Large-Scale Recurrent Neural Network Based Modelling of Gene Regulatory Network Using Cuckoo Search-Flower Pollination Algorithm
16 Feb 2016-Advances in Bioinformatics (Hindawi Publishing Corporation)-Vol. 2016, Iss: 2016, pp 5283937-5283937
TL;DR: The results obtained show that the proposed methodology is capable of increasing the inference of correct regulations and decreasing false regulations to a high degree and the proposed method sacrifices computational time complexity in both cases due to the hybrid optimization process.
Abstract: The accurate prediction of genetic networks using computational tools is one of the greatest challenges in the postgenomic era. Recurrent Neural Network is one of the most popular but simple approaches to model the network dynamics from time-series microarray data. To date, it has been successfully applied to computationally derive small-scale artificial and real-world genetic networks with high accuracy. However, they underperformed for large-scale genetic networks. Here, a new methodology has been proposed where a hybrid Cuckoo Search-Flower Pollination Algorithm has been implemented with Recurrent Neural Network. Cuckoo Search is used to search the best combination of regulators. Moreover, Flower Pollination Algorithm is applied to optimize the model parameters of the Recurrent Neural Network formalism. Initially, the proposed method is tested on a benchmark large-scale artificial network for both noiseless and noisy data. The results obtained show that the proposed methodology is capable of increasing the inference of correct regulations and decreasing false regulations to a high degree. Secondly, the proposed methodology has been validated against the real-world dataset of the DNA SOS repair network of Escherichia coli. However, the proposed method sacrifices computational time complexity in both cases due to the hybrid optimization process.
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Abstract: Fil: Rubiolo, Mariano. Consejo Nacional de Investigaciones Cientificas y Tecnicas. Centro Cientifico Tecnologico Conicet - Santa Fe. Instituto de Investigacion en Senales, Sistemas e Inteligencia Computacional. Universidad Nacional del Litoral. Facultad de Ingenieria y Ciencias Hidricas. Instituto de Investigacion en Senales, Sistemas e Inteligencia Computacional; Argentina
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TL;DR: A novel elephant swarm water search algorithm inspired by the behaviour of social elephants, to solve different optimization problems, which has been observed that the proposed ESWSA is able to reach nearest to global minima and enabled inference of all true regulations of GRN correctly with less computational time compared with the other existing metaheuristics.
Abstract: The rising complexity of real-life optimization problems has constantly inspired computer researchers to develop new efficient optimization methods. Evolutionary computation and metaheuristics based on swarm intelligence are very popular nature-inspired optimization techniques. In this paper, the author has proposed a novel elephant swarm water search algorithm (ESWSA) inspired by the behaviour of social elephants, to solve different optimization problems. This algorithm is mainly based on the water search strategy of intelligent and social elephants during drought. Initially, we perform preliminary parametric sensitivity analysis for our proposed algorithm, developing guidelines for choosing the parameter values in real-life problems. In addition, the algorithm is evaluated against a number of widely used benchmark functions for global optimizations, and it is observed that the proposed algorithm has better performance for most of the cases compared with other state-of-the-art metaheuristics. Moreover, ESWSA performs better during fitness test, convergence test, computational complexity test, success rate test and scalability test for most of the benchmarks. Next, ESWSA is tested against two well-known constrained optimization problems, where ESWSA is found to be very efficient in term of execution speed and best fitness. As an application of ESWSA to real-life problem, it has been tested against a benchmark problem of computational biology, i.e., inference of Gene Regulatory Network based on Recurrent Neural Network. It has been observed that the proposed ESWSA is able to reach nearest to global minima and enabled inference of all true regulations of GRN correctly with less computational time compared with the other existing metaheuristics.
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Cites methods from "Large-Scale Recurrent Neural Networ..."
...The search space was selected as wi,j 2 [- 30,30], bi 2 [- 10,10] and si 2 [0,20], the same as in earlier work [48, 50, 57, 58]....
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...For comparison purpose, we have selected some wellknown optimization methods, namely BA [16, 45, 46], CS [17, 47, 48], FPA [18, 49] and PSO [15, 43, 44]....
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TL;DR: A new metaheuristic namely Elephant Swarm Water Search Algorithm (ESWSA) to infer Gene Regulatory Network (GRN) is proposed, mainly based on the water search strategy of intelligent and social elephants during drought, utilizing the different types of communication techniques.
Abstract: Correct inference of genetic regulations inside a cell from the biological database like time series microarray data is one of the greatest challenges in post genomic era for biologists and researchers. Recurrent Neural Network (RNN) is one of the most popular and simple approach to model the dynamics as well as to infer correct dependencies among genes. Inspired by the behavior of social elephants, we propose a new metaheuristic namely Elephant Swarm Water Search Algorithm (ESWSA) to infer Gene Regulatory Network (GRN). This algorithm is mainly based on the water search strategy of intelligent and social elephants during drought, utilizing the different types of communication techniques. Initially, the algorithm is tested against benchmark small and medium scale artificial genetic networks without and with presence of different noise levels and the efficiency was observed in term of parametric error, minimum fitness value, execution time, accuracy of prediction of true regulation, etc. Next, the proposed algorithm is tested against the real time gene expression data of Escherichia Coli SOS Network and results were also compared with others state of the art optimization methods. The experimental results suggest that ESWSA is very efficient for GRN inference problem and performs better than other methods in many ways.
14 citations
References
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01 Dec 2009
TL;DR: A new meta-heuristic algorithm, called Cuckoo Search (CS), is formulated, based on the obligate brood parasitic behaviour of some cuckoo species in combination with the Lévy flight behaviour ofSome birds and fruit flies, for solving optimization problems.
Abstract: In this paper, we intend to formulate a new meta-heuristic algorithm, called Cuckoo Search (CS), for solving optimization problems. This algorithm is based on the obligate brood parasitic behaviour of some cuckoo species in combination with the Levy flight behaviour of some birds and fruit flies. We validate the proposed algorithm against test functions and then compare its performance with those of genetic algorithms and particle swarm optimization. Finally, we discuss the implication of the results and suggestion for further research.
5,521 citations
TL;DR: This review focuses on the much more mundane but indispensable tasks of 'normalizing' data from individual hybridizations to make meaningful comparisons of expression levels, and of 'transforming' them to select genes for further analysis and data mining.
Abstract: Underlying every microarray experiment is an experimental question that one would like to address. Finding a useful and satisfactory answer relies on careful experimental design and the use of a variety of data-mining tools to explore the relationships between genes or reveal patterns of expression. While other sections of this issue deal with these lofty issues, this review focuses on the much more mundane but indispensable tasks of 'normalizing' data from individual hybridizations to make meaningful comparisons of expression levels, and of 'transforming' them to select genes for further analysis and data mining.
2,024 citations
TL;DR: The compendium of expression data compiled in this study, coupled with RegulonDB, provides a valuable model system for further improvement of network inference algorithms using experimental data.
Abstract: Machine learning approaches offer the potential to systematically identify transcriptional regulatory interactions from a compendium of microarray expression profiles. However, experimental validation of the performance of these methods at the genome scale has remained elusive. Here we assess the global performance of four existing classes of inference algorithms using 445 Escherichia coli Affymetrix arrays and 3,216 known E. coli regulatory interactions from RegulonDB. We also developed and applied the context likelihood of relatedness (CLR) algorithm, a novel extension of the relevance networks class of algorithms. CLR demonstrates an average precision gain of 36% relative to the next-best performing algorithm. At a 60% true positive rate, CLR identifies 1,079 regulatory interactions, of which 338 were in the previously known network and 741 were novel predictions. We tested the predicted interactions for three transcription factors with chromatin immunoprecipitation, confirming 21 novel interactions and verifying our RegulonDB-based performance estimates. CLR also identified a regulatory link providing central metabolic control of iron transport, which we confirmed with real-time quantitative PCR. The compendium of expression data compiled in this study, coupled with RegulonDB, provides a valuable model system for further improvement of network inference algorithms using experimental data.
1,587 citations
03 Sep 2012
TL;DR: This paper proposes a new algorithm, namely, flower pollination algorithm, inspired by the pollination process of flowers, and uses it to solve a nonlinear design benchmark, which shows the convergence rate is almost exponential.
Abstract: Flower pollination is an intriguing process in the natural world. Its evolutionary characteristics can be used to design new optimization algorithms. In this paper, we propose a new algorithm, namely, flower pollination algorithm, inspired by the pollination process of flowers. We first use ten test functions to validate the new algorithm, and compare its performance with genetic algorithms and particle swarm optimization. Our simulation results show the flower algorithm is more efficient than both GA and PSO. We also use the flower algorithm to solve a nonlinear design benchmark, which shows the convergence rate is almost exponential.
1,525 citations
TL;DR: In this article, a new algorithm, namely, flower pollination algorithm, inspired by the pollination process of flowers, was proposed, which is more efficient than both GA and PSO.
Abstract: Flower pollination is an intriguing process in the natural world. Its evolutionary characteristics can be used to design new optimization algorithms. In this paper, we propose a new algorithm, namely, flower pollination algorithm, inspired by the pollination process of flowers. We first use ten test functions to validate the new algorithm, and compare its performance with genetic algorithms and particle swarm optimization. Our simulation results show the flower algorithm is more efficient than both GA and PSO. We also use the flower algorithm to solve a nonlinear design benchmark, which shows the convergence rate is almost exponential.
1,415 citations