Argumentation and artifacts for intelligent multi-agent systems

Reasoning under uncertainty is a human capacity that in software system is necessary and often hidden. Argumentation theory and logic make explicit non-monotonic information in order to enable automatic forms of reasoning under uncertainty. In human organization Distributed Cognition and Activity Theory explain how artifacts are fundamental in all cognitive process. Then, in this thesis we search to understand the use of cognitive artifacts in an new argumentation framework for an agent-based artificial society.

Multi-level models and infrastructures for simulating biological system development

The hierarchical organisation of biological systems plays a crucial role in the pattern formation of gene expression resulting from the morphogenetic processes, where autonomous internal dynamics of cells, as well as cell-to-cell interactions through membranes, are responsible for the emergent peculiar structures of the individual phenotype. Being able to reproduce the systems dynamics at different levels of such a hierarchy might be very useful for studying such a complex phenomenon of self-organisation. The idea is to model the phenomenon in terms of a large and dynamic network of compartments, where the interplay between inter-compartment and intra-compartment events determines the emergent behaviour resulting in the formation of spatial patterns. According to these premises the thesis proposes a review of the different approaches already developed in modelling developmental biology problems, as well as the main models and infrastructures available in literature for modelling biological systems, analysing their capabilities in tackling multi-compartment / multi-level models. The thesis then introduces a practical framework, MS-BioNET, for modelling and simulating these scenarios exploiting the potential of multi-level dynamics. This is based on (i) a computational model featuring networks of compartments and an enhanced model of chemical reaction addressing molecule transfer, (ii) a logic-oriented language to flexibly specify complex simulation scenarios, and (iii) a simulation engine based on the many-species/many-channels optimised version of Gillespie’s direct method. The thesis finally proposes the adoption of the agent-based model as an approach capable of capture multi-level dynamics. To overcome the problem of parameter tuning in the model, the simulators are supplied with a module for parameter optimisation. The task is defined as an optimisation problem over the parameter space in which the objective function to be minimised is the distance between the output of the simulator and a target one. The problem is tackled with a metaheuristic algorithm. As an example of application of the MS-BioNET framework and of the agent-based model, a model of the first stages of Drosophila Melanogaster development is realised. The model goal is to generate the early spatial pattern of gap gene expression. The correctness of the models is shown comparing the simulation results with real data of gene expression with spatial and temporal resolution, acquired in free on-line sources.

Engineering Agent-Oriented Technologies and Programming Languages for Computer Programming and Software Development

Mainstream hardware is becoming parallel, heterogeneous, and distributed on every desk, every home and in every pocket. As a consequence, in the last years software is having an epochal turn toward concurrency, distribution, interaction which is pushed by the evolution of hardware architectures and the growing of network availability. This calls for introducing further abstraction layers on top of those provided by classical mainstream programming paradigms, to tackle more effectively the new complexities that developers have to face in everyday programming. A convergence it is recognizable in the mainstream toward the adoption of the actor paradigm as a mean to unite object-oriented programming and concurrency. Nevertheless, we argue that the actor paradigm can only be considered a good starting point to provide a more comprehensive response to such a fundamental and radical change in software development. Accordingly, the main objective of this thesis is to propose Agent-Oriented Programming (AOP) as a high-level general purpose programming paradigm, natural evolution of actors and objects, introducing a further level of human-inspired concepts for programming software systems, meant to simplify the design and programming of concurrent, distributed, reactive/interactive programs. To this end, in the dissertation first we construct the required background by studying the state-of-the-art of both actor-oriented and agent-oriented programming, and then we focus on the engineering of integrated programming technologies for developing agent-based systems in their classical application domains: artificial intelligence and distributed artificial intelligence. Then, we shift the perspective moving from the development of intelligent software systems, toward general purpose software development. Using the expertise maturated during the phase of background construction, we introduce a general-purpose programming language named simpAL, which founds its roots on general principles and practices of software development, and at the same time provides an agent-oriented level of abstraction for the engineering of general purpose software systems.

A mesoscopic simulation method for electrolyte solutions

This thesis deals with the development of a novel simulation technique for macromolecules in electrolyte solutions, with the aim of a performance improvement over current molecular-dynamics based simulation methods. In solutions containing charged macromolecules and salt ions, it is the complex interplay of electrostatic interactions and hydrodynamics that determines the equilibrium and non-equilibrium behavior. However, the treatment of the solvent and dissolved ions makes up the major part of the computational effort. Thus an efficient modeling of both components is essential for the performance of a method. With the novel method we approach the solvent in a coarse-grained fashion and replace the explicit-ion description by a dynamic mean-field treatment. Hence we combine particle- and field-based descriptions in a hybrid method and thereby effectively solve the electrokinetic equations. The developed algorithm is tested extensively in terms of accuracy and performance, and suitable parameter sets are determined. As a first application we study charged polymer solutions (polyelectrolytes) in shear flow with focus on their viscoelastic properties. Here we also include semidilute solutions, which are computationally demanding. Secondly we study the electro-osmotic flow on superhydrophobic surfaces, where we perform a detailed comparison to theoretical predictions.

Simulations- und VR-basierte Steuerungsverifikation zellularer Intralogistiksysteme

Die hohe Komplexität zellularer intralogistischer Systeme und deren Steuerungsarchitektur legt die Verwendung moderner Simulations- und Visualisierungstechniken nahe, um schon im Vorfeld Aussagen über die Leistungsfähigkeit und Zukunftssicherheit eines geplanten Systems treffen zu können. In dieser Arbeit wird ein Konzept für ein Simulationssystem zur VR-basierten Steuerungsverifikation zellularer Intralogistiksysteme vorgestellt. Beschrieben wird die Erstellung eines Simulationsmodells für eine real existierende Anlage und es wird ein Überblick über die Bestandteile der Simulation, insbesondere die Anbindung der Steuerung des realen agentenbasierten Systems, gegeben.

Evaluation of control and surveillance strategies for classical swine fever using a simulation model

Classical swine fever (CSF) outbreaks can cause enormous losses in naïve pig populations. How to best minimize the economic damage and number of culled animals caused by CSF is therefore an important research area. The baseline CSF control strategy in the European Union and Switzerland consists of culling all animals in infected herds, movement restrictions for animals, material and people within a given distance to the infected herd and epidemiological tracing of transmission contacts. Additional disease control measures such as pre-emptive culling or vaccination have been recommended based on the results from several simulation models; however, these models were parameterized for areas with high animal densities. The objective of this study was to explore whether pre-emptive culling and emergency vaccination should also be recommended in low- to moderate-density areas such as Switzerland. Additionally, we studied the influence of initial outbreak conditions on outbreak severity to improve the efficiency of disease prevention and surveillance. A spatial, stochastic, individual-animal-based simulation model using all registered Swiss pig premises in 2009 (n=9770) was implemented to quantify these relationships. The model simulates within-herd and between-herd transmission (direct and indirect contacts and local area spread). By varying the four parameters (a) control measures, (b) index herd type (breeding, fattening, weaning or mixed herd), (c) detection delay for secondary cases during an outbreak and (d) contact tracing probability, 112 distinct scenarios were simulated. To assess the impact of scenarios on outbreak severity, daily transmission rates were compared between scenarios. Compared with the baseline strategy (stamping out and movement restrictions) vaccination and pre-emptive culling neither reduced outbreak size nor duration. Outbreaks starting in a herd with weaning piglets or fattening pigs caused higher losses regarding to the number of culled premises and were longer lasting than those starting in the two other index herd types. Similarly, larger transmission rates were estimated for these index herd type outbreaks. A longer detection delay resulted in more culled premises and longer duration and better transmission tracing increased the number of short outbreaks. Based on the simulation results, baseline control strategies seem sufficient to control CSF in low-medium animal-dense areas. Early detection of outbreaks is crucial and risk-based surveillance should be focused on weaning piglet and fattening pig premises.

Imaging properties of scanning equalization digital radiography: A simulation study

We have developed an empirically based simulation system to create images equivalent in SNR and SPR to those that would be acquired with various possible SEDR configurations. This system uses a collection of spot collimated full-field images (SCFFIs) of an anthropomorphic chest phantom, taken at high exposure levels and rescaled in noise and intensity, then digitally collimated and combined to produce the simulated SEDR images. This system allows for the study of design trade-offs between different equalization feedback schemes and scatter rejection geometries in addition to estimating the clinical benefits of SEDR over traditional imaging techniques. Data from this simulation system has demonstrated that SEDR techniques offer potential significant improvements over currently used digital radiography techniques for chest imaging. ^

Simulation Model of Benthic Antarctic Assemblages (SIMBAA), link to PC-executable

SIMBAA is a spatially explicit, individual-based simulation model. It was developed to analyse the response of populations of Antarctic benthic species and their diversity to iceberg scouring. This disturbance is causing a high local mortality providing potential space for new colonisation. Traits can be attributed to model species, e.g. in terms of reproduction, dispersal, and life span. Physical disturbances can be designed in space and time, e.g. in terms of size, shape, and frequency. Environmental heterogeneity can be considered by cell-specific capacities to host a certain number of individuals. When grid cells become empty (after a disturbance event or due to natural mortality of of an individual), a lottery decides which individual from which species stored in a pool of candidates (for this cell) will recruit in that cell. After a defined period the individuals become mature and their offspring are dispersed and stored in the pool of candidates. The biological parameters and disturbance regimes decide on how long an individual lives. Temporal development of single populations of species as well as Shannon diversity are depicted in the main window graphically and primary values are listed. Examples for simulations can be loaded and saved as sgf-files. The results are also shown in an additional window in a dimensionless area with 50 x 50 cells, which contain single individuals depicted as circles; their colour indicates the assignment to the self-designed model species and the size represents their age. Dominant species per cell and disturbed areas can also be depicted. Output of simulation runs can be saved as images, which can be assembled to video-clips by standard computer programs (see GIF-examples of which "Demo 1" represents the response of the Antarctic benthos to iceberg scouring and "Demo 2" represents a simulation of a deep-sea benthic habitat).

Enhancing iDynoMiCS framework with a plasmid conjugation module

Actualmente existen aplicaciones que permiten simular el comportamiento de bacterias en distintos hábitats y los procesos que ocurren en estos para facilitar su estudio y experimentación sin la necesidad de un laboratorio. Una de las aplicaciones de software libre para la simulación de poblaciones bacteriológicas mas usada es iDynoMiCS (individual-based Dynamics of Microbial Communities Simulator), un simulador basado en agentes que permite trabajar con varios modelos computacionales de bacterias en 2D y 3D. Este simulador permite una gran libertad al configurar una numerosa cantidad de variables con respecto al entorno, reacciones químicas y otros detalles importantes. Una característica importante es el poder simular de manera sencilla la conjugación de plásmidos entre bacterias. Los plásmidos son moléculas de ADN diferentes del cromosoma celular, generalmente circularles, que se replican, transcriben y conjugan independientemente del ADN cromosómico. Estas están presentes normalmente en bacterias procariotas, y en algunas ocasiones en eucariotas, sin embargo, en este tipo de células son llamados episomas. Dado el complejo comportamiento de los plásmidos y la gama de posibilidades que estos presentan como mecanismos externos al funcionamiento básico de la célula, en la mayoría de los casos confiriéndole distintas ventajas evolutivas, como por ejemplo: resistencia antibiótica, entre otros, resulta importante su estudio y subsecuente manipulación. Sin embargo, el marco operativo del iDynoMiCS, en cuanto a simulación de plásmidos se refiere, es demasiado sencillo y no permite realizar operaciones más complejas que el análisis de la propagación de un plásmido en la comunidad. El presente trabajo surge para resolver esta deficiencia de iDynomics. Aquí se analizarán, desarrollarán e implementarán las modificaciones necesarias para que iDynomics pueda simular satisfactoriamente y mas apegado a la realidad la conjugación de plásmidos y permita así mismo resolver distintas operaciones lógicas, como lo son los circuitos genéticos, basadas en plásmidos. También se analizarán los resultados obtenidos de acuerdo a distintos estudios relevantes y a la comparación de los resultados obtenidos con el código original de iDynomics. Adicionalmente se analizará un estudio comparando la eficiencia de detección de una sustancia mediante dos circuitos genéticos distintos. Asimismo el presente trabajo puede tener interés para el grupo LIA de la Facultad de Informática de la Universidad Politécnica de Madrid, el cual está participando en el proyecto europeo BACTOCOM que se centra en el estudio de la conjugación de plásmidos y circuitos genéticos. --ABSTRACT--Currently there are applications that simulate the behavior of bacteria in different habitats and the ongoing processes inside them to facilitate their study and experimentation without the need for an actual laboratory. One of the most used open source applications to simulate bacterial populations is iDynoMiCS (individual-based Dynamics of Microbial Communities Simulator), an agent-based simulator that allows working with several computer models of 2D and 3D bacteria in biofilms. This simulator allows great freedom by means of a large number of configurable variables regarding environment, chemical reactions and other important details of the simulation. Within these characteristics there exists a very basic framework to simulate plasmid conjugation. Plasmids are DNA molecules physically different from the cell’s chromosome, commonly found as small circular, double-stranded DNA molecules that are replicated, conjugated and transcribed independently of chromosomal DNA. These bacteria are normally present in prokaryotes and sometimes in eukaryotes, which in this case these cells are called episomes. Plasmids are external mechanisms to the cells basic operations, and as such, in the majority of the cases, confer to the host cell various evolutionary advantages, like antibiotic resistance for example. It is mperative to further study plasmids and the possibilities they present. However, the operational framework of the iDynoMiCS plasmid simulation is too simple, and does not allow more complex operations that the analysis of the spread of a plasmid in the community. This project was conceived to resolve this particular deficiency in iDynomics, moreover, in this paper is discussed, developed and implemented the necessary changes to iDynomics simulation software so it can satisfactorily and realistically simulate plasmid conjugation, and allow the possibility to solve various ogic operations, such as plasmid-based genetic circuits. Moreover the results obtained will be analyzed and compared with other relevant studies and with those obtained with the original iDynomics code. Conjointly, an additional study detailing the sensing of a substance with two different genetic circuits will be presented. This work may also be relevant to the LIA group of the Faculty of Informatics of the Polytechnic University of Madrid, which is participating in the European project BACTOCOM that focuses on the study of the of plasmid conjugation and genetic circuits.

Desenvolvimento de um modelo baseado em agentes para investigar a conformação e evolução de padrões populacionais de atividade física no lazer em adultos

Introdução: Grande parte das ações para promover a atividade física no lazer em populações tem apresentado tamanhos de efeito pequenos ou inexistentes, ou resultados inconsistentes. Abordar o problema a partir da perspectiva sistêmica pode ser uma das formas de superar esse descompasso. Objetivo: Desenvolver um modelo baseado em agentes para investigar a conformação e evolução de padrões populacionais de atividade física no lazer em adultos a partir da interação entre atributos psicológicos dos indivíduos e atributos dos ambientes físico construído e social em que vivem. Métodos: O processo de modelagem foi composto por três etapas: elaboração de um mapa conceitual, com base em revisão da literatura e consulta com especialistas; criação e verificação do algoritmo do modelo; e parametrização e análise de consistência e sensibilidade. Os resultados da revisão da literatura foram consolidados e relatados de acordo com os domínios da busca (aspectos psicológicos, ambiente social e ambiente físico construído). Os resultados quantitativos da consulta com os especialistas foram descritos por meio de frequências e o conteúdo das respostas questões abertas foi analisado e compilado pelo autor desta tese. O algoritmo do modelo foi criado no software NetLogo, versão 5.2.1., seguindo-se um protocolo de verificação para garantir que o algoritmo fosse implementado acuradamente. Nas análises de consistência e sensibilidade, utilizaram-se o Teste A de Vargha-Delaney, coeficiente de correlação de postos parcial, boxplots e gráficos de linha e de dispersão. Resultados: Definiram-se como elementos do mapa conceitual a intenção da pessoa, o comportamento de pessoas próximas e da comunidade, e a percepção da qualidade, do acesso e das atividades disponíveis nos locais em que atividade física no lazer pode ser praticada. O modelo representa uma comunidade hipotética contendo dois tipos de agentes: pessoas e locais em que atividade física no lazer pode ser praticada. As pessoas interagem entre si e com o ambiente construído, gerando tendências temporais populacionais de prática de atividade física no lazer e de intenção. As análises de sensibilidade indicaram que as tendências temporais de atividade física no lazer e de intenção são altamente sensíveis à influência do comportamento atual da pessoa sobre a sua intenção futura, ao tamanho do raio de percepção da pessoa e à proporção de locais em que a atividade física no lazer pode ser praticada. Considerações finais: O mapa conceitual e o modelo baseado em agentes se mostraram adequados para investigar a conformação e evolução de padrões populacionais de atividade física no lazer em adultos. A influência do comportamento da pessoa sobre a sua intenção, o tamanho do raio de percepção da pessoa e a proporção de locais em que a atividade física no lazer pode ser praticada são importantes determinantes da conformação e evolução dos padrões populacionais de atividade física no lazer entre adultos no modelo.

Time-series Luminance Distribution Maps: implementation of annual daylight simulation methods for occupant visual comfort analysis

Thesis (Master's)--University of Washington, 2016-06

Contributions to Physics-Based Aeroservoelastic Uncertainty Analysis

Thesis (Ph.D.)--University of Washington, 2016-06

Patterns in complex systems modeling

The design, development, and use of complex systems models raises a unique class of challenges and potential pitfalls, many of which are commonly recurring problems. Over time, researchers gain experience in this form of modeling, choosing algorithms, techniques, and frameworks that improve the quality, confidence level, and speed of development of their models. This increasing collective experience of complex systems modellers is a resource that should be captured. Fields such as software engineering and architecture have benefited from the development of generic solutions to recurring problems, called patterns. Using pattern development techniques from these fields, insights from communities such as learning and information processing, data mining, bioinformatics, and agent-based modeling can be identified and captured. Collections of such 'pattern languages' would allow knowledge gained through experience to be readily accessible to less-experienced practitioners and to other domains. This paper proposes a methodology for capturing the wisdom of computational modelers by introducing example visualization patterns, and a pattern classification system for analyzing the relationship between micro and macro behaviour in complex systems models. We anticipate that a new field of complex systems patterns will provide an invaluable resource for both practicing and future generations of modelers.

An iterative agent bidding mechanism for responsive manufacturing

In today's market, the global competition has put manufacturing businesses in great pressures to respond rapidly to dynamic variations in demand patterns across products and changing product mixes. To achieve substantial responsiveness, the manufacturing activities associated with production planning and control must be integrated dynamically, efficiently and cost-effectively. This paper presents an iterative agent bidding mechanism, which performs dynamic integration of process planning and production scheduling to generate optimised process plans and schedules in response to dynamic changes in the market and production environment. The iterative bidding procedure is carried out based on currency-like metrics in which all operations (e.g. machining processes) to be performed are assigned with virtual currency values, and resource agents bid for the operations if the costs incurred for performing them are lower than the currency values. The currency values are adjusted iteratively and resource agents re-bid for the operations based on the new set of currency values until the total production cost is minimised. A simulated annealing optimisation technique is employed to optimise the currency values iteratively. The feasibility of the proposed methodology has been validated using a test case and results obtained have proven the method outperforming non-agent-based methods.

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.