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A Bayesian Updating Framework for Long-term Multi-Environment Trial Data in Plant Breeding

Bark, Stephan, Malik, Waqas Ahmed, Prus, Maryna, Piepho, Hans-Peter, Schmid, Volker

arXiv.org Machine Learning

In variety testing, multi-environment trials (MET) are essential for evaluating the genotypic performance of crop plants. A persistent challenge in the statistical analysis of MET data is the estimation of variance components, which are often still inaccurately estimated or shrunk to exactly zero when using residual (restricted) maximum likelihood (REML) approaches. At the same time, institutions conducting MET typically possess extensive historical data that can, in principle, be leveraged to improve variance component estimation. However, these data are rarely incorporated sufficiently. The purpose of this paper is to address this gap by proposing a Bayesian framework that systematically integrates historical information to stabilize variance component estimation and better quantify uncertainty. Our Bayesian linear mixed model (BLMM) reformulation uses priors and Markov chain Monte Carlo (MCMC) methods to maintain the variance components as positive, yielding more realistic distributional estimates. Furthermore, our model incorporates historical prior information by managing MET data in successive historical data windows. Variance component prior and posterior distributions are shown to be conjugate and belong to the inverse gamma and inverse Wishart families. While Bayesian methodology is increasingly being used for analyzing MET data, to the best of our knowledge, this study comprises one of the first serious attempts to objectively inform priors in the context of MET data. This refers to the proposed Bayesian updating approach. To demonstrate the framework, we consider an application where posterior variance component samples are plugged into an A-optimality experimental design criterion to determine the average optimal allocations of trials to agro-ecological zones in a sub-divided target population of environments (TPE).


Exponential Family Discriminant Analysis: Generalizing LDA-Style Generative Classification to Non-Gaussian Models

Lakkapragada, Anish

arXiv.org Machine Learning

We introduce Exponential Family Discriminant Analysis (EFDA), a unified generative framework that extends classical Linear Discriminant Analysis (LDA) beyond the Gaussian setting to any member of the exponential family. Under the assumption that each class-conditional density belongs to a common exponential family, EFDA derives closed-form maximum-likelihood estimators for all natural parameters and yields a decision rule that is linear in the sufficient statistic, recovering LDA as a special case and capturing nonlinear decision boundaries in the original feature space. We prove that EFDA is asymptotically calibrated and statistically efficient under correct specification, and we generalise it to $K \geq 2$ classes and multivariate data. Through extensive simulation across five exponential-family distributions (Weibull, Gamma, Exponential, Poisson, Negative Binomial), EFDA matches the classification accuracy of LDA, QDA, and logistic regression while reducing Expected Calibration Error (ECE) by $2$-$6\times$, a gap that is structural: it persists for all $n$ and across all class-imbalance levels, because misspecified models remain asymptotically miscalibrated. We further prove and empirically confirm that EFDA's log-odds estimator approaches the Cramér-Rao bound under correct specification, and is the only estimator in our comparison whose mean squared error converges to zero. Complete derivations are provided for nine distributions. Finally, we formally verify all four theoretical propositions in Lean 4, using Aristotle (Harmonic) and OpenGauss (Math, Inc.) as proof generators, with all outputs independently machine-checked by AXLE (Axiom).








A Proofs of Linear Case Throughout the appendix, for ease of notation, we overload the definition of the function d

Neural Information Processing Systems

The proof of this lemma requires Lemma A.1, which characterizes the distribution of the residual By Pinsker's inequality, this implies d By Lemma A.1, we have E[ X ( null w w The proof is inspired by Theorem 11.2 in [20], with modifications to our setting. First, we construct a "ghost" dataset The most challenging aspect of the ReLU setting is that we do not have an expression for the TV suffered by the MLE, such as Lemma 4.2 in the linear case. The proof of this Lemma, as well as other Lemmas in this section, can be found in Appendix B.1. Using Lemma B.2 and Lemma B.3, we can form a uniform bound, such that all A straight forward combination of Lemma 4.3 and Lemma B.4 gives the following Theorem. Now we can apply Bernstein's inequality (Theorem 2.10 of [8]).