MotivationPrecision medicine requires the ability to predict the efficacies of different treatments for a given individual using high-dimensional genomic measurements. However, identifying predictive features remains a challenge when the sample size is small. Incorporating expert knowledge offers a promising approach to improve predictions, but collecting such knowledge is laborious if the number of candidate features is very large.ResultsWe introduce a probabilistic framework to incorporate expert feedback about the impact of genomic measurements on the outcome of interest and present a novel approach to collect the feedback efficiently, based on Bayesian experimental design. The new approach outperformed other recent alternatives in two medical applications: prediction of metabolic traits and prediction of sensitivity of cancer cells to different drugs, both using genomic features as predictors. Furthermore, the intelligent approach to collect feedback reduced the workload of the expert to approximately 11%, compared to a baseline approach.Availability and implementationSource code implementing the introduced computational methods is freely available at https://github.com/AaltoPML/knowledge-elicitation-for-precision-medicine.Supplementary information Supplementary data are available at Bioinformatics online.

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Least squares twin support vector machine (LSTSVM) is a relatively new version of support vector machine (SVM) based on non-parallel twin hyperplanes. Although, LSTSVM is an extremely efficient and fast algorithm for binary classification, its parameters depend on the nature of the problem. Problem dependent parameters make the process of tuning the algorithm with best values for parameters very difficult, which affects the accuracy of the algorithm. Simulated annealing (SA) is a random search technique proposed to find the global minimum of a cost function. It works by emulating the process where a metal slowly cooled so that its structure finally "freezes". This freezing point happens at a minimum energy configuration. The goal of this paper is to improve the accuracy of the LSTSVM algorithm by hybridizing it with simulated annealing. Our research to date suggests that this improvement on the LSTSVM is made for the first time in this paper. Experimental results on several benchmark datasets demonstrate that the accuracy of the proposed algorithm is very promising when compared to other classification methods in the literature. In addition, computational time analysis of the algorithm showed the practicality of the proposed algorithm where the computational time of the algorithm falls between LSTSVM and SVM.

Regression under the "small n, large p" conditions, of small sample size n and large number of features p in the learning data set, is a recurring setting in which learning from data is difficult. With prior knowledge about relationships of the features, p can effectively be reduced, but explicating such prior knowledge is difficult for experts. In this paper we introduce a new method for eliciting expert prior knowledge about the similarity of the roles of features in the prediction task. The key idea is to use an interactive multidimensionalscaling (MDS) type scatterplot display of the features to elicit the similarity relationships, and then use the elicited relationships in the prior distribution of prediction parameters. Specifically, for learning to predict a target variable with Bayesian linear regression, the feature relationships are used to construct a Gaussian prior with a full covariance matrix for the regression coefficients. Evaluation of our method in experiments with simulated and real users on text data confirm that prior elicitation of feature similarities improves prediction accuracy. Furthermore, elicitation with an interactive scatterplot display outperforms straightforward elicitation where the users choose feature pairs from a feature list.