Mixtures of Skew-t Factor Analyzers

In this paper, we introduce a mixture of skew-t factor analyzers as well as a family of mixture models based thereon. The mixture of skew-t distributions model that we use arises as a limiting case of the mixture of generalized hyperbolic distributions. Like their Gaussian and t-distribution analogues, our mixture of skew-t factor analyzers are very well-suited to the model-based clustering of high-dimensional data. Imposing constraints on components of the decomposed covariance parameter results in the development of eight flexible models. The alternating expectation-conditional maximization algorithm is used for model parameter estimation and the Bayesian information criterion is used for model selection. The models are applied to both real and simulated data, giving superior clustering results compared to a well-established family of Gaussian mixture models

Mixtures of Shifted Asymmetric Laplace Distributions

A mixture of shifted asymmetric Laplace distributions is introduced and used for clustering and classification. A variant of the EM algorithm is developed for parameter estimation by exploiting the relationship with the general inverse Gaussian distribution. This approach is mathematically elegant and relatively computationally straightforward. Our novel mixture modelling approach is demonstrated on both simulated and real data to illustrate clustering and classification applications. In these analyses, our mixture of shifted asymmetric Laplace distributions performs favourably when compared to the popular Gaussian approach. This work, which marks an important step in the non-Gaussian model-based clustering and classification direction, concludes with discussion as well as suggestions for future work

DeepGene: an advanced cancer type classifier based on deep learning and somatic point mutations

BACKGROUND: With the developments of DNA sequencing technology, large amounts of sequencing data have become available in recent years and provide unprecedented opportunities for advanced association studies between somatic point mutations and cancer types/subtypes, which may contribute to more accurate somatic point mutation based cancer classification (SMCC). However in existing SMCC methods, issues like high data sparsity, small volume of sample size, and the application of simple linear classifiers, are major obstacles in improving the classification performance. RESULTS: To address the obstacles in existing SMCC studies, we propose DeepGene, an advanced deep neural network (DNN) based classifier, that consists of three steps: firstly, the clustered gene filtering (CGF) concentrates the gene data by mutation occurrence frequency, filtering out the majority of irrelevant genes; secondly, the indexed sparsity reduction (ISR) converts the gene data into indexes of its non-zero elements, thereby significantly suppressing the impact of data sparsity; finally, the data after CGF and ISR is fed into a DNN classifier, which extracts high-level features for accurate classification. Experimental results on our curated TCGA-DeepGene dataset, which is a reformulated subset of the TCGA dataset containing 12 selected types of cancer, show that CGF, ISR and DNN all contribute in improving the overall classification performance. We further compare DeepGene with three widely adopted classifiers and demonstrate that DeepGene has at least 24% performance improvement in terms of testing accuracy. CONCLUSIONS: Based on deep learning and somatic point mutation data, we devise DeepGene, an advanced cancer type classifier, which addresses the obstacles in existing SMCC studies. Experiments indicate that DeepGene outperforms three widely adopted existing classifiers, which is mainly attributed to its deep learning module that is able to extract the high level features between combinatorial somatic point mutations and cancer types

MMKK++ algorithm for clustering heterogeneous images into an unknown number of clusters

In this paper we present an automatic clustering procedure with the main aim to predict the number of clusters of unknown, heterogeneous images. We used the Fisher-vector for mathematical representation of the images and these vectors were considered as input data points for the clustering algorithm. We implemented a novel variant of K-means, the kernel K-means++, furthermore the min-max kernel K-means plusplus (MMKK++) as clustering method. The proposed approach examines some candidate cluster numbers and determines the strength of the clustering to estimate how well the data fit into K clusters, as well as the law of large numbers was used in order to choose the optimal cluster size. We conducted experiments on four image sets to demonstrate the efficiency of our solution. The first two image sets are subsets of different popular collections; the third is their union; the fourth is the complete Caltech101 image set. The result showed that our approach was able to give a better estimation for the number of clusters than the competitor methods. Furthermore, we defined two new metrics for evaluation of predicting the appropriate cluster number, which are capable of measuring the goodness in a more sophisticated way, instead of binary evaluation