Chemical Reaction Optimization: A tutorial

Chemical Reaction Optimization (CRO) is a recently established metaheuristics for optimization, inspired by the nature of chemical reactions. A chemical reaction is a natural process of transforming the unstable substances to the stable ones. In microscopic view, a chemical reaction starts with some unstable molecules with excessive energy. The molecules interact with each other through a sequence of elementary reactions. At the end, they are converted to those with minimum energy to support their existence. This property is embedded in CRO to solve optimization problems. CRO can be applied to tackle problems in both the discrete and continuous domains. We have successfully exploited CRO to solve a broad range of engineering problems, including the quadratic assignment problem, neural network training, multimodal continuous problems, etc. The simulation results demonstrate that CRO has superior performance when compared with other existing optimization algorithms. This tutorial aims to assist the readers in implementing CRO to solve their problems. It also serves as a technical overview of the current development of CRO and provides potential future research directions. © 2012 The Author(s).published_or_final_versionSpringer Open Choice, 25 May 201

A Computational Framework for Host-Pathogen Protein-Protein Interactions

Infectious diseases cause millions of illnesses and deaths every year, and raise great health concerns world widely. How to monitor and cure the infectious diseases has become a prevalent and intractable problem. Since the host-pathogen interactions are considered as the key infection processes at the molecular level for infectious diseases, there have been a large amount of researches focusing on the host-pathogen interactions towards the understanding of infection mechanisms and the development of novel therapeutic solutions. For years, the continuously development of technologies in biology has benefitted the wet lab-based experiments, such as small-scale biochemical, biophysical and genetic experiments and large-scale methods (for example yeast-two-hybrid analysis and cryogenic electron microscopy approach). As a result of past decades of efforts, there has been an exploded accumulation of biological data, which includes multi omics data, for example, the genomics data and proteomics data. Thus, an initiative review of omics data has been conducted in Chapter 2, which has exclusively demonstrated the recent update of ‘omics’ study, particularly focusing on proteomics and genomics. With the high-throughput technologies, the increasing amount of ‘omics’ data, including genomics and proteomics, has even further boosted. An upsurge of interest for data analytics in bioinformatics comes as no surprise to the researchers from a variety of disciplines. Specifically, the astonishing rate at which genomics and proteomics data are generated leads the researchers into the realm of ‘Big Data’ research. Chapter 2 is thus developed to providing an update of the omics background and the state-of-the-art developments in the omics area, with a focus on genomics data, from the perspective of big data analytics..

Querying the web of data with low latency: high performance distributed SPARQL processing and benchmarking

The Web of Data extends the World Wide Web (WWW) in a way that applications can understand information and cooperate with humans on complex tasks. The basis of performing complex tasks is low latency queries over the Web of Data. The large scale and distributed nature of the Web of Data have negative impacts on several critical factors for efficient query processing, including fast data transmission between datasets, predictable data distribution and statistics that summarise and describe certain patterns in the data. Moreover, it is common on the Web of Data that the same resource is identified by multiple URIs. This phenomenon, named co-reference, potentially increases the complexity of query processing, and makes it even harder to obtain accurate statistics. With the aforementioned challenges, it is not clear whether it is possible to achieve efficient queries on the Web of Data on a large scale.In this thesis, we explore techniques to improve the efficiency of querying the Web of Data on a large scale. More specifically, we investigate two typical scenarios on the Web of Data, which are: 1) the scenario in which all datasets provide detailed statistics that are possibly available on a large scale, and 2) the scenario in which co-reference is taken into account, and datasets’ statistics are not reliable. For each scenario we explore existing and novel optimisation techniques that are tailored for querying the Web of Data, as well as well developed techniques with careful adjustments.For the scenario with detailed statistics we provide a scheme that implements a statistics query optimisation approach that requires detailed statistics, and intensively exploits parallelism. We propose an efficient algorithm called Parallel Sub-query Identification () to increase the degree of parallelism. () breaks a SPARQL query into sub-queries that can be processed in parallel while not increasing network traffic. We combine with dynamic programming to produce query plans with both minimum costs and a fair degree of parallelism. Furthermore, we develop a mechanism that maximally exploits bandwidth and computing power of datasets. For the scenario having co-reference and without reliable statistics we provide a scheme that implements a dynamic query optimisation approach that takes co-reference into account, and utilises runtime statistics to elevate query efficiency even further. We propose a model called Virtual Graph to transform a query and all its co-referent siblings into a single query with pre-defined bindings. Virtual Graph reduces the large number of outgoing and incoming requests that is required to process co-referent queries individually. Moreover, Virtual Graph enables query optimisers to find the optimal plan with respect to all co-referent queries as a whole. () is used in this scheme as well but provides a higher degree of parallelism with the help of runtime statistics. A Minimum-Spanning-Tree-based algorithm is used in this scheme as a result of using runtime statistics. The same parallel execution mechanism used in the previous scenario is adopted here as well.In order to examine the effectiveness of our schemes in practice, we deploy the above approaches in two distributed SPARQL engines, LHD-s and LHD-d respectively. Both engines are implemented using a popular Java-based platform for building Semantic Web applications. They can be used as either standalone applications or integrated into existing systems that require quick response of Linked Data queries.We also propose a scalable and flexible benchmark, called Distributed SPARQL Evaluation Framework (DSEF), for evaluating optimisation approaches in the Web of Data. DSEF adopts a expandable virtual-machine-based structure and provides a set of efficient tools to help easily set up RDF networks of arbitrary sizes. We further investigate the proportion and distribution of co-reference in the real world, based on which DESF is able to simulate co-reference for given RDF datasets. DSEF bases its soundness in the usage of widely accepted assessment data and queries.By comparing both LHD-s and LHD-d with existing approaches using DSEF, we provide evidence that neither existing statistics provided by datasets nor cost estimation methods, are sufficiently accurate. On the other hand, dynamic optimisation using runtime statistics together with carefully tuned parallelism are promising for significantly reducing the latency of large scale queries on the Web of Data. We also demonstrate that () and Virtual Graph algorithms significantly increase query efficiency for queries with or without co-reference.In summary, the contributions of this these include: 1) proposing two schemes for improving query efficiency in two typical scenarios in the Web of Data; 2) providing implementations, named LHD-s and LHD-d, for the two schemes respectively; 3) proposing a scalable and flexible evaluation framework for distributed SPARQL engines called DSEF; and 4) showing evidence that runtime-statistics-based dynamic optimisation with parallelism are promising to reduce latency of Linked Data queries on a large scale

Inductive biases and metaknowledge representations for search-based optimization

"What I do not understand, I can still create."- H. Sayama The following work follows closely the aforementioned bonmot. Guided by questions such as: ``How can evolutionary processes exhibit learning behavior and consolidate knowledge?´´, ``What are cognitive models of problem-solving?´´ and ``How can we harness these altogether as computational techniques?´´, we clarify within this work essentials required to implement them for metaheuristic search and optimization.We therefore look into existing models of computational problem-solvers and compare these with existing methodology in literature. Particularly, we find that the meta-learning model, which frames problem-solving in terms of domain-specific inductive biases and the arbitration thereof through means of high-level abstractions resolves outstanding issues with methodology proposed within the literature. Noteworthy, it can be also related to ongoing research on algorithm selection and configuration frameworks. We therefore look in what it means to implement such a model by first identifying inductive biases in terms of algorithm components and modeling these with density estimation techniques. And secondly, propose methodology to process metadata generated by optimization algorithms in an automated manner through means of deep pattern recognition architectures for spatio-temporal feature extraction. At last we look into an exemplary shape optimization problem which allows us to gain insight into what it means to apply our methodology to application scenarios. We end our work with a discussion on future possible directions to explore and discuss the limitations of such frameworks for system deployment

Predicting effective control parameters for differential evolution using cluster analysis of objective function features

A methodology is introduced which uses three simple objectivefunction features to predict effective control parameters for differential evolution. This is achieved using cluster analysis techniques to classify objectivefunctions using these features. Information on prior performance of variouscontrol parameters for each classification is then used to determine which control parameters to use in future optimisations. Our approach is compared tostate–of–the–art adaptive and non–adaptive techniques. Two accepted benchmark suites are used to compare performance and in all cases we show thatthe improvement resulting from our approach is statistically significant. Themajority of the computational effort of this methodology is performed off–line, however even when taking into account the additional on–line cost ourapproach outperforms other adaptive techniques. We also study the key tuning parameters of our methodology, such as number of clusters, which furthersupport the finding that the simple features selected are predictors of effectivecontrol parameters. The findings presented in this paper are significant becausethey show that simple to calculate features of objective functions can help toselect control parameters for optimisation algorithms. This can have an immediate positive impact the application of these optimisation algorithms on realworld problems where it is often difficult to select effective control parameters

Self adaptation in evolutionary algorithms

Evolutionary Algorithms are search algorithms based on the Darwinian metaphor of “Natural Selection”. Typically these algorithms maintain a population of individual solutions, each of which has a fitness attached to it, which in some way reflects the quality of the solution. The searchproceeds via the iterative generation, evaluation and possible incorporation of new individuals based on the current population, using a number of parameterisedgenetic operators. In this thesis the phenomenon of Self Adaptation of the genetic operators is investigated.A new framework for classifying adaptive algorithms is proposed, based on the scope of the adaptation, and on the nature of the transition function guiding the search through the space of possible configurations of the algorithm. Mechanisms are investigated for achieving the self adaptation of recombination and mutation operators within a genetic algorithm, and means of combining them are investigated. These are shown to produce significantly better results than any of the combinations of fixed operators tested, across a range of problem types. These new operators reduce the need for the designer of an algorithm to select appropriate choices of operators and parameters, thus aiding the implementation of geneticalgorithms. The nature of the evolving search strategies are investigated and explained in terms of the known properties of the landscapes used, and it is suggested how observations of evolving strategies on unknown landscapes may be used to categorise them, and guide further changes in other facets of the genetic algorithm.This work provides a contribution towards the study of adaptation in Evolutionary Algorithms, and towards the design of robust search algorithms for “real world” problems

The 1st International Electronic Conference on Algorithms

This book presents 22 of the accepted presentations at the 1st International Electronic Conference on Algorithms which was held completely online from September 27 to October 10, 2021. It contains 16 proceeding papers as well as 6 extended abstracts. The works presented in the book cover a wide range of fields dealing with the development of algorithms. Many of contributions are related to machine learning, in particular deep learning. Another main focus among the contributions is on problems dealing with graphs and networks, e.g., in connection with evacuation planning problems