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Register a new userBinary Particle Swarm Optimization versus Hybrid Genetic Algorithm for Inferring Well Supported Phylogenetic Trees
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The amount of completely sequenced chloroplast genomes increases rapidly every day, leading to the possibility to build large-scale phylogenetic trees of plant species. Considering a subset of close plant species defined according to their chloroplasts, the phylogenetic tree that can be inferred by their core genes is not necessarily well supported, due to the possible occurrence of problematic genes (i.e., homoplasy, incomplete lineage sorting, horizontal gene transfers, etc.) which may blur the phylogenetic signal. However, a trustworthy phylogenetic tree can still be obtained provided such a number of blurring genes is reduced. The problem is thus to determine the largest subset of core genes that produces the best-supported tree. To discard problematic genes and due to the overwhelming number of possible combinations, this article focuses on how to extract the largest subset of sequences in order to obtain the most supported species tree. Due to computational complexity, a distributed Binary Particle Swarm Optimization (BPSO) is proposed in sequential and distributed fashions. Obtained results from bo
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Increasing nature-inspired metaheuristic algorithms are applied to solving the real-world optimization problems, as they have some advantages over the classical methods of numerical optimization. This paper has proposed a new nature-inspired metaheuristic called Whale Swarm Algorithm for function optimization, which is inspired by the whales behavior of communicating with each other via ultrasound for hunting. The proposed Whale Swarm Algorithm has been compared with several popular metaheuristic algorithms on comprehensive performance metrics. According to the experimental results, Whale Swarm Algorithm has a quite competitive performance when compared with other algorithms.
Microarray techniques are widely used in Gene expression analysis. These techniques are based on discovering submatrices of genes that share similar expression patterns across a set of experimental conditions with coherence constraint. Actually, these submatrices are called biclusters and the extraction process is called biclustering. In this paper we present a novel binary particle swarm optimization model for the gene expression biclustering problem. Hence, we apply the binary particle swarm optimization algorithm with a proposed measure, called Discretized Column-based Measure (DCM) as a novel cost function for evaluating biclusters where biological relevance, MSR and the size of the bicluster are considered as evaluation metrics for our results. Results are compared to the existing algorithms and they show the validity of our proposed approach.
Transcriptome assembly from RNA-Seq reads is an active area of bioinformatics research. The ever-declining cost and the increasing depth of RNA-Seq have provided unprecedented opportunities to better identify expressed transcripts. However, the nonlinear transcript structures and the ultra-high throughput of RNA-Seq reads pose significant algorithmic and computational challenges to the existing transcriptome assembly approaches, either reference-guided or de novo. While reference-guided approaches offer good sensitivity, they rely on alignment results of the splice-aware aligners and are thus unsuitable for species with incomplete reference genomes. In contrast, de novo approaches do not depend on the reference genome but face a computational daunting task derived from the complexity of the graph built for the whole transcriptome. In response to these challenges, we present a hybrid approach to exploit an incomplete reference genome without relying on splice-aware aligners. We have designed a split-and-align procedure to efficiently localize the reads to individual genomic loci, which is followed by an accurate de novo assembly to assemble reads falling into each locus. Using extensive simulation data, we demonstrate a high accuracy and precision in transcriptome reconstruction by comparing to selected transcriptome assembly tools. Our method is implemented in assemblySAM, a GUI software freely available at http://sammate.sourceforge.net.
This paper discusses a new variant of the Henry Gas Solubility Optimization (HGSO) Algorithm, called Hybrid HGSO (HHGSO). Unlike its predecessor, HHGSO allows multiple clusters serving different individual meta-heuristic algorithms (i.e., with its own defined parameters and local best) to coexist within the same population. Exploiting the dynamic cluster-to-algorithm mapping via penalized and reward model with adaptive switching factor, HHGSO offers a novel approach for meta-heuristic hybridization consisting of Jaya Algorithm, Sooty Tern Optimization Algorithm, Butterfly Optimization Algorithm, and Owl Search Algorithm, respectively. The acquired results from the selected two case studies (i.e., involving team formation problem and combinatorial test suite generation) indicate that the hybridization has notably improved the performance of HGSO and gives superior performance against other competing meta-heuristic and hyper-heuristic algorithms.
While a fully-coherent all-sky search is known to be optimal for detecting signals from compact binary coalescences (CBCs), its high computational cost has limited current searches to less sensitive coincidence-based schemes. For a network of first generation GW detectors, it has been demonstrated that Particle Swarm Optimization (PSO) can reduce the computational cost of this search, in terms of the number of likelihood evaluations, by a factor of $approx 10$ compared to a grid-based optimizer. Here, we extend the PSO-based search to a network of second generation detectors and present further substantial improvements in its performance by adopting the local-best variant of PSO and an effective strategy for tuning its configuration parameters. It is shown that a PSO-based search is viable over the entire binary mass range relevant to second generation detectors at realistic signal strengths.
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