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4th International Workshop on Reversible Computation, RC 2012

作者： Seiter, Julia Soeken, Mathias Wille, Robert Drechsler, Rolf Group of Computer Architecture Institute of Computer Science University of Bremen D-28359 Bremen Germany DFKI GmbH Cyber-Physical Systems D-28359 Bremen Germany

ISBN: (纸本)9783642363146

For the validation and verification of quantum circuits mainly techniques based on simulation are applied. Although lots of effort has been put into the improvement of these techniques, ensuring the correctness still requires an exhaustive consideration of all input vectors. As a result, these techniques are particularly insufficient to prove a circuit to be error free. As an alternative, we present a symbolic formal verification method that is based on Quantum Multiple-Valued Decision Diagrams (QMDDs), a data-structure allowing for a compact representation of quantum circuits. As a result, using QMDDs it is possible to check the correctness of a circuit without exhaustively considering all input patterns. © 2013 Springer-Verlag Berlin Heidelberg.

关键词： Timing circuits

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Reducing the depth of quantum circuits using additional circuit lines

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5th International Conference on Reversible Computation, RC 2013

作者： Abdessaied, Nabila Wille, Robert Soeken, Mathias Drechsler, Rolf Institute of Computer Science University of Bremen Group of Computer Architecture D-28359 Bremen Germany Cyber-Physical Systems DFKI GmbH D-28359 Bremen Germany

ISBN: (纸本)9783642389856

The synthesis of Boolean functions, as they are found in many quantum algorithms, is usually conducted in two steps. First, the function is realized in terms of a reversible circuit followed by a mapping into a corresponding quantum realization. During this process, the number of lines and the quantum costs of the resulting circuits have mainly been considered as optimization objectives thus far. However, beyond that also the depth of a quantum circuit is vital. Although first synthesis approaches that consider depth have recently been introduced, the majority of design methods did not consider this metric. In this paper, we introduce an optimization approach aiming for the reduction of depth in the process of mapping a reversible circuit into a quantum circuit. For this purpose, we present an improved (local) mapping of single gates as well as a (global) optimization scheme considering the whole circuit. In both cases, we incorporate the idea of exploiting additional circuit lines which are used in order to split a chain of serial gates. Our optimization techniques enable a concurrent application of gates which significantly reduces the depth of the circuit. Experiments show that reductions of approx. 40% on average can be achieved when following this scheme. © 2013 Springer-Verlag Berlin Heidelberg.

关键词： Mapping

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Highlights from the 11th ISCB Student Council Symposium 2015. Dublin, Ireland. 10 July 2015

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BMC bioinformatics 2016年第3期17 Suppl 3卷 95页

作者： Katie Wilkins Mehedi Hassan Margherita Francescatto Jakob Jespersen R. Gonzalo Parra Bart Cuypers Dan DeBlasio Alexander Junge Anupama Jigisha Farzana Rahman Griet Laenen Sander Willems Lieven Thorrez Yves Moreau Nagarajan Raju Sonia Pankaj Chothani C. Ramakrishnan Masakazu Sekijima M. Michael Gromiha Paddy J Slator Nigel J Burroughs Przemysław Szałaj Zhonghui Tang Paul Michalski Oskar Luo Xingwang Li Yijun Ruan Dariusz Plewczynski Giulia Fiscon Emanuel Weitschek Massimo Ciccozzi Paola Bertolazzi Giovanni Felici Pieter Meysman Manu Vanaerschot Maya Berg Hideo Imamura Jean-Claude Dujardin Kris Laukens Westa Domanova James R. Krycer Rima Chaudhuri Pengyi Yang Fatemeh Vafaee Daniel J. Fazakerley Sean J. Humphrey David E. James Zdenka Kuncic Plant Pathology and Plant-Microbe Biology Section School of Integrative Plant Science Cornell University Ithaca USA Graduate Field of Computational Biology Cornell University Ithaca USA School of Computing & Mathematics University of South Wales Cardiff UK Department of Genome Biology for Neurodegenerative Diseases German Center for Neurodegenerative Diseases (DZNE) within the Helmholtz Association ᅟ Germany Department of Surgery Massachusetts General Hospital The Broad Institute of MIT and Harvard Boston USA Department of Systems Biology Technical University of Denmark Kemitorvet Denmark Protein Physiology Lab Facultad de Ciencias Exactas y Naturales Universidad de Buenos Aires Buenos Aires Argentina Molecular Parasitology Unit (MPU) Institute of Tropical Medicine Antwerp Belgium Advanced Database Research and Modeling (ADReM) research group University of Antwerp Antwerpen Belgium Department of Computer Science University of Arizona Tucson USA Department of Veterinary Clinical and Animal Sciences Center for non-coding RNA in Technology and Health University of Copenhagen Copenhagen Denmark University College Dublin Dublin Ireland Department of Electrical Engineering (ESAT) STADIUS Center for Dynamical Systems Signal Processing and Data Analytics KU Leuven Leuven Belgium Minds Medical IT Department Leuven Belgium Scientific Institute of Public Health (WIV-ISP) Platform of Biotechnology and Molecular Biology (PBB) Brussels Belgium Department of Development and Regeneration @ Kulak KU Leuven Kortrijk Belgium Department of Biotechnology Bhupat and Jyoti Metha School of Biosciences Indian Institute of Technology Madras Chennai India Philips Research North America Briarcliff Manor USA Global Scientific Information and Computing Center (GSIC) Tokyo Institute of Technology Tokyo Japan Systems Biology Centre University of Warwick Senate House Coventry UK Systems Biology Doctoral Training Centre University of Warwick Senate House Coventry UK Center for B

A1 Highlights from the eleventh ISCB Student Council Symposium 2015 Katie Wilkins, Mehedi Hassan, Margherita Francescatto, Jakob Jespersen, R. Gonzalo Parra, Bart Cuypers, Dan DeBlasio, Alexander Junge, Anupama Jigisha, Farzana Rahman O1 Prioritizing a drug’s targets using both gene expression and structural similarity Griet Laenen, Sander Willems, Lieven Thorrez, Yves Moreau O2 Organism specific protein-RNA recognition: A computational analysis of protein-RNA complex structures from different organisms Nagarajan Raju, Sonia Pankaj Chothani, C. Ramakrishnan, Masakazu Sekijima; M. Michael Gromiha O3 Detection of Heterogeneity in Single Particle Tracking Trajectories Paddy J Slator, Nigel J Burroughs O4 3D-NOME: 3D NucleOme Multiscale Engine for data-driven modeling of three-dimensional genome architecture Przemysław Szałaj, Zhonghui Tang, Paul Michalski, Oskar Luo, Xingwang Li, Yijun Ruan, Dariusz Plewczynski O5 A novel feature selection method to extract multiple adjacent solutions for viral genomic sequences classification Giulia Fiscon, Emanuel Weitschek, Massimo Ciccozzi, Paola Bertolazzi, Giovanni Felici O6 A systems Biology Compendium for Leishmania donovani Bart Cuypers, Pieter Meysman, Manu Vanaerschot, Maya Berg, Hideo Imamura, Jean-Claude Dujardin, Kris Laukens O7 Unravelling signal coordination from large scale phosphorylation kinetic data Westa Domanova, James R. Krycer, Rima Chaudhuri, Pengyi Yang, Fatemeh Vafaee, Daniel J. Fazakerley, Sean J. Humphrey, David E. James, Zdenka Kuncic

关键词： Visceral Leishmaniasis Feature Selection Method Frequent Itemset Mining Leishmania Donovani Student Council

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Applying "functional scenario-based" test case generation method in unit testing and integration testing

Applying "functional scenario-based" test case generation me...

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2nd International Workshop on Structured Object-Oriented Formal Language and Method, SOFL 2012

作者： Li, Cencen Li, Mo Liu, Shaoying Nakajima, Shin Graduate School of Computer and Information Sciences Hosei University Tokyo Japan Department of Computer and Information Sciences Hosei University Tokyo Japan Information Systems Architecture Science Research Division National Institute of Informatics Tokyo Japan

ISBN: (纸本)9783642392764

Specification-based testing enables us to detect errors in the implementation of functions defined in given specifications. Its effectiveness in achieving high path coverage and efficiency in generating test cases are always major concerns of testers. The automatic test case generation approach based on formal specifications proposed by Liu and Nakajima is aimed at ensuring high effectiveness and efficiency, but this approach has not been used under different testing environments. In this paper, we first present the statical analysis of the characteristics of the test case generation approach, and then show the experiments of using this approach in two different real testing environments. The two practical testing cases include a unit testing and an integration testing. We perform the testing not only for assessing Liu's approach in practice, but also trying to get some experience of using this approach in practice. The static analysis and the results of experiments indicate that this test case generation approach may not be effective in some circumstances, especially in integration testing. We discuss the results, analyze the specific causes for the ineffectiveness, namely the low path coverage, and propose some suggestions for improvement. © 2013 Springer-Verlag.

关键词： Integration testing

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Towards a socially-aware management of new overlay application traffic combined with energy efficiency in the Internet (SmartenIT)

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2013 Annual Future Internet Assembly, FIA 2013

作者： Stiller, Burkhard Hausheer, David Hofßeld, Tobias University of Zürich Department of Informatics Communication Systems Group Switzerland P2P Systems Engineering TU Darmstadt Germany University of Würzburg Institute of Computer Science Würzburg Germany

ISBN: (纸本)9783642380815

The Internet has seen a strong move to support overlay applications, which demand a coherent and integrated control in underlying heterogeneous networks in a scalable, resilient, and energy-efficient manner. A tighter integration of network management and overlay service functionality can lead to crosslayer optimization of operations and management, which is a promising approach as it offers a large business potential in operational perspectives for all players involved. Therefore, the objective of this paper is to present SmartenIT (Socially-aware Management of New Overlay Application Traffic combined with Energy Efficiency in the Internet), which targets at an incentive-compatible cross-layer network management for providers of overlay-based application (e.g., cloud applications, content delivery, and social networks), network providers, and end-users. The goal is to ensure a QoE-awareness, by addressing accordingly load and traffic patterns or special application requirements, and exploiting at the same time social awareness (in terms of user relations and interests). Moreover, energy efficiency with respect to both end-user devices and underlying networking infrastructure is tackled to ensure an operationally efficient management. Incentive-compatible network management mechanisms for improving metrics on an inter-domain basis for ISPs serve as the major mechanism to deal with and investigate real-life scenarios. © The Author(s).

关键词： Energy efficiency

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Using πdDs in the design of reversible circuits (work-in-progress)

Using πdDs in the design of reversible circuits (work-in-pr...

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4th International Workshop on Reversible Computation, RC 2012

作者： Soeken, Mathias Wille, Robert Minato, Shin-Ichi Drechsler, Rolf Institute of Computer Science University of Bremen Group of Computer Architecture D-28359 Bremen Germany Hokkaido University Sapporo 060-0814 Japan DFKI GmbH Cyber-Physical Systems D-28359 Bremen Germany

ISBN: (纸本)9783642363146

With πDDs a data structure has recently been introduced that offers a compact representation for sets of permutations. Since reversible functions constitute permutations on the input assignments, they can naturally be expressed using this data structure. However, its potential has not been exploited so far. In this work-in-progress report, we present and discuss possible applications of πDDs within the design of reversible circuits including techniques for synthesis, debugging, and an efficient determination of the number of minimal circuits. We observed that πDDs inhibit the same space complexities as truth tables and, hence, do not superior existing design methods in many cases. However, they are advantageous when dealing with several functions or gates at once. © 2013 Springer-Verlag Berlin Heidelberg.

关键词： Data structures

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Sequence data and association statistics from 12,940 type 2 diabetes cases and controls

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Scientific data 2017年第1期4卷 170179页

作者： Jason Flannick Christian Fuchsberger Anubha Mahajan Tanya M Teslovich Vineeta Agarwala Kyle J Gaulton Lizz Caulkins Ryan Koesterer Clement Ma Loukas Moutsianas Davis J McCarthy Manuel A Rivas John R B Perry Xueling Sim Thomas W Blackwell Neil R Robertson N William Rayner Pablo Cingolani Adam E Locke Juan Fernandez Tajes Heather M Highland Josee Dupuis Peter S Chines Cecilia M Lindgren Christopher Hartl Anne U Jackson Han Chen Jeroen R Huyghe Martijn van de Bunt Richard D Pearson Ashish Kumar Martina Müller-Nurasyid Niels Grarup Heather M Stringham Eric R Gamazon Jaehoon Lee Yuhui Chen Robert A Scott Jennifer E Below Peng Chen Jinyan Huang Min Jin Go Michael L Stitzel Dorota Pasko Stephen C J Parker Tibor V Varga Todd Green Nicola L Beer Aaron G Day-Williams Teresa Ferreira Tasha Fingerlin Momoko Horikoshi Cheng Hu Iksoo Huh Mohammad Kamran Ikram Bong-Jo Kim Yongkang Kim Young Jin Kim Min-Seok Kwon Juyoung Lee Selyeong Lee Keng-Han Lin Taylor J Maxwell Yoshihiko Nagai Xu Wang Ryan P Welch Joon Yoon Weihua Zhang Nir Barzilai Benjamin F Voight Bok-Ghee Han Christopher P Jenkinson Teemu Kuulasmaa Johanna Kuusisto Alisa Manning Maggie C Y Ng Nicholette D Palmer Beverley Balkau Alena Stančáková Hanna E Abboud Heiner Boeing Vilmantas Giedraitis Dorairaj Prabhakaran Omri Gottesman James Scott Jason Carey Phoenix Kwan George Grant Joshua D Smith Benjamin M Neale Shaun Purcell Adam S Butterworth Joanna M M Howson Heung Man Lee Yingchang Lu Soo-Heon Kwak Wei Zhao John Danesh Vincent K L Lam Kyong Soo Park Danish Saleheen Wing Yee So Claudia H T Tam Uzma Afzal David Aguilar Rector Arya Tin Aung Edmund Chan Carmen Navarro Ching-Yu Cheng Domenico Palli Adolfo Correa Joanne E Curran Dennis Rybin Vidya S Farook Sharon P Fowler Barry I Freedman Michael Griswold Daniel Esten Hale Pamela J Hicks Chiea-Chuen Khor Satish Kumar Benjamin Lehne Dorothée Thuillier Wei Yen Lim Jianjun Liu Marie Loh Solomon K Musani Sobha Puppala William R Scott Loïc Yengo Sian-Tsung Tan Herman A Taylor Farook Thameem Gregory Wilson Tien Yin Wong Pål Rasmu Department of Molecular Biology Massachusetts General Hospital Boston Massachusetts USA. Program in Medical and Population Genetics Broad Institute Cambridge Massachusetts USA. Department of Biostatistics and Center for Statistical Genetics University of Michigan Ann Arbor Michigan USA. Wellcome Trust Centre for Human Genetics Nuffield Department of Medicine University of Oxford Oxford UK. Harvard-MIT Division of Health Sciences and Technology Massachusetts Institute of Technology Cambridge Massachusetts USA. Department of Statistics University of Oxford Oxford UK. Genetics of Complex Traits University of Exeter Medical School University of Exeter Exeter UK. MRC Epidemiology Unit Institute of Metabolic Science University of Cambridge Cambridge UK. Department of Twin Research and Genetic Epidemiology King's College London London UK. Oxford Centre for Diabetes Endocrinology and Metabolism Radcliffe Department of Medicine University of Oxford Oxford UK. Department of Human Genetics Wellcome Trust Sanger Institute Hinxton Cambridgeshire UK. School of Computer Science McGill University Montreal Quebec Canada. McGill University and Génome Québec Innovation Centre Montreal Quebec Canada. Human Genetics Center The University of Texas Graduate School of Biomedical Sciences at Houston The University of Texas Health Science Center at Houston Houston Texas USA. Department of Biostatistics Boston University School of Public Health Boston Massachusetts USA. National Heart Lung and Blood Institute's Framingham Heart Study Framingham Massachusetts USA. Medical Genomics and Metabolic Genetics Branch National Human Genome Research Institute National Institutes of Health Bethesda Maryland USA. Department of Biostatistics Harvard School of Public Health Boston Massachusetts USA. Chronic Disease Epidemiology Swiss Tropical and Public Health Institute University of Basel Basel Switzerland. Institute of Genetic Epidemiology Helmholtz Zentrum München German R

To investigate the genetic basis of type 2 diabetes (T2D) to high resolution, the GoT2D and T2D-GENES consortia catalogued variation from whole-genome sequencing of 2,657 European individuals and exome sequencing of 12,940 individuals of multiple ancestries. Over 27M SNPs, indels, and structural variants were identified, including 99% of low-frequency (minor allele frequency [MAF] 0.1-5%) non-coding variants in the whole-genome sequenced individuals and 99.7% of low-frequency coding variants in the whole-exome sequenced individuals. Each variant was tested for association with T2D in the sequenced individuals, and, to increase power, most were tested in larger numbers of individuals (>80% of low-frequency coding variants in ~82 K Europeans via the exome chip, and ~90% of low-frequency non-coding variants in ~44 K Europeans via genotype imputation). The variants, genotypes, and association statistics from these analyses provide the largest reference to date of human genetic information relevant to T2D, for use in activities such as T2D-focused genotype imputation, functional characterization of variants or genes, and other novel analyses to detect associations between sequence variation and T2D.

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Guided merging of sequence diagrams

Guided merging of sequence diagrams

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5th International Conference on Software Language Engineering, SLE 2012

作者： Widl, Magdalena Biere, Armin Brosch, Petra Egly, Uwe Heule, Marijn Kappel, Gerti Seidl, Martina Tompits, Hans Institute of Information Systems Vienna University of Technology Austria Business Informatics Group Vienna University of Technology Austria Institute for Formal Models and Verification Johannes Kepler University Austria Department of Computer Science University of Texas Austin United States

ISBN: (纸本)9783642360886

The employment of optimistic model versioning systems allows multiple developers of a team to work independently on their local copies of a software model. The merging process towards one consolidated version can be error-prone and time-consuming when performed without any tool support. Recently, several sophisticated approaches for model merging have been presented. However, even for multi-view modeling languages like UML, which distribute the information on the modeled system over different views, these views are merged independently of each other. Hence, inconsistencies are likely to be introduced into the merged model. We suggest to solve this problem by exploiting information stored in one view as constraint for the computation of a consolidated version of another view. More specifically, we demonstrate how state machines can guide the integration of parallel changes performed on a sequence diagram. We give a concise formal description of this problem and suggest a translation to the satisfiability problem of propositional logic. © 2013 Springer-Verlag Berlin Heidelberg.

关键词： Merging

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Erratum: Large meta-analysis of genome-wide association studies identifies five loci for lean body mass

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Nature communications 2017年第1期8卷 1414页

作者： M Carola Zillikens Serkalem Demissie Yi-Hsiang Hsu Laura M Yerges-Armstrong Wen-Chi Chou Lisette Stolk Gregory Livshits Linda Broer Toby Johnson Daniel L Koller Zoltán Kutalik Jian'an Luan Ida Malkin Janina S Ried Albert V Smith Gudmar Thorleifsson Liesbeth Vandenput Jing Hua Zhao Weihua Zhang Ali Aghdassi Kristina Åkesson Najaf Amin Leslie J Baier Inês Barroso David A Bennett Lars Bertram Rainer Biffar Murielle Bochud Michael Boehnke Ingrid B Borecki Aron S Buchman Liisa Byberg Harry Campbell Natalia Campos Obanda Jane A Cauley Peggy M Cawthon Henna Cederberg Zhao Chen Nam H Cho Hyung Jin Choi Melina Claussnitzer Francis Collins Steven R Cummings Philip L De Jager Ilja Demuth Rosalie A M Dhonukshe-Rutten Luda Diatchenko Gudny Eiriksdottir Anke W Enneman Mike Erdos Johan G Eriksson Joel Eriksson Karol Estrada Daniel S Evans Mary F Feitosa Mao Fu Melissa Garcia Christian Gieger Thomas Girke Nicole L Glazer Harald Grallert Jagvir Grewal Bok-Ghee Han Robert L Hanson Caroline Hayward Albert Hofman Eric P Hoffman Georg Homuth Wen-Chi Hsueh Monica J Hubal Alan Hubbard Kim M Huffman Lise B Husted Thomas Illig Erik Ingelsson Till Ittermann John-Olov Jansson Joanne M Jordan Antti Jula Magnus Karlsson Kay-Tee Khaw Tuomas O Kilpeläinen Norman Klopp Jacqueline S L Kloth Heikki A Koistinen William E Kraus Stephen Kritchevsky Teemu Kuulasmaa Johanna Kuusisto Markku Laakso Jari Lahti Thomas Lang Bente L Langdahl Lenore J Launer Jong-Young Lee Markus M Lerch Joshua R Lewis Lars Lind Cecilia Lindgren Yongmei Liu Tian Liu Youfang Liu Östen Ljunggren Mattias Lorentzon Robert N Luben William Maixner Fiona E McGuigan Carolina Medina-Gomez Thomas Meitinger Håkan Melhus Dan Mellström Simon Melov Karl Michaëlsson Braxton D Mitchell Andrew P Morris Leif Mosekilde Anne Newman Carrie M Nielson Jeffrey R O'Connell Ben A Oostra Eric S Orwoll Aarno Palotie Stephen C J Parker Munro Peacock Markus Perola Annette Peters Ozren Polasek Richard L Prince Katri Räikkönen Stuart H Ralston Samuli Ripatti John A Robbins Jerome I Rotter Igor Rudan Veikko Department of Internal Medicine Erasmus MC Rotterdam 3000 The Netherlands. Netherlands Genomics Initiative (NGI)-sponsored Netherlands Consortium for Healthy Aging (NCHA) Leiden 2593 The Netherlands. Department of Biostatistics Boston University School of Public Health Boston MA 02118 USA. Hebrew SeniorLife Institute for Aging Research Roslindale MA 02131 USA. Harvard Medical School Boston MA 02115 USA. Molecular and Integrative Physiological Sciences Program Harvard School of Public Health Boston MA 02115 USA. Program in Personalized and Genomic Medicine and Department of Medicine Division of Endocrinology Diabetes and Nutrition University of Maryland School of Medicine Baltimore MD 21201 USA. Broad Institute Cambridge MA 02142 USA. Sackler Faculty of Medicine Department of Anatomy and Anthropology Tel Aviv University Tel Aviv 6997801 Israel. Department of Twin Research and Genetic Epidemiology King's College London St Thomas' Campus London WC2R 2LS UK. Department of Epidemiology Erasmus MC Rotterdam 3000 The Netherlands. Department of Medical Genetics University of Lausanne Lausanne 1011 Switzerland. Swiss Institute of Bioinformatics Lausanne 1015 Switzerland. Centre Hospitalier Universitaire (CHUV) University Institute for Social and Preventive Medicine Lausanne 1010 Switzerland. Department of Medical and Molecular Genetics Indiana University School of Medicine Indianapolis IN 46202 USA. MRC Epidemiology Unit University of Cambridge School of Clinical Medicine Cambridge Biomedical Campus Cambridge CB2 OQQ UK. Institute of Epidemiology II Helmholtz Zentrum München - German Research Center for Environmental Health Neuherberg 85764 Germany. Icelandic Heart Association Kopavogur 201 Iceland. Faculty of Medicine University of Iceland Reykjavik 101 Iceland. deCODE Genetics Reykjavik 101 Iceland. Department of Internal Medicine Institute of Medicine Sahlgrenska Academy University of Gothenburg Gothenburg SE-405 30 Sweden. Dep

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A system for perspective-aware search 3

A system for perspective-aware search

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3rd European Workshop on Human-computer Interaction and Information Retrieval, EuroHCIR 2013 - Co-located with the 36th International ACM SIGIR Conference on Research and Development in Information Retrieval, SIGIR 2013

作者： Qureshi, M. Atif Younus, Arjumand O'Riordan, Colm Pasr, Gabriella Touheed, Nasir Computational Intelligence Research Group Information Technology National University of Ireland Galway Ireland Information Retrieval Lab. Informatics Systems and Communication University of Milan Bicocca Milan Italy Web Science Research Group Faculty of Computer Science Institute of Business Administration Karachi Pakistan

Traditional search engines fail to capture the notion of "perspective" in their search results and at times present the results skewed towards a particular topic. Under most of these cases even query reformulation fails to retrieve desired search results and the underlying reason for such failure is often the bias within the document collection itself (e.g., news articles). A perspective-aware search interface enabling users to look into search results for some "perspective" terms may be of great use for certain information needs. In this paper we describe such a system. Copyright © 2013 for the individual papers by the papers' authors.

关键词： Search engines

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