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Background: Cancer is one of the leading death causes around the world. Accurate prediction of its survival time is significant, which can help clinicians make appropriate therapeutic schemes. Cancer data can be characterized by varied molecular features, clinical behaviors and morphological appearances. However, the cancer heterogeneity problem usually makes patient samples with different risks (i.e., short and long survival time) inseparable, thereby causing unsatisfactory prediction results. Clinical studies have shown that genetic data tends to contain more molecular biomarkers associated with cancer, and hence integrating multi-type genetic data may be a feasible way to deal with cancer heterogeneity. Although multi-type gene data have been used in the existing work, how to learn more effective features for cancer survival prediction has not been well studied. Results: To this end, we propose a deep learning approach to reduce the negative impact of cancer heterogeneity and improve the cancer survival prediction effect. It represents each type of genetic data as the shared and specific features, which can capture the consensus and complementary information among all types of data. We collect mRNA expression, DNA methylation and microRNA expression data for four cancers to conduct experiments. Conclusions: Experimental results demonstrate that our approach substantially outperforms established integrative methods and is effective for cancer survival prediction. Availability and implementation: https://github.com/githyr/ComprehensiveSurvival. [ABSTRACT FROM AUTHOR]

Background: As a highly aggressive disease, cancer has been becoming the leading death cause around the world. Accurate prediction of the survival expectancy for cancer patients is significant, which can help clinicians make appropriate therapeutic schemes. With the high-throughput sequencing technology becoming more and more cost-effective, integrating multi-type genome-wide data has been a promising method in cancer survival prediction. Based on these genomic data, some data-integration methods for cancer survival prediction have been proposed. However, existing methods fail to simultaneously utilize feature information and structure information of multi-type genome-wide data. Results: We propose a Multi-type Data Joint Learning (MDJL) approach based on multi-type genome-wide data, which comprehensively exploits feature information and structure information. Specifically, MDJL exploits correlation representations between any two data types by cross-correlation calculation for learning discriminant features. Moreover, based on the learned multiple correlation representations, MDJL constructs sample similarity matrices for capturing global and local structures across different data types. With the learned discriminant representation matrix and fused similarity matrix, MDJL constructs graph convolutional network with Cox loss for survival prediction. Conclusions: Experimental results demonstrate that our approach substantially outperforms established integrative methods and is effective for cancer survival prediction. [ABSTRACT FROM AUTHOR]

Heterogeneous defect prediction (HDP) refers to identifying more likely defect-proneness of software modules in a target project using heterogeneous metric data from other source projects, which solves the heterogeneous metric problem in cross-project defect prediction. Recently, several mixed-project HDP methods have been presented. However, these models neglect to address the linear inseparability and cross-project class imbalance issues simultaneously. These limitations usually lead to the unsatisfactory performance of HDP. In this paper, we propose an improved transfer learning approach for mixed-project HDP to deal with the above limitations, called data sampling and kernel manifold discriminant alignment (DSKMDA). DSKMDA firstly applies data sampling technique to handle the class imbalance issue. Then it uses kernel manifold discriminant alignment technique to handle the linear inseparability issue. Extensive experiments on 13 projects from three public benchmark datasets with four evaluation measures demonstrate that DSKMDA can produce better or comparable results against a range of competing methods. [ABSTRACT FROM AUTHOR]

Cross-project defect prediction (CPDP) refers to identifying defect-prone software modules in one project (target) using historical data collected from other projects (source), which can help developers find bugs and prioritize their testing efforts. Recently, CPDP has attracted great research interest. However, the source and target data usually exist redundancy and nonlinearity characteristics. Besides, most CPDP methods do not exploit source label information to uncover the underlying knowledge for label propagation. These factors usually lead to unsatisfactory CPDP performance. To address the above limitations, we propose a landmark selection-based kernelized discriminant subspace alignment (LSKDSA) approach for CPDP. LSKDSA not only reduces the discrepancy of the data distributions between the source and target projects, but also characterizes the complex data structures and increases the probability of linear separability of the data. Moreover, LSKDSA encodes label information of the source data into domain adaptation learning process and makes itself with good discriminant ability. Extensive experiments on 13 public projects from three benchmark datasets demonstrate that LSKDSA performs better than a range of competing CPDP methods. The improvement is 3.44%-11.23% in g-measure, 5.75%-11.76% in AUC, and 9.34%-33.63% in MCC, respectively. [ABSTRACT FROM AUTHOR]

The heterogeneous defect prediction (HDP) technique can predict defects in a target company using heterogeneous metric data from external company, which has received substantial research attention. However, existing HDP methods assume that source data is labeled but labeling data is expensive. Semi-supervised defect prediction technique can perform defect prediction with few labeled data. In this paper, we investigate a new problem — semi-supervised HDP (SHDP). To solve this problem, we propose a new approach named cost-sensitive kernel semi-supervised correlation analysis (CKSCA) as a solution of SHDP problem. It introduces unified metric representation and canonical correlation analysis to make the data distributions of different company projects more similar. CKSCA also designs a cost-sensitive kernel semi-supervised discriminant analysis mechanism to utilize the limited labeled data and sufficient real-life unlabeled data from different companies. Besides we collect lots of open-source projects from GitHub website to construct a new large-scale unlabeled dataset called GITHUB dataset. It contains 26,407 modules and is greater than each public project dataset. It has been public online and can be extended continuously. Experiments on the GITHUB dataset and other public datasets indicate that unlabeled GITHUB data can help prediction model improve prediction performance, and CKSCA is effective and efficient for solving SHDP problem. [ABSTRACT FROM AUTHOR]

Sparse additive models have shown competitive performance for high-dimensional variable selection and prediction due to their representation flexibility and interpretability. Despite their theoretical properties have been studied extensively, few works have addressed the robustness for the sparse additive models. In this paper, we employ the robust average top-k (AT k) loss as classification error measure and propose a new sparse algorithm, named AT k group sparse additive machine (AT k -GSAM). Besides the robust concern, the AT k -GSAM has well adaptivity by integrating the data dependent hypothesis space and group sparse regularizer together. Generalization error bound is established by the concentration estimate with empirical covering numbers. In particular, our error analysis shows that AT k -GSAM can achieve the learning rate O (n − 1 / 2) under appropriate conditions. We further analyze the robustness of AT k -GSAM via a sample-weighted procedure interpretation, and the theoretical guarantees on grouped variable selection. Experimental evaluations on both simulated and benchmark datasets validate the effectiveness and robustness of the new algorithm. [ABSTRACT FROM AUTHOR]