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Open Access Research

Prediction of lung tumor types based on protein attributes by machine learning algorithms

Faezeh Hosseinzadeh1, Amir Hossein KayvanJoo2, Mansuor Ebrahimi2* and Bahram Goliaei1

Author Affiliations

1 Laboratory of biophysics and molecular biology, Institute of Biophysics and Biochemistry (IBB), University of Tehran, Tehran, Iran

2 Department of Biology at Basic science School & Bioinformatics Research Group, Green Research Center, University of Qom, Qom, Iran

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SpringerPlus 2013, 2:238  doi:10.1186/2193-1801-2-238

Published: 24 May 2013

Abstract

Early diagnosis of lung cancers and distinction between the tumor types (Small Cell Lung Cancer (SCLC) and Non-Small Cell Lung Cancer (NSCLC) are very important to increase the survival rate of patients. Herein, we propose a diagnostic system based on sequence-derived structural and physicochemical attributes of proteins that involved in both types of tumors via feature extraction, feature selection and prediction models. 1497 proteins attributes computed and important features selected by 12 attribute weighting models and finally machine learning models consist of seven SVM models, three ANN models and two NB models applied on original database and newly created ones from attribute weighting models; models accuracies calculated through 10-fold cross and wrapper validation (just for SVM algorithms). In line with our previous findings, dipeptide composition, autocorrelation and distribution descriptor were the most important protein features selected by bioinformatics tools. The algorithms performances in lung cancer tumor type prediction increased when they applied on datasets created by attribute weighting models rather than original dataset. Wrapper-Validation performed better than X-Validation; the best cancer type prediction resulted from SVM and SVM Linear models (82%). The best accuracy of ANN gained when Neural Net model applied on SVM dataset (88%). This is the first report suggesting that the combination of protein features and attribute weighting models with machine learning algorithms can be effectively used to predict the type of lung cancer tumors (SCLC and NSCLC).

Keywords:
Lung cancer; Prediction; Structural and physicochemical features; Attributes weighting; Support vector machine; Artificial neural network; Naïve bayes