Evolutionary Computation

This book presents several recent advances on Evolutionary Computation, specially evolution-based optimization methods and hybrid algorithms for several applications, from optimization and learning to pattern recognition and bioinformatics. This book also presents new algorithms based on several analogies and metafores, where one of them is based on philosophy, specifically on the philosophy of praxis and dialectics. In this book it is also presented interesting applications on bioinformatics, specially the use of particle swarms to discover gene expression patterns in DNA microarrays. Therefore, this book features representative work on the field of evolutionary computation and applied sciences. The intended audience is graduate, undergraduate, researchers, and anyone who wishes to become familiar with the latest research work on this field

A Framework for Evaluating Traceability Benchmark Metrics

Many software traceability techniques have been developed in the past decade, but suffer from inaccuracy. To address this shortcoming, the software traceability research community seeks to employ benchmarking. Benchmarking will help the community agree on whether improvements to traceability techniques have addressed the challenges faced by the research community. A plethora of evaluation methods have been applied, with no consensus on what should be part of a community benchmark. The goals of this paper are: to identify recurring problems in evaluation of traceability techniques, to identify essential properties that evaluation methods should possess to overcome the identified problems, and to provide guidelines for benchmarking software traceability techniques. We illustrate the properties and guidelines using empirical evaluation of three software traceability techniques on nine data sets. The proposed benchmarking framework can be broadly applied to domains beyond traceability research

Automated incremental software verification

Software continuously evolves to meet rapidly changing human needs. Each evolved transformation of a program is expected to preserve important correctness and security properties. Aiming to assure program correctness after a change, formal verification techniques, such as Software Model Checking, have recently benefited from fully automated solutions based on symbolic reasoning and abstraction. However, the majority of the state-of-the-art model checkers are designed that each new software version has to be verified from scratch. In this dissertation, we investigate the new Formal Incremental Verification (FIV) techniques that aim at making software analysis more efficient by reusing invested efforts between verification runs. In order to show that FIV can be built on the top of different verification techniques, we focus on three complementary approaches to automated formal verification. First, we contribute the FIV technique for SAT-based Bounded Model Checking developed to verify programs with (possibly recursive) functions with respect to the set of pre-defined assertions. We present the function-summarization framework based on Craig interpolation that allows extracting and reusing over- approximations of the function behaviors. We introduce the algorithm to revalidate the summaries of one program locally in order to prevent re-verification of another program from scratch. Second, we contribute the technique for simulation relation synthesis for loop-free programs that do not necessarily contain assertions. We introduce an SMT-based abstraction- refinement algorithm that proceeds by guessing a relation and checking whether it is a simulation relation. We present a novel algorithm for discovering simulations symbolically, by means of solving ∀∃-formulas and extracting witnessing Skolem relations. Third, we contribute the FIV technique for SMT-based Unbounded Model Checking developed to verify programs with (possibly nested) loops. We present an algorithm that automatically derives simulations between programs with different loop structures. The automatically synthesized simulation relation is then used to migrate the safe inductive invariants across the evolution boundaries. Finally, we contribute the implementation and evaluation of all our algorithmic contributions, and confirm that the state-of-the-art model checking tools can successfully be extended by the FIV capabilities

Transformations in the Scale of Behaviour and the Global Optimisation of Constraints in Adaptive Networks

The natural energy minimisation behaviour of a dynamical system can be interpreted as a simple optimisation process, finding a locally optimal resolution of problem constraints. In human problem solving, high-dimensional problems are often made much easier by inferring a low-dimensional model of the system in which search is more effective. But this is an approach that seems to require top-down domain knowledge; not one amenable to the spontaneous energy minimisation behaviour of a natural dynamical system. However, in this paper we investigate the ability of distributed dynamical systems to improve their constraint resolution ability over time by self-organisation. We use a ‘self-modelling’ Hopfield network with a novel type of associative connection to illustrate how slowly changing relationships between system components can result in a transformation into a new system which is a low-dimensional caricature of the original system. The energy minimisation behaviour of this new system is significantly more effective at globally resolving the original system constraints. This model uses only very simple, and fully-distributed positive feedback mechanisms that are relevant to other ‘active linking’ and adaptive networks. We discuss how this neural network model helps us to understand transformations and emergent collective behaviour in various non-neural adaptive networks such as social, genetic and ecological networks

Model-based compositional verification approaches and tools development for cyber-physical systems

The model-based design for embedded real-time systems utilizes the veriable reusable components and proper architectures, to deal with the verification scalability problem caused by state-explosion. In this thesis, we address verification approaches for both low-level individual component correctness and high-level system correctness, which are equally important under this scheme. Three prototype tools are developed, implementing our approaches and algorithms accordingly. For the component-level design-time verification, we developed a symbolic verifier, LhaVrf, for the reachability verification of concurrent linear hybrid systems (LHA). It is unique in translating a hybrid automaton into a transition system that preserves the discrete transition structure, possesses no continuous dynamics, and preserves reachability of discrete states. Afterward, model-checking is interleaved in the counterexample fragment based specification relaxation framework. We next present a simulation-based bounded-horizon reachability analysis approach for the reachability verification of systems modeled by hybrid automata (HA) on a run-time basis. This framework applies a dynamic, on-the-fly, repartition-based error propagation control method with the mild requirement of Lipschitz continuity on the continuous dynamics. The novel features allow state-triggered discrete jumps and provide eventually constant over-approximation error bound for incremental stable dynamics. The above approaches are implemented in our prototype verifier called HS3V. Once the component properties are established, the next thing is to establish the system-level properties through compositional verication. We present our work on the role and integration of quantier elimination (QE) for property composition and verication. In our approach, we derive in a single step, the strongest system property from the given component properties for both time-independent and time-dependent scenarios. The system initial condition can also be composed, which, alongside the strongest system property, are used to verify a postulated system property through induction. The above approaches are implemented in our prototype tool called ReLIC

United Kingdom Frozen Shoulder Trial (UK FROST), multi-centre, randomised, 12 month, parallel group, superiority study to compare the clinical and cost-effectiveness of Early Structured Physiotherapy versus manipulation under anaesthesia versus arthroscopic capsular release for patients referred to secondary care with a primary frozen shoulder : study protocol for a randomised controlled trial

BACKGROUND: Frozen shoulder (also known as adhesive capsulitis) occurs when the capsule, or the soft tissue envelope around the ball and socket shoulder joint, becomes scarred and contracted, making the shoulder tight, painful and stiff. It affects around 1 in 12 men and 1 in 10 women of working age. Although this condition can settle with time (typically taking 1 to 3 years), for some people it causes severe symptoms and needs referral to hospital. Our aim is to evaluate the clinical and cost-effectiveness of two invasive and costly surgical interventions that are commonly used in secondary care in the National Health Service (NHS) compared with a non-surgical comparator of Early Structured Physiotherapy. METHODS: We will conduct a randomised controlled trial (RCT) of 500 adult patients with a clinical diagnosis of frozen shoulder, and who have radiographs that exclude other pathology. Early Structured Physiotherapy with an intra-articular steroid injection will be compared with manipulation under anaesthesia with a steroid injection or arthroscopic (keyhole) capsular release followed by manipulation. Both surgical interventions will be followed with a programme of post-procedural physiotherapy. These treatments will be undertaken in NHS hospitals across the United Kingdom. The primary outcome and endpoint will be the Oxford Shoulder Score (a patient self-reported assessment of shoulder function) at 12 months. This will also be measured at baseline, 3 and 6 months after randomisation; and on the day that treatment starts and 6 months later. Secondary outcomes include the Disabilities of Arm Shoulder and Hand (QuickDASH) score, the EQ-5D-5 L score, pain, extent of recovery and complications. We will explore the acceptability of the different treatments to patients and health care professionals using qualitative methods. DISCUSSION: The three treatments being compared are the most frequently used in secondary care in the NHS, but there is uncertainty about which one works best and at what cost. UK FROST is a rigorously designed and adequately powered study to inform clinical decisions for the treatment of this common condition in adults. TRIAL REGISTRATION: International Standard Randomised Controlled Trial Register, ID: ISRCTN48804508 . Registered on 25 July 2014