Stacked penalized logistic regression for selecting views in multi-view learning

In biomedical research, many different types of patient data can be collected, such as various types of omics data and medical imaging modalities. Applying multi-view learning to these different sources of information can increase the accuracy of medical classification models compared with single-view procedures. However, collecting biomedical data can be expensive and/or burdening for patients, so that it is important to reduce the amount of required data collection. It is therefore necessary to develop multi-view learning methods which can accurately identify those views that are most important for prediction. In recent years, several biomedical studies have used an approach known as multi-view stacking (MVS), where a model is trained on each view separately and the resulting predictions are combined through stacking. In these studies, MVS has been shown to increase classification accuracy. However, the MVS framework can also be used for selecting a subset of important views. To study the view selection potential of MVS, we develop a special case called stacked penalized logistic regression (StaPLR). Compared with existing view-selection methods, StaPLR can make use of faster optimization algorithms and is easily parallelized. We show that nonnegativity constraints on the parameters of the function which combines the views play an important role in preventing unimportant views from entering the model. We investigate the performance of StaPLR through simulations, and consider two real data examples. We compare the performance of StaPLR with an existing view selection method called the group lasso and observe that, in terms of view selection, StaPLR is often more conservative and has a consistently lower false positive rate.