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arXiv 2024年

作者： Willett, Francis R. Li, Jingyuan Le, Trung Fan, Chaofei Chen, Mingfei Shlizerman, Eli Chen, Yue Zheng, Xin Okubo, Tatsuo S. Benster, Tyler Lee, Hyun Dong Kounga, Maxwell Buchanan, E. Kelly Zoltowski, David Linderman, Scott W. Henderson, Jaimie M. Department of Neurosurgery Stanford University United States Department of Electrical & Computer Engineering University of Washington United States Department of Computer Science Stanford University United States Department of Applied Mathematics University of Washington United States China Neurosciences Phd Program Stanford University United States Wu Tsai Neurosciences Institute Department of Statistics Stanford University United States

Speech brain-computer interfaces aim to decipher what a person is trying to say from neural activity alone, restoring communication to people with paralysis who have lost the ability to speak intelligibly. The Brain-to-Text Benchmark’24 and associated competition was created to foster the advancement of decoding algorithms that convert neural activity to text. Here, we summarize the lessons learned from the competition ending on June 1, 2024 (the top 4 entrants also presented their experiences in a recorded webinar). The largest improvements in accuracy were achieved using an ensembling approach, where the output of multiple independent decoders was merged using a fine-tuned large language model (an approach used by all 3 top entrants). Performance gains were also found by improving how the baseline recurrent neural network (RNN) model was trained, including by optimizing learning rate scheduling and by using a diphone training objective. Improving upon the model architecture itself proved more difficult, however, with attempts to use deep state space models or transformers not yet appearing to offer a benefit over the RNN baseline. The benchmark will remain open indefinitely to support further work towards increasing the accuracy of brain-to-text algorithms. © 2024, CC BY.

关键词： Recurrent neural networks

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Ciwars: A Web Server for Antibiotic Resistance Surveillance Using Longitudinal Metagenomic Data

SSRN

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SSRN 2024年

作者： Emon, Muhit Islam Cheung, Yat Fei Stoll, James Rumi, Monjura Afrin Brown, Connor Choi, Joung Min Moumi, Nazifa Ahmed Ahmed, Shafayat Song, Haoqiu Sein, Justin Yao, Shunyu Khan, Ahmad Gupta, Suraj Kulkarni, Rutwik Butt, Ali Vikesland, Peter Pruden, Amy Zhang, Liqing Department of Computer Science Virginia Tech BlacksburgVA24060 United States Fralin Life Science Institute Virginia Tech BlacksburgVA24060 United States Department of Civil and Environmental Engineering Virginia Tech BlacksburgVA24060 United States The Interdisciplinary PhD Program in Genetics Bioinformatics and Computational Biology Virginia Tech BlacksburgVA24060 United States

The rise of antibiotic resistance (AR) poses substantial threats to human and animal health, food security, and economic stability. Wastewater-based surveillance (WBS) has emerged as a powerful strategy for population-level AR monitoring, providing valuable data to guide public health and policy decisions. Metagenomic sequencing is especially promising, as it can yield comprehensive profiles of antibiotic resistance genes (ARGs) and other genes relevant to AR in a single run. However, online analytical platforms to facilitate continuous AR monitoring through longitudinal metagenomic data are lacking. To address this, we introduce Cyberinfrastructure for Waterborne Antibiotic Resistance Surveillance (CIWARS), a web server configured for characterizing key AR trends from longitudinal metagenomic WBS data. CIWARS offers comprehensive ARG and taxonomic profiling, along with detection of anomalous AR indicators over time, aiding in identifying potential events of concern, such as the emergence of resistant strains or outbreaks. Through interactive temporal data visualization, CIWARS enables AR monitoring and demonstrates its potential for informing effective and timely interventions to mitigate the spread and transmission of AR. CIWARS is broadly applicable to longitudinal metagenomic data from any environment and thus could be a valuable tool to support global efforts to combat the evolution and spread of AR, while also guiding agricultural and public health efforts aimed at optimizing antibiotic use when it is needed. The web server is freely available at https://***/. © 2024, The Authors. All rights reserved.

关键词： Gene encoding

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Full-privacy secured search engine empowered by efficient genome-mapping algorithms

arXiv

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arXiv 2021年

作者： Chang, Yuan-Yu Wong, Sheng-Tang Salawu, Emmanuel O. Wang, Yu-Xuan Hung, Jui-Hung Yang, Lee-Wei Institute of Bioinformatics and Structural Biology National Tsing Hua University Hsinchu300044 Taiwan Praexisio Taiwan Inc. New Taipei221425 Taiwan Bioinformatics Program Institute of Information Sciences Academia Sinica Taipei115201 Taiwan HerndonVA United States Department of Computer Science College of Computer Science National Yang Ming Chiao Tung University Hsinchu300044 Taiwan Physics Division National Center for Theoretical Sciences Taipei106216 Taiwan PhD Program in Biomedical Artificial Intelligence National Tsing Hua University Hsinchu300044 Taiwan

Search engine privacy has not been an option for web exploration in the past. Search history returns to users as personalized merchandise promotion from search engine companies. Here we demonstrate a privacy-guaranteed internet search method, provided with the entire article as a query, can be correctly carried out without revealing users' sensitive content by a degenerate, irreversible, encoding scheme and an efficient FM-index search routine, generally used in the next-generation sequencing. In our solution, Sapiens Aperio Veritas Engine (S.A.V.E.), every word in the query is encoded into one of 12 "amino acids" comprising a pseudo-biological sequence (PBS) at users' local machines. The PBS-mediated plagiarism detection is done by users' submission of locally encoded PBS through our cloud service to locate duplicates in the collected web contents, currently including all the English and Chinese Wikipedia pages and Open Access journal articles, as of April 2021, which had been encoded in the same way as the query. It is found that PBSs with a length longer than 12, comprising a combination of more than 12 "amino acids", can return correct results with a false positive rate © 2021, CC BY-NC-ND.

关键词： Search engines

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Review on Engineering and Regulatory aspects associated with Frequency Control Capabilities of Wind Power Plants

Review on Engineering and Regulatory aspects associated with...

引用

IEEE Energytech

作者： Venkatesh Yadav Singarao Vittal Rao Mark A. Harral multi-disciplinary Wind Science and Engineering PhD program Texas Tech University Department of Electrical & Computer Engineering Texas Tech University GroupNIRE clean energy development company

ISBN: (纸本)9781467344456

With the increasing grid penetration levels of wind power, there is an increasing need to study both the power control systems and the regulatory aspects associated with frequency control capabilities of wind power plants at various levels (turbine, wind farm and power system levels). This is especially very important in the United States with a goal of achieving 20% nation's electricity from wind energy by 2030. This paper provides observations and challenges identified with wind energy integration with respect to active power control strategies used in implementing frequency regulation at various levels. This paper also discusses the current and future aspects of market regulation of frequency responsive services offered by converter based variable generation technologies and the need for an appropriate utility market structure in order to provide settlements for these capabilities.

关键词： Inertial and Primary Frequency Response Frequency Regulation Standards Ancillary Service Markets Wind Power Plants

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Probabilistic Genotype-Phenotype Maps Reveal Mutational Robustness of RNA Folding, Spin Glasses, and Quantum Circuits

arXiv

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arXiv 2023年

作者： Sappington, Anna Mohanty, Vaibhav Department of Electrical Engineering and Computer Science Massachusetts Institute of Technology CambridgeMA02139 United States Program for Health Sciences and Technology Harvard Medical School BostonMA02115 United States Massachusetts Institute of Technology CambridgeMA02139 United States Harvard/MIT MD-PhD Program Harvard Medical School BostonMA02115 United States Department of Chemistry and Chemical Biology Harvard University CambridgeMA02138 United States

Recent studies of genotype-phenotype (GP) maps have reported universally enhanced phenotypic robustness to genotype mutations, a feature essential to evolution. Virtually all of these studies make a simplifying assumption that each genotype—represented as a sequence—maps deterministically to a single phenotype, such as a discrete structure. Here, we introduce probabilistic genotype-phenotype (PrGP) maps, where each genotype maps to a vector of phenotype probabilities, as a more realistic and universal language for investigating robustness in a variety of physical, biological, and computational systems. We study three model systems to show that PrGP maps offer a generalized framework which can handle uncertainty emerging from various physical sources: (1) thermal fluctuation in RNA folding, (2) external field disorder in spin glass ground state finding, and (3) superposition and entanglement in quantum circuits, which are realized experimentally on IBM quantum computers. In all three cases, we observe a novel biphasic robustness scaling which is enhanced relative to random expectation for more frequent phenotypes and approaches random expectation for less frequent phenotypes. We derive an analytical theory for the behavior of PrGP robustness, and we demonstrate that the theory is highly predictive of empirical robustness. © 2023, CC BY.

关键词： Quantum computers

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ANALYSIS AND CAD TECHNIQUES FOR PERIODIC LEAKY-WAVE PRINTED ANTENNAS - NUMERICAL AND EXPERIMENTAL RESULTS

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INTERNATIONAL JOURNAL OF MICROWAVE AND MILLIMETER-WAVE computer-AIDED ENGINEERING 1994年第1期4卷 88-99页

作者： ENCINAR, JA Department of Electromagnetism and Circuit Theory Universidad Politécnica de Madrid 28040 Madrid Spain Jose A. Encinar was born in Madrid Spain in 1957. He received the “Ingeniero de Telecomunicacion” and PhD degrees both from the Universidad PolitCcnica de Madrid in 1979 and 1985 respectively. Starting in January of 1980 he was with the Grupo de Electromagnetismo Aplicad0 y Microondas at the Universidad Politecnica de Madrid as a teaching and research assistant from 1980 to 1982 and as an assistant professor from 1983 to 1986. In 1986 he became associate professor. From February to October of 1987 he was at Polytechnic University Brooklyn NY as a postdoctoral fellow of the NATO Science Program. He is currently a professor in the Electromagnetism and Circuit Theory Department at the Universidad Politecnica de Madrid. His research interests include analytical and computer-aided techniques for solving electromagnetic problems in waveguide structures and radiating systems.

Theoretical and experimental results are presented for a printed leaky-wave antenna. Mode-matching and EDC methods have been used to analyze the antenna and to design the prototypes. Reflection, transmission, and radiation measurements have been compared with theoretical predictions with good agreement. A CAD procedure is proposed to reduce the sidelobe level by tapering width and separation of metal strips. (C) 1994 John Wiley & Sons, Inc.

关键词： Antennas

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Thermalization of fluorescent protein exciton-polaritons at room temperature

arXiv

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arXiv 2022年

作者： Satapathy, Sitakanta Liu, Bin Deshmukh, Prathmesh Molinaro, Paul M. Dirnberger, Florian Khatoniar, Mandeep Koder, Ronald L. Menon, Vinod M. Department of Physics Center for Discovery and Innovation The City College of New York 85 St. Nicholas Terrace New YorkNY10031 United States The PhD Program in Physics The Graduate Center of the City University of New York 365 5th Ave New YorkNY10016 United States Department of Electrical Engineering and Computer Science University of Michigan Ann ArborMI48109 United States

Fluorescent proteins (FPs) have recently emerged as a serious contender for realizing ultra-low threshold room temperature exciton-polariton condensation and lasing. Our contribution investigates the thermalization of FP microcavity exciton-polaritons upon optical pumping under ambient conditions. We realize polariton cooling using a new FP molecule, called mScarlet, coupled strongly to the optical modes in a Fabry-Pérot cavity. Interestingly, at the threshold excitation energy (fluence) of ~9 nJ/pulse (15.6 mJ/cm2), we observe an effective temperature, Teff ~350 ± 35 K close to the lattice temperature indicative of strongly thermalized exciton-polaritons at equilibrium. This efficient thermalization results from the interplay of radiative pumping facilitated by the energetics of the lower polariton branch and the cavity Qfactor. Direct evidence for dramatic switching from an equilibrium state into a metastable state is observed for the organic cavity polariton device at room temperature via deviation from the Maxwell-Boltzmann statistics at k1 = 0 above the threshold. Thermalized polariton gases in organic systems at equilibrium hold substantial promise for designing room temperature polaritonic circuits, switches, and lattices for analog simulation. © 2022, CC BY-NC-SA.

关键词： Polariton

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A Framework for Interpretability in Machine Learning for Medical Imaging

arXiv

引用

arXiv 2023年

作者： Wang, Alan Q. Karaman, Batuhan K. Kim, Heejong Rosenthal, Jacob Saluja, Rachit Young, Sean I. Sabuncu, Mert R. School of Electrical and Computer Engineering Cornell University Cornell Tech New YorkNY10044 United States Department of Radiology Weill Cornell Medical School New YorkNY10065 United States Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program New YorkNY10065 United States Martinos Center for Biomedical Imaging Harvard Medical School BostonMA02129 United States Computer Science and Artificial Intelligence Laboratory MIT CambridgeMA02139 United States

Interpretability for machine learning models in medical imaging (MLMI) is an important direction of research. However, there is a general sense of murkiness in what interpretability means. Why does the need for interpretability in MLMI arise? What goals does one actually seek to address when interpretability is needed? To answer these questions, we identify a need to formalize the goals and elements of interpretability in MLMI. By reasoning about real-world tasks and goals common in both medical image analysis and its intersection with machine learning, we identify five core elements of interpretability: localization, visual recognizability, physical attribution, model transparency, and actionability. From this, we arrive at a framework for interpretability in MLMI, which serves as a step-by-step guide to approaching interpretability in this context. Overall, this paper formalizes interpretability needs in the context of medical imaging, and our applied perspective clarifies concrete MLMI-specific goals and considerations in order to guide method design and improve real-world usage. Our goal is to provide practical and didactic information for model designers and practitioners, inspire developers of models in the medical imaging field to reason more deeply about what interpretability is achieving, and suggest future directions of interpretability research. © 2023, CC0.

关键词： Machine learning

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Statistical Power Analysis for Designing Bulk, Single-Cell, and Spatial Transcriptomics Experiments: Review, Tutorial, and Perspectives

arXiv

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arXiv 2023年

作者： Jeon, Hyeongseon Xie, Juan Jeon, Yeseul Jung, Kyeong Joo Gupta, Arkobrato Chang, Won Chung, Dongjun Department of Biomedical Informatics The Ohio State University ColumbusOH United States Pelotonia Institute for Immuno-Oncology The James Comprehensive Cancer Center The Ohio State University ColumbusOH43210 United States The Interdisciplinary PhD program in Biostatistics The Ohio State University ColumbusOH United States Department of Statistics and Data Science Yonsei University Seoul Korea Republic of Department of Applied Statistics Yonsei University Seoul Korea Republic of Department of Computer Science and Engineering The Ohio State University ColumbusOH United States Division of Statistics and Data Science University of Cincinnati CincinnatiOH United States

Gene expression profiling technologies have been used in various applications such as cancer biology. The development of gene expression profiling has expanded the scope of target discovery in transcriptomic studies, and each technology produces data with distinct characteristics. In order to guarantee biologically meaningful findings using transcriptomic experiments, it is important to consider various experimental factors in a systematic way through statistical power analysis. In this paper, we review and discuss the power analysis for three types of gene expression profiling technologies from a practical standpoint, including bulk RNA-seq, single-cell RNA-seq, and high-throughput spatial transcriptomics. Specifically, we describe the existing power analysis tools for each research objective for each of the bulk RNA-seq and scRNA-seq experiments, along with recommendations. On the other hand, since there are no power analysis tools for high-throughput spatial transcriptomics at this point, we instead investigate the factors that can influence power analysis. © 2023, CC BY-NC-ND.

关键词： RNA

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Segmenting Alzheimer's Disease MRI Slices for Hippocampal Volume Calculation

Segmenting Alzheimer's Disease MRI Slices for Hippocampal Vo...

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IEEE International Conference on Consumer Electronics-Taiwan (ICCE-TW)

作者： Hsiao-Chuan Tan Gilang Titah Ramadhan Wei-Cheng Shen Wen-Thong Chang Chih-Yang Lin Ben-Yi Liau Yih-Kuen Jan Yori Pusparani Chi-Wen Lung Department of Artificial Intelligence PhD Program Asia University Taichung Taiwan Department of Computer Science and Information Engineering Asia University Taichung Taiwan Department of Creative Product Design Asia University Taichung Taiwan Department of Mechanical Engineering National Central University Taoyuan Taiwan Department of Automatic Control Engineering Feng Chia University Taichung Taiwan Department of Kinesiology and Community Health University of Illinois Urbana America Department of Digital Media Design Asia University Taichung Taiwan

ISBN: (数字)9798350386844

ISBN: (纸本)9798350386851

Alzheimer's is a neurodegenerative disease that quietly steals human memory. This study analyzed hippocampal volume in Alzheimer's Disease (AD), Mild Cognitive Impairment (MCI), and Normal Cognition (NC) using MRI image slices from the ADNI database and YOLOv8 instance segmentation. We used 300 images to segment the left and right hippocampal. This study focused on volume calculation from five MRI image slices. The results showed 0.98 (AD), 0.92 (MCI), and 0.90 (NC) and revealed significant volumetric differences showed in the NC class (P = 0.045). This suggests early neuroanatomical changes can occur without cognitive symptoms, highlighting the potential of deep learning in the early detection of neurodegenerative diseases.

关键词： Instance segmentation Deep learning Accuracy Databases Magnetic resonance imaging Cognition Alzheimer's disease

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