Evolving cell models for systems and synthetic biology

This paper proposes a new methodology for the automated design of cell models for systems and synthetic biology. Our modelling framework is based on P systems, a discrete, stochastic and modular formal modelling language. The automated design of biological models comprising the optimization of the model structure and its stochastic kinetic constants is performed using an evolutionary algorithm. The evolutionary algorithm evolves model structures by combining different modules taken from a predefined module library and then it fine-tunes the associated stochastic kinetic constants. We investigate four alternative objective functions for the fitness calculation within the evolutionary algorithm: (1) equally weighted sum method, (2) normalization method, (3) randomly weighted sum method, and (4) equally weighted product method. The effectiveness of the methodology is tested on four case studies of increasing complexity including negative and positive autoregulation as well as two gene networks implementing a pulse generator and a bandwidth detector. We provide a systematic analysis of the evolutionary algorithm’s results as well as of the resulting evolved cell models

Illuminating meaningful diversity in complex feature spaces through adaptive grid-based genetic algorithms

In many fields there exist problems for which multiple solutions of suitably high performance may be found across distinct regions of the search space. Optimisation of the search towards including these distinct solutions is important not only to understanding these spaces but also to avoiding local optima. This is the goal of a type of genetic algorithms called illumination algorithms. In Chapter 2, we demonstrate the use of an illumination algorithm in the exploration of networks sharing only a given set of structural features (valid networks). This method produces a population of valid networks that are more diverse than those produced using state of the art methods, however, it was found to be too inefficient to be usable in real-world problems. Additionally, setting an appropriate resolution of the search requires some amount of prior knowledge of the space of solutions. Addressing this problem is the focus of Chapter 3, in which we develop three extensions to the method: a) an exact method of mutation whereby only valid networks are explored, b) an adaptive mechanism for setting the resolution of the search, c) a principle for tuning mutations parameters to the search’ s resolution. We show that with these additions our method is able to increase the diversity of solutions found in significantly fewer iterations. Finally, in Chapter 4 we expand our method for use in more general problem spaces. We benchmark it against the state of the art. In all tested landscapes, we show that our method is able to identify more meaningful niches in the spaces in the same number of iterations. We conclude by highlighting the limits of our framework and discuss further directions

Novel sampling techniques for reservoir history matching optimisation and uncertainty quantification in flow prediction

Modern reservoir management has an increasing focus on accurately predicting the likely range of field recoveries. A variety of assisted history matching techniques has been developed across the research community concerned with this topic. These techniques are based on obtaining multiple models that closely reproduce the historical flow behaviour of a reservoir. The set of resulted history matched models is then used to quantify uncertainty in predicting the future performance of the reservoir and providing economic evaluations for different field development strategies. The key step in this workflow is to employ algorithms that sample the parameter space in an efficient but appropriate manner. The algorithm choice has an impact on how fast a model is obtained and how well the model fits the production data. The sampling techniques that have been developed to date include, among others, gradient based methods, evolutionary algorithms, and ensemble Kalman filter (EnKF). This thesis has investigated and further developed the following sampling and inference techniques: Particle Swarm Optimisation (PSO), Hamiltonian Monte Carlo, and Population Markov Chain Monte Carlo. The inspected techniques have the capability of navigating the parameter space and producing history matched models that can be used to quantify the uncertainty in the forecasts in a faster and more reliable way. The analysis of these techniques, compared with Neighbourhood Algorithm (NA), has shown how the different techniques affect the predicted recovery from petroleum systems and the benefits of the developed methods over the NA. The history matching problem is multi-objective in nature, with the production data possibly consisting of multiple types, coming from different wells, and collected at different times. Multiple objectives can be constructed from these data and explicitly be optimised in the multi-objective scheme. The thesis has extended the PSO to handle multi-objective history matching problems in which a number of possible conflicting objectives must be satisfied simultaneously. The benefits and efficiency of innovative multi-objective particle swarm scheme (MOPSO) are demonstrated for synthetic reservoirs. It is demonstrated that the MOPSO procedure can provide a substantial improvement in finding a diverse set of good fitting models with a fewer number of very costly forward simulations runs than the standard single objective case, depending on how the objectives are constructed. The thesis has also shown how to tackle a large number of unknown parameters through the coupling of high performance global optimisation algorithms, such as PSO, with model reduction techniques such as kernel principal component analysis (PCA), for parameterising spatially correlated random fields. The results of the PSO-PCA coupling applied to a recent SPE benchmark history matching problem have demonstrated that the approach is indeed applicable for practical problems. A comparison of PSO with the EnKF data assimilation method has been carried out and has concluded that both methods have obtained comparable results on the example case. This point reinforces the need for using a range of assisted history matching algorithms for more confidence in predictions

New Fundamental Technologies in Data Mining

The progress of data mining technology and large public popularity establish a need for a comprehensive text on the subject. The series of books entitled by "Data Mining" address the need by presenting in-depth description of novel mining algorithms and many useful applications. In addition to understanding each section deeply, the two books present useful hints and strategies to solving problems in the following chapters. The contributing authors have highlighted many future research directions that will foster multi-disciplinary collaborations and hence will lead to significant development in the field of data mining

Multi-objective Search-based Mobile Testing

Despite the tremendous popularity of mobile applications, mobile testing still relies heavily on manual testing. This thesis presents mobile test automation approaches based on multi-objective search. We introduce three approaches: Sapienz (for native Android app testing), Octopuz (for hybrid/web JavaScript app testing) and Polariz (for using crowdsourcing to support search-based mobile testing). These three approaches represent the primary scientific and technical contributions of the thesis. Since crowdsourcing is, itself, an emerging research area, and less well understood than search-based software engineering, the thesis also provides the first comprehensive survey on the use of crowdsourcing in software testing (in particular) and in software engineering (more generally). This survey represents a secondary contribution. Sapienz is an approach to Android testing that uses multi-objective search-based testing to automatically explore and optimise test sequences, minimising their length, while simultaneously maximising their coverage and fault revelation. The results of empirical studies demonstrate that Sapienz significantly outperforms both the state-of-the-art technique Dynodroid and the widely-used tool, Android Monkey, on all three objectives. When applied to the top 1,000 Google Play apps, Sapienz found 558 unique, previously unknown crashes. Octopuz reuses the Sapienz multi-objective search approach for automated JavaScript testing, aiming to investigate whether it replicates the Sapienz’ success on JavaScript testing. Experimental results on 10 real-world JavaScript apps provide evidence that Octopuz significantly outperforms the state of the art (and current state of practice) in automated JavaScript testing. Polariz is an approach that combines human (crowd) intelligence with machine (computational search) intelligence for mobile testing. It uses a platform that enables crowdsourced mobile testing from any source of app, via any terminal client, and by any crowd of workers. It generates replicable test scripts based on manual test traces produced by the crowd workforce, and automatically extracts from these test traces, motif events that can be used to improve search-based mobile testing approaches such as Sapienz

3rd EGEE User Forum

We have organized this book in a sequence of chapters, each chapter associated with an application or technical theme introduced by an overview of the contents, and a summary of the main conclusions coming from the Forum for the chapter topic. The first chapter gathers all the plenary session keynote addresses, and following this there is a sequence of chapters covering the application flavoured sessions. These are followed by chapters with the flavour of Computer Science and Grid Technology. The final chapter covers the important number of practical demonstrations and posters exhibited at the Forum. Much of the work presented has a direct link to specific areas of Science, and so we have created a Science Index, presented below. In addition, at the end of this book, we provide a complete list of the institutes and countries involved in the User Forum

Computation in Complex Networks

Complex networks are one of the most challenging research focuses of disciplines, including physics, mathematics, biology, medicine, engineering, and computer science, among others. The interest in complex networks is increasingly growing, due to their ability to model several daily life systems, such as technology networks, the Internet, and communication, chemical, neural, social, political and financial networks. The Special Issue “Computation in Complex Networks" of Entropy offers a multidisciplinary view on how some complex systems behave, providing a collection of original and high-quality papers within the research fields of: • Community detection • Complex network modelling • Complex network analysis • Node classification • Information spreading and control • Network robustness • Social networks • Network medicin