TY - CONF T1 - C2MS: Dynamic Monitoring and Management of Cloud Infrastructures T2 - IEEE CloudCom Y1 - 2013 A1 - Gary McGilvary A1 - Josep Rius A1 - Íñigo Goiri A1 - Francesc Solsona A1 - Barker, Adam A1 - Atkinson, Malcolm P. AB - Server clustering is a common design principle employed by many organisations who require high availability, scalability and easier management of their infrastructure. Servers are typically clustered according to the service they provide whether it be the application(s) installed, the role of the server or server accessibility for example. In order to optimize performance, manage load and maintain availability, servers may migrate from one cluster group to another making it difficult for server monitoring tools to continuously monitor these dynamically changing groups. Server monitoring tools are usually statically configured and with any change of group membership requires manual reconfiguration; an unreasonable task to undertake on large-scale cloud infrastructures. In this paper we present the Cloudlet Control and Management System (C2MS); a system for monitoring and controlling dynamic groups of physical or virtual servers within cloud infrastructures. The C2MS extends Ganglia - an open source scalable system performance monitoring tool - by allowing system administrators to define, monitor and modify server groups without the need for server reconfiguration. In turn administrators can easily monitor group and individual server metrics on large-scale dynamic cloud infrastructures where roles of servers may change frequently. Furthermore, we complement group monitoring with a control element allowing administrator-specified actions to be performed over servers within service groups as well as introduce further customized monitoring metrics. This paper outlines the design, implementation and evaluation of the C2MS. JF - IEEE CloudCom CY - Bristol, UK ER - TY - JOUR T1 - The Cloud Paradigm Applied to e-Health JF - BMC Med. Inf. {&} Decision Making Y1 - 2013 A1 - Jordi Vilaplana A1 - Francesc Solsona A1 - Francesc Abella A1 - Rosa Filgueira A1 - Josep Rius Torrento VL - 13 ER - TY - JOUR T1 - Computed Tomography Perfusion Imaging Denoising Using Gaussian Process Regression JF - Physics in Medicine and Biology Y1 - 2012 A1 - Fan Zhu A1 - Carpenter, Trevor A1 - Rodríguez, David A1 - Malcolm Atkinson A1 - Wardlaw, Joanna AB - Objective: Brain perfusion weighted images acquired using dynamic contrast studies have an important clinical role in acute stroke diagnosis and treatment decisions. However, Computed Tomography (CT) images suffer from low contrast-to-noise ratios (CNR) as a consequence of the limitation of the exposure to radiation of the patient. As a consequence, the developments of methods for improving the CNR are valuable. Methods: The majority of existing approaches for denoising CT images are optimized for 3D (spatial) information, including spatial decimation (spatially weighted mean filters) and techniques based on wavelet and curvelet transforms. However, perfusion imaging data is 4D as it also contains temporal information. Our approach using Gaussian process regression (GPR), which takes advantage of the temporal information, to reduce the noise level. Results: Over the entire image, GPR gains a 99% CNR improvement over the raw images and also improves the quality of haemodynamic maps allowing a better identification of edges and detailed information. At the level of individual voxel, GPR provides a stable baseline, helps us to identify key parameters from tissue time- concentration curves and reduces the oscillations in the curve. Conclusion: GPR is superior to the comparable techniques used in this study. ER - TY - JOUR T1 - Consistency and repair for XML write-access control policies JF - VLDB J. Y1 - 2012 A1 - Loreto Bravo A1 - James Cheney A1 - Irini Fundulaki A1 - Ricardo Segovia VL - 21 ER - TY - CONF T1 - A Core Calculus for Provenance T2 - POST Y1 - 2012 A1 - Umut A. Acar A1 - Amal Ahmed A1 - James Cheney A1 - Roly Perera JF - POST ER - TY - JOUR T1 - Comparing Clinical Decision Support Systems for Recruitment in Clinical Trials JF - Journal of Medical Informatics Y1 - 2010 A1 - Marc Cuggia A1 - Paolo Besana A1 - David Glasspool. ER - TY - JOUR T1 - Correcting for intra-experiment variation in Illumina BeadChip data is necessary to generate robust gene-expression profiles JF - BMC Genomics Y1 - 2010 A1 - R. R. Kitchen A1 - V. S. Sabine A1 - A. H. Sims A1 - E. J. Macaskill A1 - L. Renshaw A1 - J. S. Thomas A1 - van Hemert, J. I. A1 - J. M. Dixon A1 - J. M. S. Bartlett AB - Background Microarray technology is a popular means of producing whole genome transcriptional profiles, however high cost and scarcity of mRNA has led many studies to be conducted based on the analysis of single samples. We exploit the design of the Illumina platform, specifically multiple arrays on each chip, to evaluate intra-experiment technical variation using repeated hybridisations of universal human reference RNA (UHRR) and duplicate hybridisations of primary breast tumour samples from a clinical study. Results A clear batch-specific bias was detected in the measured expressions of both the UHRR and clinical samples. This bias was found to persist following standard microarray normalisation techniques. However, when mean-centering or empirical Bayes batch-correction methods (ComBat) were applied to the data, inter-batch variation in the UHRR and clinical samples were greatly reduced. Correlation between replicate UHRR samples improved by two orders of magnitude following batch-correction using ComBat (ranging from 0.9833-0.9991 to 0.9997-0.9999) and increased the consistency of the gene-lists from the duplicate clinical samples, from 11.6% in quantile normalised data to 66.4% in batch-corrected data. The use of UHRR as an inter-batch calibrator provided a small additional benefit when used in conjunction with ComBat, further increasing the agreement between the two gene-lists, up to 74.1%. Conclusion In the interests of practicalities and cost, these results suggest that single samples can generate reliable data, but only after careful compensation for technical bias in the experiment. We recommend that investigators appreciate the propensity for such variation in the design stages of a microarray experiment and that the use of suitable correction methods become routine during the statistical analysis of the data. VL - 11 UR - http://www.biomedcentral.com/1471-2164/11/134 IS - 134 ER - TY - JOUR T1 - The Circulate Architecture: Avoiding Workflow Bottlenecks Caused By Centralised Orchestration JF - Cluster Computing Y1 - 2009 A1 - Barker, A. A1 - Weissman, J. A1 - van Hemert, J. I. KW - grid computing KW - workflow VL - 12 UR - http://www.springerlink.com/content/080q5857711w2054/?p=824749739c6a432ea95a0c3b59f4025f&pi=1 ER - TY - CONF T1 - CoMPI: Enhancing MPI Based Applications Performance and Scalability Using Run-Time Compression. T2 - EUROPVM/MPI 2009.Espoo, Finland. September 2009 Y1 - 2009 A1 - Rosa Filgueira A1 - David E. Singh A1 - Alejandro Calderón A1 - Jesús Carretero AB - This paper presents an optimization of MPI communications, called CoMPI, based on run-time compression of MPI messages exchanged by applications. A broad number of compression algorithms have been fully implemented and tested for both MPI collective and point to point primitives. In addition, this paper presents a study of several compression algorithms that can be used for run-time compression, based on the datatype used by applications. This study has been validated by using several MPI benchmarks and real HPC applications. Show that, in most of the cases, using compression reduces the application communication time enhancing application performance and scalability. In this way, CoMPI obtains important improvements in the overall execution time for many of the considered scenarios. JF - EUROPVM/MPI 2009.Espoo, Finland. September 2009 PB - Springer CY - Espoo. Finland VL - 5759/2009 ER - TY - Generic T1 - Crossing boundaries: computational science, e-Science and global e-Infrastructure I T2 - All Hands meeting 2008 Y1 - 2009 A1 - Coveney, P. V. A1 - Atkinson, M. P. ED - Coveney, P. V. ED - Atkinson, M. P. JF - All Hands meeting 2008 T3 - Philosophical Transactions of the Royal Society Series A PB - Royal Society Publishing CY - Edinburgh VL - 367 UR - http://rsta.royalsocietypublishing.org/content/367/1897.toc ER - TY - Generic T1 - Crossing boundaries: computational science, e-Science and global e-Infrastructure II T2 - All Hands Meeting 2008 Y1 - 2009 A1 - Coveney, P. V. A1 - Atkinson, M. P. ED - Coveney, P. V. ED - Atkinson, M. P. JF - All Hands Meeting 2008 T3 - Philosophical Transactions of the Royal Society Series A PB - Royal Society Publishing CY - Edinburgh VL - 367 UR - http://rsta.royalsocietypublishing.org/content/367/1898.toc ER - TY - CHAP T1 - Contraction-Based Heuristics to Improve the Efficiency of Algorithms Solving the Graph Colouring Problem T2 - Studies in Computational Intelligence Y1 - 2008 A1 - Juhos, I. A1 - van Hemert, J. I. ED - Cotta, C. ED - van Hemert, J. I. KW - constraint satisfaction KW - evolutionary computation KW - graph colouring JF - Studies in Computational Intelligence PB - Springer ER - TY - CHAP T1 - COBrA and COBrA-CT: Ontology Engineering Tools T2 - Anatomy Ontologies for Bioinformatics: Principles and Practice Y1 - 2007 A1 - Stuart Aitken A1 - Yin Chen ED - Albert Burger ED - Duncan Davidson ED - Richard Baldock AB - COBrA is a Java-based ontology editor for bio-ontologies and anatomies that dif- fers from other editors by supporting the linking of concepts between two ontologies, and providing sophisticated analysis and verification functions. In addition to the Gene Ontology and Open Biology Ontologies formats, COBrA can import and export ontologies in the Se- mantic Web formats RDF, RDFS and OWL. COBrA is being re-engineered as a Prot ́eg ́e plug-in, and complemented by an ontology server and a tool for the management of ontology versions and collaborative ontology de- velopment. We describe both the original COBrA tool and the current developments in this chapter. JF - Anatomy Ontologies for Bioinformatics: Principles and Practice PB - Springer SN - ISBN-10:1846288843 UR - http://www.amazon.ca/Anatomy-Ontologies-Bioinformatics-Principles-Practice/dp/1846288843 ER - TY - CONF T1 - Complexity Transitions in Evolutionary Algorithms: Evaluating the impact of the initial population T2 - Proceedings of the Congress on Evolutionary Computation Y1 - 2005 A1 - Defaweux, A. A1 - Lenaerts, T. A1 - van Hemert, J. I. A1 - Parent, J. KW - constraint satisfaction KW - transition models AB - This paper proposes an evolutionary approach for the composition of solutions in an incremental way. The approach is based on the metaphor of transitions in complexity discussed in the context of evolutionary biology. Partially defined solutions interact and evolve into aggregations until a full solution for the problem at hand is found. The impact of the initial population on the outcome and the dynamics of the process is evaluated using the domain of binary constraint satisfaction problems. JF - Proceedings of the Congress on Evolutionary Computation PB - {IEEE} Press ER - TY - JOUR T1 - A Criticality-Based Framework for Task Composition in Multi-Agent Bioinformatics Integration Systems JF - Bioinformatics Y1 - 2005 A1 - Karasavvas, K. A1 - Baldock, R. A1 - Burger, A. VL - 21 ER - TY - CONF T1 - Cross-Layer Peer-to-Peer Traffic Identification and Optimization Based on Active Networking T2 - 7th International Working Conference on Active and Programmable Networks Y1 - 2005 A1 - Dedinski, I. A1 - De Meer, H. A1 - Liangxiu Han A1 - Mathy, L. A1 - Pezaros, D. A1 - P. , Sventek, J. S. A1 - Xiaoying, Z. JF - 7th International Working Conference on Active and Programmable Networks CY - Sophia Antipolis, French Riviera, La Cote d'Azur, France, November 21-23, 2005. ER - TY - JOUR T1 - Comparing Evolutionary Algorithms on Binary Constraint Satisfaction Problems JF - IEEE Transactions on Evolutionary Computation Y1 - 2003 A1 - Craenen, B. G. W. A1 - Eiben, A. E. A1 - van Hemert, J. I. KW - constraint satisfaction AB - Constraint handling is not straightforward in evolutionary algorithms (EA) since the usual search operators, mutation and recombination, are `blind' to constraints. Nevertheless, the issue is highly relevant, for many challenging problems involve constraints. Over the last decade numerous EAs for solving constraint satisfaction problems (CSP) have been introduced and studied on various problems. The diversity of approaches and the variety of problems used to study the resulting algorithms prevents a fair and accurate comparison of these algorithms. This paper aligns related work by presenting a concise overview and an extensive performance comparison of all these EAs on a systematically generated test suite of random binary CSPs. The random problem instance generator is based on a theoretical model that fixes deficiencies of models and respective generators that have been formerly used in the Evolutionary Computing (EC) field. VL - 7 UR - http://ieeexplore.ieee.org/xpl/abs_free.jsp?isNumber=27734&prod=JNL&arnumber=1237162&arSt=+424&ared=+444&arAuthor=+Craenen%2C+B.G.W.%3B++Eiben%2C+A.E.%3B++van+Hemert%2C+J.I.&arNumber=1237162&a_id0=1237161&a_id1=1237162&a_id2=1237163&a_id3=1237164&a_id4=12 ER - TY - RPRT T1 - Computer Challenges to emerge from e-Science. Y1 - 2003 A1 - Atkinson, M. A1 - Crowcroft, J. A1 - Goble, C. A1 - Gurd, J. A1 - Rodden, T. A1 - Shadbolt, N. A1 - Sloman, M. A1 - Sommerville, I. A1 - Storey, T. AB - The UK e-Science programme has initiated significant developments that allow networked grid technology to be used to form virtual colaboratories. The e-Science vision of a globally connected community has broader application than science with the same fundamental technologies being used to support eCommerce and e-Government. The broadest vision of e-Science outlines a challenging research agenda for the computing community. New theories and models will be needed to provide a sound foundation for the tools used to specify, design, analyse and prove the properties of future grid technologies and applications. Fundamental research is needed in order to build a future e-Science infrastructure and to understand how to exploit the infrastructure to best effect. A future infrastructure needs to be dynamic, universally available and promote trust. Realising this infrastructure will need new theories, methods and techniques to be developed and deployed. Although often not directly visible these fundamental infrastructure advances will provide the foundation for future scientific advancement, wealth generation and governance. • We need to move from the current data focus to a semantic grid with facilities for the generation, support and traceability of knowledge. • We need to make the infrastructure more available and more trusted by developing trusted ubiquitous systems. • We need to reduce the cost of development by enabling the rapid customised assembly of services. • We need to reduce the cost and complexity of managing the infrastructure by realising autonomic computing systems. JF - EPSRC ER - TY - CONF T1 - Comparing Classical Methods for Solving Binary Constraint Satisfaction Problems with State of the Art Evolutionary Computation T2 - Springer Lecture Notes on Computer Science Y1 - 2002 A1 - van Hemert, J. I. ED - S. Cagnoni ED - J. Gottlieb ED - E. Hart ED - M. Middendorf ED - G. Raidl KW - constraint satisfaction AB - Constraint Satisfaction Problems form a class of problems that are generally computationally difficult and have been addressed with many complete and heuristic algorithms. We present two complete algorithms, as well as two evolutionary algorithms, and compare them on randomly generated instances of binary constraint satisfaction prob-lems. We find that the evolutionary algorithms are less effective than the classical techniques. JF - Springer Lecture Notes on Computer Science PB - Springer-Verlag, Berlin ER - TY - CONF T1 - Criticality-Based Task Composition in Distributed Bioinformatics Systems T2 - Proceedings of the Twelfth International Conference on Intelligent Systems for Molecular Biology Y1 - 2002 A1 - Karasavvas, K. A1 - Baldock, R. A1 - Burger, A. JF - Proceedings of the Twelfth International Conference on Intelligent Systems for Molecular Biology ER - TY - JOUR T1 - The characterizing network traffic based on the wavelet technique JF - Journal of Mini-Micro Computer System Y1 - 2001 A1 - Liangxiu Han A1 - Cong Suo VL - 22 IS - 9 ER - TY - CONF T1 - Constraint Satisfaction Problems and Evolutionary Algorithms: A Reality Check T2 - Proceedings of the Twelfth Belgium/Netherlands Conference on Artificial Intelligence (BNAIC'00) Y1 - 2000 A1 - van Hemert, J. I. ED - van den Bosch, A. ED - H. Weigand KW - constraint satisfaction AB - Constraint satisfaction has been the subject of many studies. Different areas of research have tried to solve all kind of constraint problems. Here we will look at a general model for constraint satisfaction problems in the form of binary constraint satisfaction. The problems generated from this model are studied in the research area of constraint programming and in the research area of evolutionary computation. This paper provides an empirical comparison of two techniques from each area. Basically, this is a check on how well both areas are doing. It turns out that, although evolutionary algorithms are doing well, classic approaches are still more successful. JF - Proceedings of the Twelfth Belgium/Netherlands Conference on Artificial Intelligence (BNAIC'00) PB - BNVKI, Dutch and the Belgian AI Association ER - TY - CONF T1 - Comparing genetic programming variants for data classification T2 - Proceedings of the Eleventh Belgium/Netherlands Conference on Artificial Intelligence (BNAIC'99) Y1 - 1999 A1 - Eggermont, J. A1 - Eiben, A. E. A1 - van Hemert, J. I. ED - E. Postma ED - M. Gyssens KW - classification KW - data mining KW - genetic programming AB - This article is a combined summary of two papers written by the authors. Binary data classification problems (with exactly two disjoint classes) form an important application area of machine learning techniques, in particular genetic programming (GP). In this study we compare a number of different variants of GP applied to such problems whereby we investigate the effect of two significant changes in a fixed GP setup in combination with two different evolutionary models JF - Proceedings of the Eleventh Belgium/Netherlands Conference on Artificial Intelligence (BNAIC'99) PB - BNVKI, Dutch and the Belgian AI Association ER - TY - CONF T1 - A comparison of genetic programming variants for data classification T2 - Springer Lecture Notes on Computer Science Y1 - 1999 A1 - Eggermont, J. A1 - Eiben, A. E. A1 - van Hemert, J. I. ED - D. J. Hand ED - J. N. Kok ED - M. R. Berthold KW - classification KW - data mining KW - genetic programming AB - In this paper we report the results of a comparative study on different variations of genetic programming applied on binary data classification problems. The first genetic programming variant is weighting data records for calculating the classification error and modifying the weights during the run. Hereby the algorithm is defining its own fitness function in an on-line fashion giving higher weights to `hard' records. Another novel feature we study is the atomic representation, where `Booleanization' of data is not performed at the root, but at the leafs of the trees and only Boolean functions are used in the trees' body. As a third aspect we look at generational and steady-state models in combination of both features. JF - Springer Lecture Notes on Computer Science PB - Springer-Verlag, Berlin SN - 3-540-66332-0 ER -