW power per detector ‘layer’ in our design. Using 3×3×10 mm³ "LGSO" crystals coupled to arrays of 3×3 mm² SiPMs, energy resolution of 13.8±0.1%, 13.9±0.3%, and 17.1±0.6% were experimentally achieved for conventional pulse height, DynTOT, and conventional TOT methods, respectively. Including the DynTOT method, coincidence data were experimentally acquired using a low jitter FPGA-based TDC, and 103.6 ± 1.1 ps FWHM CTR was achieved, demonstrating the robustness of our novel and scalable timing electronic chain.

关键词： Multiplexing Energy resolution Linearity Detectors Crystals Jitter Robustness

Sag and Flicker Reduction Using Hysteresis-Fuzzy Control-Based SMES Unit

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Canadian Journal of electrical and computer engineering 2019年第1期42卷 52-57页

作者： Yunus, A. M. Shiddiq Habriansyah, Imran Abu-Siada, Ahmed Masoum, Mohammad A.S. Energy Conversion Study Program Mechanical Engineering Department State Polytechnic of Ujung Pandang Makassar90245 Indonesia Mechatronics Study Program Mechanical Engineering Department State Polytechnic of Ujung Pandang Makassar90245 Indonesia Electrical and Computer Engineering Department University of Curtin University BentleyWA6102 United States Department of Engineering Utah Valley University OremUT84058 United States

The issue of power quality is one of the prominent factors in determining the reliability of power systems. It is inevitable to consider power quality issues and include appropriate mitigation techniques in the design of any future power system project construction. Voltage sag and flicker are the two most common short disturbance types of power quality issues that frequently occur in power systems. A widely accepted mitigation strategy to enhance the power quality of disturbed networks is by connecting a flexible ac transmission system. In this paper, a superconducting magnetic energy storage (SMES) unit along with hysteresis-fuzzy controller to suppress the severe impacts of voltage sag and flicker events on the power quality of a power system is proposed, implemented, and tested. The proposed SMES configuration with hysteresis current control and fuzzy logic controller is effective, simple, and easy to implement. Simulation results show the ability of the proposed SMES controller in compensating sag and/or flicker distortions. © 2003-2010 IEEE Canada.

关键词： Power quality

Machine learning full 3-D lower-body kinematics and kinetics on patients with osteoarthritis from electromyography

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biomedical engineering Advances 2023年 5卷

作者： Richard Byfield Matthew Guess Kianoosh Sattari Yunchao Xie Trent Guess Jian Lin Department of Mechanical and Aerospace Engineering George W. Woodruff School of Mechanical Engineering and the Center for Human-Centric Interfaces and Engineering Institute for Electronics and Nanotechnology Georgia Institute of Technology Atlanta USA 30332 Department of Physical Therapy Department of Orthopedic Surgery Department of Electrical Engineering and Computer Science Department of Biomedical Biological and Chemical Engineering University of Missouri Columbia USA 65211

Osteoarthritis (OA) is a degenerative disease that causes severe pain and reduces the range of motion of the joint, decreasing the quality of life for millions of individuals in the United States. Electromyography (EMG) sensors have been widely studied in biomechanics, showing applications in prosthetics, robotics, and control. While complex musculoskeletal models have been well established, the attempt of directly correlating EMG with kinematics and kinetics is still quite limited. Particularly, little work has been conducted on OA patients. In this work, we propose a method for estimating lower body joint angles (JAs) and ground reaction forces (GRFs) from surface-EMG sensors during a step-down task for individuals diagnosed with OA. The JAs and GRFs were measured by a Vicon motion capture system and force plates, respectively. EMG, JAs, and GRFs were used to train an echo state network (ESN) which afforded JAs with relative errors of 3.78% and 3.71% and the GRFs with relative errors of 3.619% and 4.596% for training and testing datasets, respectively. This study suggests the high fidelity of the ESN in automatically predicting full lower body kinematics and kinetics from the EMG signals. The results of this work promote the development of an EMG-controlled lower limb rehabilitation robot system for patients with OA.

关键词： Echo state network Electromyography Kinematics Kinetics Machine learning Osteoarthritis