Multi-task prediction models are widely being used to couple regressors or classification models by sharing information across related tasks. A common pitfall of these models is that they assume that the output tasks are independent conditioned on the inputs. Here, we propose a multi-task Gaussian process approach to model both the relatedness between regressors as well as the task correlations in the residuals, in order to more accurately identify true sharing between regressors. The resulting Gaussian model has a covariance term that is the sum of Kronecker products, for which efficient parameter inference and out of sample prediction are feasible. On both synthetic examples and applications to phenotype prediction in genetics, we find substantial benefits of modeling structured noise compared to established alternatives.
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