Dependence model and network for biomarker identification and cancer classification

Of particular interest in this paper is to develop statistical and modeling approaches for protein biomarker discovery to provide new insights into the early detection and diagnosis of cancer, based on mass spectrometry (MS) data. In this paper, we propose to employ an ensemble dependence model (EDM)-based framework for cancer classification, protein dependence network reconstruction, and further for biomarker identification. The dependency revealed by the EDM reflects the functional relationships between MS peaks and thus provides some insights into the underlying cancer development mechanism. The EDM-based classification scheme is applied to real cancer MS datasets, and provides superior performance for cancer classification when compared with the popular Support Vector Machine algorithm. From the eigenvalue pattern of the dependence model, the dependence networks are constructed to identify cancer biomarkers. Furthermore, for the purpose of comparison, a classification-performance-based biomarker identification criterion is examined. The dependence-network-based biomarkers show much greater consistency in cross validation. Therefore, the proposed dependence-network-based scheme is promising for use as a cancer diagnostic classifier and predictor.