High dimensionality has become a typical feature of biomolecular data. In this paper, a novel dimension reduction method named p-norm singular value decomposition (PSVD) is proposed to seek the low-rank approximation matrix to the biomolecular data. To enhance the robustness to outliers, the Lp-norm is taken as the error function and the Schatten p-norm is used as the regularization function in the optimization model. To evaluate the performance of PSVD, the Kmeans clustering method is then employed for tumor clustering based on the low-rank approximation matrix. Extensive experiments are carried out on five gene expression data sets including two benchmark data sets and three higher dimensional data sets from the cancer genome atlas. The experimental results demonstrate that the PSVD-based method outperforms many existing methods. Especially, it is experimentally proved that the proposed method is more efficient for processing higher dimensional data with good robustness, stability, and superior time performance.
BackgroundIn recent years, identification of differentially expressed genes and sample clustering have become hot topics in bioinformatics. Principal Component Analysis (PCA) is a widely used method in gene expression data. However, it has two limitations: first, the geometric structure hidden in data, e.g., pair-wise distance between data points, have not been explored. This information can facilitate sample clustering; second, the Principal Components (PCs) determined by PCA are dense, leading to hard interpretation. However, only a few of genes are related to the cancer. It is of great significance for the early diagnosis and treatment of cancer to identify a handful of the differentially expressed genes and find new cancer biomarkers.ResultsIn this study, a new method gLSPCA is proposed to integrate both graph Laplacian and sparse constraint into PCA. gLSPCA on the one hand improves the clustering accuracy by exploring the internal geometric structure of the data, on the other hand identifies differentially expressed genes by imposing a sparsity constraint on the PCs.ConclusionsExperiments of gLSPCA and its comparison with existing methods, including Z-SPCA, GPower, PathSPCA, SPCArt, gLPCA, are performed on real datasets of both pancreatic cancer (PAAD) and head & neck squamous carcinoma (HNSC). The results demonstrate that gLSPCA is effective in identifying differentially expressed genes and sample clustering. In addition, the applications of gLSPCA on these datasets provide several new clues for the exploration of causative factors of PAAD and HNSC.
Many studies on automatic speech emotion recognition (SER) have been devoted to extracting meaningful emotional features for generating emotion-relevant representations. However, they generally ignore the complementary learning of static and dynamic features, leading to limited performances. In this paper, we propose a novel hierarchical network called HNSD that can efficiently integrate the static and dynamic features for SER. Specifically, the proposed HNSD framework consists of three different modules. To capture the discriminative features, an effective encoding module is firstly designed to simultaneously encode both static and dynamic features. By taking the obtained features as inputs, the Gated Multi-features Unit (GMU) is conducted to explicitly determine the emotional intermediate representations for framelevel features fusion, instead of directly fusing these acoustic features. In this way, the learned static and dynamic features can jointly and comprehensively generate the unified feature representations. Benefiting from a well-designed attention mechanism, the last classification module is applied to predict the emotional states at the utterance level. Extensive experiments on the IEMOCAP benchmark dataset demonstrate the superiority of our method in comparison with state-of-the-art baselines.
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