TY - CHAP T1 - Evolutionary Computation and Constraint Satisfaction Y1 - 2015 A1 - van Hemert, J. ED - Kacpryk, J. ED - Pedrycz, W. KW - constraint satisfaction KW - evolutionary computation AB - In this chapter we will focus on the combination of evolutionary computation techniques and constraint satisfaction problems. Constraint Programming (CP) is another approach to deal with constraint satisfaction problems. In fact, it is an important prelude to the work covered here as it advocates itself as an alternative approach to programming (Apt). The first step is to formulate a problem as a CSP such that techniques from CP, EC, combinations of the two (c.f., Hybrid) or other approaches can be deployed to solve the problem. The formulation of a problem has an impact on its complexity in terms of effort required to either find a solution or proof no solution exists. It is therefore vital to spend time on getting this right. Main differences between CP and EC. CP defines search as iterative steps over a search tree where nodes are partial solutions to the problem where not all variables are assigned values. The search then maintain a partial solution that satisfies all variables assigned values. Instead, in EC most often solver sample a space of candidate solutions where variables are all assigned values. None of these candidate solutions will satisfy all constraints in the problem until a solution is found. Another major difference is that many constraint solvers from CP are sound whereas EC solvers are not. A solver is sound if it always finds a solution if it exists. PB - Springer ER - TY - JOUR T1 - Precise montaging and metric quantification of retinal surface area from ultra-widefield fundus photography and fluorescein angiography JF - Ophthalmic Surg Lasers Imaging Retina Y1 - 2014 A1 - Croft, D.E. A1 - van Hemert, J. A1 - Wykoff, C.C. A1 - Clifton, D. A1 - Verhoek, M. A1 - Fleming, A. A1 - Brown, D.M. KW - medical KW - retinal imaging AB - BACKGROUND AND OBJECTIVE: Accurate quantification of retinal surface area from ultra-widefield (UWF) images is challenging due to warping produced when the retina is projected onto a two-dimensional plane for analysis. By accounting for this, the authors sought to precisely montage and accurately quantify retinal surface area in square millimeters. PATIENTS AND METHODS: Montages were created using Optos 200Tx (Optos, Dunfermline, U.K.) images taken at different gaze angles. A transformation projected the images to their correct location on a three-dimensional model. Area was quantified with spherical trigonometry. Warping, precision, and accuracy were assessed. RESULTS: Uncorrected, posterior pixels represented up to 79% greater surface area than peripheral pixels. Assessing precision, a standard region was quantified across 10 montages of the same eye (RSD: 0.7%; mean: 408.97 mm(2); range: 405.34-413.87 mm(2)). Assessing accuracy, 50 patients' disc areas were quantified (mean: 2.21 mm(2); SE: 0.06 mm(2)), and the results fell within the normative range. CONCLUSION: By accounting for warping inherent in UWF images, precise montaging and accurate quantification of retinal surface area in square millimeters were achieved. [Ophthalmic Surg Lasers Imaging Retina. 2014;45:312-317.]. VL - 45 ER - TY - JOUR T1 - Quantification of Ultra-Widefield Retinal Images JF - Retina Today Y1 - 2014 A1 - D.E. Croft A1 - C.C. Wykoff A1 - D.M. Brown A1 - van Hemert, J. A1 - M. Verhoek KW - medical KW - retinal imaging AB - Advances in imaging periodically lead to dramatic changes in the diagnosis, management, and study of retinal disease. For example, the innovation and wide-spread application of fluorescein angiography and optical coherence tomography (OCT) have had tremendous impact on the management of retinal disorders.1,2 Recently, ultra-widefield (UWF) imaging has opened a new window into the retina, allowing the capture of greater than 80% of the fundus with a single shot.3 With montaging, much of the remaining retinal surface area can be captured.4,5 However, to maximize the potential of these new modalities, accurate quantification of the pathology they capture is critical. UR - http://www.bmctoday.net/retinatoday/pdfs/0514RT_imaging_Croft.pdf 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 - Towards automatic detection of abnormal retinal capillaries in ultra-widefield-of-view retinal angiographic exams T2 - Conf Proc IEEE Eng Med Biol Soc Y1 - 2013 A1 - Zutis, K. A1 - Trucco, E. A1 - Hubschman, J. P. A1 - Reed, D. A1 - Shah, S. A1 - van Hemert, J. KW - retinal imaging AB - Retinal capillary abnormalities include small, leaky, severely tortuous blood vessels that are associated with a variety of retinal pathologies. We present a prototype image-processing system for detecting abnormal retinal capillary regions in ultra-widefield-of-view (UWFOV) fluorescein angiography exams of the human retina. The algorithm takes as input an UWFOV FA frame and returns the candidate regions identified. An SVM classifier is trained on regions traced by expert ophthalmologists. Tests with a variety of feature sets indicate that edge features and allied properties differentiate best between normal and abnormal retinal capillary regions. Experiments with an initial set of images from patients showing branch retinal vein occlusion (BRVO) indicate promising area under the ROC curve of 0.950 and a weighted Cohen's Kappa value of 0.822. JF - Conf Proc IEEE Eng Med Biol Soc ER - TY - JOUR T1 - Generating web-based user interfaces for computational science JF - Concurrency and Computation: Practice and Experience Y1 - 2011 A1 - van Hemert, J. A1 - Koetsier, J. A1 - Torterolo, L. A1 - Porro, I. A1 - Melato, M. A1 - Barbera, R. AB - Scientific gateways in the form of web portals are becoming the popular approach to share knowledge and resources around a topic in a community of researchers. Unfortunately, the development of web portals is expensive and requires specialists skills. Commercial and more generic web portals have a much larger user base and can afford this kind of development. Here we present two solutions that address this problem in the area of portals for scientific computing; both take the same approach. The whole process of designing, delivering and maintaining a portal can be made more cost-effective by generating a portal from a description rather than programming in the traditional sense. We show four successful use cases to show how this process works and the results it can deliver. PB - Wiley VL - 23 ER - TY - JOUR T1 - Special Issue: Portals for life sciences---Providing intuitive access to bioinformatic tools JF - Concurrency and Computation: Practice and Experience Y1 - 2011 A1 - Gesing, Sandra A1 - van Hemert, J. A1 - Kacsuk, P. A1 - Kohlbacher, O. AB - The topic ‘Portals for life sciences’ includes various research fields, on the one hand many different topics out of life sciences, e.g. mass spectrometry, on the other hand portal technologies and different aspects of computer science, such as usability of user interfaces and security of systems. The main aspect about portals is to simplify the user’s interaction with computational resources that are concerted to a supported application domain. PB - Wiley VL - 23 IS - 23 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 - CHAP T1 - Molecular Orbital Calculations of Inorganic Compounds T2 - Inorganic Experiments Y1 - 2010 A1 - C. A. Morrison A1 - N. Robertson A1 - Turner, A. A1 - van Hemert, J. A1 - Koetsier, J. ED - J. Derek Woollins JF - Inorganic Experiments PB - Wiley-VCH SN - 978-3527292530 ER - TY - CONF T1 - Resource management of enterprise cloud systems using layered queuing and historical performance models T2 - IEEE International Symposium on Parallel Distributed Processing Y1 - 2010 A1 - Bacigalupo, D. A. A1 - van Hemert, J. A1 - Usmani, A. A1 - Dillenberger, D. N. A1 - Wills, G. B. A1 - Jarvis, S. A. KW - e-Science AB - The automatic allocation of enterprise workload to resources can be enhanced by being able to make `what-if' response time predictions, whilst different allocations are being considered. It is important to quantitatively compare the effectiveness of different prediction techniques for use in cloud infrastructures. To help make the comparison of relevance to a wide range of possible cloud environments it is useful to consider the following. 1.) urgent cloud customers such as the emergency services that can demand cloud resources at short notice (e.g. for our FireGrid emergency response software). 2.) dynamic enterprise systems, that must rapidly adapt to frequent changes in workload, system configuration and/or available cloud servers. 3.) The use of the predictions in a coordinated manner by both the cloud infrastructure and cloud customer management systems. 4.) A broad range of criteria for evaluating each technique. However, there have been no previous comparisons meeting these requirements. This paper, meeting the above requirements, quantitatively compares the layered queuing and (\^A¿HYDRA\^A¿) historical techniques - including our initial thoughts on how they could be combined. Supporting results and experiments include the following: i.) defining, investigating and hence providing guidelines on the use of a historical and layered queuing model; ii.) using these guidelines showing that both techniques can make low overhead and typically over 70% accurate predictions, for new server architectures for which only a small number of benchmarks have been run; and iii.) defining and investigating tuning a prediction-based cloud workload and resource management algorithm. JF - IEEE International Symposium on Parallel Distributed Processing 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 - Data Integration in eHealth: A Domain/Disease Specific Roadmap T2 - Studies in Health Technology and Informatics Y1 - 2007 A1 - Ure, J. A1 - Proctor, R. A1 - Martone, M. A1 - Porteous, D. A1 - Lloyd, S. A1 - Lawrie, S. A1 - Job, D. A1 - Baldock, R. A1 - Philp, A. A1 - Liewald, D. A1 - Rakebrand, F. A1 - Blaikie, A. A1 - McKay, C. A1 - Anderson, S. A1 - Ainsworth, J. A1 - van Hemert, J. A1 - Blanquer, I. A1 - Sinno ED - N. Jacq ED - Y. Legr{\'e} ED - H. Muller ED - I. Blanquer ED - V. Breton ED - D. Hausser ED - V. Hern{\'a}ndez ED - T. Solomonides ED - M. Hofman-Apitius KW - e-Science AB - The paper documents a series of data integration workshops held in 2006 at the UK National e-Science Centre, summarizing a range of the problem/solution scenarios in multi-site and multi-scale data integration with six HealthGrid projects using schizophrenia as a domain-specific test case. It outlines emerging strategies, recommendations and objectives for collaboration on shared ontology-building and harmonization of data for multi-site trials in this domain. JF - Studies in Health Technology and Informatics PB - IOPress VL - 126 SN - 978-1-58603-738-3 ER - TY - Generic T1 - Genetic Programming, Proceedings of the 8th European Conference T2 - Lecture Notes in Computer Science Y1 - 2005 A1 - Keijzer, M. A1 - Tettamanzi, A. A1 - Collet, P. A1 - van Hemert, J. A1 - Tomassini, M. ED - M. Keijzer ED - A. Tettamanzi ED - P. Collet ED - van Hemert, J. ED - M. Tomassini KW - evolutionary computation JF - Lecture Notes in Computer Science PB - Springer VL - 3447 SN - 3-540-25436-6 UR - http://www.springeronline.com/sgw/cda/frontpage/0,11855,3-40100-22-45347265-0,00.html?changeHeader=true ER -