Nonnegative principal component analysis for mass spectral serum profiles and biomarker discovery

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Abstract
As a novel cancer diagnostic paradigm, mass spectroscopic serum proteomic pattern diagnostics was reported superior to the conventional serologic cancer biomarkers. However, its clinical use is not fully validated yet. An important factor to prevent this young technology to become a mainstream cancer diagnostic paradigm is that robustly identifying cancer molecular patterns from high-dimensional protein expression data is still a challenge in machine learning and oncology research. As a well-established dimension reduction technique, PCA is widely integrated in pattern recognition analysis to discover cancer molecular patterns. However, its global feature selection mechanism prevents it from capturing local features. This may lead to difficulty in achieving high-performance proteomic pattern discovery, because only features interpreting global data behavior are used to train a learning machine.

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