Clustering Sparse Data With Feature Correlation With Application to Discover Subtypes in Cancer

• Main Authors: Jipeng Qiang, Wei Ding, Marieke Kuijjer, John Quackenbush, Ping Chen
• Format: Article
• Language: English
• Published: IEEE 2020-01-01
• Series: IEEE Access
• Subjects: Cancer subtype; feature interaction network; similarity metric; somatic mutational data
• Online Access: https://ieeexplore.ieee.org/document/9048133/

In this paper, given data with high-dimensional features, we study this problem of how to calculate the similarity between two samples by considering feature interaction network, where a feature interaction network represents the relationship between features. This is different from some traditional methods, those of which learn similarities based on a sample network that represents the relationship between samples. Therefore, we propose a novel network-based similarity metric for computing the similarity between samples, which incorporates the knowledge of feature interaction network, in order to overcome the data sparseness problem. Our similarity metric uses a new Feature Alignment Similarity measure, which does not directly compute the similarities among samples, but projects each sample into a feature interaction network and measures the similarities between two samples using the similarities between the vertices of the samples in the network. As such, when two samples do not share any common features, they are likely to have higher similarity values when their features share the similar network regions. For ensuring that the metric is useful in a real-world application, we apply our metric to discover subtypes in tumor mutational data by incorporating the information of the gene interaction network. Our experimental results from using synthetic data and real-world tumor mutational data show that our approach outperforms the top competitors in cancer subtype discovery. Furthermore, our approach can identify cancer subtypes that cannot be detected by other clustering algorithms in real cancer data.