Stable Bagging Feature Selection on Medical Data

In the medical field, distinguishing genes that are relevant to a specific disease, let's say colon cancer, is crucial to finding a cure and understanding its causes and subsequent complications. Usually, medical datasets are comprised of immensely complex dimensions with considerably small sample size. Thus, for domain experts, such as biologists, the task of identifying these genes have become a very challenging one, to say the least. Feature selection is a technique that aims to select these genes, or features in machine learning field with respect to the disease. However, learning from a medical dataset to identify relevant features suffers from the curse-of-dimensionality. Due to a large number of features with a small sample size, the selection usually returns a different subset each time a new sample is introduced into the dataset. This selection instability is intrinsically related to data variance. We assume that reducing data variance improves selection stability. In this paper, we propose an ensemble approach based on the bagging technique to improve feature selection stability in medical datasets via data variance reduction. We conducted an experiment using four microarray datasets each of which suffers from high dimensionality and relatively small sample size. On each dataset, we applied five well-known feature selection algorithms to select varying number of features. The results of the selection stability and accuracy show the improvement in terms of both the stability and the accuracy with the bagging technique.