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

A Formal Framework for Modeling Trust and Reputation in Collective Adaptive Systems

Trust and reputation models for distributed, collaborative systems have been studied and applied in several domains, in order to stimulate cooperation while preventing selfish and malicious behaviors. Nonetheless, such models have received less attention in the process of specifying and analyzing formally the functionalities of the systems mentioned above. The objective of this paper is to define a process algebraic framework for the modeling of systems that use (i) trust and reputation to govern the interactions among nodes, and (ii) communication models characterized by a high level of adaptiveness and flexibility. Hence, we propose a formalism for verifying, through model checking techniques, the robustness of these systems with respect to the typical attacks conducted against webs of trust.Comment: In Proceedings FORECAST 2016, arXiv:1607.0200

Collaborative Environments. Considerations Concerning Some Collaborative Systems

It is obvious, that all collaborative environments (workgroups, communities of practice, collaborative enterprises) are based on knowledge and between collaboration and knowledge management there is a strong interdependence. The evolution of information systems in these collaborative environments led to the sudden necessity to adopt, for maintaining the virtual activities and processes, the latest technologies/systems, which are capable to support integrated collaboration in business services. In these environments, portal-based IT platforms will integrate multi-agent collaborative systems, collaborative tools, different enterprise applications and other useful information systems.collaboration, collaborative environments, knowledge management, collaborative systems, portals, knowledge portals, agile development of portals

Mapping Big Data into Knowledge Space with Cognitive Cyber-Infrastructure

Big data research has attracted great attention in science, technology, industry and society. It is developing with the evolving scientific paradigm, the fourth industrial revolution, and the transformational innovation of technologies. However, its nature and fundamental challenge have not been recognized, and its own methodology has not been formed. This paper explores and answers the following questions: What is big data? What are the basic methods for representing, managing and analyzing big data? What is the relationship between big data and knowledge? Can we find a mapping from big data into knowledge space? What kind of infrastructure is required to support not only big data management and analysis but also knowledge discovery, sharing and management? What is the relationship between big data and science paradigm? What is the nature and fundamental challenge of big data computing? A multi-dimensional perspective is presented toward a methodology of big data computing.Comment: 59 page

Automated user modeling for personalized digital libraries

Digital libraries (DL) have become one of the most typical ways of accessing any kind of digitalized information. Due to this key role, users welcome any improvements on the services they receive from digital libraries. One trend used to improve digital services is through personalization. Up to now, the most common approach for personalization in digital libraries has been user-driven. Nevertheless, the design of efficient personalized services has to be done, at least in part, in an automatic way. In this context, machine learning techniques automate the process of constructing user models. This paper proposes a new approach to construct digital libraries that satisfy user’s necessity for information: Adaptive Digital Libraries, libraries that automatically learn user preferences and goals and personalize their interaction using this information

The Distributed Ontology Language (DOL): Use Cases, Syntax, and Extensibility

The Distributed Ontology Language (DOL) is currently being standardized within the OntoIOp (Ontology Integration and Interoperability) activity of ISO/TC 37/SC 3. It aims at providing a unified framework for (1) ontologies formalized in heterogeneous logics, (2) modular ontologies, (3) links between ontologies, and (4) annotation of ontologies. This paper presents the current state of DOL's standardization. It focuses on use cases where distributed ontologies enable interoperability and reusability. We demonstrate relevant features of the DOL syntax and semantics and explain how these integrate into existing knowledge engineering environments.Comment: Terminology and Knowledge Engineering Conference (TKE) 2012-06-20 to 2012-06-21 Madrid, Spai

Formal approaches to modelling and verifying resource-bounded agents-state of the art and future prospects

This paper reviews formal approaches to modelling and verifying resource-bounded agents focusing on state of the Art and future prospects

Towards a Formal Model of Privacy-Sensitive Dynamic Coalitions

The concept of dynamic coalitions (also virtual organizations) describes the temporary interconnection of autonomous agents, who share information or resources in order to achieve a common goal. Through modern technologies these coalitions may form across company, organization and system borders. Therefor questions of access control and security are of vital significance for the architectures supporting these coalitions. In this paper, we present our first steps to reach a formal framework for modeling and verifying the design of privacy-sensitive dynamic coalition infrastructures and their processes. In order to do so we extend existing dynamic coalition modeling approaches with an access-control-concept, which manages access to information through policies. Furthermore we regard the processes underlying these coalitions and present first works in formalizing these processes. As a result of the present paper we illustrate the usefulness of the Abstract State Machine (ASM) method for this task. We demonstrate a formal treatment of privacy-sensitive dynamic coalitions by two example ASMs which model certain access control situations. A logical consideration of these ASMs can lead to a better understanding and a verification of the ASMs according to the aspired specification.Comment: In Proceedings FAVO 2011, arXiv:1204.579

Transitioning Applications to Semantic Web Services: An Automated Formal Approach

Semantic Web Services have been recognized as a promising technology that exhibits huge commercial potential, and attract significant attention from both industry and the research community. Despite expectations being high, the industrial take-up of Semantic Web Service technologies has been slower than expected. One of the main reasons is that many systems have been developed without considering the potential of the web in integrating services and sharing resources. Without a systematic methodology and proper tool support, the migration from legacy systems to Semantic Web Service-based systems can be a very tedious and expensive process, which carries a definite risk of failure. There is an urgent need to provide strategies which allow the migration of legacy systems to Semantic Web Services platforms, and also tools to support such a strategy. In this paper we propose a methodology for transitioning these applications to Semantic Web Services by taking the advantage of rigorous mathematical methods. Our methodology allows users to migrate their applications to Semantic Web Services platform automatically or semi-automatically