Integrative subspace clustering by common and specific decomposition for applications on cancer subtype identification

Abstract

Background: Recent high throughput technologies have been applied for collecting heterogeneous biomedical omics datasets. Computational analysis of the multi-omics datasets could potentially reveal deep insights for a given disease. Most existing clustering methods by multi-omics data assume strong consistency among different sources of datasets, and thus may lose efficacy when the consistency is relatively weak. Furthermore, they could not identify the conflicting parts for each view, which might be important in applications such as cancer subtype identification. Methods: In this work, we propose an integrative subspace clustering method (ISC) by common and specific decomposition to identify clustering structures with multi-omics datasets. The main idea of our ISC method is that the original representations for the samples in each view could be reconstructed by the concatenation of a common part and a view-specific part in orthogonal subspaces. The problem can be formulated as a matrix decomposition problem and solved efficiently by our proposed algorithm. Results: The experiments on simulation and text datasets show that our method outperforms other state-of-Art methods. Our method is further evaluated by identifying cancer types using a colorectal dataset. We finally apply our method to cancer subtype identification for five cancers using TCGA datasets, and the survival analysis shows that the subtypes we found are significantly better than other compared methods. Conclusion: We conclude that our ISC model could not only discover the weak common information across views but also identify the view-specific information.