Sparse coding is a popular technique for achieving compact data representation and has been used in many applications. However, the instability issue often causes degeneration in practice and thus attracts a lot of studies. While the traditional graph sparse coding preserves the neighborhood structure of the data, this study integrates the low-rank representation(LRR) to fix the inconsistency of sparse coding by holding the subspace structures of the high-dimensional observations. The proposed method is dubbed low-rank graph regularized sparse coding (LogSC), which learns sparse codes and low-rank representations jointly rather than the traditional two-step approach. Since the two data representations share a dictionary matrix, the resulted sparse representation on this dictionary could be benefited from LRR. We solved the optimization problem of LogSC by using the linearized alternating direction method with adaptive penalty. Experimental results show the proposed method is discriminative in feature learning and robust to various noises. This work provides a one-step approach to integrating graph embedding in representation learning. INDEX TERMS Graph sparse coding, graph embedding, data structure preserving, robust data representation, image representation, one-step integrated graph sparse coding.
Different subtypes of the same cancer often show distinct genomic signatures and require targeted treatments. The differences at the cellular and molecular levels of tumor microenvironment in different cancer subtypes have significant effects on tumor pathogenesis and prognostic outcomes. Although there have been significant researches on the prognostic association of tumor infiltrating lymphocytes in selected histological subtypes, few investigations have systemically reported the prognostic impacts of immune cells in molecular subtypes, as quantified by machine learning approaches on multi-omics datasets. This paper describes a new computational framework, ProTICS, to quantify the differences in the proportion of immune cells in tumor microenvironment and estimate their prognostic effects in different subtypes. First, we stratified patients into molecular subtypes based on gene expression and methylation profiles by applying nonnegative tensor factorization technique. Then we quantified the proportion of cell types in each specimen using an mRNA-based deconvolution method. For tumors in each subtype, we estimated the prognostic effects of immune cell types by applying Cox proportional hazard regression. At the molecular level, we also predicted the prognosis of signature genes for each subtype. Finally, we benchmarked the performance of ProTICS on three TCGA datasets and another independent METABRIC dataset. ProTICS successfully stratified tumors into different molecular subtypes manifested by distinct overall survival. Furthermore, the different immune cell types showed distinct prognostic patterns with respect to molecular subtypes. This study provides new insights into the prognostic association between immune cells and molecular subtypes, showing the utility of immune cells as potential prognostic markers. Availability: R code is available at https://github.com/liu-shuhui/ProTICS
In current research processes, mathematical learning has significantly impacted the brain’s plasticity and cognitive functions. While biochemical changes in brain have been investigated by magnetic resonance spectroscopy, our study attempts to identify non-math students by using magnetic resonance imaging scans (MRIs). The proposed method crops the left middle front gyrus (MFG) region from the MRI, resulting in a multi-instance classification problem. Then, subspace enhanced contrastive learning is employed on all instances to learn robust deep features, followed by an ensemble classifier based on multiple-layer-perceptron models for student identification. The experiments were conducted on 123 MRIs taken from 72 math students and 51 non-math students. The proposed method arrived at an accuracy of 73.7% for image classification and 91.8% for student classification. Results show the proposed workflow successfully identifies the students who lack mathematical education by using MRI data. This study provides insights into the impact of mathematical education on brain development from structural imaging.
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