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11th German Conference on Chemoinformatics (GCC 2015) Abstracts

JOURNAL OF CHEMINFORMATICS 2016年第SUPPL 1期8卷 1-27页

作者： [Anonymous] GDCh-CIC Division Associated Board Member Beilstein-Institut zur Förderung der Chemischen Wissenschaften Trakehner Str. 7-9 60487 Frankfurt Germany. ufechner@beilstein-institut.de. Division Medicinal Chemistry Amsterdam Institute for Molecules Medicines and Systems (AIMMS) VU University Amsterdam The Netherlands. Centre for Bioinformatics Uni Hamburg Bundesstr. 43 20146 Hamburg Germany. Sanofi-Aventis Deutschland GmbH 65926 Frankfurt am Main Germany. stefan.guessregen@***. Sanofi-Aventis Deutschland GmbH 65926 Frankfurt am Main Germany. GlaxoSmithKline Stevenage SG1 2NY UK. nicola.j.richmond@***. Discngine Paris 75011 France. Organisch-Chemisches Institut Westfälische Wilhelms-Universität Münster Germany. marwin.segler@wwu.de. Organisch-Chemisches Institut Westfälische Wilhelms-Universität Münster Germany. Bundeskriminalamt Wiesbaden Central Analytics II 65173 Wiesbaden Germany. Department of Chemistry and Biochemistry University of California Santa Barbara CA 93111 USA. shea@chem.ucsb.edu. Department of Chemistry and Biochemistry University of California Santa Barbara CA 93111 USA. Chemistry Department Ludwig-Maximilians-Universität München Butenandtstr. 7 81377 Munich Germany. Inorganic Chemistry and Center for Nanointegration University of Duisburg-Essen Essen Germany. CAM-D Technologies Essen Germany. Institute for Bioinformatics and Chemoinformatics Westphalian University of Applied Sciences Recklinghausen Germany. Institute for Bioinformatics and Chemoinformatics Westphalian University of Applied Sciences Recklinghausen Germany. achim.zielesny@w-hs.de. Leiden University Leiden Netherlands. j.fraaije@chem.leidenuniv.nl. Culgi BV Berlin Germany. Physikalische Chemie III TU Dortmund 44227 Dortmund Germany. stefan.kast@tu-dortmund.de. Centre for Molecular Informatics Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW United Kingdom. kcb27@cam.ac.uk. Centre for Molecular Informatics Department of Chemistry

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Constraint programming based large neighbourhood search for energy minimisation in data centres

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10th International Conference on the Economics of Grids, Clouds, Systems, and Services, GECON 2013

作者： Cambazard, Hadrien Mehta, Deepak O'Sullivan, Barry Simonis, Helmut G-SCOP Université de Grenoble CNRS France INSIGHT Centre for Data Analytics Department of Computer Science University College Cork Ireland

ISBN: (纸本)9783319024134

EnergeTIC is a recent industrial research project carried out in Grenoble on optimising energy consumption in data centres. We study the problem formulation proposed by EnergeTIC. The problem focuses on the allocation of virtual machines to servers with time-variable resource demands in data centres in order to minimise energy costs while ensuring service quality. We present a scalable constraint programming-based large neighbourhood search (CP-LNS) method to solving this challenging problem. We present empirical results that demonstrate that the industrial benchmarks can be solved to near optimality using our approach. Our CP-LNS method provides a fast and practical approach for finding high quality solutions for lowering electricity costs in data centres. © 2013 Springer International Publishing.

关键词： Industrial research

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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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What users care about: A framework for social content alignment

What users care about: A framework for social content alignm...

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23rd International Joint Conference on Artificial Intelligence, IJCAI 2013

作者： Hou, Lei Li, Juanzi Li, Xiaoli Qu, Jiangfeng Guo, Xiaofei Hui, Ou Tang, Jie Dept. of Computer Science and Technology Tsinghua University Tsinghua 100084 China Data Analytics Department Institute for Infocomm Research Singapore 138632 Singapore

ISBN: (纸本)9781577356332

With the rapid proliferation of social media, more and more people freely express their opinions (or comments) on news, products, and movies through online services such as forums, discussion groups, and microblogs. Those comments may be concerned with different aspects (topics) of the target Web document (e.g., a news page). It would be interesting to align the social comments to the corresponding subtopics contained in the Web document. In this paper, we propose a novel framework that is able to automatically detect the subtopics from a given Web document, and also align the associated social comments with the detected subtopics. This provides a new view of the Web standard document and its associated user generated content through topics, which facilitates the readers to quickly focus on those hot topics or grasp topics that they are interested in. Extensive experiments show that our proposed framework significantly outperforms the existing state-of-the-art methods in social content alignment.

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Multiresolution similarity search in time series data: An application to EEG signals 13

Multiresolution similarity search in time series data: An ap...

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6th ACM International Conference on PErvasive Technologies Related to Assistive Environments, PETRA 2013

作者： Charisi, Amalia Malliaros, Fragkiskos D. Zacharaki, Evangelia I. Megalooikonomou, Vasileios Department of Computer Engineering and Informatics University of Patras Greece Computer Science Laboratory École Polytechnique France Center for Data Analytics and Biomedical Informatics Temple University PA United States

ISBN: (纸本)9781450319737

Time series constitute a prevalent data type that arise in several diverse disciplines (e.g., biomedical data, sensor data, images, video data), and therefore analyzing time series is a significant task with a plethora of important applications. In this paper, we study the general problem of similarity search in time series databases and we propose a novel multiresolution indexing (i.e., representation) and retrieval method for time series similarity search. Our approach is motivated by the idea that if we examine a time series at different resolution levels, we could possibly acquire further insights about the data. The proposed algorithm adopts a combined, two-step pruning (filtering) strategy to further reduce data dimensionality by discarding irrelevant time series (i.e., false alarms). At a first level, the time series are represented by line segments and filtered by the triangular inequality property. Then, a Vector Quantization like scheme is applied to encode data and thus to reduce dimensionality. We test and demonstrate the performance of the proposed method, analyzing EEG time series data for retrieval of one of the constituent brain waveforms in EEG recordings, the K-complex, but the method can as well be applied for retrieval of other patterns of interest in time series analysis. The automatic detection and categorization of the EEG patterns will allow the advanced correlation analysis of large amounts of data and will lead to advanced decision making capabilities assisting diagnosis by medical professionals. © 2013 ACM.

关键词： Decision making

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Novel SNP improves differential survivability and mortality in non-small cell lung cancer patients

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BMC Genomics 2014年第9期15卷 1-7页

作者： Mah, Tzia Liang Yap, Xin Ning Adeline Limviphuvadh, Vachiranee Li, Nanpu Sridharan, Srinath Kuralmani, Vellaisemy Feng, Mengling Liem, Natalia Adhikari, Sharmila Yong, Wei Peng Soo, Ross A Maurer-Stroh, Sebastian Eisenhaber, Frank Tong, Joo Chuan Institute for Infocomm Research Data Analytics Department 1 Fusionopolis Way #21-01 Connexis South Tower Singapore 138632 Singapore National University Health System Department of Haematology-Oncology 5 Lower Kent Ridge Road Singapore 119074 Singapore Bioinformatics Institute 30 Biopolis Street #07-01 Matrix Singapore 138671 Singapore Nanyang Technological University (NTU) School of Biological Sciences (SBS) 60 Nanyang Drive 637551 Singapore Nanyang Technological University (NTU) School of Computer Engineering (SCE) 50 Nanyang Drive 637553 Singapore National University of Singapore (NUS) Department of Biological Sciences (DBS) 8 Medical Drive 4 117597 Singapore National University of Singapore Department of Biochemistry Yong Loo Lin School of Medicine Singapore 117597 Singapore Institute of High Performance Computing 1 Fusionopolis Way #16-16 Connexis 138632 Singapore National University of Singapore Cancer Science Institute of Singapore Singapore

Background: Non-small cell lung cancer (NSCLC) is a major cause of cancer-related death worldwide due to poor patient prognosis and clinical outcome. Here, we studied the genetic variations underlying NSCLC pathogenesis based on their association to patient outcome after gemcitabine therapy. Results: Bioinformatics analysis was used to investigate possible effects of POLA2 G583R (POLA2+1747 GG/GA, dbSNP ID: rs487989) in terms of protein function. Using biostatistics, POLA2+1747 GG/GA (rs487989, POLA2 G583R) was identified as strongly associated with mortality rate and survival time among NSCLC patients. It was also shown that POLA2+1747 GG/GA is functionally significant for protein localization via green fluorescent protein (GFP)-tagging and confocal laser scanning microscopy analysis. The single nucleotide polymorphism (SNP) causes DNA polymerase alpha subunit B to localize in the cytoplasm instead of the nucleus. This inhibits DNA replication in cancer cells and confers a protective effect in individuals with this SNP. Conclusions: The results suggest that POLA2+1747 GG/GA may be used as a prognostic biomarker of patient outcome in NSCLC pathogenesis. © 2014 Mah et al.;licensee BioMed Central Ltd.

关键词： Biomarker Genetic variant Mortality Non-small cell lung cancer Survival Outcome

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Lazy Branching for Constraint Satisfaction

Lazy Branching for Constraint Satisfaction

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International Conference on Tools with Artificial Intelligence

作者： Deepak Mehta Barry O'Sullivan Lars Kotthoff Yuri Malitsky INSIGHT Centre for Data Analytics Department of Computer Science University College of Cork

ISBN: (纸本)9781479929733

When solving a constraint satisfaction problem using a systematic backtracking method the branching scheme normally selects a variable to which a value is assigned. In this paper we refer to such strategies as eager branching schemes. These contrast with the alternative class of novel branchings considered in this paper whereby having selected a variable we proceed by removing values from its domain. In this paper we study such lazy branching schemes in depth. We define three lazy branchings based on k-way, binary and split branching. We show how each can be incorporated into MAC, and define a novel value ordering heuristic that is suitable in this setting. Our results show that lazy branching can significantly outperform traditional branching schemes across a variety of problem classes. While, in general, neither lazy nor eager branching dominates the other, our results clearly show that choosing the correct branching scheme for a given problem instances can significantly reduce search effort. Therefore, we implemented a variety of branching portfolios for choosing amongst all of the branching strategies studied in this paper. The results demonstrate that a good branching scheme can be automatically selected for a given problem instances and that including lazy branching schemes in the portfolio significantly reduces runtime.

关键词： Portfolios Search problems Runtime Input variables Educational institutions Systematics Conferences

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A Constraint Programming Approach to the Additional Relay Placement Problem in Wireless Sensor Networks

A Constraint Programming Approach to the Additional Relay Pl...

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International Conference on Tools with Artificial Intelligence

作者： Luis Quesada Kenneth N. Brown Barry O'Sullivan Lanny Sitanayah Cormac J. Sreenan INSIGHT Centre for Data Analytics Department of Computer Science University College Cork Mobile and Internet Systems Laboratory Department of Computer Science University College Cork

ISBN: (纸本)9781479929733

A Wireless Sensor Network (WSN) is composed of many sensor nodes which transmit their data wirelessly over a multi-hop network to data sinks. Since WSNs are subject to node failures, the network topology should be robust, so that when a failure does occur, data delivery can continue from all surviving nodes. A WSN is k-robust if an alternate length-constrained route to a sink is available for each surviving node after the failure of up to k-1 nodes. Determining whether a network is k-robust is an NP-complete problem. We develop a Constraint Programming (CP) approach for solving this problem which outperforms a Mixed-Integer Programming (MIP) model on larger problems. A network can be made robust by deploying extra relay nodes, and we extend our CP approach to an optimisation problem by using QuickXplain to search for a minimal set of relays, and compare it to a state-of-the-art local search approach.

关键词： Wireless sensor networks relay constraint handling wireless multi-hop networks Nondeterministic polynomial-time hard Minimal Set Sinks Ganglia Network topology WSN gene failures

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Erratum to: Methods for evaluating medical tests and biomarkers

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Diagnostic and prognostic research 2017年第1期1卷 11页

作者： Gowri Gopalakrishna Miranda Langendam Rob Scholten Patrick Bossuyt Mariska Leeflang Anna Noel-Storr James Thomas Iain Marshall Byron Wallace Penny Whiting Clare Davenport Gowri GopalaKrishna Isabel de Salis Sue Mallett Robert Wolff Richard Riley Marie Westwood Jos Kleinen Gary Collins Hans Reitsma Karel Moons Antonia Zapf Annika Hoyer Katharina Kramer Oliver Kuss J Ensor J J Deeks E C Martin R D Riley Gerta Rücker Susanne Steinhauser Martin Schumacher Joie Ensor Kym Snell Brian Willis Thomas Debray Jon Deeks Lavinia Ferrante di Ruffano Sian Taylor-Phillips Chris Hyde Stuart A Taylor Gauraang Batnagar Lavinia Ferrante Di Ruffano Farah Seedat Aileen Clarke Sarah Byron Frances Nixon Rebecca Albrow Thomas Walker Carla Deakin Zhivko Zhelev Harriet Hunt Yaling Yang Lucy Abel James Buchanan Thomas Fanshawe Bethany Shinkins Laure Wynants Jan Verbakel Sabine Van Huffel Dirk Timmerman Ben Van Calster Aeliko Zwinderman Jason Oke Jack O'Sullivan Rafael Perera Brian Nicholson Hannah L Bromley Tracy E Roberts Adele Francis Denniis Petrie G Bruce Mann Kinga Malottki Holly Smith Lucinda Billingham Alice Sitch Oke Gerke Mie Holm-Vilstrup Eivind Antonsen Segtnan Ulrich Halekoh Poul Flemming Høilund-Carlsen Bernard G Francq Jac Dinnes Julie Parkes Walter Gregory Jenny Hewison Doug Altman William Rosenberg Peter Selby Julien Asselineau Paul Perez Aïssatou Paye Emilie Bessede Cécile Proust-Lima Christiana Naaktgeboren Joris de Groot Anne Rutjes Johannes Reitsma Emmanuel Ogundimu Jonathan Cook Yannick Le Manach Yvonne Vergouwe Romin Pajouheshnia Rolf Groenwold Karen Moons Linda Peelen Daan Nieboer Bavo De Cock Micael J Pencina Ewout W Steyerberg Jennifer Cooper Nick Parsons Chris Stinton Steve Smith Andy Dickens Rachel Jordan Alexandra Enocson David Fitzmaurice Peymane Adab Charles Boachie Gaj Vidmar Karoline Freeman Martin Connock Rachel Court Carl Moons Jessica Harris Andrew Mumford Zoe Plummer Kurtis Lee Barnaby Reeves Chris Rogers Veerle Verheyden Gianni D Angelini Gavin J Murphy Jeremy Huddy Melody Ni Katherine Good Graham Cooke 1Department of Clinical Epidemiology Biostatistics & Bioinformatics Academic Medical Center University of Amsterdam Amsterdam The Netherlands. 2Cochrane Netherlands Julius Center for Health Sciences and Primary Care University Medical Center Utrecht Utrecht Netherlands. 234Department of Clinical Epidemiology Biostatistics & Bioinformatics Academic Medical Center University of Amsterdam Amsterdam The Netherlands. 49Department of Clinical Epidemiology Biostatistics & Bioinformatics Academic Medical Center University of Amsterdam Amsterdam The Netherlands. 3Cochrane Dementia and Cognitive Improvement Group University of Oxford Oxford UK. 4EPPI-Centre Department of Social Science University College London London UK. 5Division of Health and Social Care Research King's College London London UK. 6College of Computer and Information Science Northeastern University Boston USA. 13University Hospitals Bristol NHS Foundation Trust School of Social and Community Medicine Bristol UK. 275Institute of Applied Health Research University of Birmingham Birmingham UK. 9Department of Clinical Epidemiology Biostatistics & Bioinformatics Academic Medical Center University of Amsterdam Amsterdam The Netherlands. 10School of Social and Community Medicine University of Bristol Bristol UK. 179Institute of Applied Health Research University of Birmingham Birmingham UK. 12Kleijnen Systematic Reviews Ltd York UK. 25Research Institute for Primary Care and Health Sciences Keele University Keele UK. 188Centre for Statistics in Medicine Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Sciences University of Oxford Oxford UK. 191Julius Center for Health Sciences and Primary Care University Medical Center Utrecht 3584 CG Utrecht Netherlands. 237Julius Center for Health Sciences and Primary Care University Medical Center Utrecht 3584 CG Utrecht Netherlands. 18Department of Medical Statistics University Medical Center Göttingen Göttingen Germany. 19Institute for B

[This corrects the article DOI: 10.1186/s41512-016-0001-y.].

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Detecting click fraud in online advertising: a data mining approach

The Journal of Machine Learning Research

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The Journal of Machine Learning Research 2014年第1期15卷

作者： Kevin Murphy Bernhard Schölkopf Richard Oentaryo Ee-Peng Lim Michael Finegold David Lo Feida Zhu Clifton Phua Eng-Yeow Cheu Ghim-Eng Yap Kelvin Sim Minh Nhut Nguyen Kasun Perera Bijay Neupane Mustafa Faisal Zeyar Aung Wei Lee Woon Wei Chen Dhaval Patel Daniel Berrar Google Living Analytics Research Centre Singapore Management University Singapore SAS Institute Pte. Ltd. Singapore Data Analytics Department Institute for Infocomm Research Singapore Masdar Institute of Science and Technology Abu Dhabi United Arab Emirates Institute for Infocomm Research Singapore Department of Computer Science and Engineering Indian Institute of Technology Roorkee Roorkee Uttarakhand India Interdisciplinary Graduate School of Science and Engineering Tokyo Institute of Technology Yokohama Japan

Click fraud-the deliberate clicking on advertisements with no real interest on the product or service offered-is one of the most daunting problems in online advertising. Building an effective fraud detection method is thus pivotal for online advertising businesses. We organized a Fraud Detection in Mobile Advertising (FDMA) 2012 Competition, opening the opportunity for participants to work on real-world fraud data from BuzzCity Pte. Ltd., a global mobile advertising company based in Singapore. In particular, the task is to identify fraudulent publishers who generate illegitimate clicks, and distinguish them from normal publishers. The competition was held from September 1 to September 30, 2012, attracting 127 teams from more than 15 countries. The mobile advertising data are unique and complex, involving heterogeneous information, noisy patterns with missing values, and highly imbalanced class distribution. The competition results provide a comprehensive study on the usability of data mining-based fraud detection approaches in practical setting. Our principal findings are that features derived from fine-grained time-series analysis are crucial for accurate fraud detection, and that ensemble methods offer promising solutions to highly-imbalanced nonlinear classification tasks with mixed variable types and noisy/missing patterns. The competition data remain available for further studies at http://***/fdma2012/.

关键词： ensemble learning feature engineering fraud detection imbalanced classification

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