TY  - CONF
T1  - Ad hoc Cloud Computing
T2  - IEEE Cloud
Y1  - 2015
A1  - Gary McGilvary
A1  - Barker, Adam
A1  - Malcolm Atkinson
KW  - ad hoc
KW  - cloud computing
KW  - reliability
KW  - virtualization
KW  - volunteer computing
AB  - This paper presents the first complete, integrated and end-to-end solution for ad hoc cloud computing environments. Ad hoc clouds harvest resources from existing sporadically available, non-exclusive (i.e. primarily used for some other purpose) and unreliable infrastructures. In this paper we discuss the problems ad hoc cloud computing solves and outline our architecture which is based on BOINC.
JF  - IEEE Cloud
UR  - http://arxiv.org/abs/1505.08097
ER  - 

TY  - BOOK
T1  - Ad hoc Cloud Computing (PhD Thesis)
Y1  - 2014
A1  - Gary McGilvary
AB  - Commercial and private cloud providers offer virtualized resources via a set of co-located and dedicated hosts that are exclusively reserved for the purpose of offering a cloud service. While both cloud models appeal to the mass market, there are many cases where outsourcing to a remote platform or procuring an in-house infrastructure may not be ideal or even possible.    To offer an attractive alternative, we introduce and develop an <i>ad hoc</i> cloud computing platform to transform spare resource capacity from an infrastructure owner's locally available, but non-exclusive and unreliable infrastructure, into an overlay cloud platform. The foundation of the <i>ad hoc</i> cloud relies on transferring and instantiating lightweight virtual machines on-demand upon near-optimal hosts while virtual machine checkpoints are distributed in a P2P fashion to other members of the <i>ad hoc</i> cloud. Virtual machines found to be non-operational are restored elsewhere ensuring the continuity of cloud jobs.     In this thesis <i>we investigate the feasibility, reliability and performance of ad hoc cloud computing infrastructures</i>. We firstly show that the combination of both volunteer computing and virtualization is the backbone of the <i>ad hoc</i> cloud. We outline the process of virtualizing the volunteer system BOINC to create V-BOINC. V-BOINC distributes virtual machines to volunteer hosts allowing volunteer applications to be executed in the sandbox environment to solve many of the downfalls of BOINC; this however also provides the basis for an <i>ad hoc</i> cloud computing platform to be developed.    We detail the challenges of transforming V-BOINC into an <i>ad hoc</i> cloud and outline the transformational process and integrated extensions. These include a BOINC job submission system, cloud job and virtual machine restoration schedulers and a periodic P2P checkpoint distribution component. Furthermore, as current monitoring tools are unable to cope with the dynamic nature of <i>ad hoc</i> clouds, a dynamic infrastructure monitoring and management tool called the Cloudlet Control Monitoring System is developed and presented.    We evaluate each of our individual contributions as well as the reliability, performance and overheads associated with an <i>ad hoc</i> cloud deployed on a realistically simulated unreliable infrastructure. We conclude that the <i>ad hoc</i> cloud is not only a feasible concept but also a viable computational alternative that offers high levels of reliability and can at least offer reasonable performance, which at times may exceed the performance of a commercial cloud infrastructure.
PB  - The University of Edinburgh
CY  - Edinburgh
ER  - 

TY  - CONF
T1  - Applying selectively parallel IO compression to parallel storage systems
T2  - Euro-Par
Y1  - 2014
A1  - Rosa Filgueira
A1  - Malcolm Atkinson
A1  - Yusuke Tanimura
A1  - Isao Kojima
JF  - Euro-Par
ER  - 

TY  - JOUR
T1  - Automatic extraction of retinal features from colour retinal images for glaucoma diagnosis: A review
JF  - Computerized Medical Imaging and Graphics
Y1  - 2013
A1  - Haleem, M.S.
A1  - Han, L.
A1  - van Hemert, J.
A1  - Li, B.
KW  - retinal imaging
AB  - Glaucoma is a group of eye diseases that have common traits such as, high eye pressure, damage to the Optic Nerve Head and gradual vision loss. It affects peripheral vision and eventually leads to blindness if left untreated. The current common methods of pre-diagnosis of Glaucoma include measurement of Intra-Ocular Pressure (IOP) using Tonometer, Pachymetry, Gonioscopy; which are performed manually by the clinicians. These tests are usually followed by Optic Nerve Head (ONH) Appearance examination for the confirmed diagnosis of Glaucoma. The diagnoses require regular monitoring, which is costly and time consuming. The accuracy and reliability of diagnosis is limited by the domain knowledge of different ophthalmologists. Therefore automatic diagnosis of Glaucoma attracts a lot of attention. This paper surveys the state-of-the-art of automatic extraction of anatomical features from retinal images to assist early diagnosis of the Glaucoma. We have conducted critical evaluation of the existing automatic extraction methods based on features including Optic Cup to Disc Ratio (CDR), Retinal Nerve Fibre Layer (RNFL), Peripapillary Atrophy (PPA), Neuroretinal Rim Notching, Vasculature Shift, etc., which adds value on efficient feature extraction related to Glaucoma diagnosis.
VL  - 37
SN  - 0895-6111
UR  - http://linkinghub.elsevier.com/retrieve/pii/S0895611113001468?showall=true
ER  - 

TY  - CONF
T1  - Automatic Extraction of the Optic Disc Boundary for Detecting Retinal Diseases
T2  - 14th {IASTED} International Conference on Computer Graphics and Imaging (CGIM)
Y1  - 2013
A1  - M.S. Haleem
A1  - L. Han
A1  - B. Li
A1  - A. Nisbet
A1  - van Hemert, J.
A1  - M. Verhoek
ED  - L. Linsen
ED  - M. Kampel
KW  - retinal imaging
AB  - In this paper, we propose an algorithm based on active shape model for the extraction of Optic Disc boundary. The determination of Optic Disc boundary is fundamental to the automation of retinal eye disease diagnosis because the Optic Disc Center is typically used as a reference point to locate other retinal structures, and any structural change in Optic Disc, whether textural or geometrical, can be used to determine the occurrence of retinal diseases such as Glaucoma. The algorithm is based on determining a model for the Optic Disc boundary by learning patterns of variability from a training set of annotated Optic Discs. The model can be deformed so as to reflect the boundary of Optic Disc in any feasible shape. The algorithm provides some initial steps towards automation of the diagnostic process for retinal eye disease in order that more patients can be screened with consistent diagnoses. The overall accuracy of the algorithm was 92% on a set of 110 images.
JF  - 14th {IASTED} International Conference on Computer Graphics and Imaging (CGIM)
PB  - {ACTA} Press
ER  - 

TY  - CONF
T1  - Abstract: Reservation-Based I/O Performance Guarantee for MPI-IO Applications Using Shared Storage Systems
T2  - SC Companion
Y1  - 2012
A1  - Yusuke Tanimura
A1  - Rosa Filgueira
A1  - Isao Kojima
A1  - Malcolm P. Atkinson
JF  - SC Companion
ER  - 

TY  - CONF
T1  - An adaptive, scalable, and portable technique for speeding up MPI-based applications
T2  - International European Conference on Parallel and Distributed Computing, Europar-2012
Y1  - 2012
A1  - Rosa Filgueira
A1  - Alberto Nuñez
A1  - Javier Fernandez
A1  - Malcolm Atkinson
JF  - International European Conference on Parallel and Distributed Computing, Europar-2012
ER  - 

TY  - CONF
T1  - Automatic Agent Protocol Generation from Argumentation
T2  - 13th European Agent Systems Summer Schoo
Y1  - 2011
A1  - Ashwag Omar Maghraby
JF  - 13th European Agent Systems Summer Schoo
ER  - 

TY  - JOUR
T1  - Automatically Identifying and Annotating Mouse Embryo Gene Expression Patterns
JF  - Bioinformatics
Y1  - 2011
A1  - Liangxiu Han
A1  - van Hemert, Jano
A1  - Richard Baldock
KW  - classification
KW  - e-Science
AB  - Motivation: Deciphering the regulatory and developmental mechanisms for multicellular organisms requires detailed knowledge of gene interactions and gene expressions. The availability of large datasets with both spatial and ontological annotation of the spatio-temporal patterns of gene-expression in mouse embryo provides a powerful resource to discover the biological function of embryo organisation. Ontological annotation of gene expressions consists of labelling images with terms from the anatomy ontology for mouse development. If the spatial genes of an anatomical component are expressed in an image, the image is then tagged with a term of that anatomical component. The current annotation is done manually by domain experts, which is both time consuming and costly. In addition, the level of detail is variable and inevitably, errors arise from the tedious nature of the task. In this paper, we present a new method to automatically identify and annotate gene expression patterns in the mouse embryo with anatomical terms.    Results: The method takes images from in situ hybridisation studies and the ontology for the developing mouse embryo, it then combines machine learning and image processing techniques to produce classifiers that automatically identify and annotate gene expression patterns in these images.We evaluate our method on image data from the EURExpress-II study where we use it to automatically classify nine anatomical terms: humerus, handplate, fibula, tibia, femur, ribs, petrous part, scapula and head mesenchyme. The accuracy of our method lies between 70–80% with few exceptions.     Conclusions: We show that other known methods have lower classification performance than ours. We have investigated the images misclassified by our method and found several cases where the original annotation was not correct. This shows our method is robust against this kind of noise.     Availability: The annotation result and the experimental dataset in the paper can be freely accessed at http://www2.docm.mmu.ac.uk/STAFF/L.Han/geneannotation/    Contact: l.han@mmu.ac.uk, j.vanhemert@ed.ac.uk and Richard.Baldock@hgu.mrc.ac.uk
VL  - 27
UR  - http://bioinformatics.oxfordjournals.org/content/early/2011/02/25/bioinformatics.btr105.abstract
ER  - 

TY  - CONF
T1  - Accelerating Data-Intensive Applications: a Cloud Computing Approach Image Pattern Recognition Tasks
T2  - The Fourth International Conference on Advanced Engineering Computing and Applications in Sciences
Y1  - 2010
A1  - Han, L
A1  - Saengngam, T.
A1  - van Hemert, J.
JF  - The Fourth International Conference on Advanced Engineering Computing and Applications in Sciences
ER  - 

TY  - JOUR
T1  - Adaptive CoMPI: Enhancing MPI based applications performance and scalability by using adaptive compression.
JF  - International Journal of High Performance Computing and Applications, 2010. Sage
Y1  - 2010
A1  - Rosa Filgueira
A1  - David E. Singh
A1  - Alejandro Calderón
A1  - Félix García Carballeira
A1  - Jesús Carretero
AB  - This paper presents an optimization of MPI communication, called Adaptive-CoMPI, based on runtime compression of MPI messages exchanged by applications. The technique developed can be used for any application, because its implementation is transparent for the user, and integrates different compression algorithms for both MPI collective and point-to-point primitives. Furthermore, compression is turned on and off and the most appropriate compression algorithms are selected at runtime, depending on the characteristics of each message, the network behavior, and compression algorithm behavior, following a runtime adaptive strategy. Our system can be optimized for a specific application, through a guided strategy, to reduce the runtime strategy overhead. Adaptive-CoMPI has been validated using several MPI benchmarks and real HPC applications. Results show that, in most cases, by using adaptive compression, communication time is reduced, enhancing application performance and scalability.
IS  - 25 (3)
ER  - 

TY  - RPRT
T1  - ADMIRE D1.5 – Report defining an iteration of the model and language: PM3 and DL3
Y1  - 2009
A1  - Peter Brezany
A1  - Ivan Janciak
A1  - Alexander Woehrer
A1  - Carlos Buil Aranda
A1  - Malcolm Atkinson
A1  - van Hemert, Jano
AB  - This document is the third deliverable to report on the progress of the model, language and ontology research conducted within Workpackage 1 of the ADMIRE project. Significant progress has been made on each of the above areas. The new results that we achieved are recorded against the targets defined for project month 18 and are reported in four sections of this document
PB  - ADMIRE project
UR  - http://www.admire-project.eu/docs/ADMIRE-D1.5-model-language-ontology.pdf
ER  - 

TY  - CONF
T1  - Adoption of e-Infrastructure Services: inhibitors, enablers and opportunities
T2  - 5th International Conference on e-Social Science
Y1  - 2009
A1  - Voss, A.
A1  - Asgari-Targhi, M.
A1  - Procter, R.
A1  - Halfpenny, P.
A1  - Fragkouli, E.
A1  - Anderson, S.
A1  - Hughes, L.
A1  - Fergusson, D.
A1  - Vander Meer, E.
A1  - Atkinson, M.
AB  - Based on more than 100 interviews with respondents from the academic community and information services, we present findings from our study of inhibitors and enablers of adoption of e-Infrastructure services for research. We discuss issues raised and potential ways of addressing them.
JF  - 5th International Conference on e-Social Science
CY  - Maternushaus, Cologne
ER  - 

TY  - CONF
T1  - Advanced Data Mining and Integration Research for Europe
T2  - All Hands Meeting 2009
Y1  - 2009
A1  - Atkinson, M.
A1  - Brezany, P.
A1  - Corcho, O.
A1  - Han, L
A1  - van Hemert, J.
A1  - Hluchy, L.
A1  - Hume, A.
A1  - Janciak, I.
A1  - Krause, A.
A1  - Snelling, D.
A1  - Wöhrer, A.
AB  - There is a rapidly growing wealth of data [1]. The number of sources of data is increasing,  while, at the same time, the diversity, complexity and scale of these data resources are also increasing  dramatically. This cornucopia of data oers much potential; a combinatorial explosion of opportunities  for knowledge discovery, improved decisions and better policies. Today, most of these opportunities are  not realised because composing data from multiple sources and extracting information is too dicult.  Every business, organisation and government faces problems that can only be addressed successfully if  we improve our techniques for exploiting the data we gather.
JF  - All Hands Meeting 2009
CY  - Oxford
ER  - 

TY  - CONF
T1  - Automating Gene Expression Annotation for Mouse Embryo
T2  - Lecture Notes in Computer Science (Advanced Data Mining and Applications, 5th International Conference)
Y1  - 2009
A1  - Liangxiu Han
A1  - van Hemert, Jano
A1  - Richard Baldock
A1  - Atkinson, Malcolm P.
ED  - Ronghuai Huang
ED  - Qiang Yang
ED  - Jian Pei
ED  - et al
JF  - Lecture Notes in Computer Science (Advanced Data Mining and Applications, 5th International Conference)
PB  - Springer
VL  - LNAI 5678
ER  - 

TY  - CONF
T1  - An Architecture for an Integrated Fire Emergency Response System for the Built Environment
T2  - 9th Symposium of the International Association for Fire Safety Science (IAFSS)
Y1  - 2008
A1  - Rochan Upadhyay
A1  - Galvin Pringle
A1  - George Beckett
A1  - Stephen Potter
A1  - Liangxiu Han
A1  - Stephen Welch
A1  - Asif Usmani
A1  - Jose Torero
KW  - emergency response system
KW  - FireGrid
KW  - system architecture
KW  - technology integration
AB  - FireGrid is a modern concept that aims to leverage a number of modern technologies to aid   fire emergency response. In this paper we provide a brief introduction to the FireGrid project. A number   of different technologies such as wireless sensor networks, grid-enabled High Performance Computing   (HPC) implementation of fire models, and artificial intelligence tools need to be integrated to build up a   modern fire emergency response system. We propose a system architecture that provides the framework for integration of the various technologies. We describe the components of the generic FireGrid system architecture in detail. Finally we present a small-scale demonstration experiment which has been completed to highlight the concept and application of the FireGrid system to an actual fire. Although our proposed system architecture provides a versatile framework for integration, a number of new and interesting research problems need to be solved before actual deployment of the system. We outline some of the challenges involved which require significant interdisciplinary collaborations.
JF  - 9th Symposium of the International Association for Fire Safety Science (IAFSS)
PB  - IAFSS
CY  - Karlsruhe, GERMANY
ER  - 

TY  - CONF
T1  - Accessing Data in Grids Using OGSA-DAI
T2  - Knowledge and Data Management in Grids
Y1  - 2007
A1  - Chue Hong, N. P.
A1  - Antonioletti, M.
A1  - Karasavvas, K. A.
A1  - Atkinson, M.
ED  - Talia, D.
ED  - Bilas, A.
ED  - Dikaiakos, M.
AB  - The grid provides a vision in which resources, including storage and data, can be shared across organisational boundaries. The original emphasis of grid computing lay in the sharing of computational resources but technological and scientific advances have led to an ongoing data explosion in many fields. However, data is stored in many different storage systems and data formats, with different schema, access rights, metadata attributes, and ontologies all of which are obstacles to the access, integration and management of this information.    In this chapter we examine some of the ways in which these differences can be addressed by grid technology to enable the meaningful sharing of data. In particular, we present an overview of the OGSA-DAI (Open Grid Service Architecture - Data Access and Integration) software, which provides a uniform, extensible framework for accessing structured and semi-structured data and provide some examples of its use in other projects. The open-source OGSA-DAI software is freely available from http://www.ogsadai.org.uk.
JF  - Knowledge and Data Management in Grids
SN  - 978-0-387-37830-5
UR  - http://www.springer.com/computer/communication+networks/book/978-0-387-37830-5
ER  - 

TY  - CONF
T1  - The Architectural Design of Multi Interface-Device Binding (MID-B) System
T2  - The 3rd Workshop on Context Awareness for Proactive Systems
Y1  - 2007
A1  - Srihathai Prammanee
A1  - Klaus Moessner
AB  - The Multi Interface-Device Binding (MID-B) System enhances a multimodal interaction in a virtual-device environment. The system promises to overcome the drawbacks of classic multimodal interaction. In the classic sense,  multimodality uses a strategy of simultaneously utilising several modalities  generally offered on a single device. In contrast, the MID-B’s mechanism gets  multimodality out of the solitary-device scenario. In MID-B, a ‘controller- device’ (UE_C) is aware of the availability of various devices in the vicinity,  each of which may host one or more user interfaces (modalities). The   capabilities of each of the co-located devices, together with the context in which the user acts, is exploited to dynamically customise the interface services available. This paper describes the MID-B architecture and its mechanisms to collect and exploit device and user context information to dynamically adapt the user interfaces.
JF  - The 3rd Workshop on Context Awareness for Proactive Systems
CY  - Guildford, UK
UR  - http://www.geocities.com/sprammanee/
ER  - 

TY  - JOUR
T1  - Application of the methodology combined formal method with Object-Oriented technology in E-commerce
JF  - Journal of Computer Engineering
Y1  - 2002
A1  - Liangxiu Han
VL  - 29
IS  - z1
ER  - 

TY  - CONF
T1  - Adaptive Genetic Programming Applied to New and Existing Simple Regression Problems
T2  - Springer Lecture Notes on Computer Science
Y1  - 2001
A1  - Eggermont, J.
A1  - van Hemert, J. I.
ED  - J. Miller
ED  - Tomassini, M.
ED  - P. L. Lanzi
ED  - C. Ryan
ED  - A. G. B. Tettamanzi
ED  - W. B. Langdon
KW  - data mining
AB  - In this paper we continue our study on adaptive genetic pro-gramming. We use Stepwise Adaptation of Weights to boost performance of a genetic programming algorithm on simple symbolic regression problems. We measure the performance of a standard GP and two variants of SAW extensions on two different symbolic regression prob-lems from literature. Also, we propose a model for randomly generating polynomials which we then use to further test all three GP variants.
JF  - Springer Lecture Notes on Computer Science
PB  - Springer-Verlag, Berlin
SN  - 9-783540-418993
ER  - 

TY  - CONF
T1  - Adapting the Fitness Function in GP for Data Mining
T2  - Springer Lecture Notes on Computer Science
Y1  - 1999
A1  - Eggermont, J.
A1  - Eiben, A. E.
A1  - van Hemert, J. I.
ED  - R. Poli
ED  - P. Nordin
ED  - W. B. Langdon
ED  - T. C. Fogarty
KW  - data mining
KW  - genetic programming
AB  - In this paper we describe how the Stepwise Adaptation of Weights (SAW) technique can be applied in genetic programming. The SAW-ing mechanism has been originally developed for and successfully used in EAs for constraint satisfaction problems. Here we identify the very basic underlying ideas behind SAW-ing and point out how it can be used for different types of problems. In particular, SAW-ing is well suited for data mining tasks where the fitness of a candidate solution is composed by `local scores' on data records. We evaluate the power of the SAW-ing mechanism on a number of benchmark classification data sets. The results indicate that extending the GP with the SAW-ing feature increases its performance when different types of misclassifications are not weighted differently, but leads to worse results when they are.
JF  - Springer Lecture Notes on Computer Science
PB  - Springer-Verlag, Berlin
SN  - 3-540-65899-8
ER  -