Multiple clustering aims at exploring alternative clusterings to organize the data into meaningful groups from different perspectives. Existing multiple clustering algorithms are designed for singleview data. We assume that the individuality and commonality of multi-view data can be leveraged to generate high-quality and diverse clusterings. To this end, we propose a novel multi-view multiple clustering (MVMC) algorithm. MVMC first adapts multi-view self-representation learning to explore the individuality encoding matrices and the shared commonality matrix of multi-view data. It additionally reduces the redundancy (i.e., enhancing the individuality) among the matrices using the Hilbert-Schmidt Independence Criterion (HSIC), and collects shared information by forcing the shared matrix to be smooth across all views. It then uses matrix factorization on the individual matrices, along with the shared matrix, to generate diverse clusterings of high-quality. We further extend multiple co-clustering on multi-view data and propose a solution called multi-view multiple co-clustering (MVMCC). Our empirical study shows that MVMC (MVMCC) can exploit multiview data to generate multiple high-quality and diverse clusterings (co-clusterings), with superior performance to the state-of-the-art methods.
DNA methylation plays a significant role in transcriptional regulation by repressing activity. Change of the DNA methylation level is an important factor affecting the expression of target genes and downstream phenotypes. Because current experimental technologies can only assay a small proportion of CpG sites in the human genome, it is urgent to develop reliable computational models for predicting genome-wide DNA methylation. Here, we proposed a novel algorithm that accurately extracted sequence complexity features (seven features) and developed a support-vector-machine-based prediction model with integration of the reported DNA composition features (trinucleotide frequency and GC content, 65 features) by utilizing the methylation profiles of embryonic stem cells in human. The prediction results from 22 human chromosomes with size-varied windows showed that the 600-bp window achieved the best average accuracy of 94.7%. Moreover, comparisons with two existing methods further showed the superiority of our model, and cross-species predictions on mouse data also demonstrated that our model has certain generalization ability. Finally, a statistical test of the experimental data and the predicted data on functional regions annotated by ChromHMM found that six out of 10 regions were consistent, which implies reliable prediction of unassayed CpG sites. Accordingly, we believe that our novel model will be useful and reliable in predicting DNA methylation.
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