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ANDREAS PIERIS School of Informatics, University of Edinburgh 10 Crichton Street, Edinburgh, EH8 9AB, UK [email protected]
ANDREAS PIERIS School of Informatics, University of Edinburgh 10 Crichton Street, Edinburgh, EH8 9AB, UK [email protected] UNIVERSITY EDUCATION • D.Phil. in Computer Science, 2011 Department of Computer Science, University of Oxford Thesis: Ontological Query Answering: New Languages, Algorithms and Complexity Supervisor: Professor Georg Gottlob • M.Sc. in Mathematics anD FounDations oF Computer Science (with Distinction), 2007 Mathematical Institute, University of Oxford Thesis: Data Exchange and Schema Mappings Supervisor: Professor Georg Gottlob • B.Sc. in Computer Science (with Distinction, GPA: 9.06/10), 2006 Department of Computer Science, University of Cyprus Thesis: The Fully Mixed Nash Equilibrium Conjecture Supervisor: Professor Marios Mavronicolas EMPLOYMENT HISTORY • Lecturer (equivalent to Assistant ProFessor) in Databases, 09/2016 – present School of Informatics, University of Edinburgh • PostDoctoral Researcher, 11/2014 – 09/2016 Institute of Logic and Computation, Vienna University of Technology • PostDoctoral Researcher, 09/2011 – 10/2014 Department of Computer Science, University of Oxford RESEARCH Major research interests • Data management: knowledge-enriched data, uncertain data • Knowledge representation and reasoning: ontology languages, complexity of reasoning • Computational logic and its applications to computer science Research grants • EfFicient Querying oF Inconsistent Data, 09/2018 – 08/2022 Principal Investigator Funding agency: Engineering and Physical Sciences Research Council (EPSRC) Total award: £758,049 • Value AdDeD Data Systems: Principles anD Architecture, 04/2015 – 03/2020 Co-Investigator Funding agency: Engineering and Physical Sciences Research Council (EPSRC) Total award: £1,546,471 Research supervision experience • Marco Calautti, postdoctoral supervision, University of Edinburgh, 09/2016 – present • Markus Schneider, Ph.D. supervisor, University of Edinburgh, 09/2018 – present • Gerald Berger, Ph.D. -
120421-24Recombschedule FINAL.Xlsx
Friday 20 April 18:00 20:00 REGISTRATION OPENS in Fira Palace 20:00 21:30 WELCOME RECEPTION in CaixaForum (access map) Saturday 21 April 8:00 8:50 REGISTRATION 8:50 9:00 Opening Remarks (Roderic GUIGÓ and Benny CHOR) Session 1. Chair: Roderic GUIGÓ (CRG, Barcelona ES) 9:00 10:00 Richard DURBIN The Wellcome Trust Sanger Institute, Hinxton UK "Computational analysis of population genome sequencing data" 10:00 10:20 44 Yaw-Ling Lin, Charles Ward and Steven Skiena Synthetic Sequence Design for Signal Location Search 10:20 10:40 62 Kai Song, Jie Ren, Zhiyuan Zhai, Xuemei Liu, Minghua Deng and Fengzhu Sun Alignment-Free Sequence Comparison Based on Next Generation Sequencing Reads 10:40 11:00 178 Yang Li, Hong-Mei Li, Paul Burns, Mark Borodovsky, Gene Robinson and Jian Ma TrueSight: Self-training Algorithm for Splice Junction Detection using RNA-seq 11:00 11:30 coffee break Session 2. Chair: Bonnie BERGER (MIT, Cambrige US) 11:30 11:50 139 Son Pham, Dmitry Antipov, Alexander Sirotkin, Glenn Tesler, Pavel Pevzner and Max Alekseyev PATH-SETS: A Novel Approach for Comprehensive Utilization of Mate-Pairs in Genome Assembly 11:50 12:10 171 Yan Huang, Yin Hu and Jinze Liu A Robust Method for Transcript Quantification with RNA-seq Data 12:10 12:30 120 Zhanyong Wang, Farhad Hormozdiari, Wen-Yun Yang, Eran Halperin and Eleazar Eskin CNVeM: Copy Number Variation detection Using Uncertainty of Read Mapping 12:30 12:50 205 Dmitri Pervouchine Evidence for widespread association of mammalian splicing and conserved long range RNA structures 12:50 13:10 169 Melissa Gymrek, David Golan, Saharon Rosset and Yaniv Erlich lobSTR: A Novel Pipeline for Short Tandem Repeats Profiling in Personal Genomes 13:10 13:30 217 Rory Stark Differential oestrogen receptor binding is associated with clinical outcome in breast cancer 13:30 15:00 lunch break Session 3. -
Python for Bioinformatics, Second Edition
PYTHON FOR BIOINFORMATICS SECOND EDITION CHAPMAN & HALL/CRC Mathematical and Computational Biology Series Aims and scope: This series aims to capture new developments and summarize what is known over the entire spectrum of mathematical and computational biology and medicine. It seeks to encourage the integration of mathematical, statistical, and computational methods into biology by publishing a broad range of textbooks, reference works, and handbooks. The titles included in the series are meant to appeal to students, researchers, and professionals in the mathematical, statistical and computational sciences, fundamental biology and bioengineering, as well as interdisciplinary researchers involved in the field. The inclusion of concrete examples and applications, and programming techniques and examples, is highly encouraged. Series Editors N. F. Britton Department of Mathematical Sciences University of Bath Xihong Lin Department of Biostatistics Harvard University Nicola Mulder University of Cape Town South Africa Maria Victoria Schneider European Bioinformatics Institute Mona Singh Department of Computer Science Princeton University Anna Tramontano Department of Physics University of Rome La Sapienza Proposals for the series should be submitted to one of the series editors above or directly to: CRC Press, Taylor & Francis Group 3 Park Square, Milton Park Abingdon, Oxfordshire OX14 4RN UK Published Titles An Introduction to Systems Biology: Statistical Methods for QTL Mapping Design Principles of Biological Circuits Zehua Chen Uri Alon -
Toward an Open Knowledge Research Graph.Pdf
THE SERIALS LIBRARIAN https://doi.org/10.1080/0361526X.2019.1540272 Toward an Open Knowledge Research Graph Sören Auera and Sanjeet Mann b aPresenter; bRecorder ABSTRACT KEYWORDS Knowledge graphs facilitate the discovery of information by organizing it into Knowledge graph; scholarly entities and describing the relationships of those entities to each other and to communication; Semantic established ontologies. They are popular with search and e-commerce com- Web; linked data; scientific panies and could address the biggest problems in scientific communication, research; machine learning according to Sören Auer of the Technische Informationsbibliothek and Leibniz University of Hannover. In his NASIG vision session, Auer introduced attendees to knowledge graphs and explained how they could make scientific research more discoverable, efficient, and collaborative. Challenges include incentiviz- ing researchers to participate and creating the training data needed to auto- mate the generation of knowledge graphs in all fields of research. Change in the digital world Thank you to Violeta Ilik and the NASIG Program Planning Committee for inviting me to this conference. I would like to show you where I come from. Leibniz University of Hannover has a castle that belonged to a prince, and next to the castle is the Technische Informationsbibliothek (TIB), responsible for supporting the scientific and technology community in Germany with publications, access, licenses, and digital information services. Figure 1 is an example of a knowledge graph about TIB. The basic ingredients of a knowledge graph are entities and relationships. We are the library of Leibniz University of Hannover and we are a member of Leibniz Association (a German research association). -
AAAI-11 Program Schedule.IAAI.EAAI
AAAI-11 Technical Program Schedule Monday, August 8 6:00 – 7:00 pm AAAI-11 Opening Reception Tuesday, August 9 8:30 - 9:00 am Grand Ballroom, Street Level AAAI-11/IAAI-11 Opening Ceremony Welcome and Opening Remarks Outstanding Award Presentations -- Papers, SPC Member, PC Member Wolfram Burgard and Dan Roth, AAAI-11 Program Cochairs IAAI Welcome, Robert S. Engelmore Award, Deployed Application Award Announcements Daniel Shapiro, IAAI-11 Conference Chair, Markus Fromherz, IAAI-11 Program Cochair, and David Leake, AI Magazine Editor-in-Chief Feigenbaum Prize, AAAI Classic Paper Award, Distinguished Service Award Fellows Announcement, Senior Member Recognition Eric Horvitz, AAAI Past President and Awards Committee Chair Henry Kautz, AAAI President 9:15 – 10:00 am AAAI-11 25th Conference Anniversary Panel Moderator: Manuela Veloso, AAAI President-Elect (Carnegie Mellon University) 10:00 – 10:20 am Coffee Break 10:20 - 11:20 am IAAI-11/AAAI-11 Joint Invited Talk: Building Watson: An Overview of DeepQA for the Jeopardy! Challenge David Ferrucci (IBM T J Watson Research Center) 11:30 am – 12:30 pm Description Logics 1 281: Revisiting Semantics for Epistemic Extensions of Description Logics Anees Mehdi, Sebastian Rudolph 242: Integrating Rules and Description Logics by Circumscription Qian Yang, Jia-Huai You, Zhiyong Feng 626: Conjunctive Query Inseparability of OWL 2QL TBoxes B. Konev, R. Kontchakov, M. Ludwig, T. Schneider, F. Wolter, M. Zakharyaschev Machine Learning 1 6024: Nectar: Quantity Makes Quality: Learning with Partial Views Nicolò Cesa-Bianchi, Shai Shalev-Shwartz, Ohad Shamir 31: Symmetric Graph Regularized Constraint Propagation Zhenyong Fu, Zhiwu Lu, Horace H. S. -
Internationale Mathematische Nachrichten
INTERNATIONALE MATHEMATISCHE NACHRICHTEN INTERNATIONAL MATHEMATICAL NEWS NOUVELLES MATHEMA¶ TIQUES INTERNATIONALES NACHRICHTEN DER OSTERREICHISCHENÄ MATHEMATISCHEN GESELLSCHAFT EDITED BY OSTERREICHISCHEÄ MATHEMATISCHE GESELLSCHAFT Nr. 181 August 1999 WIEN INTERNATIONALE MATHEMATISCHE NACHRICHTEN INTERNATIONAL MATHEMATICAL NEWS NOUVELLES MATHEMA¶ TIQUES INTERNATIONALES GegrundetÄ 1947 von R. Inzinger, fortgefuhrtÄ von W. Wunderlich Herausgeber: OSTERREICHISCHEÄ MATHEMATISCHE GESELLSCHAFT Redaktion: P. Flor (U Graz; Herausgeber), U. Dieter (TU Graz), M. Drmota (TU Wien), L. Reich (U Graz) und J. Schwaiger (U Graz), unter stÄandiger Mit- arbeit von R. Mlitz (TU Wien) und E. Seidel (U Graz). ISSN 0020-7926. Korrespondenten DANEMARK:Ä M. E. Larsen (Dansk Matematisk Forening, Kopenhagen) FRANKREICH: B. Rouxel (Univ. Bretagne occ., Brest) GRIECHENLAND: N. K. Stephanidis (Univ. Saloniki) GROSSBRITANNIEN: The Institute of Mathematics and Its Applications (Southend-on-Sea), The London Mathematical Society JAPAN: K. Iseki¶ (Japanese Asoc. of Math. Sci) JUGOSLAWIEN: S. Pre·sic¶ (Univ. Belgrad) KROATIEN: M. Alic¶ (Zagreb) NORWEGEN: Norsk Matematisk Forening (Oslo) OSTERREICH:Ä C. Binder (TU Wien) RUMANIEN:Ä F.-K. Klepp (Timisoara) SCHWEDEN: Svenska matematikersamfundet (GÄoteborg) 2 SLOWAKEI: J. Sira· n· (Univ. Pre¼burg) SLOWENIEN: M. Razpet (Univ. Laibach) TSCHECHISCHE REPUBLIK: B. Maslowski (Akad. Wiss. Prag) USA: A. Jackson (Amer. Math. Soc., Providende RI) INTERNATIONALE MATHEMATISCHE NACHRICHTEN INTERNATIONAL MATHEMATICAL NEWS NOUVELLES MATHEMA¶ -
Conference Program
Twenty-Fifth AAAI Conference on Artificial Intelligence (AAAI-11) Twenty-Third Conference on Innovative Applications of Artificial Intelligence (IAAI-11) Second Symposium on Educational Advances in Artificial Intelligence (EAAI-11) August 7 – 11, 2011 Hyatt Regency San Francisco San Francisco, California, USA Sponsored by the Association for the Advancement of Artificial Intelligence Cosponsored by the National Science Foundation, AI Journal, Google, Inc. Microsoft Research, Cornell University Institute for Computational Sustainability Naval Research Laboratory, Yahoo! Research Labs, NASA Ames Research Center University of Southern California/Information Sciences Institute, ACM/SIGART IBM Research, Videolectures.net, and David E. Smith Conference Program Acknowledgments Robotics Program Chair Contents The Association for the Advancement of Artifi- Andrea Thomaz (Georgia Institute of Technology, USA) cial Intelligence acknowledges and thanks the Acknowledgments / 2 following individuals for their generous contri- Poker Competition Cohairs AI Video Competition / 18 butions of time and energy to the successful Nolan Bard (University of Alberta, Canada) Awards / 2–4 creation and planning of the Twenty-Fifth AAAI Jonathan Rubin (University of Auckland, New Competitions / 18–19 Conference on Artificial Intelligence and the Zealand) Conference at a Glance / 5 Twenty-Third Conference on Innovative Appli- AI Video Competition Cochairs Doctoral Consortium / 8 cations of Artificial Intelligence. David Aha (Naval Research Laboratory, USA) EAAI-11 Program / 9 Arnav Jhala (University of California, Santa Cruz, Exhibition / 16 AAAI-11 Conference Committee USA) General Information / 20 IAAI-11 Program / 10–15 AAAI Conference Committee Chair A complete listing of the AAAI-11 / IAAI-11 / Invited Presentations / 3, 6–7 Dieter Fox (University of Washington, USA) EAAI-11 Program Committee members appears in Poker Competition / 18 AAAI-11 Program Cochairs the conference proceedings. -
Today Oxford
www.oxfordtoday.ox.ac.uk Michaelmas Term 2010 Volume 23 No 1 OX FOR D TODAY THE UNIVERSITY MAGAZINE 20 | WILFRED THESIGER AFRICA SEEN THROUGH HIS LENS 30 | SCIENCE WHEN TO SHARE GENE DATA? 45 | GEOFFREY HILL SEAMUS PERRY ON OUR GREATEST LIVING POET PRIME MINISTERS Why has Oxford produced so many? OXF01.cover 1 8/10/10 3:37:5 pm FROM HOME Since 1821 the Oxfordand Cambridge Club has provided alumni of both universities with an exclusive home from home in the heartofthe Capital. Todaymembers can relax, dine and meetfriends in supremely elegant surroundings thatalso featurewell stocked libraries,sports facilities and first-class bedroom accommodation. Reciprocal clubs welcome members of the Oxfordand Cambridge Club in 35 countriesaround the world. Formoreinformation, please contact: [email protected] or call +44 (0)20 7321 5110 Oxfordand Cambridge Club,71Pall Mall,LondonSW1Y 5HD www.oxfordandcambridgeclub.co.uk OX FOR D TODAY EDITOR: Dr Richard Lofthouse DEPUTY ART EDITOR: Steven Goldring DESIGNER: Victoria Ford HEAD OF PUBLICATIONS AND WEB OFFICE: Anne Brunner-Ellis PRODUCTION EDITOR: Kate Lloyd SUB EDITOR: Elizabeth Tatham PICTURE EDITOR: Joanna Kay DESIGN DIRECTOR: Dylan Channon Thanks to Simon Kirrane, Esther Woodman, Helen Cox, Emma Swift EDITORIAL ENQUIRIES: Janet Avison Public Affairs Directorate Tel: 01865 280545 Fax: 01865 270178 [email protected] www.oxfordtoday.ox.ac.uk ALUMNI ENQUIRIES, INCLUDING CHANGE OF ADDRESS: Claire Larkin Alumni Offi ce Tel: 01865 611610 Michaelmas [email protected] COVER IMAGE: HARRY BORDEN/CORBIS OUTLINE, ROB JUDGES www.alumni.ox.ac.uk Term 2010 University of Oxford, University Offi ces, Wellington Square, Oxford OX1 2JD ADVERTISING ENQUIRIES: Marie Longstaff Future Plus, Beaufort Court, 30 Monmouth Street, Bath BA1 2BW Tel: 01225 822849 [email protected] www.futureplc.com Oxford Today is published in February, June and October. -
Size and Treewidth Bounds for Conjunctive Queries
Size and Treewidth Bounds for Conjunctive Queries GEORG GOTTLOB University of Oxford, UK STEPHANIE TIEN LEE University of Oxford, UK GREGORY VALIANT University of California, Berkeley and PAUL VALIANT University of California, Berkeley This paper provides new worst-case bounds for the size and treewith of the result Q(D) of a conjunctive query Q applied to a database D. We derive bounds for the result size |Q(D)| in terms of structural properties of Q, both in the absence and in the presence of keys and functional dependencies. These bounds are based on a novel “coloring” of the query variables that associates a coloring number C(Q) to each query Q. Intuitively, each color used represents some possible entropy of that variable. Using this coloring number, we derive tight bounds for the size of Q(D) in case (i) no functional dependencies or keys are specified, and (ii) simple functional dependencies (keys) are given. These results generalize recent size-bounds for join queries obtained by Atserias et al. [2008]. In the case of arbitrary (compound) functional dependencies, we use tools from information theory to provide lower and upper bounds, establishing a close connection between size bounds and a basic question in information theory. Our new coloring scheme also allows us to precisely characterize (both in the absence of keys and with simple keys) the treewidth-preserving queries—the queries for which the treewidth of the output relation is bounded by a function of the treewidth of the input database. Finally, we give some results on the computational complexity of determining the size bounds, and of deciding whether the treewidth is preserved. -
F. Alex Feltus, Ph.D
F. Alex Feltus, Ph.D. Curriculum Vitae 001010101000001000100001011001010101001000101001010010000100001010101001001000010010001000100001010001001010100100010001000101001000011110101000110010100010101010101010110101010100001000010010101010100100100000101001010010001010110100010 Clemson University • Department of Genetics & Biochemistry Biosystems Research Complex Rm 302C • 105 Collings St. • Clemson, SC 29634 (864)656-3231 (office) • (864) 654-5403 (home) • Skype: alex.feltus • [email protected] https://www.clemson.edu/science/departments/genetics-biochemistry/people/profiles/ffeltus https://orcid.org/0000-0002-2123-6114 https://www.linkedin.com/in/alex-feltus-86a0073a 001010101000001010101010101010101010100110000101100101010100100010100101001000010000101010100100100001001000100010000101000100101010010001000100010100100001111010100011001010001000001000010010101010100100100000101001010010001010110100010 Educational Background: Ph.D. Cell Biology (2000) Vanderbilt University (Nashville, TN) B.Sc. Biochemistry (1992) Auburn University (Auburn, AL) Ph.D. Dissertation Title: Transcriptional Regulation of Human Type II 3β-Hydroxysteroid Dehydrogenase: Stat5- Centered Control by Steroids, Prolactin, EGF, and IL-4 Hormones. Professional Experience: 2018- Professor, Clemson University Department of Genetics and Biochemistry 2017- Core Faculty, Biomedical Data Science and Informatics (BDSI) PhD Program 2018- Faculty Member, Clemson Center for Human Genetics 2020- Faculty Scholar, Clemson University School of Health Research (CUSHR) 2019- co-Founder, -
Prof. Dr. Georg Gottlob Univ
Speaker: Prof. Dr. Georg Gottlob Univ. Oxford, TU Wien Title: My adventures with Datalog: Walking the thin line between theory and practice Abstract: I have worked on various subjects, but ever since my years as PostDoc, I have been fascinated by Datalog, a logical programming language for reasoning and database querying. I will start this talk with a short introduction to Datalog, followed by an overview of some theoretical results on Datalog variants. This will be interleaved with a tale of four Datalog-related companies I co-founded: DLVSystem, Lixto, Wrapidity, and DeepReason.ai. I will also comment on the difficulties an academic has to face when spinning out a start-up, and on the satisfaction you may experience when your results are used in practice. Short Bio: Georg Gottlob is a Royal Society Research Professor and a Professor of Informatics at Oxford University. and at TU Wien. At Oxford he is a Fellow of St John's College. His interests include knowledge representation, logic and complexity, and database and Web querying. He has received various awards, among which the Wittgenstein Award (Austria) and the Ada Lovelace Medal (UK). He is a Fellow of the Royal Society, of the Austrian and German National Academies of Science, and of the Academia Europaea. He was a founder of Lixto, a company specialised in semi-automatic web data extraction which was acquired by McKinsey in 2013. Gottlob was awarded an ERC Advanced Investigator's Grant for the project "DIADEM: Domain-centric Intelligent Automated Data Extraction Methodology". Based on the results of this project, he co-founded Wrapidity Ltd, a company that specialised in fully automated web data extraction, which was acquired in 2016 by Meltwater. -
ACM-BCB 2016 the 7Th ACM Conference on Bioinformatics
ACM-BCB 2016 The 7th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics October 2-5, 2016 Organizing Committee General Chairs: Steering Committee: Ümit V. Çatalyürek, Georgia Institute of Technology Aidong Zhang, State University of NeW York at Buffalo, Genevieve Melton-Meaux, University of Minnesota Co-Chair May D. Wang, Georgia Institute of Technology and Program Chairs: Emory University, Co-Chair John Kececioglu, University of Arizona Srinivas Aluru, Georgia Institute of Technology Adam Wilcox, University of Washington Tamer Kahveci, University of Florida Christopher C. Yang, Drexel University Workshop Chair: Ananth Kalyanaraman, Washington State University Tutorial Chair: Mehmet Koyuturk, Case Western Reserve University Demo and Exhibit Chair: Robert (Bob) Cottingham, Oak Ridge National Laboratory Poster Chairs: Lin Yang, University of Florida Dongxiao Zhu, Wayne State University Registration Chair: Preetam Ghosh, Virginia CommonWealth University Publicity Chairs Daniel Capurro, Pontificia Univ. Católica de Chile A. Ercument Cicek, Bilkent University Pierangelo Veltri, U. Magna Graecia of Catanzaro Student Travel Award Chairs May D. Wang, Georgia Institute of Technology and Emory University JaroslaW Zola, University at Buffalo, The State University of NeW York Student Activity Chair Marzieh Ayati, Case Western Reserve University Dan DeBlasio, Carnegie Mellon University Proceedings Chairs: Xinghua Mindy Shi, U of North Carolina at Charlotte Yang Shen, Texas A&M University Web Admins: Anas Abu-Doleh, The