Agents in Bioinformatics

The scope of the Technical Forum Group (TFG) on Agents in Bioinformatics (BIOAGENTS) was to inspire collaboration between the agent and bioinformatics communities with the aim of creating an opportunity to propose a different (agent-based) approach to the development of computational frameworks both for data analysis in bioinformatics and for system modelling in computational biology. During the day, the participants examined the future of research on agents in bioinformatics primarily through 12 invited talks selected to cover the most relevant topics. From the discussions, it became clear that there are many perspectives to the field, ranging from bio-conceptual languages for agent-based simulation, to the definition of bio-ontology-based declarative languages for use by information agents, and to the use of Grid agents, each of which requires further exploration. The interactions between participants encouraged the development of applications that describe a way of creating agent-based simulation models of biological systems, starting from an hypothesis and inferring new knowledge (or relations) by mining and analysing the huge amount of public biological data. In this report we summarise and reflect on the presentations and discussions

Analysis and design of multiagent systems using MAS-CommonKADS

This article proposes an agent-oriented methodology called MAS-CommonKADS and develops a case study. This methodology extends the knowledge engineering methodology CommonKADSwith techniquesfrom objectoriented and protocol engineering methodologies. The methodology consists of the development of seven models: Agent Model, that describes the characteristics of each agent; Task Model, that describes the tasks that the agents carry out; Expertise Model, that describes the knowledge needed by the agents to achieve their goals; Organisation Model, that describes the structural relationships between agents (software agents and/or human agents); Coordination Model, that describes the dynamic relationships between software agents; Communication Model, that describes the dynamic relationships between human agents and their respective personal assistant software agents; and Design Model, that refines the previous models and determines the most suitable agent architecture for each agent, and the requirements of the agent network

Overview on agent-based social modelling and the use of formal languages

Transdisciplinary Models and Applications investigates a variety of programming languages used in validating and verifying models in order to assist in their eventual implementation. This book will explore different methods of evaluating and formalizing simulation models, enabling computer and industrial engineers, mathematicians, and students working with computer simulations to thoroughly understand the progression from simulation to product, improving the overall effectiveness of modeling systems.Postprint (author's final draft

Multi-level agent-based modeling - A literature survey

During last decade, multi-level agent-based modeling has received significant and dramatically increasing interest. In this article we present a comprehensive and structured review of literature on the subject. We present the main theoretical contributions and application domains of this concept, with an emphasis on social, flow, biological and biomedical models.Comment: v2. Ref 102 added. v3-4 Many refs and text added v5-6 bibliographic statistics updated. v7 Change of the name of the paper to reflect what it became, many refs and text added, bibliographic statistics update

A group learning management method for intelligent tutoring systems

In this paper we propose a group management specification and execution method that seeks a compromise between simple course design and complex adaptive group interaction. This is achieved through an authoring method that proposes predefined scenarios to the author. These scenarios already include complex learning interaction protocols in which student and group models use and update are automatically included. The method adopts ontologies to represent domain and student models, and object Petri nets to specify the group interaction protocols. During execution, the method is supported by a multi-agent architecture

Socionic Multi-Agent Systems Based on Reflexive Petri Nets and Theories of Social Self-Organisation

This contribution summarises the core results of the transdisciplinary ASKO project, part of the German DFG's programme Sozionik, which combines sociologists' and computer scientists' skills in order to create improved theories and models of artificial societies. Our research group has (a) formulated a social theory, which is able to explain fundamental mechanisms of self-organisation in both natural and artificial societies, (b) modelled this in a mathematical way using a visual formalism, and (c) developed a novel multi-agent system architecture which is conceptually coherent, recursively structured (hence non-eclectic) and based on our social theory. The article presents an outline of both a sociological middle-range theory of social self-organisation in educational institutions, its formal, Petri net based model, including a simulation of one of its main mechanisms, and the multi-agent system architecture SONAR. It describes how the theory was created by a re-analysis of some grand social theories, by grounding it empirically, and finally how the theory was evaluated by modelling its concepts and statements.Multi-Agents Systems, Petri Nets, Self-Organisation, Social Theories

International conference on software engineering and knowledge engineering: Session chair

The Thirtieth International Conference on Software Engineering and Knowledge Engineering (SEKE 2018) will be held at the Hotel Pullman, San Francisco Bay, USA, from July 1 to July 3, 2018. SEKE2018 will also be dedicated in memory of Professor Lofti Zadeh, a great scholar, pioneer and leader in fuzzy sets theory and soft computing. The conference aims at bringing together experts in software engineering and knowledge engineering to discuss on relevant results in either software engineering or knowledge engineering or both. Special emphasis will be put on the transference of methods between both domains. The theme this year is soft computing in software engineering & knowledge engineering. Submission of papers and demos are both welcome

Rewiring strategies for changing environments

A typical pervasive application executes in a changing environment: people, computing resources, software services and network connections come and go continuously. A robust pervasive application needs adapt to this changing context as long as there is an appropriate rewiring strategy that guarantees correct behavior. We combine the MERODE modeling methodology with the ReWiRe framework for creating interactive pervasive applications that can cope with changing environments. The core of our approach is a consistent environment model, which is essential to create (re)configurable context-aware pervasive applications. We aggregate different ontologies that provide the required semantics to describe almost any target environment. We present a case study that shows a interactive pervasive application for media access that incorporates parental control on media content and can migrate between devices. The application builds upon models of the run-time environment represented as system states for dedicated rewiring strategies

Multi-level agent-based modeling with the Influence Reaction principle

This paper deals with the specification and the implementation of multi-level agent-based models, using a formal model, IRM4MLS (an Influence Reaction Model for Multi-Level Simulation), based on the Influence Reaction principle. Proposed examples illustrate forms of top-down control in (multi-level) multi-agent based-simulations