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IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

作者： Yetian Fan Xiaohua Hu Xiwei Tang Qing Ping Wei Wu School of Mathematical Sciences Dalian University of Technology Dalian China College of Computing and Informatics Drexel University Philadelphia PA USA Department of Information Science and Engineering Hunan First Normal University Changsha China

ISBN: (纸本)9781509016129

Essential proteins play a crucial role in the survival and development process of life, as they provide all available nutrients to maintain life. Therefore, many researchers pay attention to the identification of essential proteins. As experiments methods are usually costly and time-consuming, more and more computational algorithms have been developed to discover essential proteins based on biological and topological features. Given that the subcellular localization is very important in understanding protein-protein interaction, in this paper, a novel method is proposed to predict essential proteins, which integrates the subcellular compartments information with Pearson correlation coefficient (PCC) of gene expression data. We name this method SCP in this paper. In order to evaluate the prediction performance of our method, several experiments are carried out to compare SCP with other methods. The results demonstrate that SCP has a better prediction performance of essential proteins than other methods.

关键词： Proteins Gene expression Prediction algorithms Correlation Sparse matrices Databases Fans

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A algorithm for identifying disease genes by incorporating the subcellular localization information into the protein-protein interaction networks

A algorithm for identifying disease genes by incorporating t...

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IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

作者： Xiwei Tang Xiaohua Hu Xuejun Yang Yuan Sun School of Information Science and Engineering Hunan First Normal University Changsha China College of Computer National University of Defense Technology Changsha China College of Computing and Informatics Drexel University Philadelphia PA USA

ISBN: (纸本)9781509016129

Disease gene identification is a key step to understand the cellular mechanisms associated with a specific disease. Compared with biological experiments, computational predictions of disease genes are cheaper and more effortless. Many computational methods are used to detect causal genes for diseases on the protein-protein interaction (PPI) networks generated by the high-throughput technology. However, the accuracy of these methods need to be improved due to the false interactions in the PPI data. To deal with the challenge, other methods are proposed via the integration of biological information from different sources with the PPI networks. In this work, a new algorithm AIDG is developed to predict disease genes. First, the weighted PPI networks are built by incorporating the protein subcellular localization information into the human PPI networks. Next, all of disease candidate genes are scored in terms of a iteration function. Finally, they are ranked on descending order of their scores. The top candidates are considered as potential disease genes. The results from the leave-one-out crossing validation (LOOCV) show that AIDG outperforms other similar methods like DADA and ToppNet.

关键词： Proteins Databases Cancer Training Bioinformatics Protein engineering

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Topic Discovery from Heterogeneous Texts

Topic Discovery from Heterogeneous Texts

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International Conference on Tools for Artificial Intelligence (ICTAI)

作者： Jipeng Qiang Ping Chen Wei Ding Tong Wang Fei Xie Xindong Wu School of Computer Science and Information Engineering Hefei University of Technology Hefei China Department of Computer Science University of Massachusetts Boston Boston MA Department of Computer Science and Technology Hefei Normal University Hefei China School of Computing and Informatics University of Louisiana at Lafayette Lafayette Louisiana

ISBN: (纸本)9781509044603

Recently many topic models such as Latent Dirich-let Allocation (LDA) have made important progress towards generating high-level knowledge from a large corpus. They assume that a text consists of a mixture of topics, which is usually the case for regular articles but may not hold for a short text that usually contains only one topic. In practice, a corpus may include both short texts and long texts, in this case neither methods developed for only long texts nor methods for only short texts can generate satisfying results. In this paper, we present an innovative method to discover latent topics from a heterogeneous corpus including both long and short texts. A new topic model based on collapsed Gibbs sampling algorithm is developed for modeling such heterogeneous texts. The experiments on real-world datasets validate the effectiveness of the proposed model in comparison with other state-of-the-art models.

关键词： Rockets Companies Solid modeling Twitter Headphones Mobile communication Computer science

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Antipattern and Code Smell False Positives: Preliminary Conceptualization and Classification

Antipattern and Code Smell False Positives: Preliminary Conc...

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IEEE International Conference on Software Analysis, Evolution and Reengineering (SANER)

作者： Francesca Arcelli Fontana Jens Dietrich Bartosz Walter Aiko Yamashita Marco Zanoni Department of Informatics Systems and Communication University of Milano-Bicocca Milano Italy School of Engineering and Advanced Technology Massey University Palmerston North New Zealand Faculty of Computing Poznań University of Technology Poznań Poland Department of Information Technology Oslo and Akershus University Oslo Norway

Anti-patterns and code smells are archetypes used for describing software design shortcomings that can negatively affect software quality, in particular maintainability. Tools, metrics and methodologies have been developed to identify these archetypes, based on the assumption that they can point at problematic code. However, recent empirical studies have shown that some of these archetypes are ubiquitous in real world programs, and many of them are found not to be as detrimental to quality as previously conjectured. We are therefore interested in revisiting common anti-patterns and code smells, and building a catalogue of cases that constitute candidates for "false positives". We propose a preliminary classification of such false positives with the aim of facilitating a better understanding of the effects of anti-patterns and code smells in practice. We hope that the development and further refinement of such a classification can support researchers and tool vendors in their endeavour to develop more pragmatic, context-relevant detection and analysis tools for anti-patterns and code smells.

关键词： Production facilities Generators Software quality Graphical user interfaces Maintenance engineering Systematics Concrete

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PennyLane: Automatic differentiation of hybrid quantum-classical computations

arXiv

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arXiv 2018年

作者： Bergholm, Ville Izaac, Josh Schuld, Maria Gogolin, Christian Ahmed, Shahnawaz Ajith, Vishnu Alam, M. Sohaib Alonso-Linaje, Guillermo AkashNarayanan, B. Asadi, Ali Arrazola, Juan Miguel Azad, Utkarsh Banning, Sam Blank, Carsten Bromley, Thomas R. Cordier, Benjamin A. Ceroni, Jack Delgado, Alain Matteo, Olivia Di Dusko, Amintor Garg, Tanya Guala, Diego Hayes, Anthony Hill, Ryan Ijaz, Aroosa Isacsson, Theodor Ittah, David Jahangiri, Soran Jain, Prateek Jiang, Edward Khandelwal, Ankit Kottmann, Korbinian Lang, Robert A. Lee, Christina Loke, Thomas Lowe, Angus McKiernan, Keri Meyer, Johannes Jakob Montañez-Barrera, J.A. Moyard, Romain Niu, Zeyue O’Riordan, Lee James Oud, Steven Panigrahi, Ashish Park, Chae-Yeun Polatajko, Daniel Quesada, Nicolás Roberts, Chase Sá, Nahum Schoch, Isidor Shi, Borun Shu, Shuli Sim, Sukin Singh, Arshpreet Strandberg, Ingrid Soni, Jay Száva, Antal Thabet, Slimane Vargas-Hernández, Rodrigo A. Vincent, Trevor Vitucci, Nicola Weber, Maurice Wierichs, David Wiersema, Roeland Willmann, Moritz Wong, Vincent Zhang, Shaoming Killoran, Nathan Xanadu 777 Bay Street Toronto Canada Wallenberg Centre for Quantum Technology Department of Microtechnology and Nanoscience Chalmers University of Technology Gothenburg412 96 Sweden Indian Institute of Information Technology Kottayam India NASA Ames Research Center Moffett FieldCA94035 United States Mountain ViewCA94043 United States data cybernetics Martin-Kolmsperger-Str 26 Landsberg86899 Germany Department of Medical Informatics and Clinical Epidemiology Oregon Health and Science University PortlandOR97202 United States Dept. of Electrical and Computer Engineering The University of British Columbia VancouverBCV6T 1Z4 Canada Department of Physics Indian Institute of Technology Roorkee Uttarakhand Roorkee India qBraid 5235 South Harper Court ChicagoIL60615 United States Factal Analytics Level 2 Chimes Building Plot 61 Sector - 44 Haryana Gurgaon122003 India Centre for High Energy Physics Indian Institute of Science Karnataka Bengaluru560012 India ICFO - Institut de Ciencies Fotoniques The Barcelona Institute of Science and Technology Av. Carl Friedrich Gauss 3 Castelldefels Barcelona08860 Spain Chemical Physics Theory Group Department of Chemistry University of Toronto Canada DUG Technology 76 Kings Park Rd West PerthWA6005 Australia Rigetti Computing 2919 Seventh Street BerkeleyCA94710 United States Dahlem Center for Complex Quantum Systems Freie Universität Berlin Berlin14195 Germany Institute for Advanced Simulation Jülich Supercomputing Centre Forschungszentrum Jülich Jülich52425 Germany University of Amsterdam Netherlands School of Physical Sciences National Institute of Science Education and Research HBNI Odisha Jatni752 050 India Cervest United Kingdom Centro Brasileiro de Pesquisas Físicas Rua Dr. Xavier Sigaud 150 Rio de Janeiro22290-180 Brazil Zurich8092 Switzerland Neo4j UK Ltd United Kingdom Zapata Computing Inc. United States ITC Infotech Bangalore India Department of Microtechnology and Nanoscienc

PennyLane is a Python 3 software framework for differentiable programming of quantum computers. The library provides a unified architecture for near-term quantum computing devices, supporting both qubit and continuous-variable paradigms. PennyLane’s core feature is the ability to compute gradients of variational quantum circuits in a way that is compatible with classical techniques such as backpropagation. PennyLane thus extends the automatic differentiation algorithms common in optimization and machine learning to include quantum and hybrid computations. A plugin system makes the framework compatible with any gate-based quantum simulator or hardware. We provide plugins for hardware providers including the Xanadu Cloud, Amazon Braket, and IBM Quantum, allowing PennyLane optimizations to be run on publicly accessible quantum devices. On the classical front, PennyLane interfaces with accelerated machine learning libraries such as TensorFlow, PyTorch, JAX, and Autograd. PennyLane can be used for the optimization of variational quantum eigensolvers, quantum approximate optimization, quantum machine learning models, and many other applications. Copyright © 2018, The Authors. All rights reserved.

关键词： Machine learning

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Evaluation of wavelet transform families in image resolution enhancement 2

Evaluation of wavelet transform families in image resolution...

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2nd IET International Conference on Intelligent Signal Processing 2015, ISP 2015

作者： Bagheri Zadeh, P. Sheikh Akbari, A. School of Computer Science and Informatics Faculty of Technology De Montfort University United Kingdom School of Computing Creative Technology and Engineering Leeds Beckett University United Kingdom

ISBN: (纸本)9781785611360

Wavelet transform have been used in many image enlargement techniques and shows superior results compared to conventional image resolution enhancement techniques. However, the choice of wavelets for image enlargement has not been fully investigated. This paper presents an investigation on the performance of a generic wavelet based image enlargement technique, with respect to the choice of wavelets. A Wavelet based image enlargement technique using cycle-spinning is employed for the purpose of this investigation. Different wavelet transforms from wavelet transform families such as Daubechies, symlet, Coiflet, Biorthogonal, Reverse Biorthogonal and Discrete Meyer wavelets are used in this investigation. A summary of the process for this investigation is as follows: A high resolution image is first generated from an input low resolution image, using an inverse wavelet transform, where the coefficients in high frequency subbands are sets to zero. The cycle spinning method is then used to remove the ringing artefacts of the resulting high-resolution image. The generated results indicate that the performance of the image enlargement technique is a function of the chosen wavelet and also the frequency components or texture of the image. Results implies that the enlargement method produces superior results using Daubechi 9/7 and Symlet 2 wavelets, when enlarging images containing significantly higher frequency components. The technique generates superior results when dealing with images containing lower high frequency components using Daubechi 9/7 and LeGall 5/3.

关键词： Discrete wavelet transforms

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Screening Interacting Factors in a Wireless Network Testbed Using Locating Arrays

Screening Interacting Factors in a Wireless Network Testbed ...

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IEEE Conference on Computer Communications Workshops

作者： Randy Compton Michael T. Mehari Charles J. Colbourn Eli De Poorter Violet R. Syrotiuk School of Computing Informatics and Decision Systems Engineering Arizona State University Tempe USA 85287-8809 Ghent University - iMinds Department of Information Technology (INTEC) Gaston Crommenlaan 8 (Bus 201) B-9050 Belgium

ISBN: (纸本)9781467399562

Wireless systems exhibit a wide range of configurable parameters (factors), each with a number of values (levels), that may influence performance. Exhaustively analyzing all factor interactions is typically not feasible in experimental systems due to the large design space. We propose a method for determining which factors play a significant role in wireless network performance with multiple performance metrics (response variables). Such screening can be used to reduce the set of factors in subsequent experimental testing, whether for modelling or optimization. Our method accounts for pairwise interactions between the factors when deciding significance, because interactions play a significant role in real-world systems. We utilize locating arrays to design the experiment because they guarantee that each pairwise interaction impacts a distinct set of tests. We formulate the analysis as a problem in compressive sensing that we solve using a variation of orthogonal matching pursuit, together with statistical methods to determine which factors are significant. We evaluate the method using data collected from the w-iLab.t Zwijnaarde wireless network testbed and construct a new experiment based on the first analysis to validate the results. We find that the analysis exhibits robustness to noise and to missing data.

关键词： Data models Wireless networks Matching pursuit algorithms IEEE 802.11 Standard Compressed sensing Arrays

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Erratum to: Measurement of differential cross sections and W+/W− cross-section ratios for W boson production in association with jets at = 8 TeV with the ATLAS detector

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Journal of High Energy Physics 2020年第10期2020卷 1-20页

作者： Aaboud, M. Aad, G. Abbott, B. Abdinov, O. Abeloos, B. Abidi, S. H. AbouZeid, O. S. Abraham, N. L. Abramowicz, H. Abreu, H. Abreu, R. Abulaiti, Y. Acharya, B. S. Adachi, S. Adamczyk, L. Adelman, J. Adersberger, M. Adye, T. Affolder, A. A. Afik, Y. Agheorghiesei, C. Aguilar-Saavedra, J. A. Ahlen, S. P. Ahmadov, F. Aielli, G. Akatsuka, S. Akerstedt, H. Åkesson, T. P. A. Akilli, E. Akimov, A. V. Alberghi, G. L. Albert, J. Albicocco, P. Alconada Verzini, M. J. Alderweireldt, S. C. Aleksa, M. Aleksandrov, I. N. Alexa, C. Alexander, G. Alexopoulos, T. Alhroob, M. Ali, B. Aliev, M. Alimonti, G. Alison, J. Alkire, S. P. Allbrooke, B. M. M. Allen, B. W. Allport, P. P. Aloisio, A. Alonso, A. Alonso, F. Alpigiani, C. Alshehri, A. A. Alstaty, M. I. Alvarez Gonzalez, B. Álvarez Piqueras, D. Alviggi, M. G. Amadio, B. T. Amaral Coutinho, Y. Amelung, C. Amidei, D. Amor Dos Santos, S. P. Amoroso, S. Anastopoulos, C. Ancu, L. S. Andari, N. Andeen, T. Anders, C. F. Anders, J. K. Anderson, K. J. Andreazza, A. Andrei, V. Angelidakis, S. Angelozzi, I. Angerami, A. Anisenkov, A. V. Anjos, N. Annovi, A. Antel, C. Antonelli, M. Antonov, A. Antrim, D. J. Anulli, F. Aoki, M. Aperio Bella, L. Arabidze, G. Arai, Y. Araque, J. P. Araujo Ferraz, V. Arce, A. T. H. Ardell, R. E. Arduh, F. A. Arguin, J-F. Argyropoulos, S. Arik, M. Armbruster, A. J. Armitage, L. J. Arnaez, O. Arnold, H. Arratia, M. Arslan, O. Artamonov, A. Artoni, G. Artz, S. Asai, S. Asbah, N. Ashkenazi, A. Asquith, L. Assamagan, K. Astalos, R. Atkinson, M. Atlay, N. B. Augsten, K. Avolio, G. Axen, B. Ayoub, M. K. Azuelos, G. Baas, A. E. Baca, M. J. Bachacou, H. Bachas, K. Backes, M. Bagnaia, P. Bahmani, M. Bahrasemani, H. Baines, J. T. Bajic, M. Baker, O. K. Bakker, P. J. Baldin, E. M. Balek, P. Balli, F. Balunas, W. K. Banas, E. Bandyopadhyay, A. Banerjee, Sw. Bannoura, A. A. E. Barak, L. Barberio, E. L. Barberis, D. Barbero, M. Barillari, T. Barisits, M-S Barkeloo, J. T. Barklow, T. Barlow, N. Barnes, S. L. Barnett, B. M. Barnett, R. M. Barnovska-Blenessy, Z. Baroncelli, A. Bar Faculté des Sciences Université Mohamed Premier and LPTPM Oujda Morocco CPPM Aix-Marseille Université and CNRS/IN2P3 Marseille France Homer L. Dodge Department of Physics and Astronomy University of Oklahoma Norman United States of America Institute of Physics Azerbaijan Academy of Sciences Baku Azerbaijan LAL Univ. Paris-Sud CNRS/IN2P3 Université Paris-Saclay Orsay France Department of Physics University of Toronto Toronto Canada Santa Cruz Institute for Particle Physics University of California Santa Cruz Santa Cruz United States of America Department of Physics and Astronomy University of Sussex Brighton United Kingdom Raymond and Beverly Sackler School of Physics and Astronomy Tel Aviv University Tel Aviv Israel Department of Physics Technion: Israel Institute of Technology Haifa Israel Center for High Energy Physics University of Oregon Eugene United States of America Department of Physics Stockholm University Stockholm Sweden The Oskar Klein Centre Stockholm Sweden INFN Gruppo Collegato di Udine Sezione di Trieste Udine Italy ICTP Trieste Italy Department of Physics King’s College London London United Kingdom International Center for Elementary Particle Physics and Department of Physics The University of Tokyo Tokyo Japan AGH University of Science and Technology Faculty of Physics and Applied Computer Science Krakow Poland Department of Physics Northern Illinois University DeKalb United States of America Fakultät für Physik Ludwig-Maximilians-Universität München München Germany Particle Physics Department Rutherford Appleton Laboratory Didcot United Kingdom Department of Physics Alexandru Ioan Cuza University of Iasi Iasi Romania Laboratório de Instrumentação e Física Experimental de Partículas — LIP Lisboa Portugal Departamento de Fisica Teorica y del Cosmos Universidad de Granada Granada Portugal Department of Physics Boston University Boston United States of America Joint Institute for Nuclear Research JINR Dubna Dubna Russia IN

Two additions impacting tables 3 and 4 in ref. [1] are presented in the following. No significant impact is found for other results or figures in ref. [1].

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HEVC based stereo video codec 2

HEVC based stereo video codec

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2nd IET International Conference on Intelligent Signal Processing 2015, ISP 2015

作者： Mallik, B. Sheikh Akbari, A. Bagheri Zadeh, P. School of Computing Creative Technology and Engineering Leeds Beckett University United Kingdom School of Computer Science and Informatics De Montfort University United Kingdom

ISBN: (纸本)9781785611360

Development of stereo video codecs in latest multi-view extension of HEVC (MV-HEVC) with higher compression efficiency has been an active area of research. In this paper, a frame interleaved stereo video coding scheme based on MVHEVC standard codec is proposed. The proposed codec applies a reduced layer approach to encode the frame interleaved stereo sequences. A frame interleaving algorithm is developed to reorder the stereo video frames into a monocular video, such that the proposed codec can gain advantage from inter-views and temporal correlations to improve its coding performance. To evaluate the performance of the proposed codec;three standard multi-view test video sequences, named "Poznan-Street", "Kendo" and "Newspaper1", were selected and coded using the proposed codec and the standard MV-HEVC codec at different QPs and bitrates. Experimental results show that the proposed codec gives a significantly higher coding performance to that of the standard MV-HEVC codec at all bitrates.

关键词： Image compression

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Publisher Correction: The tuatara genome reveals ancient features of amniote evolution

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Nature 2020年第7823期585卷 E3页

作者： Neil J Gemmell Kim Rutherford Stefan Prost Marc Tollis David Winter J Robert Macey David L Adelson Alexander Suh Terry Bertozzi José H Grau Chris Organ Paul P Gardner Matthieu Muffato Mateus Patricio Konstantinos Billis Fergal J Martin Paul Flicek Bent Petersen Lin Kang Pawel Michalak Thomas R Buckley Melissa Wilson Yuanyuan Cheng Hilary Miller Ryan K Schott Melissa D Jordan Richard D Newcomb José Ignacio Arroyo Nicole Valenzuela Tim A Hore Jaime Renart Valentina Peona Claire R Peart Vera M Warmuth Lu Zeng R Daniel Kortschak Joy M Raison Valeria Velásquez Zapata Zhiqiang Wu Didac Santesmasses Marco Mariotti Roderic Guigó Shawn M Rupp Victoria G Twort Nicolas Dussex Helen Taylor Hideaki Abe Donna M Bond James M Paterson Daniel G Mulcahy Vanessa L Gonzalez Charles G Barbieri Dustin P DeMeo Stephan Pabinger Tracey Van Stijn Shannon Clarke Oliver Ryder Scott V Edwards Steven L Salzberg Lindsay Anderson Nicola Nelson Clive Stone Department of Anatomy University of Otago Dunedin New Zealand. neil.gemmell@otago.ac.nz. Department of Anatomy University of Otago Dunedin New Zealand. LOEWE-Center for Translational Biodiversity Genomics Senckenberg Museum Frankfurt Germany. South African National Biodiversity Institute National Zoological Garden Pretoria South Africa. School of Life Sciences Arizona State University Tempe AZ USA. School of Informatics Computing and Cyber Systems Northern Arizona University Flagstaff AZ USA. School of Fundamental Sciences Massey University Palmerston North New Zealand. Peralta Genomics Institute Oakland CA USA. School of Biological Sciences The University of Adelaide Adelaide South Australia Australia. Department of Ecology and Genetics - Evolutionary Biology Evolutionary Biology Centre (EBC) Uppsala University Uppsala Sweden. Department of Organismal Biology - Systematic Biology Evolutionary Biology Centre (EBC) Uppsala University Uppsala Sweden. Evolutionary Biology Unit South Australian Museum Adelaide South Australia Australia. Amedes Genetics Amedes Medizinische Dienstleistungen Berlin Germany. Museum für Naturkunde Berlin Leibniz-Institut für Evolutions- und Biodiversitätsforschung an der Humboldt-Universität zu Berlin Berlin Germany. Department of Earth Sciences Montana State University Bozeman MT USA. Department of Biochemistry University of Otago Dunedin New Zealand. European Molecular Biology Laboratory European Bioinformatics Institute Hinxton UK. Section for Evolutionary Genomics The GLOBE Institute Faculty of Health and Medical Sciences University of Copenhagen Copenhagen Denmark. Edward Via College of Osteopathic Medicine Blacksburg VA USA. Center for One Health Research Virginia-Maryland College of Veterinary Medicine Blacksburg VA USA. Institute of Evolution University of Haifa Haifa Israel. Manaaki Whenua - Landcare Research Auckland New Zealand. School of Biological Sciences The University of Auckland Auckland New Z

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

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