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With the discovery of new DNAs, a fundamental problem arising is how to categorize those DNA sequences into correct species. Unfortunately, identifying all data groups correctly and assigning a set of DNAs into k clusters where k must be predefined are one of the major drawbacks in clustering analysis, especially when the data have many dimensions and the number of clusters is too large and hard to guess. Furthermore, finding a similarity measure that preserves the functionality and represents both the composition and distribution of the bases in a DNA sequence is one of the main challenges in computational biology. In this paper, a new soft computing metaheuristic framework is introduced for automatic clustering to generate the optimal cluster formation and to determine the best estimate for the number of clusters. Pulse coupled neural network (PCNN) is utilized for the calculation of DNA sequence similarity or dissimilarity. Bat algorithm is hybridized with the well-known genetic algorithm to solve the automatic data clustering problem. Extensive computational experiments are conducted on the expanded human oral microbiome database (eHOMD). A comparative study between the experimental results shows that the proposed hybrid algorithm achieved superior performance over the standard genetic algorithm and bat algorithm. Moreover, the hybrid performance was compared with competing algorithms from the literature review to ascertain its superiority. Mann-Whitney-Wilcoxon rank-sum test is conducted to statistically validate the obtained clusters.

Categorical data clustering has been attracted a lot of attention recently due to its necessary in the real-world applications. Many clustering methods have been proposed for categorical data. However, most of the existing algorithms require the predefined number of clusters which is usually unavailable in real-world problems. Only a few works focused on automatic clustering, but mainly handled for numerical data. This study develops a novel automatic fuzzy clustering using non-dominated sorting particle swarm optimization (AFC-NSPSO) algorithm for categorical data. The proposed AFC-NSPSO algorithm can automatically identify the optimal number of clusters and exploit the clustering result with the corresponding selected number of clusters. In addition, a new technique is investigated to identify the maximum number of clusters in a dataset based on the local density. To select a final solution in the first Pareto front, some internal validation indices are used. The performance of the proposed AFC-NSPSO on the real-world datasets collected from the UCI machine learning repository exhibits effectiveness compared with some other existing automatic categorical clustering algorithms. Besides, this study also applies the proposed algorithm to analyze a real-world case study with an unknown number of clusters.

Clustering by fast search and find of density peaks published on journal Science in 2014 is a density-based clustering technique, which is not only unnecessary to determine the number of clusters in advance, but also able to recognize the clusters of arbitrary shapes. Due to a manual selection of clustering centers on a decision graph, samples which belong to one cluster may be assigned to two or more clusters and vice versa. On assumption that boundary points which keep comparable densities with cluster centers should be regarded as inner points, we make a new method which not only can find all possible clusters automatically but also can combine those with similarities simultaneously to obtain the final clusters. Unlike clustering by fast search and find of density peaks, we only focus on densities with discarding the relative metric which measures the minimum distance between a cluster center and a point with a higher density. Qualitative and quantitative experimental results on sufficient datasets demonstrate the effectiveness of our method.

Resumen El presente artículo describe el algoritmo del método espectral que fue elegido para crear un programa computacional aplicado, este que hace el agrupamiento automático de datos de orientaciones de discontinuidades medidas en un macizo rocosos. La agrupación y diferenciación de familias de discontinuidades normalmente se hace a través de la selección heurística de grupos a partir de un diagrama de densidades de discontinuidades. Sin embargo, una agrupación automática y basada en un algoritmo estadístico puede ser más rápido y pasible a la réplica. Así mismo, un agrupamiento automático presentado en un programa abierto es útil para la implementación en otros cálculos dentro del análisis de datos de orientaciones de discontinuidades. El artículo explica en detalle del algoritmo y su implementación, tiene validaciones y ejemplos que garantizan que el programa puede ser usado. Abstract This article describes the algorithm of the spectral method that was chosen to create an applied computational program, which performs an automatic clustering of oriented data of discontinuities-measurements in a rock mass. The clustering differentiation of discontinuity families normally is done by a heuristic selection of sets based on a density diagram of discontinuities. But, an automatic clustering based on a statistical algorithm may be faster and passive to be replicated. In addition, an automatic clustering that has been presented as an open program is useful for the implementation in other calculi in the process of data analysis of discontinuity orientations. The article explains in detail the algorithms and its implementation; it has validations and examples that guarantees that the program can be used.

The Automatic Clustering using Differential Evolution (ACDE) is one of the grouping methods capable of automatically determining the number of the cluster. However, ACDE continues making use of the strategy manual to determine the activation threshold of k, which affects its performance. In this study, the problem of ACDE is enhanced using the U Control Chart (UCC). The performance of the proposed method was tested using five data sets from the National Administrative Department of Statistics (DANE - Departamento Administrativo Nacional de Estadisticas) and the Ministry of Commerce, Industry, and Tourism of Colombia for the innovative capacity of Small and Medium-sized Enterprises (SMEs) and were assessed by the Davies Bouldin Index (DBI) and the Cosine Similarity (CS) measure. The results show that the proposed method yields excellent performance compared to prior researches for most datasets with optimal cluster number yet lowest DBI and CS measure. It can be concluded that the UCC method is able to determine k activation threshold in ACDE that caused effective determination of the cluster number for k-means clustering.

Cluster Validity Indices (CVI) evaluate the efficiency of a clustering algorithm and Data Envelopment Analysis (DEA) evaluate the efficiency of Decision-Making Units (DMUs) using a number of inputs data and outputs data. Combination of the CVI and DEA inspired the development of a new automatic clustering algorithm called Automatic Clustering Based on Data Envelopment Analysis (ACDEA). ACDEA is able to determine the optimal number of clusters in four main steps. In the first step, a new clustering algorithm called CSA-Kmeans is introduced. In this algorithm, clustering is performed by the Crow Search Algorithm (CSA), in which the K-means algorithm generates the initial centers of the clusters. In the second step, the clustering of data is performed from kmin cluster to kmax cluster, using CSA-Kmeans. At each iteration of clustering, using correct data labels, Within-Group Scatter (WGS) index, Between-Group Scatter (BGS) index, Dunn Index (DI), the Calinski-Harabasz (CH) index, and the Silhouette index (SI) are extracted and stored, which ultimately these indices make a matrix that the columns of this matrix indicate the values of validity indices and the rows or DMUs represent the number of clustering times from kmin cluster to kmax cluster. In the third step, the efficiency of the DMUs is calculated using the DEA method based on the second stage matrix, and given that the DI, CH, and SI estimate the relationship within group scatter and between group scatter, WGS and BGS are used as input variables and the indices of DI, CH and SI are used as output variables to DEA. Finally, in step four, AP method is used to calculate the efficiency of DMUs, so that an efficiency value is obtained for each DMU that maximum efficiency represents the optimal number of clusters. In this study, three categories of data are used to measure the efficiency of the ACDEA algorithm. Also, the efficiency of ACDEA is compared with the DCPSO, GCUK and ACDE algorithms. According to the results, there is a positive significant relationship between input CVI and output CVI in data envelopment analysis, and the optimal number of clusters is achieved for many cases.

In this paper we attempt to solve an automatic clustering problem by optimizing multiple objectives such as automatic k-determination and a set of cluster validity indices concurrently. The proposed automatic clustering technique uses the most recent optimization algorithm Jaya as an underlying optimization stratagem. This evolutionary technique always aims to attain global best solution rather than a local best solution in larger datasets. The explorations and exploitations imposed on the proposed work results to detect the number of automatic clusters, appropriate partitioning present in data sets and mere optimal values towards CVIs frontiers. Twelve datasets of different intricacy are used to endorse the performance of aimed algorithm. The experiments lay bare that the conjectural advantages of multi objective clustering optimized with evolutionary approaches decipher into realistic and scalable performance paybacks.

Remote sensing image clustering is a challenging task considering its intrinsic complexity. Recently, by combining the spectral and spatial information of the remote sensing data, the clustering performance can be dramatically enhanced, termed as Spectral-Spatial Clustering (SSC). However, it has always been difficult to determine the weight parameter for balancing the spectral term and spatial term of the clustering objective function. In this paper, spectral-spatial clustering with a local weight parameter determination method for remote sensing image was proposed, i.e., L-SSC. In L-SSC, considering the large scale of remote sensing images, the weight parameter can be determined locally in a patch image instead of the whole image. Afterwards, the local weight parameter was used in constructing the objective function of L-SSC. Thus, the remote sensing image clustering problem was transformed into an optimization problem. Finally, in order to achieve a better optimization performance, a variant of differential evolution (i.e., jDE) was used as the optimizer due to its powerful optimization capability. Experimental results on three remote sensing images, including a Wuhan TM image, a Fancun Quickbird image, and an Indian Pine AVIRIS image, demonstrated that the proposed L-SSC can acquire higher clustering accuracy in comparison to other spectral-spatial clustering methods.

We develop a membrane clustering algorithm to deal with automatic clustering problem.We design a tissue-like membrane system with fully connected structure.We develop an improved velocity-position model. Membrane computing is a class of distributed parallel computing models. Inspired from the structure and inherent mechanism of membrane computing, a membrane clustering algorithm is proposed to deal with automatic clustering problem, in which a tissue-like membrane system with fully connected structure is designed as its computing framework. Moreover, based on its special structure and inherent mechanism, an improved velocity-position model is developed as evolution rules. Under the control of evolution-communication mechanism, the tissue-like membrane system cannot only find the most appropriate number of clusters but else determine a good clustering partitioning for a data set. Six benchmark data sets are used to evaluate the proposed membrane clustering algorithm. Experiment results show that the proposed algorithm is superior or competitive to three state-and-the-art automatic clustering algorithms recently reported in the literature.

We propose a clustering method which produces valid results while automatically determining an optimal number of clusters. The proposed method achieves these results with minimal user input, of which none pertains to a number of clusters. Our method’s effectiveness in clustering, including its ability to produce valid results on data sets presenting nested or interlocking shapes, is demonstrated and compared with cluster validity analysis to other methods to which a known optimal number of clusters is provided, and to other automatic clustering methods. Depending on the particularities of the data set used, our method has produced results which are roughly equivalent or better than those of the compared methods., 6th International Conference, ICAART 2014, March 6-8, 2014, Angers, France, Series: Lecture Notes in Computer Science

Flow cytometry has become a standard method to analyze bacterioplankton. Analysis of samples by flow cytometry is automatic, but it is followed by manual classification of the bacterioplankton groups in flow cytometry standard (FCS) files. This classification is a time consuming and subjective task performed by manually drawing the limits of the groups present in cytograms, a process referred to as gating. The automation of flow cytometry data processing based on pattern recognition techniques could provide an efficient tool to overcome some of these disadvantages. Here, we propose the use of model-based clustering techniques for the automatic detection of low (LNA) and high (HNA) nucleic acid bacterioplankton groups in FCS files. To validate our method, we compared the automatic classification with a flow cytometry database from a 9 yr time series collected in the central Cantabrian Sea that had been manually analyzed. The correlation between automatic and manual gating methods was >0.9 for cell counts and 0.7 to 0.95 for side scatter values, a proxy of cell size. In addition, no significant differences were found in the mean annual cycle of LNA and HNA cell abundance depicted by both methods. We also quantified the subjectivity of manual gating. The coefficient of variation for heterotrophic bacteria counts obtained by different analysts was around 10 to 20%. Our results suggest that the combination of flow cytometry and automatic gating provides a valuable tool to analyze microbial communities objectively and accurately, allowing us to safely compare bacterioplankton samples from different environments., SI