Dimensionality Reduction of Protein Mass Spectrometry Data Using Random Projection

Abstract. Protein mass spectrometry (MS) pattern recognition has recently emerged as a new method for cancer diagnosis. Unfortunately, classification performance may degrade owing to the enormously high dimensionality of the data. This paper investigates the use of Random Projection in protein MS data dimensionality reduction. The effectiveness of Random Projection (RP) is ana-lyzed and compared against Principal Component Analysis (PCA) by using three classification algorithms, namely Support Vector Machine, Feed-forward Neural Networks and K-Nearest Neighbour. Three real-world cancer data sets are employed to evaluate the performances of RP and PCA. Through the inves-tigations, RP method demonstrated better or at least comparable classification performance as PCA if the dimensionality of the projection matrix is suffi-ciently large. This paper also explores the use of RP as a pre-processing step prior to PCA. The results show that without sacrificing classification accuracy, performing RP prior to PCA significantly improves the computational time.