Variational Inference for Additive Main and Multiplicative Interaction Effects Models
This work addresses computational bottlenecks in plant breeding data analysis, offering a faster alternative to MCMC for incremental improvements in modeling GxE interactions.
The authors tackled the computational inefficiency of MCMC for high-dimensional genotype by environment interaction models in plant breeding by proposing a variational inference approach, which achieved on average two times faster inference while maintaining the same predictive performance.
In plant breeding the presence of a genotype by environment (GxE) interaction has a strong impact on cultivation decision making and the introduction of new crop cultivars. The combination of linear and bilinear terms has been shown to be very useful in modelling this type of data. A widely-used approach to identify GxE is the Additive Main Effects and Multiplicative Interaction Effects (AMMI) model. However, as data frequently can be high-dimensional, Markov chain Monte Carlo (MCMC) approaches can be computationally infeasible. In this article, we consider a variational inference approach for such a model. We derive variational approximations for estimating the parameters and we compare the approximations to MCMC using both simulated and real data. The new inferential framework we propose is on average two times faster whilst maintaining the same predictive performance as MCMC.