Modelling and simulating in systems biology: an approach based on multi-agent systems

Systems Biology is an innovative way of doing biology recently raised in bio-informatics contexts, characterised by the study of biological systems as complex systems with a strong focus on the system level and on the interaction dimension. In other words, the objective is to understand biological systems as a whole, putting on the foreground not only the study of the individual parts as standalone parts, but also of their interaction and of the global properties that emerge at the system level by means of the interaction among the parts. This thesis focuses on the adoption of multi-agent systems (MAS) as a suitable paradigm for Systems Biology, for developing models and simulation of complex biological systems. Multi-agent system have been recently introduced in informatics context as a suitabe paradigm for modelling and engineering complex systems. Roughly speaking, a MAS can be conceived as a set of autonomous and interacting entities, called agents, situated in some kind of nvironment, where they fruitfully interact and coordinate so as to obtain a coherent global system behaviour. The claim of this work is that the general properties of MAS make them an effective approach for modelling and building simulations of complex biological systems, following the methodological principles identified by Systems Biology. In particular, the thesis focuses on cell populations as biological systems. In order to support the claim, the thesis introduces and describes (i) a MAS-based model conceived for modelling the dynamics of systems of cells interacting inside cell environment called niches. (ii) a computational tool, developed for implementing the models and executing the simulations. The tool is meant to work as a kind of virtual laboratory, on top of which kinds of virtual experiments can be performed, characterised by the definition and execution of specific models implemented as MASs, so as to support the validation, falsification and improvement of the models through the observation and analysis of the simulations. A hematopoietic stem cell system is taken as reference case study for formulating a specific model and executing virtual experiments.

Behaviour Driven Development for Multi-Agent Systems

This paper presents a testing methodology to apply Behaviour Driven Development (BDD) techniques while developing Multi-Agent Systems (MAS), so called BEhavioural Agent Simple Testing (BEAST) methodology. It is supported by the developed open source framework (BEAST Tool) which automatically generates test cases skeletons from BDD scenarios specifications. The developed framework allows testing MASs based on JADE or JADEX platforms and offers a set of configurable Mock Agents which allow the execution of tests while the system is under development. BEAST tool has been validated in the development of a MAS for fault diagnosis in FTTH (Fiber To The Home) networks.

Robotic control systems based on bioinspired multi-agent systems: application of the principles of neuroscience to robotics

Robotics is a field that presents a large number of problems because it depends on a large number of disciplines, devices, technologies and tasks. Its expansion from perfectly controlled industrial environments toward open and dynamic environment presents a many new challenges, such as robots household robots or professional robots. To facilitate the rapid development of robotic systems, low cost, reusability of code, its medium and long term maintainability and robustness are required novel approaches to provide generic models and software systems who develop paradigms capable of solving these problems. For this purpose, in this paper we propose a model based on multi-agent systems inspired by the human nervous system able to transfer the control characteristics of the biological system and able to take advantage of the best properties of distributed software systems.

Convergence and knowledge processing in multi-agent systems

Multi-agent systems are complex systems comprised of multiple intelligent agents that act either independently or in cooperation with one another. Agent-based modelling is a method for studying complex systems like economies, societies, ecologies etc. Due to their complexity, very often mathematical analysis is limited in its ability to analyse such systems. In this case, agent-based modelling offers a practical, constructive method of analysis. The objective of this book is to shed light on some emergent properties of multi-agent systems. The authors focus their investigation on the effect of knowledge exchange on the convergence of complex, multi-agent systems.

Stability of multi-agent systems

This work attempts to shed light to the fundamental concepts behind the stability of Multi-Agent Systems. We view the system as a discrete time Markov chain with a potentially unknown transitional probability distribution. The system will be considered to be stable when its state has converged to an equilibrium distribution. Faced with the non-trivial task of establishing the convergence to such a distribution, we propose a hypothesis testing approach according to which we test whether the convergence of a particular system metric has occurred. We describe some artificial multi-agent ecosystems that were developed and we present results based on these systems which confirm that this approach qualitatively agrees with our intuition.

Multi-agent Systems in the Harvest Prognosis

The paper presents a case study of geo-monitoring a region consisting in the capturing and encoding of human expertise into a knowledge-based system. As soon as the maps have been processed, the data patterns are detected using knowledge-based agents for the harvest prognosis.

A nested Petri net framework for modeling and analyzing multi-agent systems

In the past two decades, multi-agent systems (MAS) have emerged as a new paradigm for conceptualizing large and complex distributed software systems. A multi-agent system view provides a natural abstraction for both the structure and the behavior of modern-day software systems. Although there were many conceptual frameworks for using multi-agent systems, there was no well established and widely accepted method for modeling multi-agent systems. This dissertation research addressed the representation and analysis of multi-agent systems based on model-oriented formal methods. The objective was to provide a systematic approach for studying MAS at an early stage of system development to ensure the quality of design. ^ Given that there was no well-defined formal model directly supporting agent-oriented modeling, this study was centered on three main topics: (1) adapting a well-known formal model, predicate transition nets (PrT nets), to support MAS modeling; (2) formulating a modeling methodology to ease the construction of formal MAS models; and (3) developing a technique to support machine analysis of formal MAS models using model checking technology. PrT nets were extended to include the notions of dynamic structure, agent communication and coordination to support agent-oriented modeling. An aspect-oriented technique was developed to address the modularity of agent models and compositionality of incremental analysis. A set of translation rules were defined to systematically translate formal MAS models to concrete models that can be verified through the model checker SPIN (Simple Promela Interpreter). ^ This dissertation presents the framework developed for modeling and analyzing MAS, including a well-defined process model based on nested PrT nets, and a comprehensive methodology to guide the construction and analysis of formal MAS models.^

Robust Adaptive Control with Applications to Multi-Agent Systems and Mobile Robotics

This thesis deals with robust adaptive control and its applications, and it is divided into three main parts. The first part is about the design of robust estimation algorithms based on recursive least squares. First, we present an estimator for the frequencies of biased multi-harmonic signals, and then an algorithm for distributed estimation of an unknown parameter over a network of adaptive agents. In the second part of this thesis, we consider a cooperative control problem over uncertain networks of linear systems and Kuramoto systems, in which the agents have to track the reference generated by a leader exosystem. Since the reference signal is not available to each network node, novel distributed observers are designed so as to reconstruct the reference signal locally for each agent, and therefore decentralizing the problem. In the third and final part of this thesis, we consider robust estimation tasks for mobile robotics applications. In particular, we first consider the problem of slip estimation for agricultural tracked vehicles. Then, we consider a search and rescue application in which we need to drive an unmanned aerial vehicle as close as possible to the unknown (and to be estimated) position of a victim, who is buried under the snow after an avalanche event. In this thesis, robustness is intended as an input-to-state stability property of the proposed identifiers (sometimes referred to as adaptive laws), with respect to additive disturbances, and relative to a steady-state trajectory that is associated with a correct estimation of the unknown parameter to be found.

Multi-agent collaboration for decision support in shared zones of intelligent buildings

In domain of intelligent buildings, saving energy in buildings and increasing preferences of occupants are two important factors. These factors are the important keys for evaluating the performance of work environment. In recent years, many researchers combine these areas to create the system that can change from original to the modern work environment called intelligent work environment. Due to advance of agent technology, it has received increasing attention in the area of intelligent pervasive environments. In this paper, we review several issues in intelligent buildings, with respect to the implementation of control system for intelligent buildings via multi-agent systems. Furthermore, we present the MASBO (Multi-Agent System for Building cOntrol) that has been implemented for controlling the building facilities to reach the balancing between energy efficiency and occupant’s comfort. In addition to enhance the MASBO system, the collaboration through negotiation among agents is presented.

Upper Ontology for Multi-Agent Energy Systems’ Applications

Energy systems worldwide are complex and challenging environments. Multi-agent based simulation platforms are increasing at a high rate, as they show to be a good option to study many issues related to these systems, as well as the involved players at act in this domain. In this scope the authors research group has developed three multi-agent systems: MASCEM, which simulates the electricity markets; ALBidS that works as a decision support system for market players; and MASGriP, which simulates the internal operations of smart grids. To take better advantage of these systems, their integration is mandatory. For this reason, is proposed the development of an upper-ontology which allows an easier cooperation and adequate communication between them. Additionally, the concepts and rules defined by this ontology can be expanded and complemented by the needs of other simulation and real systems in the same areas as the mentioned systems. Each system’s particular ontology must be extended from this top-level ontology.

Multi-agent simulation of competitive electricity markets: Autonomous systems cooperation for European market modeling

The electricity market restructuring, and its worldwide evolution into regional and even continental scales, along with the increasing necessity for an adequate integration of renewable energy sources, is resulting in a rising complexity in power systems operation. Several power system simulators have been developed in recent years with the purpose of helping operators, regulators, and involved players to understand and deal with this complex and constantly changing environment. The main contribution of this paper is given by the integration of several electricity market and power system models, respecting to the reality of different countries. This integration is done through the development of an upper ontology which integrates the essential concepts necessary to interpret all the available information. The continuous development of Multi-Agent System for Competitive Electricity Markets platform provides the means for the exemplification of the usefulness of this ontology. A case study using the proposed multi-agent platform is presented, considering a scenario based on real data that simulates the European Electricity Market environment, and comparing its performance using different market mechanisms. The main goal is to demonstrate the advantages that the integration of various market models and simulation platforms have for the study of the electricity markets’ evolution.

Systems of exchange values as tools for multi-agent organizations

This paper introduces systems of exchange values as tools for the organization of multi-agent systems. Systems of exchange values are defined on the basis of the theory of social exchanges, developed by Piaget and Homans. A model of social organization is proposed, where social relations are construed as social exchanges and exchange values are put into use in the support of the continuity of the performance of social exchanges. The dynamics of social organizations is formulated in terms of the regulation of exchanges of values, so that social equilibrium is connected to the continuity of the interactions. The concept of supervisor of social equilibrium is introduced as a centralized mechanism for solving the problem of the equilibrium of the organization The equilibrium supervisor solves such problem making use of a qualitative Markov Decision Process that uses numerical intervals for the representation of exchange values.

MASGriP – a Multi-Agent Smart Grid Simulation Platform

The increasing number of players that operate in power systems leads to a more complex management. In this paper a new multi-agent platform is proposed, which simulates the real operation of power system players. MASGriP – A Multi-Agent Smart Grid Simulation Platform is presented. Several consumer and producer agents are implemented and simulated, considering real characteristics and different goals and actuation strategies. Aggregator entities, such as Virtual Power Players and Curtailment Service Providers are also included. The integration of MASGriP agents in MASCEM (Multi-Agent System for Competitive Electricity Markets) simulator allows the simulation of technical and economical activities of several players. An energy resources management architecture used in microgrids is also explained.

A multi-agent based approach for intelligent smart grid management

The spread and globalization of distributed generation (DG) in recent years has should highly influence the changes that occur in Electricity Markets (EMs). DG has brought a large number of new players to take action in the EMs, therefore increasing the complexity of these markets. Simulation based on multi-agent systems appears as a good way of analyzing players’ behavior and interactions, especially in a coalition perspective, and the effects these players have on the markets. MASCEM – Multi-Agent System for Competitive Electricity Markets was created to permit the study of the market operation with several different players and market mechanisms. MASGriP – Multi-Agent Smart Grid Platform is being developed to facilitate the simulation of micro grid (MG) and smart grid (SG) concepts with multiple different scenarios. This paper presents an intelligent management method for MG and SG. The simulation of different methods of control provides an advantage in comparing different possible approaches to respond to market events. Players utilize electric vehicles’ batteries and participate in Demand Response (DR) contracts, taking advantage on the best opportunities brought by the use of all resources, to improve their actions in response to MG and/or SG requests.

A new approach for multi-agent coalition formation and management in the scope of electricity markets

This paper presents a new methodology for the creation and management of coalitions in Electricity Markets. This approach is tested using the multi-agent market simulator MASCEM, taking advantage of its ability to provide the means to model and simulate VPP (Virtual Power Producers). VPPs are represented as coalitions of agents, with the capability of negotiating both in the market, and internally, with their members, in order to combine and manage their individual specific characteristics and goals, with the strategy and objectives of the VPP itself. The new features include the development of particular individual facilitators to manage the communications amongst the members of each coalition independently from the rest of the simulation, and also the mechanisms for the classification of the agents that are candidates to join the coalition. In addition, a global study on the results of the Iberian Electricity Market is performed, to compare and analyze different approaches for defining consistent and adequate strategies to integrate into the agents of MASCEM. This, combined with the application of learning and prediction techniques provide the agents with the ability to learn and adapt themselves, by adjusting their actions to the continued evolving states of the world they are playing in.