A review of modelling and verification approaches for computational biology

This paper reviews most frequently used computational modelling approaches and formal verification techniques in computational biology. The paper also compares a number of model checking tools and software suits used in analysing biological systems and biochemical networks and verifiying a wide range of biological properties

Evolving Test Environments to Identify Faults in Swarm Robotics Algorithms

Swarm robotic systems are often considered to be dependable. However, there is little empirical evidence or theoretical analysis showing that dependability is an inherent property of all swarm robotic systems. Recent literature has identified potential issues with respect to dependability within certain types of swarm robotic control algorithms. However, there is little research on the testing of swarm robotic systems; this provides the motivation for developing a novel testing method for swarm robotic systems. An evolutionary testing method is proposed in this thesis to identify unintended behaviours during the execution of swarm robotic systems autonomously. Three case studies are carried out on flocking control algorithm, foraging algorithm, and task partitioning algorithm. These case studies not only show that the evolutionary testing method has the ability to identify faults in swarm robotic system, but also show that this evolutionary testing method is able to reveal failures in various swarm control algorithms. The experimental results show that the evolutionary testing method can lead to worse swarm performance and reveal more failures than the random testing method within the same number of computing evaluations. Moreover, the case study of flocking control algorithm also shows that the evolutionary testing method covers more failure types than the random testing method. In all three case studies, the dependability of each swarm robotic system has been improved by tackling the faults identified during the testing phase. Consequently, the evolutionary testing method has the potential to be used to help the developers of swarm robotic systems to design and calibrate the swarm control algorithms thereby assuring the dependability of swarm robotic systems

Supervisory Control Theory for Controlling Swarm Robotics Systems

Swarm robotics systems have the potential to tackle many interesting problems. Their control software is mostly created by ad-hoc development. This makes it hard to deploy swarm robotics systems in real-world scenarios as it is difficult to analyse, maintain, or extend these systems. Formal methods can contribute to overcome these problems. However, they usually do not guarantee that the implementation matches the specification because the system’s control code is typically generated manually. This thesis studies the application of the supervisory control theory (SCT) framework in swarm robotics systems. SCT is widely applied and well established in the man- ufacturing context. It requires the system and the desired behaviours (specifications) to be defined as formal languages. In this thesis, regular languages are used. Regular languages, in the form of deterministic finite state automata, have already been widely applied for controlling swarm robotics systems, enabling a smooth transition from the ad-hoc development currently in practice. This thesis shows that the control code for swarm robotics systems can be automatically generated from formal specifications. Several case studies are presented that serve as guidance for those who want to learn how to specify swarm behaviours using SCT formally. The thesis provides the tools for the implementation of controllers using formal specifications. Controllers are validated on swarms of up to 600 physical robots through a series of systematic experiments. It is also shown that the same controllers can be automatically ported onto different robotics platforms, as long as they offer the required capabilities. The thesis extends and incorporates techniques to the supervisory control theory framework; specifically, the concepts of global events and the use of probabilistic generators. It can be seen as a step towards making formal methods a standard practice in swarm robotics

Predicting the behavior of robotic swarms in discrete simulation

Doctor of PhilosophyDepartment of Computing and Information SciencesDavid GustafsonWe use probabilistic graphs to predict the location of swarms over 100 steps in simulations in grid worlds. One graph can be used to make predictions for worlds of different dimensions. The worlds are constructed from a single 5x5 square pattern, each square of which may be either unoccupied or occupied by an obstacle or a target. Simulated robots move through the worlds avoiding the obstacles and tagging the targets. The interactions between the robots and the robots and the environment lead to behavior that, even in deterministic simulations, can be difficult to anticipate. The graphs capture the local rate and direction of swarm movement through the pattern. The graphs are used to create a transition matrix, which along with an occupancy matrix, can be used to predict the occupancy in the patterns in the 100 steps using 100 matrix multiplications. In the future, the graphs could be used to predict the movement of physical swarms though patterned environments such as city blocks in applications such as disaster response search and rescue. The predictions could assist in the design and deployment of such swarms and help rule out undesirable behavior

Stochastic modelling of spatial collective adaptive systems

Collective Adaptive Systems (CAS) are composed of individual agents with internal knowledge and rules which organize themselves into ensembles. These ensembles can often be observed to exhibit behaviour resembling that of a single entity with a clear goal and a consistent internal knowledge, even when the individual agents within the ensemble are not managed by any outside, globally-accessible entity. Because of their lack of a need for centralized control which results in high robustness, CAS are commonly observed in nature – and for similar reasons are often reflected in human engineered systems. Researching the patterns of operation observed in such systems provides meaningful insight into how to design and optimise stable multiagent systems capable of withstanding adverse conditions. Formal modelling provides valuable intellectual tools which can be applied to the problem of analysis of systems by means of modelling and simulation. In this thesis we explore the modelling of CAS in which space (topology and distances) plays a significant role. Working with CARMA (Collective Adaptive Resource-sharing Markovian Agents) a formal feature-rich language for modelling stochastic CAS, we investigate a number of spatial CAS scenarios from the realm of urban planning. When components operate in a spatial context, their behaviour can be affected by where they are located in that space. For example, their location can influence the speed at which they move, and their ability to communicate with other components. Components in CARMA have internal store, and behaviour expressed by Markov processes. They can communicate with each other through sending messages on state transitions in a unicast or broadcast fashion. Simulation with pseudo-random events can be used to obtain values of measures applied to CARMA models, providing a basis for analysis and optimisation. The CARMA models developed in the case studies are data-driven and the results of simulating these models are compared with real-world data. In particular, we explore two scenarios: crowd-routing and city transportation systems. Building on top of CARMA, we also introduce CGP (CARMA Graphical Plugin), a novel graphical software tool for graphically specifying spatial CAS systems with the feature of automatic translation into CARMA models. We also supply CARMA with additional syntax structures for expressing spatial constructs

A property-driven methodology for formal analysis of synthetic biology systems

yesThis paper proposes a formal methodology to analyse bio-systems, in particular synthetic biology systems. An integrative analysis perspective combining different model checking approaches based on different property categories is provided. The methodology is applied to the synthetic pulse generator system and several verification experiments are carried out to demonstrate the use of our approach to formally analyse various aspects of synthetic biology systems.EPSR

Formal Analysis of Artificial Collectives using Parametric Markov Models

There are many potential applications for the deployment of distributed systems composed of identical autonomous agents such as swarm robotic systems or wireless sensor networks, including remote monitoring, space exploration, or environmental clean up. Such systems need to be robust, and the loss of a small number of agents should not compromise the effectiveness of the system as they will often operate in hostile environments where individual members of that system may suffer failures, or communication may be hindered. To address this, these artificial systems are often designed to imitate the behaviour of self-organising systems found in nature, where simple reactive behaviours for individual members of a system can lead to complex global behaviours, and the collective remains robust to the loss of individuals. Despite much research being conducted into the development and evaluation of these systems, the industrial application of these technologies is still low. This issue could be addressed by further demonstrating that they can reliably, and predictably, achieve given objectives. Designing such systems is challenging, and often detailed simulations are developed for their analysis. Simulations give invaluable insight into the behaviour of such a system, however, there are often corner cases that might be overlooked. By developing a formal model of the system using some appropriate formalism, mathematical techniques can be applied during development to ensure that the system behaves correctly with respect to some given specification. These dynamic and inherently stochastic systems can be modelled as Markov processes; memoryless stochastic processes whose behaviour at any moment in time is determined solely by their current state. Model checking is an algorithmic technique to exhaustively check that a representation of a system as a Markov process exhibits some desirable property; furthermore, such an analysis can be extended to analyse systems whose parameters may not be known in an advance. However, the analysis of formal models of large systems is limited due to the resources that are required for their analysis: the size of the model may grow exponentially with the size of the system, and the subsequent analysis may prove to be impossible due to hardware or time constraints. This thesis investigates the suitability of parametric Markov models for the analysis of swarm robotic systems and wireless sensor networks. The analysis of such models is costly in terms of the size of the formal model representing a system, and the computation time required for its subsequent analysis. Modelling techniques and abstractions are developed for the construction of macroscopic models that abstract away from the identities of individual swarm robots or sensor nodes, and instead focus on the desirable global behaviours of such a system, resulting in smaller formal models. New techniques are then introduced to facilitate the analysis of large families of such models, where similarities between models who share some parameter values are exploited to speed up their analysis. In addition, new representations for such models are developed that allow for larger models to be analysed, and also significantly reduce the time required for that analysis