A comprehensive survey on cultural algorithms

Peer reviewedPostprin

Gene regulatory network modelling with evolutionary algorithms -an integrative approach

Building models for gene regulation has been an important aim of Systems Biology over the past years, driven by the large amount of gene expression data that has become available. Models represent regulatory interactions between genes and transcription factors and can provide better understanding of biological processes, and means of simulating both natural and perturbed systems (e.g. those associated with disease). Gene regulatory network (GRN) quantitative modelling is still limited, however, due to data issues such as noise and restricted length of time series, typically used for GRN reverse engineering. These issues create an under-determination problem, with many models possibly fitting the data. However, large amounts of other types of biological data and knowledge are available, such as cross-platform measurements, knockout experiments, annotations, binding site affinities for transcription factors and so on. It has been postulated that integration of these can improve model quality obtained, by facilitating further filtering of possible models. However, integration is not straightforward, as the different types of data can provide contradictory information, and are intrinsically noisy, hence large scale integration has not been fully explored, to date. Here, we present an integrative parallel framework for GRN modelling, which employs evolutionary computation and different types of data to enhance model inference. Integration is performed at different levels. (i) An analysis of cross-platform integration of time series microarray data, discussing the effects on the resulting models and exploring crossplatform normalisation techniques, is presented. This shows that time-course data integration is possible, and results in models more robust to noise and parameter perturbation, as well as reduced noise over-fitting. (ii) Other types of measurements and knowledge, such as knock-out experiments, annotated transcription factors, binding site affinities and promoter sequences are integrated within the evolutionary framework to obtain more plausible GRN models. This is performed by customising initialisation, mutation and evaluation of candidate model solutions. The different data types are investigated and both qualitative and quantitative improvements are obtained. Results suggest that caution is needed in order to obtain improved models from combined data, and the case study presented here provides an example of how this can be achieved. Furthermore, (iii), RNA-seq data is studied in comparison to microarray experiments, to identify overlapping features and possibilities of integration within the framework. The extension of the framework to this data type is straightforward and qualitative improvements are obtained when combining predicted interactions from single-channel and RNA-seq datasets

Adaptive algorithms for history matching and uncertainty quantification

Numerical reservoir simulation models are the basis for many decisions in regard to predicting, optimising, and improving production performance of oil and gas reservoirs. History matching is required to calibrate models to the dynamic behaviour of the reservoir, due to the existence of uncertainty in model parameters. Finally a set of history matched models are used for reservoir performance prediction and economic and risk assessment of different development scenarios. Various algorithms are employed to search and sample parameter space in history matching and uncertainty quantification problems. The algorithm choice and implementation, as done through a number of control parameters, have a significant impact on effectiveness and efficiency of the algorithm and thus, the quality of results and the speed of the process. This thesis is concerned with investigation, development, and implementation of improved and adaptive algorithms for reservoir history matching and uncertainty quantification problems. A set of evolutionary algorithms are considered and applied to history matching. The shared characteristic of applied algorithms is adaptation by balancing exploration and exploitation of the search space, which can lead to improved convergence and diversity. This includes the use of estimation of distribution algorithms, which implicitly adapt their search mechanism to the characteristics of the problem. Hybridising them with genetic algorithms, multiobjective sorting algorithms, and real-coded, multi-model and multivariate Gaussian-based models can help these algorithms to adapt even more and improve their performance. Finally diversity measures are used to develop an explicit, adaptive algorithm and control the algorithm’s performance, based on the structure of the problem. Uncertainty quantification in a Bayesian framework can be carried out by resampling of the search space using Markov chain Monte-Carlo sampling algorithms. Common critiques of these are low efficiency and their need for control parameter tuning. A Metropolis-Hastings sampling algorithm with an adaptive multivariate Gaussian proposal distribution and a K-nearest neighbour approximation has been developed and applied

Comprehensive Taxonomies of Nature- and Bio-inspired Optimization: Inspiration versus Algorithmic Behavior, Critical Analysis and Recommendations

In recent years, a great variety of nature- and bio-inspired algorithms has been reported in the literature. This algorithmic family simulates different biological processes observed in Nature in order to efficiently address complex optimization problems. In the last years the number of bio-inspired optimization approaches in literature has grown considerably, reaching unprecedented levels that dark the future prospects of this field of research. This paper addresses this problem by proposing two comprehensive, principle-based taxonomies that allow researchers to organize existing and future algorithmic developments into well-defined categories, considering two different criteria: the source of inspiration and the behavior of each algorithm. Using these taxonomies we review more than three hundred publications dealing with nature-inspired and bio-inspired algorithms, and proposals falling within each of these categories are examined, leading to a critical summary of design trends and similarities between them, and the identification of the most similar classical algorithm for each reviewed paper. From our analysis we conclude that a poor relationship is often found between the natural inspiration of an algorithm and its behavior. Furthermore, similarities in terms of behavior between different algorithms are greater than what is claimed in their public disclosure: specifically, we show that more than one-third of the reviewed bio-inspired solvers are versions of classical algorithms. Grounded on the conclusions of our critical analysis, we give several recommendations and points of improvement for better methodological practices in this active and growing research field.Comment: 76 pages, 6 figure