A new weighted fuzzy C-means clustering approach considering between-cluster separability

Fuzzy C-means clustering algorithm (FCM) is an effective approach for clustering. However, in most existing FCM type frameworks, only in-cluster compactness is taken into account, whereas the between-cluster separability is overlooked. In this paper, to enhance the clustering, by incorporating the feature weighting and data weighting method, we put forward a new weighted fuzzy C-means clustering approach considering between-cluster separability, in which for achieving good compactness and separability, making the in-cluster distances as small as possible and making the between-cluster distances as large as possible, the in-cluster distances and between-cluster distances are taken into account; To achieve the optimal clustering result, the iterative formulas of the feature weights, membership degrees, data weights and cluster centers are obtained by maximizing the in-cluster compactness and the between-cluster separability. Experiments on real-world datasets were carried out, the results showed that the new approach could obtain promising performance.

Accurately Clustering Single-cell RNA-seq data by Capturing Structural Relations between Cells through Graph Convolutional Network

Recent advances in single-cell RNA sequencing (scRNA-seq) technologies provide a great opportunity to study gene expression at cellular resolution, and the scRNA-seq data has been routinely conducted to unfold cell heterogeneity and diversity. A critical step for the scRNA-seq analyses is to cluster the same type of cells, and many methods have been developed for cell clustering. However, existing clustering methods are limited to extract the representations from expression data of individual cells, while ignoring the high-order structural relations between cells. Here, we proposed a new method (GraphSCC) to cluster cells based on scRNA-seq data by accounting structural relations between cells through a graph convolutional network. The representation learned from the graph convolutional network, together with another representation output from a denoising autoencoder network, are optimized by a dual self-supervised module for better cell clustering. Extensive experiments indicate that GraphSCC model outperforms state-of-the-art methods in various evaluation metrics on both simulated and real datasets. Further visualizations show that GraphSCC provides representations for better intra-cluster compactness and inter-cluster separability.

An Improved Directed Acyclic Graph Support Vector Machines Based on Inter-Cluster Separability Measure in Feature Space

For disadvantage of the methods that are used to evaluate inter-cluster separability measure, a novel separability measure is proposed and applied to directed acyclic graph support vector machine. The distance between cluster centers and distribution of samples in feature space are both considered by the algorithm. Firstly, use hyper-sphere support vector machine to obtain minimal bounding hyper-sphere of each cluster, according to the radius and centers of minimal bounding hyper-spheres, introduce the concept of inter-cluster separability measure in feature space, get the matrix of inter-cluster separability measure according to the concept, finally construct the directed acyclic graph according to the matrix. The experimental results show that the algorithm has higher classification precision, comparing with old directed acyclic graph support vector machine.

Dunn’s index for cluster tendency assessment of pharmacological data sets

Cluster tendency assessment is an important stage in cluster analysis. In this sense, a group of promising techniques named visual assessment of tendency (VAT) has emerged in the literature. The presence of clusters can be detected easily through the direct observation of a dark blocks structure along the main diagonal of the intensity image. Alternatively, if the Dunn’s index for a single linkage partition is greater than 1, then it is a good indication of the blocklike structure. In this report, the Dunn’s index is applied as a novel measure of tendency on 8 pharmacological data sets, represented by machine-learning-selected molecular descriptors. In all cases, observed values are less than 1, thus indicating a weak tendency for data to form compact clusters. Other results suggest that there is an increasing relationship between the Dunn’s index as a measure of cluster separability and the classification accuracy of various cluster algorithms tested on the same data sets.