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43rd International Conference on Very Large data Bases, VLDB 2017

作者： Chen, Lu Gao, Yunjun Zheng, Baihua Jensen, Christian S. Yang, Hanyu Yang, Keyu College of Computer Science Zhejiang University Hangzhou China The Key Lab of Big Data Intelligent Computing of Zhejiang Province Zhejiang University Hangzhou China School of Information Systems Singapore Management University Singapore Department of Computer Science Aalborg University Denmark

The general notion of a metric space encompasses a diverse range of data types and accompanying similarity measures. Hence, metric search plays an important role in a wide range of settings, including multimedia retrieval, data mining, and data integration. With the aim of accelerating metric search, a collection of pivotbased indexing techniques for metric data has been proposed, which reduces the number of potentially expensive similarity comparisons by exploiting the triangle inequality for pruning and validation. However, no comprehensive empirical study of those techniques exists. Existing studies each offers only a narrower coverage, and they use different pivot selection strategies that affect performance substantially and thus render cross-study comparisons difficult or impossible. We offer a survey of existing pivot-based indexing techniques, and report a comprehensive empirical comparison of their construction costs, update efficiency, storage sizes, and similarity search performance. As part of the study, we provide modifications for two existing indexing techniques to make them more competitive. The findings and insights obtained from the study reveal different strengths and weaknesses of different indexing techniques, and offer guidance on selecting an appropriate indexing technique for a given setting. © 2017 VLDB Endowment.

关键词： data integration

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Complete Characterization of Incorrect Orthology Assignments in Best Match Graphs

arXiv

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arXiv 2020年

作者： Schaller, David Geiß, Manuela Stadler, Peter F. Hellmuth, Marc Max Planck Institute for Mathematics in the Sciences Inselstraße 22 LeipzigD-04103 Germany Bioinformatics Group Department of Computer Science & Interdisciplinary Center for Bioinformatics Universität Leipzig Härtelstraße 16–18 LeipzigD-04107 Germany Software Competence Center Hagenberg GmbH Softwarepark 21 HagenbergA-4232 Austria Halle-Jena-Leipzig Competence Center for Scalable Data Services and Solutions Dresden-Leipzig Leipzig Research Center for Civilization Diseases Centre for Biotechnology and Biomedicine at Leipzig University Universität Leipzig Institute for Theoretical Chemistry University of Vienna Währingerstrasse 17 WienA-1090 Austria Facultad de Ciencias Universidad National de Colombia Sede Bogotá Colombia Santa Fe Insitute 1399 Hyde Park Rd. Santa FeNM87501 United States School of Computing University of Leeds EC Stoner Building LeedsLS2 9JT United Kingdom

Genome-scale orthology assignments are usually based on reciprocal best matches. In the absence of horizontal gene transfer (HGT), every pair of orthologs forms a reciprocal best match. Incorrect orthology assignments therefore are always false positives in the Reciprocal Best Match Graph. We consider duplication/loss scenarios and characterize unambiguous false-positive (u-fp) orthology assignments, that is, edges in the Best Match Graphs (BMGs) that cannot correspond to orthologs for any gene tree that explains the BMG. We characterize u-fp edges in terms of subgraphs of the BMG and show that, given a BMG, there is a unique "augmented tree" that explains the BMG and identifies all u-fp edges in terms of overlapping sets of species in certain subtrees. The augmented tree can be constructed as a refinement of the unique least resolved tree of the BMG in polynomial time. Removal of the u-fp edges from the reciprocal best matches results in a unique orthology *** Codes 92-08, MSC 92D15, MSC 68R01 Copyright © 2020, The Authors. All rights reserved.

关键词： Forestry

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database of parliamentary speeches in Ireland, 1919–2013

Database of parliamentary speeches in Ireland, 1919–2013

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International Conference on the Frontiers and Advances in data science (FADS)

作者： Alexander Herzog Slava J. Mikhaylov School of Computing Clemson University Institute for Analytics and Data Science Department of Government University of Essex

ISBN: (纸本)9781538631492

We present a database of parliamentary debates that contains the complete record of parliamentary speeches from Dail Eireann, the lower house and principal chamber of the Irish parliament, from 1919 to 2013. In addition, the database contains background information on all TDs (Teachta Dala, members of parliament), such as their party affiliations, constituencies and office positions. The current version of the database includes close to 4.5 million speeches from 1,178 TDs. In addition, we also present three applications in which we make use of the new data.

关键词： Speech databases Economic indicators Unemployment Government Finance Estimation

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Benefits from using mixed precision computations in the ELPA-AEO and ESSEX-II eigensolver projects

arXiv

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arXiv 2018年

作者： Alvermann, Andreas Basermann, Achim Bungartz, Hans-Joachim Carbogno, Christian Ernst, Dominik Fehske, Holger Futamura, Yasunori Galgon, Martin Hager, Georg Huber, Sarah Huckle, Thomas Ida, Akihiro Imakura, Akira Kawai, Masatoshi Köcher, Simone Kreutzer, Moritz Kus, Pavel Lang, Bruno Lederer, Hermann Manin, Valeriy Marek, Andreas Nakajima, Kengo Nemec, Lydia Reuter, Karsten Rippl, Michael Röhrig-Zöllner, Melven Sakurai, Tetsuya Scheffler, Matthias Scheurer, Christoph Shahzad, Faisal Brambila, Danilo Simoes Thies, Jonas Wellein, Gerhard University of Greifswald Institute of Physics Köln Germany Technical University of Munich Department of Informatics Fritz Haber Institute of the Max Planck Society Berlin Germany University of Erlangen-Nuremberg High Performance Computing University of Tsukuba Applied Mathematics University of Wuppertal Mathematics and Natural Sciences University of Tokyo Computer Science Technical University of Munich Department of Theoretical Chemistry Max Planck Computing and Data Facility Garching Germany

We first briefly report on the status and recent achievements of the ELPA-AEO (Eigenvalue Solvers for Petaflop Applications - Algorithmic Extensions and Optimizations) and ESSEX II (Equipping Sparse Solvers for Exascale) projects. In both collaboratory efforts, scientists from the application areas, mathematicians, and computer scientists work together to develop and make available efficient highly parallel methods for the solution of eigenvalue problems. Then we focus on a topic addressed in both projects, the use of mixed precision computations to enhance efficiency. We give a more detailed description of our approaches for benefiting from either lower or higher precision in three selected contexts and of the results thus obtained. Copyright © 2018, The Authors. All rights reserved.

关键词： Eigenvalues and eigenfunctions

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Introducing the HOBBIT platform into the Ontology Alignment Evaluation campaign 13

Introducing the HOBBIT platform into the Ontology Alignment ...

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13th International Workshop on Ontology Matching, OM 2018

作者： Jiménez-Ruiz, Ernesto Saveta, Tzanina Zamazal, Ondřej Hertling, Sven Röder, Michael Fundulaki, Irini Ngomo, Axel-Cyrille Ngonga Sherif, Mohamed Ahmed Annane, Amina Bellahsene, Zohra Ben Yahia, Sadok Diallo, Gayo Faria, Daniel Kachroudi, Marouen Khiat, Abderrahmane Lambrix, Patrick Li, Huanyu Mackeprang, Maximilian Mohammadi, Majid Rybinski, Maciej Balasubramani, Booma Sowkarthiga Trojahn, Cassia Alan Turing Institute London United Kingdom Department of Informatics University of Oslo Norway Institute of Computer Science - FORTH Greece University of Economics Prague Czech Republic Data and Web Science Group University of Mannheim Germany Paderborn University Data Science Group Pohlweg 51 PaderbornD-33098 Germany Ecole Nationale Superieure d'Informatique Alger Algeria LIRMM Universit de Montpellier CNRS Montpellier France Université de Tunis El Manar LIPAH-LR 1ES14 Tunis2092 Tunisia BPH Center INSERM U1219 Team ERIAS LaBRI UMR5800 University of Bordeaux France Instituto Gulbenkian de Ciência Portugal Human-Centered Computing Freie Universitat Berlin Berlin4195 Germany Linköping University Swedish e-Science Research Centre Linköping Sweden Delft University of Technology Netherlands Dpto. Lenguajes y Ciencias de la Computación University of Malaga Spain ADVIS Lab. Department of Computer Science University of Illinois Chicago United States Institut de Recherche en Informatique de Toulouse France

This paper describes the Ontology Alignment Evaluation Initiative 2017.5 pre-campaign. Like in 2012, when we transitioned the evaluation to the SEALS platform, we have also conducted a pre-campaign to assess the feasibility of moving to the HOBBIT platform. We report the experiences of this pre-campaign and discuss the future steps for the OAEI. © 2018 CEUR-WS.

关键词： Ontology

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Solution generation through hybrid intelligence and creativity based on investment portfolio

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International Journal of Performability Engineering 2018年第7期14卷 1641-1650页

作者： Liu, Qinyun Zhou, Hua Yang, Hongji Chu, William Cheng Chung Centre for Creative Computing Bath Spa University BathBA2 9BN United Kingdom College of Big Data and Intelligence Engineering Southwest Forestry University Kunming650000 China Department of Informatics University of Leicester LeicesterLE1 7RH United Kingdom Department of Computer Science Tunghai University Taichung40704 Taiwan

Artificial Intelligence (AI) has been developed to be robust on computing. Learning can be achieved by connecting to heterogeneous data using AI algorithms, such as the Artificial Neural Network. Knowledge can be learned, and rules in the database can be discovered by machines through heuristic algorithms. However, creativity has not been achieved by computers like the human brain by using AI algorithms individually. This research serves to explore a method to achieve creative solution generation by utilizing a relationship between intelligence and creativity, assuming intelligence is the subset of creativity. Under this relationship, the computing can be fulfilled using AI algorithms. The theories of achieving creativity is the guidance of this method. © 2018 Totem Publishers Ltd. All rights reserved.

关键词： Neural networks

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Tau-PET signal in Alzheimer’s disease is related to immune activation and synaptic signaling measured with CSF proteomics

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Alzheimer's & Dementia 2023年第S17期19卷

作者： Roos M. Rikken Eleonora M. Vromen Emma M. Coomans Denise Visser Frederik Barkhof Ronald Boellaard Sandeep S.V. Golla Bart N.M. van Berckel Rik Ossenkoppele Anouk den Braber Everard G.B. Vijverberg Wiesje M. van der Flier Yolande A.L. Pijnenburg Charlotte E. Teunissen Pieter Jelle Visser Elsmarieke van de Giessen Betty M. Tijms Amsterdam Neuroscience Brain Imaging Amsterdam Netherlands Radiology & Nuclear Medicine Vrije Universiteit Amsterdam Amsterdam UMC location VUmc Amsterdam Netherlands Correspondece Alzheimer Center Amsterdam Neurology Vrije Universiteit Amsterdam Amsterdam UMC location VUmc Amsterdam Netherlands Amsterdam Neuroscience Neurodegeneration Amsterdam Netherlands Queen Square Institute of Neurology and Centre for Medical Image Computing University College London United Kingdom Clinical Memory Research Unit Lund University Lund Sweden Biological Psychiatry Vrije Universiteit Amsterdam Amsterdam Netherlands Epidemiology and Data Science Vrije Universiteit Amsterdam Amsterdam UMC location VUmc Amsterdam Netherlands Amsterdam Neuroscience Neurodegeneration Amsterdam Noord-Holland Netherlands Alzheimer Center Amsterdam Neurology Vrije Universiteit Amsterdam Amsterdam UMC location VUmc Amsterdam Noord-Holland Netherlands Alzheimer Center Amsterdam Neurology Amsterdam UMC Amsterdam Netherlands Neurochemistry laboratory Clinical Chemistry Amsterdam UMC location VUmc Amsterdam Netherlands Center for Alzheimer Research Karolinska Institutet Division of Clinical Geriatrics Department of Neurobiology Care Sciences and Society Stockholm Sweden Alzheimer Center Limburg School for Mental Health and Neuroscience (MHeNs) Maastricht University Maastricht Netherlands

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Rapid simulation of glycoprotein structures by grafting and steric exclusion of glycan conformer libraries

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Cell 2024年第5期187卷 1296-1311.e26页

作者： Yu-Xi Tsai Ning-En Chang Klaus Reuter Hao-Ting Chang Tzu-Jing Yang Sören von Bülow Vidhi Sehrawat Noémie Zerrouki Matthieu Tuffery Michael Gecht Isabell Louise Grothaus Lucio Colombi Ciacchi Yong-Sheng Wang Min-Feng Hsu Kay-Hooi Khoo Gerhard Hummer Shang-Te Danny Hsu Cyril Hanus Mateusz Sikora Institute of Biological Chemistry Academia Sinica Taipei 11529 Taiwan Institute of Biochemical Sciences National Taiwan University Taipei 10617 Taiwan. Max Planck Computing and Data Facility 85748 Garching Germany. Department of Theoretical Biophysics Max Planck Institute for Biophysics 60438 Frankfurt Germany. Department of Theoretical Biophysics Max Planck Institute for Biophysics 60438 Frankfurt Germany Malopolska Centre of Biotechnology Jagiellonian University 31-007 Kraków Poland. Institute of Psychiatry and Neurosciences of Paris Inserm UMR1266 Université Paris-Cité 75014 Paris France. Hybrid Materials Interfaces Group Faculty of Production Engineering Bremen Center for Computational Materials Science and MAPEX Center for Materials and Processes University of Bremen 28359 Bremen Germany. Institute of Biological Chemistry Academia Sinica Taipei 11529 Taiwan. Institute of Biophysics Goethe University 60438 Frankfurt Germany. Institute of Biochemical Sciences National Taiwan University Taipei 10617 Taiwan International Institute for Sustainability with Knotted Chiral Meta Matter (WPI-SKCM(2)) Hiroshima University Hiroshima 739-8526 Japan. Electronic address: sthsu@gate.sinica.edu.tw. Institute of Psychiatry and Neurosciences of Paris Inserm UMR1266 Université Paris-Cité 75014 Paris France GHU Psychiatrie et Neurosciences de Paris 75014 Paris France. Electronic address: cyril.hanus@inserm.fr. Malopolska Centre of Biotechnology Jagiellonian University 31-007 Kraków Poland. Electronic address: mateusz.sikora@uj.edu.pl.

Most membrane proteins are modified by covalent addition of complex sugars through N- and O-glycosylation. Unlike proteins, glycans do not typically adopt specific secondary structures and remain very mobile, shielding potentially large fractions of protein surface. High glycan conformational freedom hinders complete structural elucidation of glycoproteins. Computer simulations may be used to model glycosylated proteins but require hundreds of thousands of computing hours on supercomputers, thus limiting routine use. Here, we describe GlycoSHIELD, a reductionist method that can be implemented on personal computers to graft realistic ensembles of glycan conformers onto static protein structures in minutes. Using molecular dynamics simulation, small-angle X-ray scattering, cryoelectron microscopy, and mass spectrometry, we show that this open-access toolkit provides enhanced models of glycoprotein structures. Focusing on N-cadherin, human coronavirus spike proteins, and gamma-aminobutyric acid receptors, we show that GlycoSHIELD can shed light on the impact of glycans on the conformation and activity of complex glycoproteins.

关键词： GABAA receptor N-cadherin SAXS coronavirus S protein cryo-EM glycans glycoproteins mass spectrometry molecular dynamics

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Improving individual predictions using social networks assortativity 12

Improving individual predictions using social networks assor...

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12th International Workshop on Self-Organizing Maps and Learning Vector Quantization, Clustering and data Visualization, WSOM 2017

作者： Mulders, Dounia De Bodt, Cyril Bjelland, Johannes Pentland, Alex Sandy Verleysen, Michel De Montjoye, Yves-Alexandre ICTEAM institute Université catholique de Louvain Belgium Telenor Research Norway MIT Media Lab Massachusetts Institute of Technology United States Data Science Institute Department of Computing Imperial College London United Kingdom

ISBN: (纸本)9781509066384

Social networks are known to be assortative with respect to many attributes, such as age, weight, wealth, level of education, ethnicity and gender. This can be explained by influences and homophilies. Independently of its origin, this assortativity gives us information about each node given its neighbors. Assortativity can thus be used to improve individual predictions in a broad range of situations, when data are missing or inaccurate. This paper presents a general framework based on probabilistic graphical models to exploit social network structures for improving individual predictions of node attributes. Using this framework, we quantify the assortativity range leading to an accuracy gain in several situations. We finally show how specific characteristics of the network can improve performances further. For instance, the gender assortativity in real-world mobile phone data changes significantly according to some communication attributes. In this case, individual predictions with 75% accuracy are improved by up to 3%. © 2017 IEEE.

关键词： Belief propagation

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Fractional kalman filter to estimate the concentration of air pollution

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Journal of Physics: Conference Series 2018年第1期1008卷

作者： Yessy Vita Oktaviana Erna Apriliani Didik Khusnul Arif Department of Mathematics Faculty of MathematicsComputing and Data Science Sepuluh Nopember Institute of Technology Indonesia

Air pollution problem gives important effect in quality environment and quality of human's life. Air pollution can be caused by nature sources or human activities. Pollutant for example Ozone, a harmful gas formed by NOx and volatile organic compounds (VOCs) emitted from various sources. The air pollution problem can be modeled by TAPM-CTM (The Air Pollution Model with Chemical Transport Model). The model shows concentration of pollutant in the air. Therefore, it is important to estimate concentration of air pollutant. Estimation method can be used for forecast pollutant concentration in future and keep stability of air quality. In this research, an algorithm is developed, based on Fractional Kalman Filter to solve the model of air pollution's problem. The model will be discretized first and then it will be estimated by the method. The result shows that estimation of Fractional Kalman Filter has better accuracy than estimation of Kalman Filter. The accuracy was tested by applying RMSE (Root Mean Square Error).

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