A consistency-based feature selection method allied with linear SVMs for HIV-1 protease cleavage site prediction.

BACKGROUND: Predicting type-1 Human Immunodeficiency Virus (HIV-1) protease cleavage site in protein molecules and determining its specificity is an important task which has attracted considerable attention in the research community. Achievements in this area are expected to result in effective drug design (especially for HIV-1 protease inhibitors) against this life-threatening virus. However, some drawbacks (like the shortage of the available training data and the high dimensionality of the feature space) turn this task into a difficult classification problem. Thus, various machine learning techniques, and specifically several classification methods have been proposed in order to increase the accuracy of the classification model. In addition, for several classification problems, which are characterized by having few samples and many features, selecting the most relevant features is a major factor for increasing classification accuracy. RESULTS: We propose for HIV-1 data a consistency-based feature selection approach in conjunction with recursive feature elimination of support vector machines (SVMs). We used various classifiers for evaluating the results obtained from the feature selection process. We further demonstrated the effectiveness of our proposed method by comparing it with a state-of-the-art feature selection method applied on HIV-1 data, and we evaluated the reported results based on attributes which have been selected from different combinations. CONCLUSION: Applying feature selection on training data before realizing the classification task seems to be a reasonable data-mining process when working with types of data similar to HIV-1. On HIV-1 data, some feature selection or extraction operations in conjunction with different classifiers have been tested and noteworthy outcomes have been reported. These facts motivate for the work presented in this paper. SOFTWARE AVAILABILITY: The software is available at http://ozyer.etu.edu.tr/c-fs-svm.rar. The software can be downloaded at esnag.etu.edu.tr/software/hiv_cleavage_site_prediction.rar; you will find a readme file which explains how to set the software in order to work.

Intracolonic multiple pebbles in young adults: radiographic imaging and conventional approach to a case.

Most of the foreign bodies detected in adult gastrointestinal systems are accidentally swallowed pins. In this study, we presented a case with intracolonic multiple pebbles. A 20-year-old man was admitted to emergency surgery policlinic for abdominal pain for 2 d without any alleviation or aggravation. His upright plain abdominal radiographic imaging revealed about 30-40 overt dense opacities in lumen of colonic segments, with oval and well shaped contours, each approximately 1 cm multiply 1 cm in size. The multiplanar reconstructions and three-dimensional images combined with sectional screening showed that all pebbles had passed completely into the colon and no foreign bodies had remained in the ileal segments. On psychiatric assessment, he was found to have immature personality features, difficulty in overcoming stressors and adaptation disorder. He recovered by conservative management and radiographic monitoring applied during his follow-up. Thus, it can be concluded that, in differential diagnosis of abdominal pain in adult ages, though less frequently seen than in children, gastrointestinal system foreign bodies should always be kept in mind and it should be considered that ingestion of pebbles may be one of the factors contributing to abdominal pain particularly in young adults with psychiatric problems. In such cases suspected of having foreign bodies which cannot be detected by plain films, abdominal tomography can be an alternative for diagnostic imaging.