Computational strategies for a system-level understanding of metabolism

Cell metabolism is the biochemical machinery that provides energy and building blocks to sustain life. Understanding its fine regulation is of pivotal relevance in several fields, from metabolic engineering applications to the treatment of metabolic disorders and cancer. Sophisticated computational approaches are needed to unravel the complexity of metabolism. To this aim, a plethora of methods have been developed, yet it is generally hard to identify which computational strategy is most suited for the investigation of a specific aspect of metabolism. This review provides an up-to-date description of the computational methods available for the analysis of metabolic pathways, discussing their main advantages and drawbacks. In particular, attention is devoted to the identification of the appropriate scale and level of accuracy in the reconstruction of metabolic networks, and to the inference of model structure and parameters, especially when dealing with a shortage of experimental measurements. The choice of the proper computational methods to derive in silico data is then addressed, including topological analyses, constraint-based modeling and simulation of the system dynamics. A description of some computational approaches to gain new biological knowledge or to formulate hypotheses is finally provided

Multi-Objective Binary PSO with Kernel P System on GPU

Computational cost is a big challenge for almost all intelligent algorithms which are run on CPU. In this regard, our proposed kernel P system multi-objective binary particle swarm optimization feature selection and classification method should perform with an efficient time that we aimed to settle via using potentials of membrane computing in parallel processing and nondeterminism. Moreover, GPUs perform better with latency-tolerant, highly parallel and independent tasks. In this study, to meet all the potentials of a membrane-inspired model particularly parallelism and to improve the time cost, feature selection method implemented on GPU. The time cost of the proposed method on CPU, GPU and Multicore indicates a significant improvement via implementing method on GPU

Optimisation of Mobile Communication Networks - OMCO NET

The mini conference “Optimisation of Mobile Communication Networks” focuses on advanced methods for search and optimisation applied to wireless communication networks. It is sponsored by Research & Enterprise Fund Southampton Solent University. The conference strives to widen knowledge on advanced search methods capable of optimisation of wireless communications networks. The aim is to provide a forum for exchange of recent knowledge, new ideas and trends in this progressive and challenging area. The conference will popularise new successful approaches on resolving hard tasks such as minimisation of transmit power, cooperative and optimal routing

Embedded, Embodied, Adaptive: Architecture and Computation

This catalogue of work marks the second year of the MSc Adaptive Architecture and Computation, UCL Bartlett\'s one-year taught MSc in the field of digital design. Bringing together research at the Bartlett with cutting edge practice, this course aims to give students a solid theoretical and technical foundation for the use of computation as a means to realise their designs, understand the built environment, and create architecture. Themes of investigation include how the built environment can be adapted to its occupants; how form may be generated or evolved parametrically; how the experience of space can be enhanced through the integrated use of new media. In each case, computational methods are sought to improve the design and use of architecture, rather than simply be a mechanical tool for its representation. With this in mind, students are taught the fundamental theory and skills necessary to manipulate their technology at a sophisticated level. Studio time is dedicated to learning scripting and programming within a series of workshops conceived especially for designers

On the dynamics of human locomotion and co-design of lower limb assistive devices

Recent developments in lower extremities wearable robotic devices for the assistance and rehabilitation of humans suffering from an impairment have led to several successes in the assistance of people who as a result regained a certain form of locomotive capability. Such devices are conventionally designed to be anthropomorphic. They follow the morphology of the human lower limbs. It has been shown previously that non-anthropomorphic designs can lead to increased comfort and better dynamical properties due to the fact that there is more morphological freedom in the design parameters of such a device. At the same time, exploitation of this freedom is not always intuitive and can be difficult to incorporate. In this work we strive towards a methodology aiding in the design of possible non-anthropomorphic structures for the task of human locomotion assistance by means of simulation and optimization. The simulation of such systems requires state of the art rigid body dynamics, contact dynamics and, importantly, closed loop dynamics. Through the course of our work, we first develop a novel, open and freely available, state of the art framework for the modeling and simulation of general coupled dynamical systems and show how such a framework enables the modeling of systems in a novel way. The resultant simulation environment is suitable for the evaluation of structural designs, with a specific focus on locomotion and wearable robots. To enable open-ended co-design of morphology and control, we employ population-based optimization methods to develop a novel Particle Swarm Optimization derivative specifically designed for the simultaneous optimization of solution structures (such as mechanical designs) as well as their continuous parameters. The optimizations that we aim to perform require large numbers of simulations to accommodate them and we develop another open and general framework to aid in large scale, population based optimizations in multi-user environments. Using the developed tools, we first explore the occurrence and underlying principles of natural human gait and apply our findings to the optimization of a bipedal gait of a humanoid robotic platform. Finally, we apply our developed methods to the co-design of a non-anthropomorphic, lower extremities, wearable robot in simulation, leading to an iterative co-design methodology aiding in the exploration of otherwise hard to realize morphological design

Computational aspects of cellular intelligence and their role in artificial intelligence.

The work presented in this thesis is concerned with an exploration of the computational aspects of the primitive intelligence associated with single-celled organisms. The main aim is to explore this Cellular Intelligence and its role within Artificial Intelligence. The findings of an extensive literature search into the biological characteristics, properties and mechanisms associated with Cellular Intelligence, its underlying machinery - Cell Signalling Networks and the existing computational methods used to capture it are reported. The results of this search are then used to fashion the development of a versatile new connectionist representation, termed the Artificial Reaction Network (ARN). The ARN belongs to the branch of Artificial Life known as Artificial Chemistry and has properties in common with both Artificial Intelligence and Systems Biology techniques, including: Artificial Neural Networks, Artificial Biochemical Networks, Gene Regulatory Networks, Random Boolean Networks, Petri Nets, and S-Systems. The thesis outlines the following original work: The ARN is used to model the chemotaxis pathway of Escherichia coli and is shown to capture emergent characteristics associated with this organism and Cellular Intelligence more generally. The computational properties of the ARN and its applications in robotic control are explored by combining functional motifs found in biochemical network to create temporal changing waveforms which control the gaits of limbed robots. This system is then extended into a complete control system by combining pattern recognition with limb control in a single ARN. The results show that the ARN can offer increased flexibility over existing methods. Multiple distributed cell-like ARN based agents termed Cytobots are created. These are first used to simulate aggregating cells based on the slime mould Dictyostelium discoideum. The Cytobots are shown to capture emergent behaviour arising from multiple stigmergic interactions. Applications of Cytobots within swarm robotics are investigated by applying them to benchmark search problems and to the task of cleaning up a simulated oil spill. The results are compared to those of established optimization algorithms using similar cell inspired strategies, and to other robotic agent strategies. Consideration is given to the advantages and disadvantages of the technique and suggestions are made for future work in the area. The report concludes that the Artificial Reaction Network is a versatile and powerful technique which has application in both simulation of chemical systems, and in robotic control, where it can offer a higher degree of flexibility and computational efficiency than benchmark alternatives. Furthermore, it provides a tool which may possibly throw further light on the origins and limitations of the primitive intelligence associated with cells

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

Methodology for identifying alternative solutions in a population based data generation approach applied to synthetic biology

This thesis was submitted for the award of Doctor of Philosophy and was awarded by Brunel University LondonDesign is an essential component of sustainable development. Computational modelling has become a useful technique that facilitates the design of complex systems. Variables that characterises a complex system are encoded into a computational model using mathematical concepts and through simulation each of these variables alone or in combination are modified to observe the changes in the outcome. This allows the researchers to make predictions on the behaviour of the real system that is being studied in response to the changes. The ultimate goal of any design process is to come up with the best design; as resources are limited, to minimize the cost and resource consumption, and to maximize the performance, profits and efficiency. To optimize means to find the best solution, the best compromise among several conflicting demands subject to predefined requirements. Therefore, computational optimization, modelling and simulation forms an integrated part of the modern design practice. This thesis defines a data analytics driven methodology which enables the identification of alternative solutions of computational design by analysing the generational history of the population based heuristic search used to generate the templates. While optimisation is focused on obtaining the optimal solution this methodology focuses on alternative solutions which are sub optimal by fitness or solutions with similar fitness but different structures. When the optimal design solution is less robust, alternative solutions can offer a sufficiently good accuracy and an achievable resource requirement. The main advantage of the methodology is that it exploits the exploration process of the solution space during a single run, by focusing also on suboptimal solutions, which usually get neglected in the search for an optimal one. The history of the heuristic search is analysed for the emergence of alternative solutions and evolving of a solution. By examining how an initial solution converts to an optimal solution core design patterns are identified, and these were used to improve the design process. Further, this method limits the number of runs of the heuristic search as more solution space is covered. The methodology is generic because it can be used to any instance where a population based heuristic search is applied to generate optimal designs. The applicability of the methodology is demonstrated using three case studies from mathematics (building of a mathematical function for a set target) and biology (obtaining alternative designs for genomic metabolic models [GEM] and DNA walker circuits). In each case a different heuristic search method was used: Gene expression programming (mathematical expressions), genetic algorithms (GEM models) and simulated annealing (DNA walker circuits). Descriptive analytics, visual analytics and clustering was mainly used to build the data analytics driven approach in identifying alternative solutions. This data analytics driven methodology is useful in optimising the computational design of complex systems

Using MapReduce Streaming for Distributed Life Simulation on the Cloud

Distributed software simulations are indispensable in the study of large-scale life models but often require the use of technically complex lower-level distributed computing frameworks, such as MPI. We propose to overcome the complexity challenge by applying the emerging MapReduce (MR) model to distributed life simulations and by running such simulations on the cloud. Technically, we design optimized MR streaming algorithms for discrete and continuous versions of Conway’s life according to a general MR streaming pattern. We chose life because it is simple enough as a testbed for MR’s applicability to a-life simulations and general enough to make our results applicable to various lattice-based a-life models. We implement and empirically evaluate our algorithms’ performance on Amazon’s Elastic MR cloud. Our experiments demonstrate that a single MR optimization technique called strip partitioning can reduce the execution time of continuous life simulations by 64%. To the best of our knowledge, we are the first to propose and evaluate MR streaming algorithms for lattice-based simulations. Our algorithms can serve as prototypes in the development of novel MR simulation algorithms for large-scale lattice-based a-life models.https://digitalcommons.chapman.edu/scs_books/1014/thumbnail.jp