Gene selection using hybrid dragonfly black hole algorithm: a case study on RNA-seq COVID-19 data

2021 ◽  
pp. 114242
Author(s):  
Elnaz Pashaei ◽  
Elham Pashaei
Keyword(s):  
Black Hole ◽  
Gene Selection ◽  
Rna Seq ◽  
Black Hole Algorithm

scholarly journals Black Hole Algorithm for Sustainable Design of Counterfort Retaining Walls

2020 ◽  
Vol 12 (7) ◽  
pp. 2767 ◽  
Author(s):  
Víctor Yepes ◽  
José V. Martí ◽  
José García
Keyword(s):  
Black Hole ◽  
Sustainable Design ◽  
Retaining Walls ◽  
The Other ◽  
Trade Off ◽  
Construction Company ◽  
Geometric Variables ◽  
The Stability ◽  
The Cost ◽  
Black Hole Algorithm

The optimization of the cost and CO 2 emissions in earth-retaining walls is of relevance, since these structures are often used in civil engineering. The optimization of costs is essential for the competitiveness of the construction company, and the optimization of emissions is relevant in the environmental impact of construction. To address the optimization, black hole metaheuristics were used, along with a discretization mechanism based on min–max normalization. The stability of the algorithm was evaluated with respect to the solutions obtained; the steel and concrete values obtained in both optimizations were analyzed. Additionally, the geometric variables of the structure were compared. Finally, the results obtained were compared with another algorithm that solved the problem. The results show that there is a trade-off between the use of steel and concrete. The solutions that minimize CO 2 emissions prefer the use of concrete instead of those that optimize the cost. On the other hand, when comparing the geometric variables, it is seen that most remain similar in both optimizations except for the distance between buttresses. When comparing with another algorithm, the results show a good performance in optimization using the black hole algorithm.

scholarly journals Optimization of Consignment-Store-Based Supply Chain with Black Hole Algorithm

Complexity ◽  
2017 ◽  
Vol 2017 ◽  
pp. 1-12 ◽  
Author(s):  
Ágota Bányai ◽  
Tamás Bányai ◽  
Béla Illés
Keyword(s):  
Black Hole ◽  
Supply Chain ◽  
Optimization Problems ◽  
Optimization Method ◽  
Chain Model ◽  
Supply Chain Optimization ◽  
Proposed Model ◽  
Supply Chain Model ◽  
Supply Model ◽  
Black Hole Algorithm

The globalization of economy and market led to increased networking in the field of manufacturing and services. These manufacturing and service processes including supply chain became more and more complex. The supply chain includes in many cases consignment stores. The design and operation of these complex supply chain processes can be described as NP-hard optimization problems. These problems can be solved using sophisticated models and methods based on metaheuristic algorithms. This research proposes an integrated supply model based on consignment stores. After a careful literature review, this paper introduces a mathematical model to formulate the problem of consignment-store-based supply chain optimization. The integrated model includes facility location and assignment problems to be solved. Next, an enhanced black hole algorithm dealing with multiobjective supply chain model is presented. The sensitivity analysis of the heuristic black hole optimization method is also described to check the efficiency of new operators to increase the convergence of the algorithm. Numerical results with different datasets demonstrate how the proposed model supports the efficiency, flexibility, and reliability of the consignment-store-based supply chain.

scholarly journals sc-REnF:An entropy guided robust feature selection for clustering of single-cell rna-seq data

2020 ◽  
Author(s):  
Snehalika Lall ◽  
Abhik Ghosh ◽  
Sumanta Ray ◽  
Sanghamitra Bandyopadhyay
Keyword(s):  
Single Cell ◽  
Gene Selection ◽  
Rna Seq ◽  
Technical Noise ◽  
Marker Selection ◽  
Cell Clustering ◽  
Typing Methods ◽  
Original Application ◽  
Downstream Analysis ◽  
Cell Typing

ABSTRACTMany single-cell typing methods require pure clustering of cells, which is susceptible towards the technical noise, and heavily dependent on high quality informative genes selected in the preliminary steps of downstream analysis. Techniques for gene selection in single-cell RNA sequencing (scRNA-seq) data are seemingly simple which casts problems with respect to the resolution of (sub-)types detection, marker selection and ultimately impacts towards cell annotation. We introduce sc-REnF, a novel and robust entropy based feature (gene) selection method, which leverages the landmark advantage of ‘Renyi’ and ‘Tsallis’ entropy achieved in their original application, in single cell clustering. Thereby, gene selection is robust and less sensitive towards the technical noise present in the data, producing a pure clustering of cells, beyond classifying independent and unknown sample with utmost accuracy. The corresponding software is available at: https://github.com/Snehalikalall/sc-REnF

scholarly journals RgCop-A regularized copula based method for gene selection in single cell rna-seq data

2021 ◽  
Vol 17 (10) ◽  
pp. e1009464
Author(s):  
Snehalika Lall ◽  
Sumanta Ray ◽  
Sanghamitra Bandyopadhyay
Keyword(s):  
Single Cell ◽  
Gene Selection ◽  
Real Life ◽  
Classification Performance ◽  
Rna Seq ◽  
Scale Invariant ◽  
Dependence Measure ◽  
Highly Expressed Genes ◽  
The Stability ◽  
Downstream Analysis

Gene selection in unannotated large single cell RNA sequencing (scRNA-seq) data is important and crucial step in the preliminary step of downstream analysis. The existing approaches are primarily based on high variation (highly variable genes) or significant high expression (highly expressed genes) failed to provide stable and predictive feature set due to technical noise present in the data. Here, we propose RgCop, a novel regularized copula based method for gene selection from large single cell RNA-seq data. RgCop utilizes copula correlation (Ccor), a robust equitable dependence measure that captures multivariate dependency among a set of genes in single cell expression data. We raise an objective function by adding a l1 regularization term with Ccor to penalizes the redundant co-efficient of features/genes, resulting non-redundant effective features/genes set. Results show a significant improvement in the clustering/classification performance of real life scRNA-seq data over the other state-of-the-art. RgCop performs extremely well in capturing dependence among the features of noisy data due to the scale invariant property of copula, thereby improving the stability of the method. Moreover, the differentially expressed (DE) genes identified from the clusters of scRNA-seq data are found to provide an accurate annotation of cells. Finally, the features/genes obtained from RgCop can able to annotate the unknown cells with high accuracy.

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