Dynamical systems for discovering protein complexes and functional modules from biological networks

Recent advances in high throughput experiments and annotations via published literature have provided a wealth of interaction maps of several biomolecular networks, including metabolic, protein-protein, and protein-DNA interaction networks. The architecture of these molecular networks reveals important principles of cellular organization and molecular functions. Analyzing such networks, i.e., discovering dense regions in the network, is an important way to identify protein complexes and functional modules. This task has been formulated as the problem of finding heavy subgraphs, the Heaviest k-Subgraph Problem (k-HSP), which itself is NPhard. However, any method based on the k-HSP requires the parameter k and an exact solution of k-HSP may still end up as a “spurious” heavy subgraph, thus reducing its practicability in analyzing large scale biological networks. We proposed a new formulation, called the rank-HSP, and two dynamical systems to approximate its results. In addition, a novel metric, called the Standard deviation and Mean Ratio (SMR), is proposed for use in “spurious” heavy subgraphs to automate the discovery by setting a fixed threshold. Empirical results on both the simulated graphs and biological networks have demonstrated the efficiency and effectiveness of our proposal.

Stability theory and numerical analysis of non-autonomous dynamical systems

The development and use of cocycles for analysis of non-autonomous behaviour is a technique that has been known for several years. Initially developed as an extension to semi-group theory for studying rion-autonornous behaviour, it was extensively used in analysing random dynamical systems [2, 9, 10, 12]. Many of the results regarding asymptotic behaviour developed for random dynamical systems, including the concept of cocycle attractors were successfully transferred and reinterpreted for deterministic non-autonomous systems primarily by P. Kloeden and B. Schmalfuss [20, 21, 28, 29]. The theory concerning cocycle attractors was later developed in various contexts specific to particular classes of dynamical systems [6, 7, 13], although a comprehensive understanding of cocycle attractors (redefined as pullback attractors within this thesis) and their role in the stability of non-autonomous dynamical systems was still at this stage incomplete. It was this purpose that motivated Chapters 1-3 to define and formalise the concept of stability within non-autonomous dynamical systems. The approach taken incorporates the elements of classical asymptotic theory, and refines the notion of pullback attraction with further development towards a study of pull-back stability arid pullback asymptotic stability. In a comprehensive manner, it clearly establishes both pullback and forward (classical) stability theory as fundamentally unique and essential components of non-autonomous stability. Many of the introductory theorems and examples highlight the key properties arid differences between pullback and forward stability. The theory also cohesively retains all the properties of classical asymptotic stability theory in an autonomous environment. These chapters are intended as a fundamental framework from which further research in the various fields of non-autonomous dynamical systems may be extended. A preliminary version of a Lyapunov-like theory that characterises pullback attraction is created as a tool for examining non-autonomous behaviour in Chapter 5. The nature of its usefulness however is at this stage restricted to the converse theorem of asymptotic stability. Chapter 7 introduces the theory of Loci Dynamics. A transformation is made to an alternative dynamical system where forward asymptotic (classical asymptotic) behaviour characterises pullback attraction to a particular point in the original dynamical system. This has the advantage in that certain conventional techniques for a forward analysis may be applied. The remainder of the thesis, Chapters 4, 6 and Section 7.3, investigates the effects of perturbations and discretisations on non-autonomous dynamical systems known to possess structures that exhibit some form of stability or attraction. Chapter 4 investigates autonomous systems with semi-group attractors, that have been non-autonomously perturbed, whilst Chapter 6 observes the effects of discretisation on non-autonomous dynamical systems that exhibit properties of forward asymptotic stability. Chapter 7 explores the same problem of discretisation, but for pullback asymptotically stable systems. The theory of Loci Dynamics is used to analyse the nature of the discretisation, but establishment of results directly analogous to those discovered in Chapter 6 is shown to be unachievable. Instead a case by case analysis is provided for specific classes of dynamical systems, for which the results generate a numerical approximation of the pullback attraction in the original continuous dynamical system. The nature of the results regarding discretisation provide a non-autonomous extension to the work initiated by A. Stuart and J. Humphries [34, 35] for the numerical approximation of semi-group attractors within autonomous systems. . Of particular importance is the effect on the system's asymptotic behaviour over non-finite intervals of discretisation.

Spatial discretization of discrete dynamical systems

Investigates what can go wrong when dynamical systems are modelled with a computer. Number theoretic techniques were used to detail the effects "discretization" errors caused by computer round-off had on characteristics of a system. In particular, a relationship was established between the occurrence of long cycles in a system and the classical result known as Artin's conjecture. Algorithms were then developed which eliminated discretization errors.

Functional observers for dynamical systems

In control theory, a state observer is an auxiliary dynamical system that mirrors the behaviour of a physical system, and it is driven by input and output measurements of the physical system in order to provide an estimate of internal states of the physical system. The primary consideration in the design of an observer is that the estimate of the states should be close to the actual value of the system states. On the other hand, the functional observation problem centers on the construction of an auxiliary dynamical system, known as the functional observer or functional reconstructor, driven by the available system inputs and outputs in order to estimate a linear function or functions of the system states. Obviously, a functional observer is a general form of the state observer because when the linear functions are chosen as the individual states of the system then the problem of functional observation reduces to the problem of state observation.

A fault detection technique for dynamical systems

This paper shows how a functional observer can be utilized to detect faults in LTI MIMO systems. The fault detection technique is designed so that the functional observer based fault indicator asymptotically converges to a fault indicator that can be derived based on the nominal system. The asymptotic value of the proposed fault indicator is not dependent on the functional observer parameters; moreover, by choosing appropriate functional observer parameters the convergence rate of the fault indicator can be altered. Observability of the system is not a requirement for the design of the fault detection scheme.

Fault detection for dynamical systems using first-order functional observers

This paper reports a new result on the fault detection of dynamical systems by employing only first-order functional observers. Indeed, we show that fault detection can be achieved by utilizing first-order functional observers. The advantages for having such simple structured observers are obvious from the economical and practical points of view as significant cost saving can be achieved. We derive existence conditions and an algorithm for the generation of residual signals to detect faults using firstorder functional observers. Two numerical examples are given to illustrate the proposed fault detection scheme. In one of the examples, a two-area interconnected power system with reheat thermal turbines is considered where only a first-order functional observer is designed to detect faults in the power system.

A functional observer based fault detection technique for dynamical systems

This paper presents a functional observer based fault detection method. The fault detection is achieved using a functional observer based fault indicator that asymptotically converges to a fault indicator that can be derived based on the nominal system. The asymptotic value of the proposed fault indicator is independent of the functional observer parameters and also the convergence rate of the fault indicator can be altered by choosing appropriate functional observer parameters. The advantage of using this new method is that the observed system is not necessarily needed to be observable; therefore, the proposed fault detection technique is also applicable for systems where state observers cannot be designed; moreover, the functional observer fault detection scheme is always of reduced order in comparison to a state observer based scheme.

Minimal-order functional observer-based residual generators for fault detection and isolation of dynamical systems

This paper examines the design of minimal-order residual generators for the purpose of detecting and isolating actuator and/or component faults in dynamical systems. We first derive existence conditions and design residual generators using only first-order observers to detect and identify the faults. When the first-order functional observers do not exist, then based on a parametric approach to the solution of a generalized Sylvester matrix equation, we develop systematic procedures for designing residual generators utilizing minimal-order functional observers. Our design approach gives lower-order residual generators than existing results in the literature. The advantages for having such lower-order residual generators are obvious from the economical and practical points of view as cost saving and simplicity in implementation can be achieved, particularly when dealing with high-order complex systems. Numerical examples are given to illustrate the proposed fault detection and isolation schemes. In all of the numerical examples, we design minimum-order residual generators to effectively detect and isolate actuator and/or component faults in the system.

Sliding mode-like learning control for SISO complex systems with T-S fuzzy models

In this paper, a sliding mode-like learning control scheme is developed for a class of single input single output (SISO) complex systems. First, the Takagi-Sugeno (T-S) fuzzy modelling technique is employed to model the uncertain complex dynamical systems. Second, a sliding mode-like learning control is designed to drive the sliding variable to converge to the sliding surface, and the system states can then asymptotically converge to zero on the sliding surface. The advantages of this scheme are that: 1) the information about the uncertain system dynamics and the system model structure is not required for the design of the learning controller; 2) the closed-loop system behaves with a strong robustness with respect to uncertainties; 3) the control input is chattering-free. The sufficient conditions for the sliding mode-like learning control to stabilise the global fuzzy model are discussed in detail. A simulation example for the control of an inverted pendulum cart is presented to demonstrate the effectiveness of the proposed control scheme.

Functional observer design with application to pre-compensated multi-variable systems

Partial state estimation of dynamical systems provides significant advantages in practical applications. Likewise, pre-compensator design for multi variable systems invokes considerable increase in the order of the original system. Hence, applying functional observer to pre-compensated systems can result in lower computational costs and more practicability in some applications such as fault diagnosis and output feedback control of these systems. In this note, functional observer design is investigated for pre-compensated systems. A lower order pre-compensator is designed based on a H2 norm optimization that is designed as the solution of a set of linear matrix inequalities (LMIs). Next, a minimum order functional observer is designed for the pre-compensated system. An LTI model of an irreversible chemical reactor is used to demonstrate our design algorithm, and to highlight the benefits of the proposed schemes.

Dynamic output feedback sliding-mode control using pole placement and linear functional observers

This paper presents a methodological approach to design dynamic output feedback sliding-mode control for a class of uncertain dynamical systems. The control action consists of the equivalent control and robust control components. The design of the equivalent control and the sliding function are based on the pole-placement technique. Linear functional observers are developed to implement the sliding function and the equivalent control. Stability of the resulting system under the proposed control scheme is guaranteed. A numerical example is given to demonstrate its efficacy.

Semi-hyperbolic mappings in Banach spaces

The definition of semi-hyperbolic dynamical systems generated by Lipschitz continuous and not necessarily invertible mappings in Banach spaces is presented in this thesis. Like hyperbolic mappings, they involve a splitting into stable and unstable spaces, but a slight leakage from the strict invariance of the spaces is possible and the unstable subspaces are assumed to be finite dimensional. Bi-shadowing is a combination of the concepts of shadowing and inverse shadowing and is usually used to compare pseudo-trajectories calculated by a computer with the true trajectories. In this thesis, the concept of bi-shadowing in a Banach space is defined and proved for semi-hyperbolic dynamical systems generated by Lipschitz mappings. As an application to the concept of bishadowing, linear delay differential equations are shown to be bi-shadowing with respect to pseudo-trajectories generated by nonlinear small perturbations of the linear delay equation. This shows robustness of solutions of the linear delay equation with respect to small nonlinear perturbations. Complicated dynamical behaviour is often a consequence of the expansivity of a dynamical system. Semi-hyperbolic dynamical systems generated by Lipschitz mappings on a Banach space are shown to be exponentially expansive, and explicit rates of expansion are determined. The result is applied to a nonsmooth noninvertible system generated by delay differential equation. It is shown that semi-hyperbolic mappings are locally φ-contracting, where -0 is the Hausdorff measure of noncompactness, and that a linear operator is semi-hyperbolic if and only if it is φ-contracting and has no spectral values on the unit circle. The definition of φ-bi-shadowing is given and it is shown that semi-hyperbolic mappings in Banach spaces are φ-bi-shadowing with respect to locally condensing continuous comparison mappings. The result is applied to linear delay differential equations of neutral type with nonsmooth perturbations. Finally, it is shown that a small delay perturbation of an ordinary differential equation with a homoclinic trajectory is ‘chaotic’.

Towards a more holistic approach to quality improvements in aluminium die casting

This work evaluates the feasibility of using a holistic approach, based on dynamical system theory,
to reduce porosity defects in high pressure aluminum die casting. Quality improvements, from a
dynamical system perspective mean the ability to move the die casting process out of its natural
equilibrium to a more beneficial state and the ability to maintain this new process state. This more beneficial state may be achieved in several ways. One way is to increase the amount of forcing to overcome natural process resistance. This forcing approach is represented by typical continuous intervention policy, with modifications in die/part design and/or process parameters. An alternative approach is to reduce the amount of natural process resistance, in particular the amount of process disturbance, allowing the process to move out of its natural equilibrium with much less forcing. This alternative uses the self-regulating ability of dynamical systems thus decreasing the amount of human intervention required. In this respect, the influence of vacuum on time on chattering at the first stage of the casting shot was identified as a good process candidate for testing using dynamical system theory. A significant reduction in porosity defects was achieved, which also set the process on a path of slow but consistent self-improvement.

A marginalised Markov Chain Monte Carlo approach for model based analysis of EEG data

The work presented in this paper focuses on fitting of a neural mass model to EEG data. Neurophysiology inspired mathematical models were developed for simulating brain's electrical activity imaged through Electroencephalography (EEG) more than three decades ago. At the present well informative models which even describe the functional integration of cortical regions also exists. However, a very limited amount of work is reported in literature on the subject of model fitting to actual EEG data. Here, we present a Bayesian approach for parameter estimation of the EEG model via a marginalized Markov Chain Monte Carlo (MCMC) approach.

Terminal sliding mode control strategy design for second-order nonlinear system

This study mainly focuses on the terminal sliding mode control (TSMC) strategy design, including an adaptive terminal sliding mode control (ATSMC) and an exact-estimator-based terminal sliding mode control (ETSMC) for second-order nonlinear dynamical systems. In the ATSMC system, an adaptive bound estimation for the lump uncertainty is proposed to ensure the system stability. On the other hand, an exact estimator is designed for exact estimating system uncertainties to solve the trouble of chattering phenomena caused by a sign function in ATSMC law in despite of the utilization of a fixed value or an adaptive tuning algorithm for the lumped uncertainty bound. The effectiveness of the proposed control schemes can be verified in numerical simulations.