A modified autoencoder approach for feature selection

As the technology improves, data sizes have become huge. This also brought difficulties in extraction of meaningful information. As a result, new data analysis methods have emerged. Since data collection is everywhere in our daily life, data includes many redundant and unnecessary records and features. To identify useful part of data, feature selection algorithms have been used for a long time. However, those algorithms should be improved to deal with large scale data. In this thesis, we developed a new autoencoder based feature selection algorithm. Unlike traditional use of autoencoder, in this study, trained weight values are utilized instead of transformed data. The main idea behind the method is if the average weight of an input is high, it should be a useful feature. This simple but effective method was tested on 5 different datasets. 4 of them are standard datasets from Kaggle and UCI repositories. One of them is drug-target prediction dataset which is very difficult to classify due to imbalance nature of the data. While proposed method provided good results on standard datasets, not only proposed method but also all other tested methods provided very low results on drug-target interaction dataset due to the imbalanced nature of the dataset. Key Words: Machine learning, Deep learning, feature selection, drug-target interaction, autoencoders