Agent-Oriented Data Curation in Bioinformatics

The practitioners of bioinformatics require increasing sophistication from their software tools to take into account the particular characteristics that make their domain complex. For example, there is a great variation of experience of researchers, from novices who would like guidance from experts in the best resources to use to experts that wish to take greater management control of the tools used in their experiments. Also, the range of available, and conflicting, data formats is growing and there is a desire to automate the many trivial manual stages of in-silico experiments. Agent-oriented software development is one approach to tackling the design of complex applications. In this paper, we argue that, in fact, agent-oriented development is a particularly well-suited approach to developing bioinformatics tools that take into account the wider domain characteristics. To illustrate this, we design a data curation tool, which manages the format of experimental data, extend it to better account for the extra requirements placed by the domain characteristics, and show how the characteristics lead to a system well suited to an agent-oriented view.

From SMART to agent systems development

n order for agent-oriented software engineering to prove effective it must use principled notions of agents and enabling specification and reasoning, while still considering routes to practical implementation. This paper deals with the issue of individual agent specification and construction, departing from the conceptual basis provided by the smart agent framework. smart offers a descriptive specification of an agent architecture but omits consideration of issues relating to construction and control. In response, we introduce two new views to complement smart: a behavioural specification and a structural specification which, together, determine the components that make up an agent, and how they operate. In this way, we move from abstract agent system specification to practical implementation. These three aspects are combined to create an agent construction model, actsmart, which is then used to define the AgentSpeak(L) architecture in order to illustrate the application of actsmart.

Modelling the Provenance of Data in Autonomous Systems

Determining the provenance of data, i.e. the process that led to that data, is vital in many disciplines. For example, in science, the process that produced a given result must be demonstrably rigorous for the result to be deemed reliable. A provenance system supports applications in recording adequate documentation about process executions to answer queries regarding provenance, and provides functionality to perform those queries. Several provenance systems are being developed, but all focus on systems in which the components are textitreactive, for example Web Services that act on the basis of a request, job submission system, etc. This limitation means that questions regarding the motives of autonomous actors, or textitagents, in such systems remain unanswerable in the general case. Such questions include: who was ultimately responsible for a given effect, what was their reason for initiating the process and does the effect of a process match what was intended to occur by those initiating the process? In this paper, we address this limitation by integrating two solutions: a generic, re-usable framework for representing the provenance of data in service-oriented architectures and a model for describing the goal-oriented delegation and engagement of agents in multi-agent systems. Using these solutions, we present algorithms to answer common questions regarding responsibility and success of a process and evaluate the approach with a simulated healthcare example.

Technology diffusion: analysing the diffusion of agent technologies

Despite several examples of deployed agent systems, there remain barriers to the large-scale adoption of agent technologies. In order to understand these barriers, this paper considers aspects of marketing theory which deal with diffusion of innovations and their relevance to the agents domain and the current state of diffusion of agent technologies. In particular, the paper examines the role of standards in the adoption of new technologies, describes the agent standards landscape, and compares the development and diffusion of agent technologies with that of object-oriented programming. The paper also reports on a simulation model developed in order to consider different trajectories for the adoption of agent technologies, with trajectories based on various assumptions regarding industry structure and the existence of competing technology standards. We present details of the simulation model and its assumptions, along with the results of the simulation exercises.

Modelling and Administration of Contract-Based Systems

Mirroring the paper versions exchanged between businesses today, electronic contracts offer the possibility of dynamic, automatic creation and enforcement of restrictions and compulsions on agent behaviour that are designed to ensure business objectives are met. However, where there are many contracts within a particular application, it can be difficult to determine whether the system can reliably fulfil them all; computer-parsable electronic contracts may allow such verification to be automated. In this paper, we describe a conceptual framework and architecture specification in which normative business contracts can be electronically represented, verified, established, renewed, etc. In particular, we aim to allow systems containing multiple contracts to be checked for conflicts and violations of business objectives. We illustrate the framework and architecture with an aerospace example.

Aprendizado por Reforço com Valores deInfluência em Sistemas Multi-Agente

We propose a new paradigm for collective learning in multi-agent systems (MAS) as a solution to the problem in which several agents acting over the same environment must learn how to perform tasks, simultaneously, based on feedbacks given by each one of the other agents. We introduce the proposed paradigm in the form of a reinforcement learning algorithm, nominating it as reinforcement learning with influence values. While learning by rewards, each agent evaluates the relation between the current state and/or action executed at this state (actual believe) together with the reward obtained after all agents that are interacting perform their actions. The reward is a result of the interference of others. The agent considers the opinions of all its colleagues in order to attempt to change the values of its states and/or actions. The idea is that the system, as a whole, must reach an equilibrium, where all agents get satisfied with the obtained results. This means that the values of the state/actions pairs match the reward obtained by each agent. This dynamical way of setting the values for states and/or actions makes this new reinforcement learning paradigm the first to include, naturally, the fact that the presence of other agents in the environment turns it a dynamical model. As a direct result, we implicitly include the internal state, the actions and the rewards obtained by all the other agents in the internal state of each agent. This makes our proposal the first complete solution to the conceptual problem that rises when applying reinforcement learning in multi-agent systems, which is caused by the difference existent between the environment and agent models. With basis on the proposed model, we create the IVQ-learning algorithm that is exhaustive tested in repetitive games with two, three and four agents and in stochastic games that need cooperation and in games that need collaboration. This algorithm shows to be a good option for obtaining solutions that guarantee convergence to the Nash optimum equilibrium in cooperative problems. Experiments performed clear shows that the proposed paradigm is theoretical and experimentally superior to the traditional approaches. Yet, with the creation of this new paradigm the set of reinforcement learning applications in MAS grows up. That is, besides the possibility of applying the algorithm in traditional learning problems in MAS, as for example coordination of tasks in multi-robot systems, it is possible to apply reinforcement learning in problems that are essentially collaborative

A multi-agent architecture for intelligent data analysis

The present study introduces a multi-agent architecture designed for doing automation process of data integration and intelligent data analysis. Different from other approaches the multi-agent architecture was designed using a multi-agent based methodology. Tropos, an agent based methodology was used for design. Based on the proposed architecture, we describe a Web based application where the agents are responsible to analyse petroleum well drilling data to identify possible abnormalities occurrence. The intelligent data analysis methods used was the Neural Network.

Metal biosorption onto dry biomass of Arthrospira (Spirulina) platensis and Chlorella vulgaris: Multi-metal systems

Binary and ternary systems of Ni2+, Zn2+, and Pb2+ were investigated at initial metal concentrations of 0.5, 1.0 and 2.0 mM as competitive adsorbates using Arthrospira platensis and Chlorella vulgaris as biosorbents. The experimental results were evaluated in terms of equilibrium sorption capacity and metal removal efficiency and fitted to the multi-component Langmuir and Freundlich isotherms. The pseudo second order model of Ho and McKay described well the adsorption kinetics, and the FT-IR spectroscopy confirmed metal binding to both biomasses. Ni2+ and Zn2+ interference on Pb2+ sorption was lower than the contrary, likely due to biosorbent preference to Pb. In general, the higher the total initial metal concentration, the lower the adsorption capacity. The results of this study demonstrated that dry biomass of C. vulgaris behaved as better biosorbent than A. platensis and suggest its use as an effective alternative sorbent for metal removal from wastewater. (C) 2012 Elsevier B.V. All rights reserved.

Self-organising coordination systems

Many research fields are pushing the engineering of large-scale, mobile, and open systems towards the adoption of techniques inspired by self-organisation: pervasive computing, but also distributed artificial intelligence, multi-agent systems, social networks, peer-topeer and grid architectures exploit adaptive techniques to make global system properties emerge in spite of the unpredictability of interactions and behaviour. Such a trend is visible also in coordination models and languages, whenever a coordination infrastructure needs to cope with managing interactions in highly dynamic and unpredictable environments. As a consequence, self-organisation can be regarded as a feasible metaphor to define a radically new conceptual coordination framework. The resulting framework defines a novel coordination paradigm, called self-organising coordination, based on the idea of spreading coordination media over the network, and charge them with services to manage interactions based on local criteria, resulting in the emergence of desired and fruitful global coordination properties of the system. Features like topology, locality, time-reactiveness, and stochastic behaviour play a key role in both the definition of such a conceptual framework and the consequent development of self-organising coordination services. According to this framework, the thesis presents several self-organising coordination techniques developed during the PhD course, mainly concerning data distribution in tuplespace-based coordination systems. Some of these techniques have been also implemented in ReSpecT, a coordination language for tuple spaces, based on logic tuples and reactions to events occurring in a tuple space. In addition, the key role played by simulation and formal verification has been investigated, leading to analysing how automatic verification techniques like probabilistic model checking can be exploited in order to formally prove the emergence of desired behaviours when dealing with coordination approaches based on self-organisation. To this end, a concrete case study is presented and discussed.