Object-Oriented Paradigms for Modelling Vascular\ud Tumour Growth: a Case Study

Motivated by a family of related hybrid multiscale models, we have built an object-oriented framework for developing and implementing multiscale models of vascular tumour growth. The models are implemented in our framework as a case study to highlight how object-oriented programming techniques and good object-oriented design may be used effectively to develop hybrid multiscale models of vascular tumour growth. The intention is that this paper will serve as a useful reference for researchers modelling complex biological systems and that these researchers will employ some of the techniques presented herein in their own projects

Component-based simulation for a reconfiguration study of transitic systems

This paper is organized as follows. Part A presents the context of reconfiguring transitic systems and the main idea in implementing the decision step. It comprises sections 1 to 3. Section 3 presents an example that illustrates the concepts presented in the next sections. Parts B and C express the models and principles used to simulate transitic systems, the result of which will be helpful for choosing the new configuration. Part B focuses mainly on models. It comprises sections 4 to 6. Part C focuses mainly on simulation principles. It comprises sections 7 to 10

GEANT4 : a simulation toolkit

Abstract Geant4 is a toolkit for simulating the passage of particles through matter. It includes a complete range of functionality including tracking, geometry, physics models and hits. The physics processes offered cover a comprehensive range, including electromagnetic, hadronic and optical processes, a large set of long-lived particles, materials and elements, over a wide energy range starting, in some cases, from 250 eV and extending in others to the TeV energy range. It has been designed and constructed to expose the physics models utilised, to handle complex geometries, and to enable its easy adaptation for optimal use in different sets of applications. The toolkit is the result of a worldwide collaboration of physicists and software engineers. It has been created exploiting software engineering and object-oriented technology and implemented in the C++ programming language. It has been used in applications in particle physics, nuclear physics, accelerator design, space engineering and medical physics. PACS: 07.05.Tp; 13; 2

Feature binding of MPEG-7 Visual Descriptors Using Chaotic Series

Due to advanced segmentation and tracking algorithms, a video can be divided into numerous objects. Segmentation and tracking algorithms output different low-level object features, resulting in a high-dimensional feature vector per object. The challenge is to generate feature vector of objects which can be mapped to human understandable description, such as object labels, e.g., person, car. MPEG-7 provides visual descriptors to describe video contents. However, generally the MPEG-7 visual descriptors are highly redundant, and the feature coefficients in these descriptors need to be pre-processed for domain specific application. Ideal case would be if MPEG-7 visual descriptor based feature vector, can be processed similar to some functional simulations of human brain activity. There has been a established link between the analysis of temporal human brain oscillatory signals and chaotic dynamics from the electroencephalography (EEG) of the brain neurons. Neural signals in limited brain activities are found to be behaviorally relevant (previously appeared to be noise) and can be simulated using chaotic series. Chaotic series is referred to as either a finite-difference or an ordinary differential equation, which presents non-random, irregular fluctuations of parameter values over time in a dynamical system. The dynamics in a chaotic series can be high - or low -dimensional, and the dimensionality can be deduced from the topological dimension of the attractor of the chaotic series. An attractor is manifested by the tendency of a non-linear finite difference equation or an ordinary differential equation, under various but delimited conditions, to go to a reproducible active state, and stay there. We propose a feature binding method, using chaotic series, to generate a new feature vector, C-MP7 , to describe video objects. The proposed method considers MPEG-7 visual descriptor coefficients as dynamical systems. Dynamical systems are excited (similar to neuronal excitation) with either high- or low-dimensional chaotic series, and then histogram-based clustering is applied on the simulated chaotic series coefficients to generate C-MP7 . The proposed feature binding offers better feature vector with high-dimensional chaotic series simulation than with low-dimensional chaotic series, over MPEG-7 visual descriptor based feature vector. Diverse video objects are grouped in four generic classes (e.g., has [barbelow]person, has [barbelow]group [barbelow]of [barbelow]persons, has [barbelow]vehicle, and has [barbelow]unknown ) to observe how well C-MP7 describes different video objects compared to MPEG-7 feature vector. In C-MP7 , with high dimensional chaotic series simulation, 1). descriptor coefficients are reduced dynamically up to 37.05% compared to 10% in MPEG-7 , 2) higher variance is achieved than MPEG-7 , 3) multi-class discriminant analysis of C-MP7 with Fisher-criteria shows increased binary class separation for clustered video objects than that of MPEG-7 , and 4) C-MP7 , specifically provides good clustering of video objects for has [barbelow]vehicle class against other classes. To test C-MP7 in an application, we deploy a combination of multiple binary classifiers for video object classification. Related work on video object classification use non-MPEG-7 features. We specifically observe classification of challenging surveillance video objects, e.g., incomplete objects, partial occlusion, background over lapping, scale and resolution variant objects, indoor / outdoor lighting variations. C-MP7 is used to train different classes of video objects. Object classification accuracy is verified with both low-dimensional and high-dimensional chaotic series based feature binding for C-MP7 . Testing of diverse video objects with high-dimensional chaotic series simulation shows, 1) classification accuracy significantly improves on average, 83% compared to the 62% with MPEG-7 , 2) excellent clustering of vehicle objects leads to above 99% accuracy for only vehicles against all other objects, and 3) with diverse video objects, including objects from poor segmentation. C-MP7 is more robust as a feature vector in classification than MPEG-7 . Initial results on sub-group classification for male and female video objects in has [barbelow]person class are also presentated as subjective observations. Earlier, chaos series properties have been used in video processing applications for compression and digital watermarking. To our best knowledge, this work is the first to use chaotic series for video object description and apply it for object classificatio

Dynamic state reconciliation and model-based fault detection for chemical processes

In this paper, we present a method for the fault detection based on the residual generation. The main idea is to reconstruct the outputs of the system from the measurements using the extended Kalman filter. The estimations are compared to the values of the reference model and so, deviations are interpreted as possible faults. The reference model is simulated by the dynamic hybrid simulator, PrODHyS. The use of this method is illustrated through an application in the field of chemical processe

ROOT - A C++ Framework for Petabyte Data Storage, Statistical Analysis and Visualization

ROOT is an object-oriented C++ framework conceived in the high-energy physics (HEP) community, designed for storing and analyzing petabytes of data in an efficient way. Any instance of a C++ class can be stored into a ROOT file in a machine-independent compressed binary format. In ROOT the TTree object container is optimized for statistical data analysis over very large data sets by using vertical data storage techniques. These containers can span a large number of files on local disks, the web, or a number of different shared file systems. In order to analyze this data, the user can chose out of a wide set of mathematical and statistical functions, including linear algebra classes, numerical algorithms such as integration and minimization, and various methods for performing regression analysis (fitting). In particular, ROOT offers packages for complex data modeling and fitting, as well as multivariate classification based on machine learning techniques. A central piece in these analysis tools are the histogram classes which provide binning of one- and multi-dimensional data. Results can be saved in high-quality graphical formats like Postscript and PDF or in bitmap formats like JPG or GIF. The result can also be stored into ROOT macros that allow a full recreation and rework of the graphics. Users typically create their analysis macros step by step, making use of the interactive C++ interpreter CINT, while running over small data samples. Once the development is finished, they can run these macros at full compiled speed over large data sets, using on-the-fly compilation, or by creating a stand-alone batch program. Finally, if processing farms are available, the user can reduce the execution time of intrinsically parallel tasks - e.g. data mining in HEP - by using PROOF, which will take care of optimally distributing the work over the available resources in a transparent way

Implementing a map based simulator for the location API for J2ME

The Java Location API for J2METM integrates generic positioning and orientation data with persistent storage of landmark objects. It can be used to develop location based service applications for small mobile devices, and these applications can be tested using simulation environments. Currently the only simulation tools in the public domain are proprietary mobile device simulators that are driven by GPS data log files, but it is sometimes useful to be able to test location based services using interactive map-based tools. In addition, we may need to experiment with extensions and changes to the standard API to support additional services, requiring an open source environment. In this paper we describe the implementation of an open source map-based simulation tool compatible with other commonly used development and deployment tools

Design and implementation of a HLA inter-federation bridge

In this paper, we discuss the design and implementation of a HLA inter-federation bridge. Our works are mainly motivated by the scalability and security problems, but we also consider the use of bridges for interoperability purposes. We describe several bridge topologies, including linear and cyclic inter-federations. We discuss problems raised by bridge federates and the use of different RTI implementations. We detail several solutions, leading to the design and implementation of a bridge prototype. Then we present our current results, and on-going works concerning performance improvements, interoperability, and security purposes