A Two-Graph Guided Multi-task Lasso Approach for eQTL Mapping

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Xiaohui Chen, Xinghua Shi, Xing Xu, Zhiyong Wang, Ryan Mills, Charles Lee, Jinbo Xu ;
Proceedings of the Fifteenth International Conference on Artificial Intelligence and Statistics, PMLR 22:208-217, 2012.

Abstract

Learning a small number of genetic variants associated with multiple complex genetic traits is of practical importance and remains challenging due to the high dimensional nature of data. In this paper, we proposed a two-graph guided multi-task Lasso to address this issue with an emphasis on estimating subnetwork-to-subnetwork associations in expression quantitative trait loci (eQTL) mapping. The proposed model can learn such subnetwork-to-subnetwork associations and therefore can be seen as a generalization of several state-of-the-art multi-task feature selection methods. Additionally, this model has a nice property of allowing flexible structured sparsity on both feature and label domains. Simulation study shows the improved performance of our model and a human eQTL data set is analyzed to further demonstrate the applications of the model.

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