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arXiv 2020年

作者： Lei, Chon Lok Ghosh, Sanmitra Whittaker, Dominic G. Aboelkassem, Yasser Beattie, Kylie A. Cantwell, Chris D. Delhaas, Tammo Houston, Charles Novaes, Gustavo Montes Panfilov, Alexander V. Pathmanathan, Pras Riabiz, Marina Weber dos Santos, Rodrigo Worden, Keith Mirams, Gary R. Wilkinson, Richard D. Computational Biology & Health Informatics Dept. of Computer Science University of Oxford United Kingdom MRC Biostatistics Unit University of Cambridge United Kingdom Centre for Mathematical Medicine & Biology School of Mathematical Sciences University of Nottingham United Kingdom Department of Bioengineering University of California San Diego United States Systems Modeling and Translational Biology GlaxoSmithKline R&D Stevenage United Kingdom ElectroCardioMaths Programme Centre for Cardiac Engineering Imperial College London United Kingdom CARIM School for Cardiovascular Diseases Maastricht University Netherlands Graduate Program in Computational Modeling Universidade Federal de Juiz de Fora Brazil Department of Physics and Astronomy Ghent University Belgium Laboratory of Computational Biology and Medicine Ural Federal University Ekaterinburg Russia U.S. Food and Drug Administration Center for Devices and Radiological Health Office of Science and Engineering Laboratories United States Department of Biomedical Engineering King’s College London Alan Turing Institute United Kingdom Dynamics Research Group Department of Mechanical Engineering University of Sheffield United Kingdom School of Mathematics and Statistics University of Sheffield United Kingdom

Uncertainty quantification (UQ) is a vital step in using mathematical models and simulations to take decisions. The field of cardiac simulation has begun to explore and adopt UQ methods to characterise uncertainty in model inputs and how that propagates through to outputs or predictions. In this perspective piece we draw attention to an important and under-addressed source of uncertainty in our predictions — that of uncertainty in the model structure or the equations themselves. The difference between imperfect models and reality is termed model discrepancy, and we are often uncertain as to the size and consequences of this discrepancy. Here we provide two examples of the consequences of discrepancy when calibrating models at the ion channel and action potential scales. Furthermore, we attempt to account for this discrepancy when calibrating and validating an ion channel model using different methods, based on modelling the discrepancy using Gaussian processes (GPs) and autoregressive-moving-average (ARMA) models, then highlight the advantages and shortcomings of each approach. Finally, suggestions and lines of enquiry for future work are provided. Copyright © 2020, The Authors. All rights reserved.

关键词： Uncertainty analysis

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Comparative cellular analysis of motor cortex in human, marmoset and mouse (vol 598, pg 111, 2021)

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NATURE 2022年第7904期604卷 E8-E8页

作者： Bakken, Trygve E. Jorstad, Nikolas L. Hu, Qiwen Lake, Blue B. Tian, Wei Kalmbach, Brian E. Crow, Megan Hodge, Rebecca D. Krienen, Fenna M. Sorensen, Staci A. Eggermont, Jeroen Yao, Zizhen Aevermann, Brian D. Aldridge, Andrew I. Bartlett, Anna Bertagnolli, Darren Casper, Tamara Castanon, Rosa G. Crichton, Kirsten Daigle, Tanya L. Dalley, Rachel Dee, Nick Dembrow, Nikolai Diep, Dinh Ding, Song-Lin Dong, Weixiu Fang, Rongxin Fischer, Stephan Goldman, Melissa Goldy, Jeff Graybuck, Lucas T. Herb, Brian R. Hou, Xiaomeng Kancherla, Jayaram Kroll, Matthew Lathia, Kanan van Lew, Baldur Li, Yang Eric Liu, Christine S. Liu, Hanqing Lucero, Jacinta D. Mahurkar, Anup McMillen, Delissa Miller, Jeremy A. Moussa, Marmar Nery, Joseph R. Nicovich, Philip R. Niu, Sheng-Yong Orvis, Joshua Osteen, Julia K. Owen, Scott Palmer, Carter R. Pham, Thanh Plongthongkum, Nongluk Poirion, Olivier Reed, Nora M. Rimorin, Christine Rivkin, Angeline Romanow, William J. Sedeno-Cortes, Adriana E. Siletti, Kimberly Somasundaram, Saroja Sulc, Josef Tieu, Michael Torkelson, Amy Tung, Herman Wang, Xinxin Xie, Fangming Yanny, Anna Marie Zhang, Renee Ament, Seth A. Behrens, M. Margarita Bravo, Hector Corrada Chun, Jerold Dobin, Alexander Gillis, Jesse Hertzano, Ronna Hof, Patrick R. Hollt, Thomas Horwitz, Gregory D. Keene, C. Dirk Kharchenko, Peter V. Ko, Andrew L. Lelieveldt, Boudewijn P. Luo, Chongyuan Mukamel, Eran A. Pinto-Duarte, Antonio Preiss, Sebastian Regev, Aviv Ren, Bing Scheuermann, Richard H. Smith, Kimberly Spain, William J. White, Owen R. Koch, Christof Hawrylycz, Michael Tasic, Bosiljka Macosko, Evan Z. McCarroll, Steven A. Ting, Jonathan T. Zeng, Hongkui Zhang, Kun Feng, Guoping Ecker, Joseph R. Linnarsson, Sten Lein, Ed S. Allen Institute for Brain Science Seattle WA USA Department of Physiology and Biophysics University of Washington Seattle WA USA Department of Biomedical Informatics Harvard Medical School Boston MA USA Department of Bioengineering University of California San Diego La Jolla CA USA The Salk Institute for Biological Studies La Jolla CA USA Epilepsy Center of Excellence Department of Veterans Affairs Medical Center Seattle WA USA Stanley Institute for Cognitive Genomics Cold Spring Harbor Laboratory Cold Spring Harbor NY USA Department of Genetics Harvard Medical School Boston MA USA Broad Institute of MIT and Harvard Cambridge MA USA LKEB Department of Radiology Leiden University Medical Center Leiden The Netherlands Pattern Recognition and Bioinformatics group Delft University of Technology Delft The Netherlands J. Craig Venter Institute La Jolla CA USA Department of Pathology University of California San Diego CA USA Division of Vaccine Discovery La Jolla Institute for Immunology La Jolla CA USA Genomic Analysis Laboratory The Salk Institute for Biological Studies La Jolla CA USA Computer Science and Engineering Program University of California San Diego La Jolla CA USA Howard Hughes Medical Institute The Salk Institute for Biological Studies La Jolla CA USA Bioinformatics and Systems Biology Graduate Program University of California San Diego La Jolla CA USA Institute for Genomes Sciences University of Maryland School of Medicine Baltimore MD USA Center for Epigenomics Department of Cellular and Molecular Medicine University of California San Diego La Jolla CA USA Ludwig Institute for Cancer Research La Jolla CA USA Department of Computer Science University of Maryland College Park College Park MD USA Sanford Burnham Prebys Medical Discovery Institute La Jolla CA USA Biomedical Sciences Program School of Medicine University of California San Diego La Jolla CA USA University of Connecticut Storrs CT USA Department

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Democratising Knowledge Representation with BioCypher

arXiv

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arXiv 2022年

作者： Lobentanzer, Sebastian Aloy, Patrick Baumbach, Jan Bohar, Balazs Charoentong, Pornpimol Danhauser, Katharina Doğan, Tunca Dreo, Johann Dunham, Ian Fernandez-Torras, Adrià Gyori, Benjamin M. Hartung, Michael Hoyt, Charles Tapley Klein, Christoph Korcsmaros, Tamas Maier, Andreas Mann, Matthias Ochoa, David Pareja-Lorente, Elena Popp, Ferdinand Preusse, Martin Probul, Niklas Schwikowski, Benno Sen, Bünyamin Strauss, Maximilian T. Turei, Denes Ulusoy, Erva Heidrun Wodke, Judith Andrea Saez-Rodriguez, Julio Heidelberg University Faculty of Medicine Heidelberg University Hospital Institute for Computational Biomedicine Bioquant Heidelberg Germany The Barcelona Institute of Science and Technology Catalonia Barcelona Spain Catalonia Barcelona Spain Institute for Computational Systems Biology University of Hamburg Germany Earlham Institute Norwich United Kingdom Biological Research Centre Szeged Hungary Heidelberg University Im Neuenheimer Feld 267 Heidelberg69120 Germany Im Neuenheimer Feld 460 Heidelberg69120 Germany Department of Pediatrics Dr. von Hauner Children’s Hospital University Hospital LMU Munich Germany Biological Data Science Lab Department of Computer Engineering Hacettepe University Ankara Turkey Department of Bioinformatics Graduate School of Health Sciences Hacettepe University Ankara Turkey Computational Systems Biomedicine Lab Department of Computational Biology Institut Pasteur Université Paris Cité Paris France Bioinformatics and Biostatistics Hub Institut Pasteur Université Paris Cité Paris France Wellcome Genome Campus Cambridgeshire HinxtonCB10 1SD United Kingdom Open Targets Wellcome Genome Campus Cambridgeshire HinxtonCB10 1SD United Kingdom Laboratory of Systems Pharmacology Harvard Medical School Boston United States Imperial College London London United Kingdom Quadram Institute Bioscience Norwich United Kingdom Proteomics Program Novo Nordisk Foundation Centre for Protein Research University of Copenhagen Copenhagen Denmark Department of Proteomics and Signal Transduction Max Planck Institute of Biochemistry Martinsried Germany Im Neuenheimer Feld 460 Heidelberg69120 Germany Neuherberg Germany Medical Informatics Laboratory University Medicine Greifswald Germany

Standardising the representation of biomedical knowledge among all researchers is an insurmountable task, hindering the effectiveness of many computational methods. To facilitate harmonisation and interoperability despite this fundamental challenge, we propose to standardise the framework of knowledge graph creation instead. We implement this standardisation in BioCypher, a FAIR (findable, accessible, interoperable, reusable) framework to transparently build biomedical knowledge graphs while preserving provenances of the source data. Mapping the knowledge onto biomedical ontologies helps to balance the needs for harmonisation, human and machine readability, and ease of use and accessibility to nonspecialist researchers. We demonstrate the usefulness of this framework on a variety of use cases, from maintenance of task-specific knowledge stores, to interoperability between biomedical domains, to on-demand building of task-specific knowledge graphs for federated learning. BioCypher (https://***) frees up valuable developer time;we encourage further development and usage by the community. © 2022, CC BY-NC-ND.

关键词： Ontology

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Real-time optimization using gradient adaptive selection and classification from infrared sensors measurement for esterification oleic acid with glycerol

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International Journal of Intelligent Computing and Cybernetics 2017年第2期10卷 130-144页

作者： Iwan Aang Soenandi Taufik Djatna Ani Suryani Irzaman Post Graduate Program of Agro-industrial Technology Bogor Agricultural UniversityBogorIndonesia and Faculty of Engineering and Computer ScienceKrida Wacana Christian UniversityJakartaIndonesia Post Graduate Program of Agro-industrial Technology Bogor Agricultural UniversityBogorIndonesia Department of Physics Faculty of Mathematics and Natural SciencesBogor Agricultural UniversityBogorIndonesia

Purpose-The production of glycerol derivatives by the esterification process is subject to many constraints related to the yield of the production target and the lack of process *** accurate monitoring and controlling of the process can improve production yield and *** purpose of this paper is to propose a real-time optimization(RTO)using gradient adaptive selection and classification from infrared sensor measurement to cover various disturbances and uncertainties in the ***/methodology/approach-The integration of the esterification process optimization using self-optimization(SO)was developed with classification process was combined with necessary condition optimum(NCO)as gradient adaptive selection,supported with laboratory scaled medium wavelength infrared(mid-IR)sensors,and measured the proposed optimization system indicator in the batch *** Process Modeling and Notation(BPMN 2.0)was built to describe the tasks of SO workflow in collaboration with NCO as an abstraction for the conceptual ***,Stateflow modeling was deployed to simulate the three states of gradient-based adaptive control combined with support vector machine(SVM)classification and Arduino microcontroller for ***-This new method shows that the real-time optimization responsiveness of control increased product yield up to 13 percent,lower error measurement with percentage error 1.11 percent,reduced the process duration up to 22 minutes,with an effective range of stirrer rotation set between 300 and 400 rpm and final temperature between 200 and 210℃ which was more efficient,as it consumed less *** limitations/implications-In this research the authors just have an experiment for the esterification process using glycerol,but as a development concept of RTO,it would be possible to apply for another chemical reaction or *** implications-This research introduces new development of an RTO approach to optimal con

关键词： Gradient technique Infrared sensor Real-time optimization Simulation and modelling Support vector machine

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Retracted: Implementation Method CUSUM to Determine the Accident Prone Areas in Web Based

Retracted: Implementation Method CUSUM to Determine the Acci...

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2018 Workshop on Multidisciplinary and Its Applications: Applied Mathematics, computer science, Information Systems, and Information Technology, WMA-Mathcomtech 2018

作者： Dinata, Rozzi Kesuma Abdullah, Dahlan Hartono, H. Erliana, Cut Ita Riasti, Berliana Kusuma Iskandar, Akbar Sari, Ifit Novita Nurmawati, N. Nanuru, Ricardo Freedom Putri, Lusi Dwi Manurung, Rosida Tiurma Sriadhi, S. Saleh, A.A. Astari, T. Khaddafi, Muammar Department of Informatics Universitas Malikussaleh Aceh Indonesia Department of Computer Science STMIK IBBI Medan Indonesia Department of Industrial Engineering Universitas Malikussaleh Aceh Indonesia Department of Informatics Universitas Sebelas Maret Surakarta Indonesia Department of Informatics STMIK AKBA Makassar Indonesia Departement Of: Social Science Education Program Post Graduate Program Universitas Kanjuruhan Malang Malang Indonesia Faculty of Industry Technique University of 45 Surabaya Indonesia Universitas Kristen Indonesia Maluku Ambon Indonesia Department of Civil Engineering Universitas Lancang Kuning Pekanbaru Indonesia Graduate Program in Scientific Psychology Universitas Kristen Maranatha Indonesia Department of Electrical Engineering Universitas Negeri Medan Indonesia Statistics Financial and Social Sciences Research Group Indonesia Department of Elementary School Teacher Education STKIP Citra Bangsa Aceh Utara Indonesia Department of Accounting Universitas Malikussaleh Aceh Indonesia

At the Unit Laka Lantas Polres Lhokseumawe determining accident-prone areas on roads in Lhokseumawe still using manual systems. Determination of accident-prone areas are less effective because the police Unit Laka Lantas Polres Lhokseumawe just using the data of the last year and had to repeatedly calculate manually accident-prone areas based on the number of human casualties. In this study the system implementation CUSUM method (Cummulative Summary) to determine the accident-prone areas designed using the web-based programming language PHP. In this system there are three processes to determine areas prone to accidents, the accident rate calculations based on the weighted severity, blacksite calculations using the Z-Score method for determining areas prone to accident blackspots and calculations using the CUSUM method to determine the critical points of an accident. The data used are secondary data obtained from the Police Unit Laka Lantas Polres Lhokseumawe years 2009-2013. © Published under licence by IOP Publishing Ltd.

关键词： Accidents

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Incremental Gaussian Granular Fuzzy Modeling Applied to Hurricane Track Forecasting

Incremental Gaussian Granular Fuzzy Modeling Applied to Hurr...

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IEEE International Conference on Fuzzy Systems

作者： Eduardo A. Soares Heloisa A. Camargo Suzana J. Camargo Daniel F. Leite Graduate Program in Computer Science of the Federal University Sao Carlos BRA Division of Ocean and Climate Physics Lamont-Doherty Earth Observatory Columbia University Department of Engineering Federal University Lavras BRA

This paper presents a Gaussian fuzzy set-based evolving modeling method, FBeM-G, to predict tropical cyclone tracks 6 hours in advance. FBeM-G summarizes similar data into Gaussian granules evolved from a sequence of data. It uses a recursive learning algorithm to update its parameters and structure over time and therefore is able to cope with nonstationarities. Past values of latitude, longitude, maximum sustained wind, pressure and wind radii in different quadrants of the Katrina, Sandy and Wilma tropical cyclones were obtained from the 'best track' analysis provided by the National Hurricane Center (NOAA). An ensemble of cloud-based and fuzzy models was considered to compare the estimated tracks. FBeM-G provided more accurate 6-hourly track estimates using a smaller number of local models and parameters. Although less accurate, longer-term estimates given by the ensemble approach became closer to those provided by FBeM-G. An outer approximation of the pointwise track prediction is a particular characteristic of the method that is useful to determine risk areas and actions to be taken.

关键词： Data models Tropical cyclones Adaptation models Atmospheric modeling Predictive models Prediction algorithms Hurricanes

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Superiorization of preconditioned conjugate gradient algorithms for tomographic image reconstruction

arXiv

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arXiv 2018年

作者： Helou, Elias S. Herman, Gabor T. Lin, Chuan Zibetti, Marcelo V.W. Institute of Mathematical Science and Computation University of São Paulo SP Brazil Department of Computer Science Graduate Center City University of New York NY United States School of Electrical Engineering Southwest Jiaotong University Chengdu China Program in Electrical and Computer Engineering Federal University of Technology PR Brazil

Properties of Superiorized Preconditioned Conjugate Gradient (SupPCG) algorithms in image reconstruction from projections are examined. Least squares (LS) is usually chosen for measuring data-inconsistency in these inverse problems. Preconditioned Conjugate Gradient algorithms are fast methods for finding an LS solution. However, for ill-posed problems, such as image reconstruction, an LS solution may not provide good image quality. This can be taken care of by superiorization. A superiorized algorithm leads to images with the value of a secondary criterion (a merit function such as the total variation) improved as compared to images with similar data-inconsistency obtained by the algorithm without superiorization. Numerical experimentation shows that SupPCG can lead to high-quality reconstructions within a remarkably short time. A theoretical analysis is also provided.15A29, 65F22, 65F10, 94A08 Copyright © 2018, The Authors. All rights reserved.

关键词： Image reconstruction

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Light-Based Analog Computing Using a Single Array of Polarizable Particles 12

Light-Based Analog Computing Using a Single Array of Polariz...

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12th International Congress on Artificial Materials for Novel Wave Phenomena, METAMATERIALS 2018

作者： Rardi, Y. Alu, A. Department of Electrical and Computer Engineering University of Texas at Austin AustinTX78712 United States Photonics Initiative Advanced Science Research Center City University of New York New YorkNY10031 United States Physics Program Graduate Center City University of New York New YorkNY10016 United States Department of Electrical Engineering City College of New York New YorkNY10031 United States

ISBN: (纸本)9781538647028

Light-based signal processing in the spatial domain enables parallel computation, resulting in faster operations in comparison to digital-based systems. We propose a basic platform to realize spatial differentiation and integration of the impinging wavefront using a basic array of electric/magnetic dipoles. We also leverage bianisotropic inclusions to realize odd operations on the impinging wavefront. Our results show that a single array of polarizable particles enables sufficient degrees of freedom to realize optical analog computing using metasurfaces. © 2018 IEEE.

关键词： Wavefronts

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Metagratings for Efficient Wavefront Manipulation 12

Metagratings for Efficient Wavefront Manipulation

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12th International Congress on Artificial Materials for Novel Wave Phenomena, METAMATERIALS 2018

ISBN: (纸本)9781538647028

Metagratings are two-dimensional periodic arrays of individual scatterers that enable highly-efficient extreme wave transformation which was impossible using conventional metasurfaces. We review our recent progress in this area and, notably, discuss metagrating designs based on asymmetric electric dipoles that are practically easier to realize compared to bianisotropic inclusions. In addition, we present the design of a tunable metagrating based on graphene strips. It will be shown that the proposed structure can provide multiple functionalities by tuning just two bias voltages. The efficiency of the proposed design is only limited by dissipation in graphene. © 2018 IEEE.

关键词： Graphene

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Stakeholder Act as an IT and General Compliance Auditor

Stakeholder Act as an IT and General Compliance Auditor

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International Conference on Sustainable Information engineering and Technology (SIET)

作者： Surjandy Erick Fernando Meyliana Raymond Kosala Suhono Harso Supangkat Diani Dwiningrum Merry Marshela Angelica Renita Amalia Information Systems Audit Program Information Systems Department Bina Nusantara University Jakarta Indonesia Information Systems Departement Bina Nusantara University Jakarta Indonesia Computer Science Department BINUS Graduate Program - Doctor of Computer Science Bina Nusantara University Jakarta Indonesia School of Electrical Engineering and Informatics Institut Teknologi Bandung Bandung Indonesia

ISBN: (纸本)9781538674086;9781538674079

Recently, the Indonesian government requires auditors, the need for auditors around 40,000 auditors in 2016, currently has only about 10,800 auditors, however, the lack of the auditors impacting the risk of financial loss for the state. Referring to the problem, this experimental research was conducted. The experiment of the research was conducted two times and the audit topic is a compliance audit in the year 2017 and year 2018. The goal of this research is to know, can the stakeholder act as an IT and general compliance auditor? The experiment was conducted by 8 university students in 2017 and 19 university students in 2018, and the supporting tools of audit activities the university student use the smartphone to capture the object as evidence. The experiment results with descriptive method show university students can act as an auditor and found several pieces of evidence that might cause future impact to the institution.

关键词： Regulation Stakeholders Companies Libraries Finance

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