An MDA approach towards integrating formal and informal modeling languages

This paper shows how formal and informal modeling languages can be cooperatively used in the MDA framework, and how transformations between models in these languages can be achieved using an MDA development environment. The integrated approach also provides an effective V&V technique for the MDA.

Patterns in complex systems modeling

The design, development, and use of complex systems models raises a unique class of challenges and potential pitfalls, many of which are commonly recurring problems. Over time, researchers gain experience in this form of modeling, choosing algorithms, techniques, and frameworks that improve the quality, confidence level, and speed of development of their models. This increasing collective experience of complex systems modellers is a resource that should be captured. Fields such as software engineering and architecture have benefited from the development of generic solutions to recurring problems, called patterns. Using pattern development techniques from these fields, insights from communities such as learning and information processing, data mining, bioinformatics, and agent-based modeling can be identified and captured. Collections of such 'pattern languages' would allow knowledge gained through experience to be readily accessible to less-experienced practitioners and to other domains. This paper proposes a methodology for capturing the wisdom of computational modelers by introducing example visualization patterns, and a pattern classification system for analyzing the relationship between micro and macro behaviour in complex systems models. We anticipate that a new field of complex systems patterns will provide an invaluable resource for both practicing and future generations of modelers.

A study of the evolution of the representational capabilities of process modeling grammars

A plethora of process modeling techniques has been proposed over the years. One way of evaluating and comparing the scope and completeness of techniques is by way of representational analysis. The purpose of this paper is to examine how process modeling techniques have developed over the last four decades. The basis of the comparison is the Bunge-Wand-Weber representation model, a benchmark used for the analysis of grammars that purport to model the real world and the interactions within it. This paper presents a comparison of representational analyses of several popular process modeling techniques and has two main outcomes. First, it provides insights, within the boundaries of a representational analysis, into the extent to which process modeling techniques have developed over time. Second, the findings also indicate areas in which the underlying theory seems to be over-engineered or lacking in specialization.

A framework of issues in large process modeling projects

As process management projects have increased in size due to globalised and company-wide initiatives, a corresponding growth in the size of process modeling projects can be observed. Despite advances in languages, tools and methodologies, several aspects of these projects have been largely ignored by the academic community. This paper makes a first contribution to a potential research agenda in this field by defining the characteristics of large-scale process modeling projects and proposing a framework of related issues. These issues are derived from a semi -structured interview and six focus groups conducted in Australia, Germany and the USA with enterprise and modeling software vendors and customers. The focus groups confirm the existence of unresolved problems in business process modeling projects. The outcomes provide a research agenda which directs researchers into further studies in global process management, process model decomposition and the overall governance of process modeling projects. It is expected that this research agenda will provide guidance to researchers and practitioners by focusing on areas of high theoretical and practical relevance.

A tool for a formal pattern modeling language

This paper presents a formal but practical approach for defining and using design patterns. Initially we formalize the concepts commonly used in defining design patterns using Object-Z. We also formalize consistency constraints that must be satisfied when a pattern is deployed in a design model. Then we implement the pattern modeling language and its consistency constraints using an existing modeling framework, EMF, and incorporate the implementation as plug-ins to the Eclipse modeling environment. While the language is defined formally in terms of Object-Z definitions, the language is implemented in a practical environment. Using the plug-ins, users can develop precise pattern descriptions without knowing the underlying formalism, and can use the tool to check the validity of the pattern descriptions and pattern usage in design models. In this work, formalism brings precision to the pattern language definition and its implementation brings practicability to our pattern-based modeling approach.

Representing part-whole relationships in conceptual modeling: An empirical evaluation

The part-of or part-whole construct is a fundamental element of many conceptual modeling grammars that is used to associate one thing (a component) with another thing (a composite). Substantive theoretical issues surrounding the part-whole construct remain to be resolved, however. For instance, contrary to widespread claims, the relationship between components and composites is not always transitive. Moreover, how the partwhole construct should be represented in a conceptual schema diagram remains a contentious issue. Some analysts argue composites should be represented as a relationship or association. Others argue they should be represented as an entity. In this paper we use an ontological theory to support our arguments that composites should be represented as entities and not relationships or associations. We also describe an experiment that we undertook to test whether representing composites as relationships or entities enables users to understand a domain better. Our results support our arguments that using entities to represent composites enables users to better understand a domain.

Off-line signature verification and forgery detection system based on fuzzy modeling

This paper presents an innovative approach for signature verification and forgery detection based on fuzzy modeling. The signature image is binarized and resized to a fixed size window and is then thinned. The thinned image is then partitioned into a fixed number of eight sub-images called boxes. This partition is done using the horizontal density approximation approach. Each sub-image is then further resized and again partitioned into twelve further sub-images using the uniform partitioning approach. The features of consideration are normalized vector angle (α) from each box. Each feature extracted from sample signatures gives rise to a fuzzy set. Since the choice of a proper fuzzification function is crucial for verification, we have devised a new fuzzification function with structural parameters, which is able to adapt to the variations in fuzzy sets. This function is employed to develop a complete forgery detection and verification system.

Fuzzy modeling based recognition of multi-font numerals

In this paper, we present a new scheme for off-line recognition of multi-font numerals using the Takagi-Sugeno (TS) model. In this scheme, the binary image of a character is partitioned into a fixed number of sub-images called boxes. The features consist of normalized vector distances (gamma) from each box. Each feature extracted from different fonts gives rise to a fuzzy set. However, when we have a small number of fonts as in the case of multi-font numerals, the choice of a proper fuzzification function is crucial. Hence, we have devised a new fuzzification function involving parameters, which take account of the variations in the fuzzy sets. The new fuzzification function is employed in the TS model for the recognition of multi-font numerals.

Towards a Modeling Environment for Earth Systems Simulations

The developments of models in Earth Sciences, e.g. for earthquake prediction and for the simulation of mantel convection, are fare from being finalized. Therefore there is a need for a modelling environment that allows scientist to implement and test new models in an easy but flexible way. After been verified, the models should be easy to apply within its scope, typically by setting input parameters through a GUI or web services. It should be possible to link certain parameters to external data sources, such as databases and other simulation codes. Moreover, as typically large-scale meshes have to be used to achieve appropriate resolutions, the computational efficiency of the underlying numerical methods is important. Conceptional this leads to a software system with three major layers: the application layer, the mathematical layer, and the numerical algorithm layer. The latter is implemented as a C/C++ library to solve a basic, computational intensive linear problem, such as a linear partial differential equation. The mathematical layer allows the model developer to define his model and to implement high level solution algorithms (e.g. Newton-Raphson scheme, Crank-Nicholson scheme) or choose these algorithms form an algorithm library. The kernels of the model are generic, typically linear, solvers provided through the numerical algorithm layer. Finally, to provide an easy-to-use application environment, a web interface is (semi-automatically) built to edit the XML input file for the modelling code. In the talk, we will discuss the advantages and disadvantages of this concept in more details. We will also present the modelling environment escript which is a prototype implementation toward such a software system in Python (see www.python.org). Key components of escript are the Data class and the PDE class. Objects of the Data class allow generating, holding, accessing, and manipulating data, in such a way that the actual, in the particular context best, representation is transparent to the user. They are also the key to establish connections with external data sources. PDE class objects are describing (linear) partial differential equation objects to be solved by a numerical library. The current implementation of escript has been linked to the finite element code Finley to solve general linear partial differential equations. We will give a few simple examples which will illustrate the usage escript. Moreover, we show the usage of escript together with Finley for the modelling of interacting fault systems and for the simulation of mantel convection.

DVMS 1.5: A user manual (the data visualization and modeling system)

The data available during the drug discovery process is vast in amount and diverse in nature. To gain useful information from such data, an effective visualisation tool is required. To provide better visualisation facilities to the domain experts (screening scientist, biologist, chemist, etc.),we developed a software which is based on recently developed principled visualisation algorithms such as Generative Topographic Mapping (GTM) and Hierarchical Generative Topographic Mapping (HGTM). The software also supports conventional visualisation techniques such as Principal Component Analysis, NeuroScale, PhiVis, and Locally Linear Embedding (LLE). The software also provides global and local regression facilities . It supports regression algorithms such as Multilayer Perceptron (MLP), Radial Basis Functions network (RBF), Generalised Linear Models (GLM), Mixture of Experts (MoE), and newly developed Guided Mixture of Experts (GME). This user manual gives an overview of the purpose of the software tool, highlights some of the issues to be taken care while creating a new model, and provides information about how to install & use the tool. The user manual does not require the readers to have familiarity with the algorithms it implements. Basic computing skills are enough to operate the software.

miniDVMS v1.8 : A user manual(The data visualization and modeling system)

Today, the data available to tackle many scientific challenges is vast in quantity and diverse in nature. The exploration of heterogeneous information spaces requires suitable mining algorithms as well as effective visual interfaces. miniDVMS v1.8 provides a flexible visual data mining framework which combines advanced projection algorithms developed in the machine learning domain and visual techniques developed in the information visualisation domain. The advantage of this interface is that the user is directly involved in the data mining process. Principled projection methods, such as generative topographic mapping (GTM) and hierarchical GTM (HGTM), are integrated with powerful visual techniques, such as magnification factors, directional curvatures, parallel coordinates, and user interaction facilities, to provide this integrated visual data mining framework. The software also supports conventional visualisation techniques such as principal component analysis (PCA), Neuroscale, and PhiVis. This user manual gives an overview of the purpose of the software tool, highlights some of the issues to be taken care while creating a new model, and provides information about how to install and use the tool. The user manual does not require the readers to have familiarity with the algorithms it implements. Basic computing skills are enough to operate the software.

A design environment for deadlock-free concurrent software

Using current software engineering technology, the robustness required for safety critical software is not assurable. However, different approaches are possible which can help to assure software robustness to some extent. For achieving high reliability software, methods should be adopted which avoid introducing faults (fault avoidance); then testing should be carried out to identify any faults which persist (error removal). Finally, techniques should be used which allow any undetected faults to be tolerated (fault tolerance). The verification of correctness in system design specification and performance analysis of the model, are the basic issues in concurrent systems. In this context, modeling distributed concurrent software is one of the most important activities in the software life cycle, and communication analysis is a primary consideration to achieve reliability and safety. By and large fault avoidance requires human analysis which is error prone; by reducing human involvement in the tedious aspect of modelling and analysis of the software it is hoped that fewer faults will persist into its implementation in the real-time environment. The Occam language supports concurrent programming and is a language where interprocess interaction takes place by communications. This may lead to deadlock due to communication failure. Proper systematic methods must be adopted in the design of concurrent software for distributed computing systems if the communication structure is to be free of pathologies, such as deadlock. The objective of this thesis is to provide a design environment which ensures that processes are free from deadlock. A software tool was designed and used to facilitate the production of fault-tolerant software for distributed concurrent systems. Where Occam is used as a design language then state space methods, such as Petri-nets, can be used in analysis and simulation to determine the dynamic behaviour of the software, and to identify structures which may be prone to deadlock so that they may be eliminated from the design before the program is ever run. This design software tool consists of two parts. One takes an input program and translates it into a mathematical model (Petri-net), which is used for modeling and analysis of the concurrent software. The second part is the Petri-net simulator that takes the translated program as its input and starts simulation to generate the reachability tree. The tree identifies `deadlock potential' which the user can explore further. Finally, the software tool has been applied to a number of Occam programs. Two examples were taken to show how the tool works in the early design phase for fault prevention before the program is ever run.

WSRF-based modeling of clinical trial information for collaborative cancer research

The CancerGrid consortium is developing open-standards cancer informatics to address the challenges posed by modern cancer clinical trials. This paper presents the service-oriented software paradigm implemented in CancerGrid to derive clinical trial information management systems for collaborative cancer research across multiple institutions. Our proposal is founded on a combination of a clinical trial (meta)model and WSRF (Web Services Resource Framework), and is currently being evaluated for use in early phase trials. Although primarily targeted at cancer research, our approach is readily applicable to other areas for which a similar information model is available.

eHabitat, a multi-purpose Web Processing Service for ecological modeling

The number of interoperable research infrastructures has increased significantly with the growing awareness of the efforts made by the Global Earth Observation System of Systems (GEOSS). One of the Societal Benefit Areas (SBA) that is benefiting most from GEOSS is biodiversity, given the costs of monitoring the environment and managing complex information, from space observations to species records including their genetic characteristics. But GEOSS goes beyond simple data sharing to encourage the publishing and combination of models, an approach which can ease the handling of complex multi-disciplinary questions. It is the purpose of this paper to illustrate these concepts by presenting eHabitat, a basic Web Processing Service (WPS) for computing the likelihood of finding ecosystems with equal properties to those specified by a user. When chained with other services providing data on climate change, eHabitat can be used for ecological forecasting and becomes a useful tool for decision-makers assessing different strategies when selecting new areas to protect. eHabitat can use virtually any kind of thematic data that can be considered as useful when defining ecosystems and their future persistence under different climatic or development scenarios. The paper will present the architecture and illustrate the concepts through case studies which forecast the impact of climate change on protected areas or on the ecological niche of an African bird.