4 research outputs found
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Computational model validation using a novel multiscale multidimensional spatio-temporal meta model checking approach
This thesis was submitted for the award of Doctor of Philosophy and was awarded by Brunel University LondonComputational models of complex biological systems can provide a better understanding of how living systems function but need to be validated before they are employed for real-life (e.g. clinical) applications. One of the most frequently employed in silico approaches for validating such models is model checking. Traditional model checking approaches are limited to uniscale non-spatial computational models because they do not explicitly distinguish between different scales, and do not take properties of (emergent) spatial structures (e.g. density of multicellular population) into account. This thesis defines a novel multiscale multidimensional spatio-temporal meta model checking methodology which enables validating multiscale (spatial) computational models of biological systems relative to how both numeric (e.g. concentrations) and spatial system properties are expected to change over time and across multiple scales. The methodology has two important advantages. First it supports computational models encoded using various high-level modelling formalisms because it is defined relative to time series data and not the models used to produce them. Secondly the methodology is generic because it can be automatically reconfigured according to case study specific types of spatial structures and properties using the meta model checking approach. In addition the methodology could
be employed for multiple domains of science, but we illustrate its applicability here only against biological case studies. To automate the computational model validation process, the approach was implemented in software tools, which are made freely available online. Their efficacy is illustrated against two uniscale and four multiscale quantitative computational models encoding phase variation in bacterial colonies and the chemotactic aggregation of cells, respectively the rat cardiovascular system dynamics, the uterine contractions of labour, the Xenopus laevis cell cycle and the acute inflammation of the gut and lung. This novel model checking approach will enable the efficient construction of
reliable multiscale computational models of complex systems.Brunel University Londo
Model checking and compositional reasoning for multi-agent systems
Multi-agent systems are distributed systems containing interacting autonomous agents designed to achieve shared and private goals. For safety-critical systems where we wish to replace a human role with an autonomous entity, we need to make assurances about the correctness of the autonomous delegate. Specialised techniques have been proposed recently for the verification of agents against mentalistic logics. Problematically, these approaches treat the system in a monolithic way. When verifying a property against a single agent, the approaches examine all behaviours of every component in the system. This is both inefficient and can lead to intractability: the so-called state-space explosion problem. In this thesis, we consider techniques to support the verification of agents in isolation. We avoid the state-space explosion problem by verifying an individual agent in the context of a specification of the rest of the system, rather than the system itself. We show that it is possible to verify an agent against its desired properties without needing to consider the behaviours of the remaining components. We first introduce a novel approach for verifying a system as a whole against specifications expressed in a logic of time and knowledge. The technique, based on automata over trees, supports an efficient procedure to verify systems in an automata-theoretic way using language containment. We show how the automata-theoretic approach can be used as an underpinning for assume-guarantee reasoning for multi-agent systems. We use a temporal logic of actions to specify the expected behaviour of the other components in the system. When performing modular verification, this specification is used to exclude behaviours that are inconsistent with the concrete system. We implement both approaches within the open-source model checker MCMAS and show that, for the relevant properties, the assume-guarantee approach can significantly increase the tractability of individual agent verification.Open Acces