Elite fuzzy clustering ensemble based on clustering diversity and quality measures

Statistical and data visualization techniques to study the role of one-electron in the energy of neutral and charged clusters of Na39

In this work, we explored the role of a single electron in the energy of neutral and charged clusters ofNa 39 using data visualization and statistical techniques as a new insight. Initially, we studied the effects of one electron, time, and temperature on energy using multiple linear regression analysis with dummy variables, and the results demonstrated that all three predictors significantly affected the energy. Time had a positive impact (direct ratio effect) on the energy ofNa - 39 , andNa 39 , and a negative impact (inverse ratio effect) on the energy ofNa + 39 , while temperature had a positive effect on the energy of all three sodium clusters. Then, to study the thermodynamic properties of each cluster, we employed the fuzzy clustering technique. The results verified that each sodium cluster is divided into three groups based on the different temperatures used to investigate the thermodynamic properties of each cluster. Finally, time series analysis was applied to investigate the behavior of the energy in each sodium cluster and each temperature. We used the statistical software R version 4.3.3 to perform all statistical computations.

Active Clustering Ensemble With Self-Paced Learning

A clustering ensemble provides an elegant framework to learn a consensus result from multiple prespecified clustering partitions. Though conventional clustering ensemble methods achieve promising performance in various applications, we observe that they may usually be misled by some unreliable instances due to the absence of labels. To tackle this issue, we propose a novel active clustering ensemble method, which selects the uncertain or unreliable data for querying the annotations in the process of the ensemble. To fulfill this idea, we seamlessly integrate the active clustering ensemble method into a self-paced learning framework, leading to a novel self-paced active clustering ensemble (SPACE) method. The proposed SPACE can jointly select unreliable data to label via automatically evaluating their difficulty and applying easy data to ensemble the clusterings. In this way, these two tasks can be boosted by each other, with the aim to achieve better clustering performance. The experimental results on benchmark datasets demonstrate the significant effectiveness of our method. The codes of this article are released in https://Doctor-Nobody.github.io/codes/space.zip.

Improving replicability in single-cell RNA-Seq cell type discovery with Dune

BACKGROUND

Single-cell transcriptome sequencing (scRNA-Seq) has allowed new types of investigations at unprecedented levels of resolution. Among the primary goals of scRNA-Seq is the classification of cells into distinct types. Many approaches build on existing clustering literature to develop tools specific to single-cell. However, almost all of these methods rely on heuristics or user-supplied parameters to control the number of clusters. This affects both the resolution of the clusters within the original dataset as well as their replicability across datasets. While many recommendations exist, in general, there is little assurance that any given set of parameters will represent an optimal choice in the trade-off between cluster resolution and replicability. For instance, another set of parameters may result in more clusters that are also more replicable.

RESULTS

Here, we propose Dune, a new method for optimizing the trade-off between the resolution of the clusters and their replicability. Our method takes as input a set of clustering results-or partitions-on a single dataset and iteratively merges clusters within each partitions in order to maximize their concordance between partitions. As demonstrated on multiple datasets from different platforms, Dune outperforms existing techniques, that rely on hierarchical merging for reducing the number of clusters, in terms of replicability of the resultant merged clusters as well as concordance with ground truth. Dune is available as an R package on Bioconductor: https://www.bioconductor.org/packages/release/bioc/html/Dune.html .

CONCLUSIONS

Cluster refinement by Dune helps improve the robustness of any clustering analysis and reduces the reliance on tuning parameters. This method provides an objective approach for borrowing information across multiple clusterings to generate replicable clusters most likely to represent common biological features across multiple datasets.

Self-Paced Clustering Ensemble

The clustering ensemble has emerged as an important extension of the classical clustering problem. It provides an elegant framework to integrate multiple weak base clusterings to generate a strong consensus result. Most existing clustering ensemble methods usually exploit all data to learn a consensus clustering result, which does not sufficiently consider the adverse effects caused by some difficult instances. To handle this problem, we propose a novel self-paced clustering ensemble (SPCE) method, which gradually involves instances from easy to difficult ones into the ensemble learning. In our method, we integrate the evaluation of the difficulty of instances and ensemble learning into a unified framework, which can automatically estimate the difficulty of instances and ensemble the base clusterings. To optimize the corresponding objective function, we propose a joint learning algorithm to obtain the final consensus clustering result. Experimental results on benchmark data sets demonstrate the effectiveness of our method.

A step edge detector based on bilinear transformation

Nowadays, Canny edge detector is considered to be one of the best edge detection approaches for the images with step form. Various overgeneralized versions of these edge detectors have been offered up to now, e.g. Saryazdi edge detector. This paper proposes a new discrete version of edge detection which is obtained from Shen-Castan and Saryazdi filters by using bilinear transformation. Different experimentations are conducted to decide the suitable parameters of the proposed edge detector and to examine its validity. To evaluate the strength of the proposed model, the results are compared to Canny, Sobel, Prewitt, LOG and Saryazdi methods. Finally, by calculation of mean square error (MSE) and peak signal-to-noise ratio (PSNR), the value of PSNR is always equal to or greater than the PSNR value of suggested methods. Moreover, by calculation of Baddeley’s error metric (BEM) on ten test images from the Berkeley Segmentation DataSet (BSDS), we show that the proposed method outperforms the other methods. Therefore, visual and quantitative comparison shows the efficiency and strength of proposed method.

GMM with parameters initialization based on SVD for network threat detection

In the field of security, the data labels are unknown or the labels are too expensive to label, so that clustering methods are used to detect the threat behavior contained in the big data. The most widely used probabilistic clustering model is Gaussian Mixture Models(GMM), which is flexible and powerful to apply prior knowledge for modelling the uncertainty of the data. Therefore, in this paper, we use GMM to build the threat behavior detection model. Commonly, Expectation Maximization (EM) and Variational Inference (VI) are used to estimate the optimal parameters of GMM. However, both EM and VI are quite sensitive to the initial values of the parameters. Therefore, we propose to use Singular Value Decomposition (SVD) to initialize the parameters. Firstly, SVD is used to factorize the data set matrix to get the singular value matrix and singular matrices. Then we calculate the number of the components of GMM by the first two singular values in the singular value matrix and the dimension of the data. Next, other parameters of GMM, such as the mixing coefficients, the mean and the covariance, are calculated based on the number of the components. After that, the initialization values of the parameters are input into EM and VI to estimate the optimal parameters of GMM. The experiment results indicate that our proposed method performs well on the parameters initialization of GMM clustering using EM and VI for estimating parameters.

A classification model based on svm and fuzzy rough set for network intrusion detection

Intrusion Detection Systems (IDS) are designed to provide security into computer networks. Different classification models such as Support Vector Machine (SVM) has been successfully applied on the network data. Meanwhile, the extension or improvement of the current models using prototype selection simultaneous with their training phase is crucial due to the serious inefficacies during training (i.e. learning overhead). This paper introduces an improved model for prototype selection. Applying proposed prototype selection along with SVM classification model increases attack discovery rate. In this article, we use fuzzy rough sets theory (FRST) for prototype selection to enhance SVM in intrusion detection. Testing and evaluation of the proposed IDS have been mainly performed on NSL-KDD dataset as a refined version of KDD-CUP99. Experimentations indicate that the proposed IDS outperforms the basic and simple IDSs and modern IDSs in terms of precision, recall, and accuracy rate.

Fuzzy clustering method to compare the spread rate of Covid-19 in the high risks countries

The numbers of confirmed cases of new coronavirus (Covid-19) are increased daily in different countries. To determine the policies and plans, the study of the relations between the distributions of the spread of this virus in other countries is critical. In this work, the distributions of the spread of Covid-19 in Unites States America, Spain, Italy, Germany, United Kingdom, France, and Iran were compared and clustered using fuzzy clustering technique. At first, the time series of Covid-19 datasets in selected countries were considered. Then, the relation between spread of Covid-19 and population's size was studied using Pearson correlation. The effect of the population's size was eliminated by rescaling the Covid-19 datasets based on the population's size of USA. Finally, the rescaled Covid-19 datasets of the countries were clustered using fuzzy clustering. The results of Pearson correlation indicated that there were positive and significant between total confirmed cases, total dead cases and population's size of the countries. The clustering results indicated that the distribution of spreading in Spain and Italy was approximately similar and differed from other countries.

Prediction of the Solubility of CO2 in Imidazolium Ionic Liquids Based on Selective Ensemble Modeling Method

Solubility data is one of the essential basic data for CO2 capture by ionic liquids. A selective ensemble modeling method, proposed to overcome the shortcomings of current methods, was developed and applied to the prediction of the solubility of CO2 in imidazolium ionic liquids. Firstly, multiple different sub–models were established based on the diversities of data, structural, and parameter design philosophy. Secondly, the fuzzy C–means algorithm was used to cluster the sub–models, and the collinearity detection method was adopted to eliminate the sub–models with high collinearity. Finally, the information entropy method integrated the sub–models into the selective ensemble model. The validation of the CO2 solubility predictions against experimental data showed that the proposed ensemble model had better performance than its previous alternative, because more effective information was extracted from different angles, and the diversity and accuracy among the sub–models were fully integrated. This work not only provided an effective modeling method for the prediction of the solubility of CO2 in ionic liquids, but also provided an effective method for the discrimination of ionic liquids for CO2 capture.

Numerical function optimization by conditionalized PSO algorithm

A lot of research has been directed to the new optimizers that can find a suboptimal solution for any optimization problem named as heuristic black-box optimizers. They can find the suboptimal solutions of an optimization problem much faster than the mathematical programming methods (if they find them at all). Particle swarm optimization (PSO) is an example of this type. In this paper, a new modified PSO has been proposed. The proposed PSO incorporates conditional learning behavior among birds into the PSO algorithm. Indeed, the particles, little by little, learn how they should behave in some similar conditions. The proposed method is named Conditionalized Particle Swarm Optimization (CoPSO). The problem space is first divided into a set of subspaces in CoPSO. In CoPSO, any particle inside a subspace will be inclined towards its best experienced location if the particles in its subspace have low diversity; otherwise, it will be inclined towards the global best location. The particles also learn to speed-up in the non-valuable subspaces and to speed-down in the valuable subspaces. The performance of CoPSO has been compared with the state-of-the-art methods on a set of standard benchmark functions.

Cluster ensemble selection using balanced normalized mutual information

A bad partition in an ensemble will be removed by a cluster ensemble selection framework from the final ensemble. It is the main idea in cluster ensemble selection to remove these partitions (bad partitions) from the selected ensemble. But still, it is likely that one of them contains some reliable clusters. Therefore, it may be reasonable to apply the selection phase on cluster level. To do this, a cluster evaluation metric is needed. Some of these metrics have been recently introduced; each of them has its limitations. The weak points of each method have been addressed in the paper. Subsequently, a new metric for cluster assessment has been introduced. The new measure is named Balanced Normalized Mutual Information (BNMI) criterion. It balances the deficiency of the traditional NMI-based criteria. Additionally, an innovative cluster ensemble approach has been proposed. To create the consensus partition considering the elected clusters, a set of different aggregation-functions (called also consensus-functions) have been utilized: the ones which are based upon the co-association matrix (CAM), the ones which are based on hyper graph partitioning algorithms, and the ones which are based upon intermediate space. The experimental study indicates that the state-of-the-art cluster ensemble methods are outperformed by the proposed cluster ensemble approach.

Analysis of University Students’ Behavior Based on a Fusion K-Means Clustering Algorithm

With the development of big data technology, creating the ‘Digital Campus’ is a hot issue. For an increasing amount of data, traditional data mining algorithms are not suitable. The clustering algorithm is becoming more and more important in the field of data mining, but the traditional clustering algorithm does not take the clustering efficiency and clustering effect into consideration. In this paper, the algorithm based on K-Means and clustering by fast search and find of density peaks (K-CFSFDP) is proposed, which improves on the distance and density of data points. This method is used to cluster students from four universities. The experiment shows that K-CFSFDP algorithm has better clustering results and running efficiency than the traditional K-Means clustering algorithm, and it performs well in large scale campus data. Additionally, the results of the cluster analysis show that the students of different categories in four universities had different performances in living habits and learning performance, so the university can learn about the students’ behavior of different categories and provide corresponding personalized services, which have certain practical significance.

An Ensemble of Locally Reliable Cluster Solutions

Clustering ensemble indicates to an approach in which a number of (usually weak) base clusterings are performed and their consensus clustering is used as the final clustering. Knowing democratic decisions are better than dictatorial decisions, it seems clear and simple that ensemble (here, clustering ensemble) decisions are better than simple model (here, clustering) decisions. But it is not guaranteed that every ensemble is better than a simple model. An ensemble is considered to be a better ensemble if their members are valid or high-quality and if they participate according to their qualities in constructing consensus clustering. In this paper, we propose a clustering ensemble framework that uses a simple clustering algorithm based on kmedoids clustering algorithm. Our simple clustering algorithm guarantees that the discovered clusters are valid. From another point, it is also guaranteed that our clustering ensemble framework uses a mechanism to make use of each discovered cluster according to its quality. To do this mechanism an auxiliary ensemble named reference set is created by running several kmeans clustering algorithms.