MOTIVATION: Epistasis or gene-gene interaction has gained increasing attention in studies of complex diseases. Its presence as an ubiquitous component of genetic architecture of common human diseases has been contemplated. However, the detection of gene-gene interaction is difficult due to combinatorial explosion. RESULTS: We present a novel feature selection method incorporating variable interaction. Three gene expression datasets are analyzed to illustrate our method, although it can also be applied to other types of high-dimensional data. The quality of variables selected is evaluated in two ways: first by classification error rates, then by functional relevance assessed using biological knowledge. We show that the classification error rates can be significantly reduced by considering interactions. Secondly, a sizable portion of genes identified by our method for breast cancer metastasis overlaps with those reported in gene-to-system breast cancer (G2SBC) database as disease associated and some of them have interesting biological implication. In summary, interaction-based methods may lead to substantial gain in biological insights as well as more accurate prediction.

Presently, inductive learning is still performed in a frustrating batch process. The user has little interaction with the system and no control over the final accuracy and training time. If the accuracy of the produced model is too low, all the computing resources are misspent. In this paper we propose a progressive modeling framework. In progressive modeling, the learning algorithm estimates online both the accuracy of the final model and remaining training time. If the estimated accuracy is far below expectation, the user can terminate training prior to completion without wasting further resources. If the user chooses to complete the learning process, progressive modeling will compute a model with expected accuracy in expected time. We describe one implementation of progressive modeling using ensemble of classifiers.