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Machine Learning for Protein Subcellular Localization Prediction by Man-Wai Mak, Shibiao Wan

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8 Experimental setup

As stated in a comprehensive review [37], valid dataset construction for training and testing, and unbiased measurements for evaluating the performance of predictors are two indispensable steps in establishing a statistical protein predictor. This chapter will focus on these two important parts for an experimental setup. Datasets construction and performance metrics for predicting single- and multi-label proteins will be presented.

8.1 Prediction of single-label proteins

This section will focus on constructing datasets and will introduce performance metrics for single-location proteins which are used in GOASVM and InterProGOSVM.

8.1.1 Datasets construction

8.1.1.1 Datasets for GOASVM

Two benchmark datasets (EU16 [46] and ...

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