Machine learning has been gaining traction in recent years to meet the demand for tools that can efficiently analyze and make sense of the ever-growing databases of biomedical data in health care systems around the world. However, effectively using machine learning methods requires considerable domain expertise, which can be a barrier of entry for bioinformaticians new to computational data science methods. Therefore, off-the-shelf tools that make machine learning more accessible can prove invaluable for bioinformaticians. To this end, we have developed an open source pipeline optimization tool (TPOT-MDR) that uses genetic programming to automatically design machine learning pipelines for bioinformatics studies. In TPOT-MDR, we implement Multifactor Dimensionality Reduction (MDR) as a feature construction method for modeling higher-order feature interactions, and combine it with a new expert knowledge-guided feature selector for large biomedical data sets. We demonstrate TPOT-MDR's capabilities using a combination of simulated and real world data sets from human genetics and find that TPOT-MDR significantly outperforms modern machine learning methods such as logistic regression and eXtreme Gradient Boosting (XGBoost). We further analyze the best pipeline discovered by TPOT-MDR for a real world problem and highlight TPOT-MDR's ability to produce a high-accuracy solution that is also easily interpretable.
@cite_32: Understanding disease-related metabolite interactions is a key issue in computational biology. We apply a modified Bayesian Optimization Algorithm to targeted metabolomics data from plasma samples of insulin-sensitive and -resistant subjects both suffering from non-alcoholic fatty liver disease. In addition to improving the classification accuracy by selecting relevant features, we extract the information that led to their selection and reconstruct networks from detected feature dependencies. We compare the influence of a variety of classifiers and different scoring metrics and examine whether the reconstructed networks represent physiological metabolite interconnections. We find that the presented method is capable of significantly improving the classification accuracy of otherwise hardly classifiable metabolomics data and that the detected metabolite dependencies can be mapped to physiological pathways, which in turn were affirmed by literature from the domain.
Narrowing the focus to automated machine learning in bioinformatics, the literature is far more sparse. One such example is @cite_32 , in which they analyze metabolomics data using a modified Bayesian optimization algorithm integrated with the classification algorithms provided in WEKA, a suite of machine learning software written in Java. The Bayesian optimization provided feature subset selection, which filtered irrelevant and redundant features from the datasets to achieve dimensionality reduction. These techniques lead to an improvement of classification accuracy.