Continuous-time temporal logic specification and verification for nonlinear biological systems in uncertain contexts

In this thesis we introduce a complete framework for modelling and verification of biological systems in uncertain contexts based on the bond-calculus process algebra and the LBUC spatio-temporal logic. The bond-calculus is a biological process algebra which captures complex patterns of interaction based on affinity patterns, a novel communication mechanism using pattern matching to express multiway interaction affinities and general kinetic laws, whilst retaining an agent-centric modelling style for biomolecular species. The bond-calculus is equipped with a novel continuous semantics which maps models to systems of Ordinary Differential Equations (ODEs) in a compositional way. We then extend the bond-calculus to handle uncertain models, featuring interval uncertainties in their species concentrations and reaction rate parameters. Our semantics is also extended to handle uncertainty in every aspect of a model, producing non-deterministic continuous systems whose behaviour depends either on time-independent uncertain parameters and initial conditions, corresponding to our partial knowledge of the system at hand, or time-varying uncertain inputs, corresponding to genuine variability in a system’s behaviour based on environmental factors. This language is then coupled with the LBUC spatio-temporal logic which combines Signal Temporal Logic (STL) temporal operators with an uncertain context operator which quantifies over an uncertain context model describing the range of environments over which a property must hold. We develop model-checking procedures for STL and LBUC properties based on verified signal monitoring over flowpipes produced by the Flow* verified integrator, including the technique of masking which directs monitoring for atomic propositions to time regions relevant to the overall verification problem at hand. This allows us to monitor many interesting nested contextual properties and frequently reduces monitoring costs by an order of magnitude. Finally, we explore the technique of contextual signal monitoring which can use a single Flow* flowpipe representing a functional dependency to complete a whole tree of signals corresponding to different uncertain contexts. This allows us to produce refined monitoring results over the whole space and to explore the variation in system behaviour in different contexts

Set-based state estimation and fault diagnosis using constrained zonotopes and applications

This doctoral thesis develops new methods for set-based state estimation and active fault diagnosis (AFD) of (i) nonlinear discrete-time systems, (ii) discrete-time nonlinear systems whose trajectories satisfy nonlinear equality constraints (called invariants), (iii) linear descriptor systems, and (iv) joint state and parameter estimation of nonlinear descriptor systems. Set-based estimation aims to compute tight enclosures of the possible system states in each time step subject to unknown-but-bounded uncertainties. To address this issue, the present doctoral thesis proposes new methods for efficiently propagating constrained zonotopes (CZs) through nonlinear mappings. Besides, this thesis improves the standard prediction-update framework for systems with invariants using new algorithms for refining CZs based on nonlinear constraints. In addition, this thesis introduces a new approach for set-based AFD of a class of nonlinear discrete-time systems. An affine parametrization of the reachable sets is obtained for the design of an optimal input for set-based AFD. In addition, this thesis presents new methods based on CZs for set-valued state estimation and AFD of linear descriptor systems. Linear static constraints on the state variables can be directly incorporated into CZs. Moreover, this thesis proposes a new representation for unbounded sets based on zonotopes, which allows to develop methods for state estimation and AFD also of unstable linear descriptor systems, without the knowledge of an enclosure of all the trajectories of the system. This thesis also develops a new method for set-based joint state and parameter estimation of nonlinear descriptor systems using CZs in a unified framework. Lastly, this manuscript applies the proposed set-based state estimation and AFD methods using CZs to unmanned aerial vehicles, water distribution networks, and a lithium-ion cell.Comment: My PhD Thesis from Federal University of Minas Gerais, Brazil. Most of the research work has already been published in DOIs 10.1109/CDC.2018.8618678, 10.23919/ECC.2018.8550353, 10.1016/j.automatica.2019.108614, 10.1016/j.ifacol.2020.12.2484, 10.1016/j.ifacol.2021.08.308, 10.1016/j.automatica.2021.109638, 10.1109/TCST.2021.3130534, 10.1016/j.automatica.2022.11042

Computer Aided Verification

This open access two-volume set LNCS 10980 and 10981 constitutes the refereed proceedings of the 30th International Conference on Computer Aided Verification, CAV 2018, held in Oxford, UK, in July 2018. The 52 full and 13 tool papers presented together with 3 invited papers and 2 tutorials were carefully reviewed and selected from 215 submissions. The papers cover a wide range of topics and techniques, from algorithmic and logical foundations of verification to practical applications in distributed, networked, cyber-physical, and autonomous systems. They are organized in topical sections on model checking, program analysis using polyhedra, synthesis, learning, runtime verification, hybrid and timed systems, tools, probabilistic systems, static analysis, theory and security, SAT, SMT and decisions procedures, concurrency, and CPS, hardware, industrial applications