A Mathematical Framework for Agent Based Models of Complex Biological Networks

Agent-based modeling and simulation is a useful method to study biological phenomena in a wide range of fields, from molecular biology to ecology. Since there is currently no agreed-upon standard way to specify such models it is not always easy to use published models. Also, since model descriptions are not usually given in mathematical terms, it is difficult to bring mathematical analysis tools to bear, so that models are typically studied through simulation. In order to address this issue, Grimm et al. proposed a protocol for model specification, the so-called ODD protocol, which provides a standard way to describe models. This paper proposes an addition to the ODD protocol which allows the description of an agent-based model as a dynamical system, which provides access to computational and theoretical tools for its analysis. The mathematical framework is that of algebraic models, that is, time-discrete dynamical systems with algebraic structure. It is shown by way of several examples how this mathematical specification can help with model analysis.Comment: To appear in Bulletin of Mathematical Biolog

Practical Use of High-level Petri Nets

This booklet contains the proceedings of the Workshop on Practical Use of High-level Petri Nets, June 27, 2000. The workshop is part of the 21st International Conference on Application and Theory of Petri Nets organised by the CPN group at the Department of Computer Science, University of Aarhus, Denmark. The workshop papers are available in electronic form via the web pages: http://www.daimi.au.dk/pn2000/proceeding

Facilitating the Quantitative Analysis ofComplexEvents through a Computational Intelligence Model-Driven Tool

Complex event processing (CEP) is a computational intelligence technology capable of analyzing big data streams for event pattern recognition in real time. In particular, this technology is vastly useful for analyzing multicriteria conditions in a pattern, which will trigger alerts (complex events) upon their fulfillment. However, one of the main challenges to be faced by CEP is how to define the quantitative analysis to be performed in response to the produced complex events. In this paper, we propose the use of the MEdit4CEP-CPN model-driven tool as a solution for conducting such quantitative analysis of events of interest for an application domain, without requiring knowledge of any scientific programming language for implementing the pattern conditions. Precisely, MEdit4CEP-CPN facilitates domain experts to graphically model event patterns, transform them into a Prioritized Colored Petri Net (PCPN) model, modify its initial marking depending on the application scenario, and make the quantitative analysis through the simulation and monitor capabilities provided by CPN tools

Second Workshop on Modelling of Objects, Components and Agents

This report contains the proceedings of the workshop Modelling of Objects, Components, and Agents (MOCA'02), August 26-27, 2002.The workshop is organized by the 'Coloured Petri Net' Group at the University of Aarhus, Denmark and the 'Theoretical Foundations of Computer Science' Group at the University of Hamburg, Germany. The homepage of the workshop is: http://www.daimi.au.dk/CPnets/workshop02

Second Workshop on Practical Use of Coloured Petri Nets and Design/CPN.

This report contains the proceedings of the Second Workshop on Practical Use of Coloured Petri Nets and Design/CPN, October 13-15, 1999. The workshop was organised by the CPN group at the Department of Computer Science at the University of Aarhus, Denmark. The individual papers are available in electronic form via the web pages: http://www.daimi.au.dk/CPnets/workshop99

Recent advances in petri nets and concurrency

CEUR Workshop Proceeding

AI Solutions for MDS: Artificial Intelligence Techniques for Misuse Detection and Localisation in Telecommunication Environments

This report considers the application of Articial Intelligence (AI) techniques to the problem of misuse detection and misuse localisation within telecommunications environments. A broad survey of techniques is provided, that covers inter alia rule based systems, model-based systems, case based reasoning, pattern matching, clustering and feature extraction, articial neural networks, genetic algorithms, arti cial immune systems, agent based systems, data mining and a variety of hybrid approaches. The report then considers the central issue of event correlation, that is at the heart of many misuse detection and localisation systems. The notion of being able to infer misuse by the correlation of individual temporally distributed events within a multiple data stream environment is explored, and a range of techniques, covering model based approaches, `programmed' AI and machine learning paradigms. It is found that, in general, correlation is best achieved via rule based approaches, but that these suffer from a number of drawbacks, such as the difculty of developing and maintaining an appropriate knowledge base, and the lack of ability to generalise from known misuses to new unseen misuses. Two distinct approaches are evident. One attempts to encode knowledge of known misuses, typically within rules, and use this to screen events. This approach cannot generally detect misuses for which it has not been programmed, i.e. it is prone to issuing false negatives. The other attempts to `learn' the features of event patterns that constitute normal behaviour, and, by observing patterns that do not match expected behaviour, detect when a misuse has occurred. This approach is prone to issuing false positives, i.e. inferring misuse from innocent patterns of behaviour that the system was not trained to recognise. Contemporary approaches are seen to favour hybridisation, often combining detection or localisation mechanisms for both abnormal and normal behaviour, the former to capture known cases of misuse, the latter to capture unknown cases. In some systems, these mechanisms even work together to update each other to increase detection rates and lower false positive rates. It is concluded that hybridisation offers the most promising future direction, but that a rule or state based component is likely to remain, being the most natural approach to the correlation of complex events. The challenge, then, is to mitigate the weaknesses of canonical programmed systems such that learning, generalisation and adaptation are more readily facilitated