A high performance profile-biomarker diagnosis for mass spectral profiles

BACKGROUND: Although mass spectrometry based proteomics demonstrates an exciting promise in complex diseases diagnosis, it remains an important research field rather than an applicable clinical routine for its diagnostic accuracy and data reproducibility. Relatively less investigation has been done yet in attaining high-performance proteomic pattern classification compared with the amount of endeavours in enhancing data reproducibility. METHODS: In this study, we present a novel machine learning approach to achieve a clinical level disease diagnosis for mass spectral data. We propose multi-resolution independent component analysis, a novel feature selection algorithm to tackle the large dimensionality of mass spectra, by following our local and global feature selection framework. We also develop high-performance classifiers by embedding multi-resolution independent component analysis in linear discriminant analysis and support vector machines. RESULTS: Our multi-resolution independent component based support vector machines not only achieve clinical level classification accuracy, but also overcome the weakness in traditional peak-selection based biomarker discovery. In addition to rigorous theoretical analysis, we demonstrate our method’s superiority by comparing it with nine state-of-the-art classification and regression algorithms on six heterogeneous mass spectral profiles. CONCLUSIONS: Our work not only suggests an alternative direction from machine learning to accelerate mass spectral proteomic technologies into a clinical routine by treating an input profile as a ‘profile-biomarker’, but also has positive impacts on large scale ‘omics' data mining. Related source codes and data sets can be found at: https://sites.google.com/site/heyaumbioinformatics/home/proteomics