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Unsupervised clustering is an essential step in identifying cell types from single-cell RNA sequencing (scRNA-seq) data. However, a common issue with unsupervised clustering models is that the optimization direction of the objective function and the final generated clustering labels in the absence of supervised information may be inconsistent or even arbitrary. To address this challenge, a dynamic ensemble pruning framework (DEPF) is proposed to identify and interpret single-cell molecular heterogeneity. In particular, a silhouette coefficient-based indicator is developed to determine the optimization direction of the bi-objective function. In addition, a hierarchical autoencoder is employed to project the high-dimensional data onto multiple low-dimensional latent space sets, and then a clustering ensemble is produced in the latent space by the basic clustering algorithm. Following that, a bi-objective fruit fly optimization algorithm is designed to prune dynamically the low-quality basic clustering in the ensemble. Multiple experiments are conducted on 28 real scRNA-seq datasets and one large real scRNA-seq dataset from diverse platforms and species to validate the effectiveness of the DEPF. In addition, biological interpretability and transcriptional and post-transcriptional regulatory are conducted to explore biological patterns from the cell types identified, which could provide novel insights into characterizing the mechanisms., (© 2023 The Authors. Advanced Science published by Wiley-VCH GmbH.)

Motivation: Single-cell RNA sequencing (scRNA-seq) is an increasingly popular technique for transcriptomic analysis of gene expression at the single-cell level. Cell-type clustering is the first crucial task in the analysis of scRNA-seq data that facilitates accurate identification of cell types and the study of the characteristics of their transcripts. Recently, several computational models based on a deep autoencoder and the ensemble clustering have been developed to analyze scRNA-seq data. However, current deep autoencoders are not sufficient to learn the latent representations of scRNA-seq data, and obtaining consensus partitions from these feature representations remains under-explored., Results: To address this challenge, we propose a single-cell deep clustering model via a dual denoising autoencoder with bipartite graph ensemble clustering called scBGEDA, to identify specific cell populations in single-cell transcriptome profiles. First, a single-cell dual denoising autoencoder network is proposed to project the data into a compressed low-dimensional space and that can learn feature representation via explicit modeling of synergistic optimization of the zero-inflated negative binomial reconstruction loss and denoising reconstruction loss. Then, a bipartite graph ensemble clustering algorithm is designed to exploit the relationships between cells and the learned latent embedded space by means of a graph-based consensus function. Multiple comparison experiments were conducted on 20 scRNA-seq datasets from different sequencing platforms using a variety of clustering metrics. The experimental results indicated that scBGEDA outperforms other state-of-the-art methods on these datasets, and also demonstrated its scalability to large-scale scRNA-seq datasets. Moreover, scBGEDA was able to identify cell-type specific marker genes and provide functional genomic analysis by quantifying the influence of genes on cell clusters, bringing new insights into identifying cell types and characterizing the scRNA-seq data from different perspectives., Availability and Implementation: The source code of scBGEDA is available at https://github.com/wangyh082/scBGEDA. The software and the supporting data can be downloaded from https://figshare.com/articles/software/scBGEDA/19657911., Supplementary Information: Supplementary data are available at Bioinformatics online., (© The Author(s) 2023. Published by Oxford University Press.)

This paper introduces versatile filters to construct efficient convolutional neural networks that are widely used in various visual recognition tasks. Considering the demands of efficient deep learning techniques running on cost-effective hardware, a number of methods have been developed to learn compact neural networks. Most of these works aim to slim down filters in different ways, e.g., investigating small, sparse or quantized filters. In contrast, we treat filters from an additive perspective. A series of secondary filters can be derived from a primary filter with the help of binary masks. These secondary filters all inherit in the primary filter without occupying more storage, but once been unfolded in computation they could significantly enhance the capability of the filter by integrating information extracted from different receptive fields. Besides spatial versatile filters, we additionally investigate versatile filters from the channel perspective. Binary masks can be further customized for different primary filters under orthogonal constraints. We conduct theoretical analysis on network complexity and an efficient convolution scheme is introduced. Experimental results on benchmark datasets and neural networks demonstrate that our versatile filters are able to achieve comparable accuracy as that of original filters, but require less memory and computation cost.

Patient stratification has been studied widely to tackle subtype diagnosis problems for effective treatment. Due to the dimensionality curse and poor interpretability of data, there is always a long-lasting challenge in constructing a stratification model with high diagnostic ability and good generalization. To address these problems, this article proposes two novel evolutionary multiobjective clustering algorithms with ensemble (NSGA-II-ECFE and MOEA/D-ECFE) with four cluster validity indices used as the objective functions. First, an effective ensemble construction method is developed to enrich the ensemble diversity. After that, an ensemble clustering fitness evaluation (ECFE) method is proposed to evaluate the ensembles by measuring the consensus clustering under those four objective functions. To generate the consensus clustering, ECFE exploits the hybrid co-association matrix from the ensembles and then dynamically selects the suitable clustering algorithm on that matrix. Multiple experiments have been conducted to demonstrate the effectiveness of the proposed algorithm in comparison with seven clustering algorithms, twelve ensemble clustering approaches, and two multiobjective clustering algorithms on 55 synthetic datasets and 35 real patient stratification datasets. The experimental results demonstrate the competitive edges of the proposed algorithms over those compared methods. Furthermore, the proposed algorithm is applied to extend its advantages by identifying cancer subtypes from five cancer-related single-cell RNA-seq datasets.

Motivation: Thanks to the development of high-throughput sequencing technologies, massive amounts of various biomolecular data have been accumulated to revolutionize the study of genomics and molecular biology. One of the main challenges in analyzing this biomolecular data is to cluster their subtypes into subpopulations to facilitate subsequent downstream analysis. Recently, many clustering methods have been developed to address the biomolecular data. However, the computational methods often suffer from many limitations such as high dimensionality, data heterogeneity and noise., Results: In our study, we develop a novel Graph-based Multiple Hierarchical Consensus Clustering (GMHCC) method with an unsupervised graph-based feature ranking (FR) and a graph-based linking method to explore the multiple hierarchical information of the underlying partitions of the consensus clustering for multiple types of biomolecular data. Indeed, we first propose to use a graph-based unsupervised FR model to measure each feature by building a graph over pairwise features and then providing each feature with a rank. Subsequently, to maintain the diversity and robustness of basic partitions (BPs), we propose multiple diverse feature subsets to generate several BPs and then explore the hierarchical structures of the multiple BPs by refining the global consensus function. Finally, we develop a new graph-based linking method, which explicitly considers the relationships between clusters to generate the final partition. Experiments on multiple types of biomolecular data including 35 cancer gene expression datasets and eight single-cell RNA-seq datasets validate the effectiveness of our method over several state-of-the-art consensus clustering approaches. Furthermore, differential gene analysis, gene ontology enrichment analysis and KEGG pathway analysis are conducted, providing novel insights into cell developmental lineages and characterization mechanisms., Availability and Implementation: The source code is available at GitHub: https://github.com/yifuLu/GMHCC. The software and the supporting data can be downloaded from: https://figshare.com/articles/software/GMHCC/17111291., Supplementary Information: Supplementary data are available at Bioinformatics online., (© The Author(s) 2022. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Detection and diagnosis of cancer are especially essential for early prevention and effective treatments. Many studies have been proposed to tackle the subtype diagnosis problems with those data, which often suffer from low diagnostic ability and bad generalization. This article studies a multiobjective PSO-based hybrid algorithm (MOPSOHA) to optimize four objectives including the number of features, the accuracy, and two entropy-based measures: the relevance and the redundancy simultaneously, diagnosing the cancer data with high classification power and robustness. First, we propose a novel binary encoding strategy to choose informative gene subsets to optimize those objective functions. Second, a mutation operator is designed to enhance the exploration capability of the swarm. Finally, a local search method based on the "best/1" mutation operator of differential evolutionary algorithm (DE) is employed to exploit the neighborhood area with sparse high-quality solutions since the base vector always approaches to some good promising areas. In order to demonstrate the effectiveness of MOPSOHA, it is tested on 41 cancer datasets including thirty-five cancer gene expression datasets and six independent disease datasets. Compared MOPSOHA with other state-of-the-art algorithms, the performance of MOPSOHA is superior to other algorithms in most of the benchmark datasets.

Chemical Reaction Optimization (CRO) is a simple and efficient evolutionary optimization algorithm by simulating chemical reactions. As far as the current research is concerned, the algorithm has been successfully used for solving a number of real-world optimization tasks. In our paper, a new real encoded chemical reaction optimization algorithm is proposed to boost the efficiency of the optimization operations in standard chemical reactions optimization algorithm. Inspired by the evolutionary operation of the differential evolution algorithm, an improved search operation mechanism is proposed based on the underlying operation. It is modeled to further explore the search space of the algorithm under the best individuals. Afterwards, to control the perturbation frequency of the search strategy, the modification rate is increased to balance between the exploration ability and mining ability of the algorithm. Meanwhile, we also propose a new population initialization method that incorporates several models to produce high-quality initialized populations. To validate the effectiveness of the algorithm, nine unconstrained optimization algorithms are used as benchmark functions. As observed from the experimental results, it is evident that the proposed algorithm is significantly better than the standard chemical reaction algorithm and other evolutionary optimization algorithms. Then, we also apply the proposed model to address the synthesis problem of two antenna array synthesis. The results also reveal that the proposed algorithm is superior to other approaches from different perspectives.

High dimensionality and sample imbalance of gene expression data promote the development of effective algorithms for classifying gene expression data. To improve the ability to distinguish different subtypes of gene expression data, we devise a hypervolume-based discrete evolutionary optimization algorithm (HYBDEOA) in this paper. Four objectives, namely the number of genes, the accuracy, the relevance, and the redundancy, are optimized simultaneously to guide the evolution. Firstly, binary encoding is used to choose some features, projecting data onto different subspaces. After that, a discrete neighborhood operation is conducted to generate a new binary-mapped population. Combining the new population with the current population, we employ the hypervolume-based mechanism to select the Pareto solutions. Finally, a discrete mutation method is proposed to find promising solutions in the binary search space. To demonstrate the performance of HYBDEOA, we apply HYBDEOA to 55 synthetic datasets and 35 cancer gene expression datasets. Extensive experiments are also conducted to reveal the effectiveness and efficiency of HYBDEOA. The experimental results demonstrate that our proposed method is a parameter-less and robust algorithm, which can group gene expression data with a finer and more informative classification. [ABSTRACT FROM AUTHOR]

Recently, many evolutionary computation methods have been developed to solve the feature selection problem. However, the studies focused mainly on small-scale issues, resulting in stagnation issues in local optima and numerical instability when dealing with large-scale feature selection dilemmas. To address these challenges, this paper proposes a novel weighted differential evolution algorithm based on self-adaptive mechanism, named SaWDE, to solve large-scale feature selection. First, a multi-population mechanism is adopted to enhance the diversity of the population. Then, we propose a new self-adaptive mechanism that selects several strategies from a strategy pool to capture the diverse characteristics of the datasets from the historical information. Finally, a weighted model is designed to identify the important features, which enables our model to generate the most suitable feature-selection solution. We demonstrate the effectiveness of our algorithm on twelve large-scale datasets. The performance of SaWDE is superior compared to six non-EC algorithms and six other EC algorithms, on both training and test datasets and on subset size, indicating that our algorithm is a favorable tool to solve the large-scale feature selection problem. Moreover, we have experimented SaWDE with six EC algorithms on twelve higher-dimensional data, which demonstrates that SaWDE is more robust and efficient compared to those state-of-the-art methods. SaWDE source code is available on Github at https://github.com/wangxb96/SaWDE. [ABSTRACT FROM AUTHOR]

Path-planning for uninhabited combat air vehicles (UCAV) is a typically complicated global optimization problem. It seeks a superior flight path in a complex battlefield environment, taking into various constraints. Many swarm intelligence (SI) algorithms have recently gained remarkable attention due to their capability to address complex optimization problems. However, different SI algorithms present various performances for UCAV path-planning since each algorithm has its own strengths and weaknesses. Therefore, this study provides an overview of different SI algorithms for UCAV path-planning research. In the experiment, twelve algorithms that published in major journals and conference proceedings are surveyed and then applied to UCAV path-planning. Moreover, to demonstrate the performance of different algorithms in further, we design different scales of problem cases for those comparative algorithms. The experimental results show that UCAV can find the safe path to avoid the threats efficiently based on most SI algorithms. In particular, the Spider Monkey Optimization is more effective and robust than other algorithms in handling the UCAV path-planning problem. The analysis from different perspectives contributes to highlight trends and open issues in the field of UCAVs. [ABSTRACT FROM AUTHOR]