Quantifying the implicit process flow abstraction in SBGN-PD diagrams with Bio-PEPA

For a long time biologists have used visual representations of biochemical networks to gain a quick overview of important structural properties. Recently SBGN, the Systems Biology Graphical Notation, has been developed to standardise the way in which such graphical maps are drawn in order to facilitate the exchange of information. Its qualitative Process Diagrams (SBGN-PD) are based on an implicit Process Flow Abstraction (PFA) that can also be used to construct quantitative representations, which can be used for automated analyses of the system. Here we explicitly describe the PFA that underpins SBGN-PD and define attributes for SBGN-PD glyphs that make it possible to capture the quantitative details of a biochemical reaction network. We implemented SBGNtext2BioPEPA, a tool that demonstrates how such quantitative details can be used to automatically generate working Bio-PEPA code from a textual representation of SBGN-PD that we developed. Bio-PEPA is a process algebra that was designed for implementing quantitative models of concurrent biochemical reaction systems. We use this approach to compute the expected delay between input and output using deterministic and stochastic simulations of the MAPK signal transduction cascade. The scheme developed here is general and can be easily adapted to other output formalisms

Working Notes from the 1992 AAAI Workshop on Automating Software Design. Theme: Domain Specific Software Design

The goal of this workshop is to identify different architectural approaches to building domain-specific software design systems and to explore issues unique to domain-specific (vs. general-purpose) software design. Some general issues that cut across the particular software design domain include: (1) knowledge representation, acquisition, and maintenance; (2) specialized software design techniques; and (3) user interaction and user interface

Continuous Improvement Through Knowledge-Guided Analysis in Experience Feedback

Continuous improvement in industrial processes is increasingly a key element of competitiveness for industrial systems. The management of experience feedback in this framework is designed to build, analyze and facilitate the knowledge sharing among problem solving practitioners of an organization in order to improve processes and products achievement. During Problem Solving Processes, the intellectual investment of experts is often considerable and the opportunities for expert knowledge exploitation are numerous: decision making, problem solving under uncertainty, and expert configuration. In this paper, our contribution relates to the structuring of a cognitive experience feedback framework, which allows a flexible exploitation of expert knowledge during Problem Solving Processes and a reuse such collected experience. To that purpose, the proposed approach uses the general principles of root cause analysis for identifying the root causes of problems or events, the conceptual graphs formalism for the semantic conceptualization of the domain vocabulary and the Transferable Belief Model for the fusion of information from different sources. The underlying formal reasoning mechanisms (logic-based semantics) in conceptual graphs enable intelligent information retrieval for the effective exploitation of lessons learned from past projects. An example will illustrate the application of the proposed approach of experience feedback processes formalization in the transport industry sector

User-centered visual analysis using a hybrid reasoning architecture for intensive care units

One problem pertaining to Intensive Care Unit information systems is that, in some cases, a very dense display of data can result. To ensure the overview and readability of the increasing volumes of data, some special features are required (e.g., data prioritization, clustering, and selection mechanisms) with the application of analytical methods (e.g., temporal data abstraction, principal component analysis, and detection of events). This paper addresses the problem of improving the integration of the visual and analytical methods applied to medical monitoring systems. We present a knowledge- and machine learning-based approach to support the knowledge discovery process with appropriate analytical and visual methods. Its potential benefit to the development of user interfaces for intelligent monitors that can assist with the detection and explanation of new, potentially threatening medical events. The proposed hybrid reasoning architecture provides an interactive graphical user interface to adjust the parameters of the analytical methods based on the users' task at hand. The action sequences performed on the graphical user interface by the user are consolidated in a dynamic knowledge base with specific hybrid reasoning that integrates symbolic and connectionist approaches. These sequences of expert knowledge acquisition can be very efficient for making easier knowledge emergence during a similar experience and positively impact the monitoring of critical situations. The provided graphical user interface incorporating a user-centered visual analysis is exploited to facilitate the natural and effective representation of clinical information for patient care

An Analysis of Service Ontologies

Services are increasingly shaping the world’s economic activity. Service provision and consumption have been profiting from advances in ICT, but the decentralization and heterogeneity of the involved service entities still pose engineering challenges. One of these challenges is to achieve semantic interoperability among these autonomous entities. Semantic web technology aims at addressing this challenge on a large scale, and has matured over the last years. This is evident from the various efforts reported in the literature in which service knowledge is represented in terms of ontologies developed either in individual research projects or in standardization bodies. This paper aims at analyzing the most relevant service ontologies available today for their suitability to cope with the service semantic interoperability challenge. We take the vision of the Internet of Services (IoS) as our motivation to identify the requirements for service ontologies. We adopt a formal approach to ontology design and evaluation in our analysis. We start by defining informal competency questions derived from a motivating scenario, and we identify relevant concepts and properties in service ontologies that match the formal ontological representation of these questions. We analyze the service ontologies with our concepts and questions, so that each ontology is positioned and evaluated according to its utility. The gaps we identify as the result of our analysis provide an indication of open challenges and future work

Requirement validation with enactable descriptions of use cases.

The validation of stakeholder requirements for a software system is a pivotal activity for any nontrivial software development project. Often, differences in knowledge regarding development issues, and knowledge regarding the problem domain, impede the elaboration of requirements amongst developers and stakeholders. A description technique that provides a user perspective of the system behaviour is likely to enhance shared understanding between the developers and stakeholders. The Unified Modelling Language (UML) use case is such a notation. Use cases describe the behaviour of a system (using natural language) in terms of interactions between the external users and the system. Since the standardisation of the UML by the Object Management Group in 1997, much research has been devoted to use cases. Some researchers have focussed on the provision of writing guidelines for use case specifications whereas others have focussed on the application of formal techniques. This thesis investigates the adequacy of the use case description for the specification and validation of software behaviour. In particular, the thesis argues that whereas the user-system interaction scheme underpins the essence of the use case notation, the UML specification of the use case does not provide a mechanism by which use cases can describe dependencies amongst constituent interaction steps. Clarifying these issues is crucial for validating the adequacy of the specification against stakeholder expectations. This thesis proposes a state-based approach (the Educator approach) to use case specification where constituent events are augmented with pre and post states to express both intra-use case and inter-use case dependencies. Use case events are enacted to visualise implied behaviour, thereby enhancing shared understanding among users and developers. Moreover, enaction provides an early "feel" of the behaviour that would result from the implementation of the specification. The Educator approach and the enaction of descriptions are supported by a prototype environment, the EducatorTool, developed to demonstrate the efficacy and novelty of the approach. To validate the work presented in this thesis an industrial study, involving the specification of realtime control software, is reported. The study involves the analysis of use case specifications of the subsystems prior to the application of the proposed approach, and the analysis of the specification where the approach and tool support are applied. This way, it is possible to determine the efficacy of the Educator approach within an industrial setting