title: Protein subcellular localization in human and hamster cell lines: employing local ternary patterns of fluorescence microscopy images.
abstract: Discriminative feature extraction technique is always required for the development of accurate and efficient prediction systems for protein subcellular localization so that effective drugs can be developed. In this work, we showed that Local Ternary Patterns (LTPs) effectively exploit small variations in pixel intensities; present in fluorescence microscopy based protein images of human and hamster cell lines. Further, Synthetic Minority Oversampling Technique is applied to balance the feature space for the classification stage. We observed that LTPs coupled with data balancing technique could enable a classifier, in this case support vector machine, to yield good performance. The proposed ensemble based prediction system, using 10-fold cross-validation, has yielded better performance compared to existing techniques in predicting various subcellular compartments for both 2D HeLa and CHO datasets. The proposed predictor is available online at: http://111.68.99.218/Protein_SubLoc/, which is freely accessible to the public.
authors.affiliation: Department of Computer and Information Sciences, PIEAS, Islamabad, Pakistan.
authors.forename: Muhammad
authors.initials: M
authors.lastname: Tahir
authors.forename: Asifullah
authors.initials: A
authors.lastname: Khan
authors.forename: Hüseyin
authors.initials: H
authors.lastname: Kaya
mesh_terms: D000465:Algorithms; D000818:Animals; D019540:Area Under Curve; D001185:Artificial Intelligence; D016466:CHO Cells; D019295:Computational Biology; D003198:Computer Simulation; D006224:Cricetinae; D003412:Cricetulus; D006367:HeLa Cells; D006801:Humans; D008856:Microscopy, Fluorescence; D015233:Models, Statistical; D009369:Neoplasms / Q000378:metabolism; D025341:Principal Component Analysis; D011506:Proteins / Q000737:chemistry*; D012372:ROC Curve; D015203:Reproducibility of Results; D060388:Support Vector Machine
chemical_list: D011506:Proteins
keywords: SMOTE; Support vector machine; mRMR