1,956 research outputs found
Evolutionary Dynamics in Gene Networks and Inference Algorithms
Dynamical interactions among sets of genes (and their products) regulate developmental processes and some dynamical diseases, like cancer. Gene regulatory networks (GRNs) are directed networks that define interactions (links) among different genes/proteins involved in such processes. Genetic regulation can be modified during the time course of the process, which may imply changes in the nodes activity that leads the system from a specific state to a different one at a later time (dynamics). How the GRN modifies its topology, to properly drive a developmental process, and how this regulation was acquired across evolution are questions that the evolutionary dynamics of gene networks tackles. In the present work we review important methodology in the field and highlight the combination of these methods with evolutionary algorithms. In recent years, this combination has become a powerful tool to fit models with the increasingly available experimental data.Junta de Andalucía FQM-12
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
Comparison of evolutionary algorithms in gene regulatory network model inference
Background: The evolution of high throughput technologies that measure gene expression levels has created a
data base for inferring GRNs (a process also known as reverse engineering of GRNs). However, the nature of
these data has made this process very di±cult. At the moment, several methods of discovering qualitative
causal relationships between genes with high accuracy from microarray data exist, but large scale quantitative
analysis on real biological datasets cannot be performed, to date, as existing approaches are not suitable for real
microarray data which are noisy and insu±cient.
Results: This paper performs an analysis of several existing evolutionary algorithms for quantitative gene
regulatory network modelling. The aim is to present the techniques used and o®er a comprehensive comparison
of approaches, under a common framework. Algorithms are applied to both synthetic and real gene expression
data from DNA microarrays, and ability to reproduce biological behaviour, scalability and robustness to noise are assessed and compared.
Conclusions: Presented is a comparison framework for assessment of evolutionary algorithms, used to infer gene
regulatory networks. Promising methods are identi¯ed and a platform for development of appropriate model
formalisms is established
Parameters identification of unknown delayed genetic regulatory networks by a switching particle swarm optimization algorithm
The official published version can be found at the link below.This paper presents a novel particle swarm optimization (PSO) algorithm based on Markov chains and competitive penalized method. Such an algorithm is developed to solve global optimization problems with applications in identifying unknown parameters of a class of genetic regulatory networks (GRNs). By using an evolutionary factor, a new switching PSO (SPSO) algorithm is first proposed and analyzed, where the velocity updating equation jumps from one mode to another according to a Markov chain, and acceleration coefficients are dependent on mode switching. Furthermore, a leader competitive penalized multi-learning approach (LCPMLA) is introduced to improve the global search ability and refine the convergent solutions. The LCPMLA can automatically choose search strategy using a learning and penalizing mechanism. The presented SPSO algorithm is compared with some well-known PSO algorithms in the experiments. It is shown that the SPSO algorithm has faster local convergence speed, higher accuracy and algorithm reliability, resulting in better balance between the global and local searching of the algorithm, and thus generating good performance. Finally, we utilize the presented SPSO algorithm to identify not only the unknown parameters but also the coupling topology and time-delay of a class of GRNs.This research was partially supported by the National Natural Science Foundation of PR China (Grant No. 60874113), the Research Fund for the Doctoral Program of Higher Education (Grant No. 200802550007), the Key Creative Project of Shanghai Education Community (Grant No. 09ZZ66), the Key Foundation Project of Shanghai (Grant No. 09JC1400700), the Engineering and Physical Sciences Research Council EPSRC of the UK under Grant No. GR/S27658/01, the International Science and Technology Cooperation Project of China under Grant No. 2009DFA32050, an International Joint Project sponsored by the Royal Society of the UK, and the Alexander von Humboldt Foundation of Germany
Accelerating ant colony optimization by using local search
This thesis report is submitted in partial fulfillment of the requirements for the degree of Bachelor of Science in Computer Science and Engineering, 2015.Cataloged from PDF version of thesis report.Includes bibliographical references (page 42-45).Optimization is very important fact in terms of taking decision in mathematics, statistics,
computer science and real life problem solving or decision making application. Many different
optimization techniques have been developed for solving such functional problem. In order to
solving various problem computer Science introduce evolutionary optimization algorithm and
their hybrid. In recent years, test functions are using to validate new optimization algorithms and
to compare the performance with other existing algorithm. There are many Single Object
Optimization algorithm proposed earlier. For example: ACO, PSO, ABC. ACO is a popular
optimization technique for solving hard combination mathematical optimization problem. In this
paper, we run ACO upon five benchmark function and modified the parameter of ACO in order
to perform SBX crossover and polynomial mutation. The proposed algorithm SBXACO is tested
upon some benchmark function under both static and dynamic to evaluate performances. We
choose wide range of benchmark function and compare results with existing DE and its hybrid
DEahcSPX from other literature are also presented here.Nabila TabassumMaruful HaqueB. Computer Science and Engineerin
Evolutionary Algorithms
Evolutionary algorithms (EAs) are population-based metaheuristics, originally
inspired by aspects of natural evolution. Modern varieties incorporate a broad
mixture of search mechanisms, and tend to blend inspiration from nature with
pragmatic engineering concerns; however, all EAs essentially operate by
maintaining a population of potential solutions and in some way artificially
'evolving' that population over time. Particularly well-known categories of EAs
include genetic algorithms (GAs), Genetic Programming (GP), and Evolution
Strategies (ES). EAs have proven very successful in practical applications,
particularly those requiring solutions to combinatorial problems. EAs are
highly flexible and can be configured to address any optimization task, without
the requirements for reformulation and/or simplification that would be needed
for other techniques. However, this flexibility goes hand in hand with a cost:
the tailoring of an EA's configuration and parameters, so as to provide robust
performance for a given class of tasks, is often a complex and time-consuming
process. This tailoring process is one of the many ongoing research areas
associated with EAs.Comment: To appear in R. Marti, P. Pardalos, and M. Resende, eds., Handbook of
Heuristics, Springe
Bioinformatics Applications Based On Machine Learning
The great advances in information technology (IT) have implications for many sectors, such as bioinformatics, and has considerably increased their possibilities. This book presents a collection of 11 original research papers, all of them related to the application of IT-related techniques within the bioinformatics sector: from new applications created from the adaptation and application of existing techniques to the creation of new methodologies to solve existing problems
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