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International Journal of Foundations of Computer science 2002年第2期13卷 223-242页

作者： Edelsbrunner, Herbert Guoy, Damrong Department of Computer Science Duke University Durham NC 27708 United States Raindrop Geomagic Research Triangle Park NC 27709 United States Center for Simulation of Advanced Rockets Computational Science and Engineering Program University of Illinois at Urbana-Champaign Urbana IL 61801 United States

We propose sink insertion as a new technique to improve the mesh quality of Delaunay triangulations. We compare it with the conventional circumcenter insertion technique under three scheduling regimes: incremental, in blocks, and in parallel. Justification for sink insertion is given in terms of mesh quality, numerical robustness, running time, and ease of parallelization. © 2002 World Scientific Publishing Company.

关键词： Delaunay triangulations dynamic data structures experimentation Mesh generation mesh quality parallel meshing

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LTE/WI-FI COEXISTENCE ON A FLEXIBLE SOFTWARE DEFINED RADIO TESTBED 57

LTE/WI-FI COEXISTENCE ON A FLEXIBLE SOFTWARE DEFINED RADIO T...

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57th Annual International Telemetering Conference, ITC 2022

作者： Elahi, Mirza M. Valdez, Kevin J. Gonzalez, Virgilio Computational Science Program The University of Texas at El Paso El PasoTX79968 United States Department of Electrical and Computer Engineering The University of Texas at El Paso El PasoTX79968 United States

The rapid rise in usage of mobile devices have not shown any signs of flattening or slowing down. Some efforts in the standardization bodies are underway to define new ways to boost data rate, network capacity and lower the latency by enhancing existing 4G technologies and by incorporating new technologies in 5G. Since lower spectrum has fewer resources, the LTE of unlicensed spectrum LTE-U is being proposed to extend LTE to unlicensed spectrum. Streaming data traffic for licensed spectrum on LTE-U can improve the performance of the system significantly. In this paper LTE-U deployment by the LAA is implemented using the LBT mechanism on a flexible SDR testbed. © 2022 International Foundation for Telemetering. All rights reserved.

关键词： Testbeds

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GranatumX:A Community-engaging, Modularized, and Flexible Webtool for Single-cell Data Analysis

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Genomics, Proteomics & Bioinformatics 2021年第3期19卷 452-460页

作者： David G.Garmire Xun Zhu Aravind Mantravadi Qianhui Huang Breck Yunits Yu Liu Thomas Wolfgruber Olivier Poirion Tianying Zhao Cédric Arisdakessian Stefan Stanojevic Lana X.Garmire Department of Electrical Engineering&Computer Science University of MichiganAnn ArborMI 48109USA Epidemiology Program University of Hawaii Cancer CenterHonoluluHI 96813USA Department of Biostatistics University of MichiganAnn ArborMI 48109USA Department of Computational Medicine and Bioinformatics University of MichiganAnn ArborMI 48105USA Molecular Biosciences and Bioengineering Graduate Program University of Hawaii at ManoaHonoluluHI 96822USA

We present GranatumX,a next-generation software environment for single-cell RNA sequencing(scRNA-seq)data *** is inspired by the interactive webtool *** enables biologists to access the latest scRNA-seq bioinformatics methods in a web-based graphical *** also offers software developers the opportunity to rapidly promote their own tools with others in customizable *** architecture of GranatumX allows for easy inclusion of plugin modules,named Gboxes,which wrap around bioinformatics tools written in various programming languages and on various *** can be run on the cloud or private servers and generate reproducible *** is a community-engaging,flexible,and evolving software ecosystem for scRNA-seq analysis,connecting developers with bench *** is freely accessible at http://***/granatumx/app.

关键词： Single-cell RNA sequencing Analysis Pipeline Webtool Module

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Transferable Learning of Reaction Pathways from Geometric Priors

arXiv

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arXiv 2025年

作者： Nam, Juno Steiner, Miguel Misterka, Max Yang, Soojung Singhal, Avni Gómez-Bombarelli, Rafael Department of Materials Science and Engineering Massachusetts Institute of Technology CambridgeMA02139 United States Energy Storage Research Alliance Argonne National Laboratory 9700 South Cass Avenue LemontIL60439 United States Department of Mathematics Massachusetts Institute of Technology CambridgeMA02139 United States Computational and Systems Biology Program Massachusetts Institute of Technology CambridgeMA02139 United States

Identifying minimum-energy paths (MEPs) is crucial for understanding chemical reaction mechanisms but remains computationally demanding. We introduce MEPIN, a scalable machine-learning method for efficiently predicting MEPs from reactant and product configurations, without relying on transition-state geometries or pre-optimized reaction paths during training. The task is defined as predicting deviations from geometric interpolations along reaction coordinates. We address this task with a continuous reaction path model based on a symmetry-broken equivariant neural network that generates a flexible number of intermediate structures. The model is trained using an energy-based objective, with efficiency enhanced by incorporating geometric priors from geodesic interpolation as initial interpolations or pre-training objectives. Our approach generalizes across diverse chemical reactions and achieves accurate alignment with reference intrinsic reaction coordinates, as demonstrated on various small molecule reactions and [3+2] cycloadditions. Our method enables the exploration of large chemical reaction spaces with efficient, data-driven predictions of reaction pathways. Copyright © 2025, The Authors. All rights reserved.

关键词： Reaction intermediates

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The anatomic determinants of conductive hearing loss secondary to tympanic membrane perforation

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Journal of Otology 2017年第3期12卷 125-131页

作者： David J.Carpenter Debara L.Tucci David M.Kaylie Dennis O.Frank-Ito Division of Head and Neck Surgery & Communication Sciences Department of Surgery Duke University Medical Center Durham NC USA Computational Biology & Bioinformatics PhD Program Duke University Durham NC USA Department of Mechanical Engineering and Materials Science Duke University Durham NC USA

Objectives: Recent studies have introduced middle ear volume(MEV) as a novel determinant of perforation-induced conductive hearing loss(CHL) in a mechanism driven by trans-tympanic membrane pressure differences. The primary aims of this preliminary report are to: 1) correlate CHL with perforation size; 2) describe the relationship between CHL and MEV; and 3) compare CHL across a range of cholesteatoma ***: A retrospective pilot study was performed in 31 subjects with audiometry indicative of conductive hearing loss, temporal bone CT scans,and no prior middle ear surgery. Perforation size and MEV were analyzed with respect to CHL in a cohort of 10 perforated ears with no cholesteatoma. CHLs were compared in 3 groups defined by extent of cholesteatoma ***: Ears with large and small perforations showed mean ABG values of 32.0 ± 15.7 dB and 16.0 ± 16.4 dB, respectively. A direct relationship was observed between MEV and CHL for ears with large perforations across all frequencies, whereas this relationship for small perforations was frequency-dependent. Finally, a statistically significant increase in CHL was found across ears with increasing cholesteatoma involvement at 1000 Hz(X^2(2) = 9.786, p = 0.008),2000 Hz(x^2(2) = 8.455, p = 0.015),and 4000 Hz(x^2(2)= 8.253, p = 0.016).Conclusions: These pilot data suggest that greater perforation-induced conductive hearing losses may be associated with larger perforation sizes and cholesteatoma. The correlation between MEV and CHL may require additional study.

关键词： Perforation-induced hearing loss Conductive hearing loss Middle ear volume Three-dimensional volume reconstruction

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A Multi-phase Deep Learning Approach for Predicting HCC Response to TACE using Complete Computed Tomography

A Multi-phase Deep Learning Approach for Predicting HCC Resp...

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2023 IEEE EMBS Special Topic Conference on Data science and engineering in Healthcare, Medicine and Biology, IEEECONF 2023

作者： Chang, Shun Cheng Liu, Chien Fu Misztal, Marta Hsieh, Yi Hsien Lin, Che Taiwan School of Electronic Engineering and Computer Science Queen Mary University of London United Kingdom Department of Electrical Engineering Ntu Taiwan Center for Computational and Systems Biology Center for Biotechnology Ntu Taiwan Smart Medicine and Health Informatics Program Ntu Taiwan

ISBN: (纸本)9798350383386

In this research study, we compare the predictive performance of two advanced deep learning-based models in order to provide a solution to TACE (Transarterial Chemoembolization) response prediction in HCC (Hepatocellular Carcinoma) patients. Using entire abdominal CT scans enabled a broader perspective available for the model, eliminating the need for segmentation during the preprocessing. Making use of both single-phase and multi-phase CT imaging, we have used DenseNet121 and have obtained an accuracy of 80% for the multi-phase *** Relevance: The ability to predict the effectiveness of TACE treatment prior to its administration makes it possible to provide a better decision-making aid for physicians and patients. © 2023 IEEE.

关键词： Computerized tomography

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Controller Design via Adaptive Critic and Model Reference Methods

Controller Design via Adaptive Critic and Model Reference Me...

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International Joint Conference on Neural Networks 2003

作者： Lendaris, G.George Santiago, Roberta McCarthy, Jay Carroll, Michael Systems Science Ph.D. Program Electrical and Computer Engineering Portland State University Portland OR 97201 United States Systems Science Ph.D. Program Portland State University Portland OR 97201 United States Electrical Engineering Department Portland State University Portland OR 97201 United States Computational Neuroscience University of Chicago Chicago IL United States

Dynamic programming (DP) is a principled way to design optimal controllers for certain classes of nonlinear systems;unfortunately, DP is computationally very expensive. The Reinforcement Learning methods known as Adaptive Critics (AC) provide computationally feasible means for performing approximate Dynamic programming (ADP). The term 'adaptive ' in A C refers to the critic 's improved estimations of the Value Function used by DP. To apply DP, the user must craft a Utility function that embodies all the problem-specific design specifications/criteria. Model Reference Adaptive Control methods have been successfully used in the control community to effect on-line redesign of a controller in response to variations in plant parameters, with the idea that the resulting closed loop system dynamics will mimic those of a Reference Model. The work reported here 1) uses a reference model in ADP as the key information input to the Utility function, and 2) uses ADP off-line to design the desired controller. Future work will extend this to on-line application. This method is demonstrated for a hypersonic shaped airplane called LoFL YTE®;its handling characteristics are natively a little "hotter" than a pilot would desire. A control augmentation subsystem is designed using ADP to make the plane "feel like " a better behaved one, as specified by a Reference Model. The number of inputs to the successfully designed controller are among the largest seen in the literature to date.

关键词： Adaptive control systems

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An efficient method for online identification of steady state for multivariate systems 13

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ASME 2018 13th International Manufacturing science and engineering Conference, MSEC 2018

作者： Xu, Honglun Wu, Jianguo Tseng, Tzu-Liang Bill Computational Science Program University of Texas El PasoTX79968 United States Department of Industrial Engineering and Management Peking University Beijing100871 China Industrial Manufacturing and Systems Engineering University of Texas El PasoTX79968 United States

ISBN: (纸本)9780791851388

Most of the existing steady state detection approaches are designed for univariate signals. For multivariate signals, the univariate approach is often applied to each process variable and the system is claimed to be steady once all signals are steady, which is computationally inefficient and also not accurate. The article proposes an efficient online method for multivariate steady state detection. It estimates the covariance matrices using two different approaches, namely, the mean-squared-deviation and mean-squared-successive-difference. To avoid the usage of a moving window, the process means and the two covariance matrices are calculated recursively through exponentially weighted moving average. A likelihood ratio test is developed to compare the difference of the two covariance matrices and to detect the steady state. The intensive numerical studies and real case study show that the proposed method can accurately detect the steady state of a multivariate system. © Copyright 2018 ASME.

关键词： Covariance matrix

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A node placement optimization method for watershed underwater sensor networks 9

A node placement optimization method for watershed underwate...

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9th ACM International Conference on Underwater Networks and Systems, WUWNet 2014

作者： Barbosa, Gentil V. Letouze, Patrick Xavier, Adilson E. Department of Computer Science UFT - Universidade Federal do Tocantins PESC Brazil Department of Computer Science UFT - Universidade Federal do Tocantins MCS - Postgraduate Program of System's Computational Modeling Brazil PESC - Postgraduate Program of System's Engineering and Computation UFRJ - Universidade Federal do Rio de Janeiro Brazil

ISBN: (纸本)9781450332774

Given a set of underwater sensors coordinates that are usually determined by a specialist for the design of a watershed monitoring system, where should be placed the sinks and the base station? The answer may be the minimization of the Variable Internode Distance. In such cases, a two dimensional architecture is acceptable because it is a shallow water system. Hence, in this paper, it is proposed a two-level node distance minimization for Underwater Wireless Sensor Network for monitoring systems. The mathematical method employed for optimization is the Hyperbolic Smoothing approach and the proposed method includes the placement of the base-station in the algorithm. Copyright 2014 ACM.

关键词： Base stations

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Annotating TSSs in Multiple Cell Types Based on DNA Sequence and RNA-seq Data via DeeReCT-TSS

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Genomics, Proteomics & Bioinformatics 2022年第5期20卷 959-973页

作者： Juexiao Zhou Bin Zhang Haoyang Li Longxi Zhou Zhongxiao Li Yongkang Long Wenkai Han Mengran Wang Huanhuan Cui Jingjing Li Wei Chen Xin Gao Computer Science Program ComputerElectrical and Mathematical Sciences and Engineering DivisionKing Abdullah University of Science and TechnologyThuwal 23955-6900Saudi Arabia Computational Bioscience Research Center King Abdullah University of Science and TechnologyThuwal 23955-6900Saudi Arabia Department of Biology School of Life SciencesSouthern University of Science and TechnologyShenzhen 518055China Shenzhen Key Laboratory of Gene Regulation and Systems Biology School of Life SciencesSouthern University of Science and TechnologyShenzhen 518055China Academy for Advanced Interdisciplinary Studies Southern University of Science and TechnologyShenzhen 518055China

The accurate annotation of transcription start sites(TSSs)and their usage are critical for the mechanistic understanding of gene regulation in different biological *** fulfill this,specific high-throughput experimental technologies have been developed to capture TSSs in a genome-wide manner,and various computational tools have also been developed for in silico prediction of TSSs solely based on genomic *** of these computational tools cast the problem as a binary classification task on a balanced dataset,thus resulting in drastic false positive predictions when applied on the genome ***,we present Dee Re CT-TSS,a deep learningbased method that is capable of identifying TSSs across the whole genome based on both DNA sequence and conventional RNA sequencing *** show that by effectively incorporating these two sources of information,Dee Re CT-TSS significantly outperforms other solely sequence-based methods on the precise annotation of TSSs used in different cell ***,we develop a meta-learning-based extension for simultaneous TSS annotations on 10 cell types,which enables the identification of cell type-specific ***,we demonstrate the high precision of DeeReCT-TSS on two independent datasets by correlating our predicted TSSs with experimentally defined TSS chromatin *** source code for Dee Re CT-TSS is available at https://github.-com/Joshua Chou2018/Dee Re CT-TSS_release and https://***/biocode/tools/BT007316.

关键词： Transcription start site Machine learning Deep learning Meta-learning RNA sequencing

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