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Protein Subcellular Localization Prediction Based on Internal Micro-similarities of Markov Chains

Elucidating protein subcellular localization is an essential topic in proteomics research due to its importance in the process of drug discovery. Unfortunately, experimentally uncovering protein subcellular targets is an arduous process that may not result in a successful localization. In contrast, computational methods can rapidly predict protein subcellular targets and are an efficient alternative to experimental methods for unannotated proteins. In this work, we introduce a new method to predict protein subcellular localization which increases the predictive power of generative probabilistic models while preserving their explanatory benefit. Our method exploits Markov models to produce a feature vector that records micro-similarities between the underlying probability distributions of a given sequence and their counterparts in reference models. Compared to ordinary Markov chain inference, we show that our method improves overall accuracy by 10% under 10-fold cross-validation on a dataset consisting of 10 subcellular locations. The source code is publicly available on https://github.com/aametwally/MC MicroSimilarities.