The handbook of engineering self-aware and self-expressive systems

When faced with the task of designing and implementing a new self-aware and self-expressive computing system, researchers and practitioners need a set of guidelines on how to use the concepts and foundations developed in the Engineering Proprioception in Computing Systems (EPiCS) project. This report provides such guidelines on how to design self-aware and self-expressive computing systems in a principled way. We have documented different categories of self-awareness and self-expression level using architectural patterns. We have also documented common architectural primitives, their possible candidate techniques and attributes for architecting self-aware and self-expressive systems. Drawing on the knowledge obtained from the previous investigations, we proposed a pattern driven methodology for engineering self-aware and self-expressive systems to assist in utilising the patterns and primitives during design. The methodology contains detailed guidance to make decisions with respect to the possible design alternatives, providing a systematic way to build self-aware and self-expressive systems. Then, we qualitatively and quantitatively evaluated the methodology using two case studies. The results reveal that our pattern driven methodology covers the main aspects of engineering self-aware and self-expressive systems, and that the resulted systems perform significantly better than the non-self-aware systems.

Optimizing amino acid groupings for GPCR classification

MOTIVATION: There is much interest in reducing the complexity inherent in the representation of the 20 standard amino acids within bioinformatics algorithms by developing a so-called reduced alphabet. Although there is no universally applicable residue grouping, there are numerous physiochemical criteria upon which one can base groupings. Local descriptors are a form of alignment-free analysis, the efficiency of which is dependent upon the correct selection of amino acid groupings. RESULTS: Within the context of G-protein coupled receptor (GPCR) classification, an optimization algorithm was developed, which was able to identify the most efficient grouping when used to generate local descriptors. The algorithm was inspired by the relatively new computational intelligence paradigm of artificial immune systems. A number of amino acid groupings produced by this algorithm were evaluated with respect to their ability to generate local descriptors capable of providing an accurate classification algorithm for GPCRs.

Subject identification via ECG fiducial-based systems:influence of the type of QT interval correction

Electrocardiography (ECG) has been recently proposed as biometric trait for identification purposes. Intra-individual variations of ECG might affect identification performance. These variations are mainly due to Heart Rate Variability (HRV). In particular, HRV causes changes in the QT intervals along the ECG waveforms. This work is aimed at analysing the influence of seven QT interval correction methods (based on population models) on the performance of ECG-fiducial-based identification systems. In addition, we have also considered the influence of training set size, classifier, classifier ensemble as well as the number of consecutive heartbeats in a majority voting scheme. The ECG signals used in this study were collected from thirty-nine subjects within the Physionet open access database. Public domain software was used for fiducial points detection. Results suggested that QT correction is indeed required to improve the performance. However, there is no clear choice among the seven explored approaches for QT correction (identification rate between 0.97 and 0.99). MultiLayer Perceptron and Support Vector Machine seemed to have better generalization capabilities, in terms of classification performance, with respect to Decision Tree-based classifiers. No such strong influence of the training-set size and the number of consecutive heartbeats has been observed on the majority voting scheme.

Visualising and controlling the flow in biomolecular systems at and between multiple scales:from atoms to hydrodynamics at different locations in time and space

A novel framework for modelling biomolecular systems at multiple scales in space and time simultaneously is described. The atomistic molecular dynamics representation is smoothly connected with a statistical continuum hydrodynamics description. The system behaves correctly at the limits of pure molecular dynamics (hydrodynamics) and at the intermediate regimes when the atoms move partly as atomistic particles, and at the same time follow the hydrodynamic flows. The corresponding contributions are controlled by a parameter, which is defined as an arbitrary function of space and time, thus, allowing an effective separation of the atomistic 'core' and continuum 'environment'. To fill the scale gap between the atomistic and the continuum representations our special purpose computer for molecular dynamics, MDGRAPE-4, as well as GPU-based computing were used for developing the framework. These hardware developments also include interactive molecular dynamics simulations that allow intervention of the modelling through force-feedback devices.

Representing human expertise by the OWL web ontology language to support knowledge engineering in decision support systems

Clinical decision support systems (CDSSs) often base their knowledge and advice on human expertise. Knowledge representation needs to be in a format that can be easily understood by human users as well as supporting ongoing knowledge engineering, including evolution and consistency of knowledge. This paper reports on the development of an ontology specification for managing knowledge engineering in a CDSS for assessing and managing risks associated with mental-health problems. The Galatean Risk and Safety Tool, GRiST, represents mental-health expertise in the form of a psychological model of classification. The hierarchical structure was directly represented in the machine using an XML document. Functionality of the model and knowledge management were controlled using attributes in the XML nodes, with an accompanying paper manual for specifying how end-user tools should behave when interfacing with the XML. This paper explains the advantages of using the web-ontology language, OWL, as the specification, details some of the issues and problems encountered in translating the psychological model to OWL, and shows how OWL benefits knowledge engineering. The conclusions are that OWL can have an important role in managing complex knowledge domains for systems based on human expertise without impeding the end-users' understanding of the knowledge base. The generic classification model underpinning GRiST makes it applicable to many decision domains and the accompanying OWL specification facilitates its implementation.

Biologically inspired features for scene classification in video surveillance

Inspired by human visual cognition mechanism, this paper first presents a scene classification method based on an improved standard model feature. Compared with state-of-the-art efforts in scene classification, the newly proposed method is more robust, more selective, and of lower complexity. These advantages are demonstrated by two sets of experiments on both our own database and standard public ones. Furthermore, occlusion and disorder problems in scene classification in video surveillance are also first studied in this paper. © 2010 IEEE.

Formal methods for the development and verification of autonomic IT systems

This chapter explores ways in which rigorous mathematical techniques, termed formal methods, can be employed to improve the predictability and dependability of autonomic computing. Model checking, formal specification, and quantitative verification are presented in the contexts of conflict detection in autonomic computing policies, and of implementation of goal and utility-function policies in autonomic IT systems, respectively. Each of these techniques is illustrated using a detailed case study, and analysed to establish its merits and limitations. The analysis is then used as a basis for discussing the challenges and opportunities of this endeavour to transition the development of autonomic IT systems from the current practice of using ad-hoc methods and heuristic towards a more principled approach. © 2012, IGI Global.

Revisiting goal-oriented models for self-aware systems-of-systems

Systems-of-systems (SoS) are systems resulted from the interaction among other independent constituent systems that collaborate to offer new functionalities towards accomplishing global missions. Each of these constituent systems accomplishes its individual missions and is able to contribute to the achievement of the global missions of the SoS, both being viewed as a set of associated goals. In the perspective of self-aware systems, SoS need to exhibit goal-awareness, i.e., They need to be aware of their own goals and of how their constituent systems contribute to their accomplishment. In this paper, we revisit goal-oriented concepts aiming at identifying and modeling goals at both SoS level and the constituent systems level. Moreover, we take advantage of such goal-oriented models to express the relationship among goals at these levels as well as to define how each constituent system can contribute to the accomplishment of global goals of an SoS. In addition, we shed light on important issues related to goal modeling in self-aware SoS to be addressed in future research.

Mobile bluetooth-based multi-player game development in ubiquitous computing

This paper describes the use of Bluetooth and Java-Based technologies in developing a multi-player mobile game in ubiquitous computing, which strongly depends on automatic contextual reconfiguration and context-triggered actions. Our investigation focuses on an extended form of ubiquitous computing which game software developers utilize to develop games for players. We have developed an experimental ubiquitous computing application that provides context-aware services to game server and game players in a mobile distributed computing system. Obviously, contextual services provide useful information in a context-aware system. However, designing a context-aware game is still a daunting task and much theoretical and practical research remains to be done to reach the ubiquitous computing era. In this paper, we present the overall architecture and discuss, in detail, the implementation steps taken to create a Bluetooth and Java based context-aware game. We develop a multi-player game server and prepare the client and server codes in ubiquitous computing, providing adaptive routines to handle connection information requests, logging and context formatting and delivery for automatic contextual reconfiguration and context-triggered actions. © 2010 Binary Information Press.