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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).


A theory of learning data statistics in diffusion models, from easy to hard

Bardone, Lorenzo, Merger, Claudia, Goldt, Sebastian

arXiv.org Machine Learning

While diffusion models have emerged as a powerful class of generative models, their learning dynamics remain poorly understood. We address this issue first by empirically showing that standard diffusion models trained on natural images exhibit a distributional simplicity bias, learning simple, pair-wise input statistics before specializing to higher-order correlations. We reproduce this behaviour in simple denoisers trained on a minimal data model, the mixed cumulant model, where we precisely control both pair-wise and higher-order correlations of the inputs. We identify a scalar invariant of the model that governs the sample complexity of learning pair-wise and higher-order correlations that we call the diffusion information exponent, in analogy to related invariants in different learning paradigms. Using this invariant, we prove that the denoiser learns simple, pair-wise statistics of the inputs at linear sample complexity, while more complex higher-order statistics, such as the fourth cumulant, require at least cubic sample complexity. We also prove that the sample complexity of learning the fourth cumulant is linear if pair-wise and higher-order statistics share a correlated latent structure. Our work describes a key mechanism for how diffusion models can learn distributions of increasing complexity.


A Locally Adaptive Normal Distribution

Georgios Arvanitidis, Lars K. Hansen, Søren Hauberg

Neural Information Processing Systems

The underlyingmetricis,however,non-parametric.Wedevelopamaximumlikelihood algorithm to infer the distribution parameters that relies on a combination of gradient descent and Monte Carlo integration. We further extend the LAND to mixture models, andprovidethecorresponding EMalgorithm.


8ccfb1140664a5fa63177fb6e07352f0-Supplemental.pdf

Neural Information Processing Systems

A.1 Notationandpreliminaries We consider the metric space(X,d( , )) where d : X X R+. We consider`( , ) to be the cross-entropyloss `log(M(x),y), ylogσ(M(x)) (1 y)logσ((1 M(x))) (whereσ(x) = 11+exp( x) isthe sigmoid function) orthe`2 loss.



SupplementaryMaterial MatrixCompletionwithHierarchical GraphSideInformation

Neural Information Processing Systems

This implies that M(δ) = T(δ), i.e., the constraint(13) made in T(δ) does not lose any generality in matrix representation. One technical distinction relative to the previous works [2,3] arises from the fact that in our setting, the hamming distances(dx1(`),dx2(`),dx3(`)) defined w.r.t. We focus on the family of rating matrices{Mhci: c T`}. First, we present the following lemma that guarantees the existence of two subsets of users with certainproperties. The proof of this case follows the same structure as that of the grouping-limited regime. It is shown that the groups within each cluster are recovered with a vanishing fraction of errors if Ig = ω(1/n).




1c364d98a5cdc426fd8c76fbb2c10e34-Supplemental-Conference.pdf

Neural Information Processing Systems

The way to instantiate BACON will be similar to MFN. The following Lemma will showthat Definition 1.2 can be extended toanalyzing functions from differentdomain. Let F = gL g1 γ, with gi being a multivariate polynomial. The inductive hypothesis is: fork 1, if zk[j] is linear sum ofB for all j, then zk+1[l]islinearsumsofB foralll. By definition ofz, we know thatzk+1 = gk(zk), where gk is a multivariate polynomial of finite degreed.


Improving multiple-try Metropolis with local balancing

Gagnon, Philippe, Maire, Florian, Zanella, Giacomo

arXiv.org Machine Learning

Multiple-try Metropolis (MTM) is a popular Markov chain Monte Carlo method with the appealing feature of being amenable to parallel computing. At each iteration, it samples several candidates for the next state of the Markov chain and randomly selects one of them based on a weight function. The canonical weight function is proportional to the target density. We show both theoretically and empirically that this weight function induces pathological behaviours in high dimensions, especially during the convergence phase. We propose to instead use weight functions akin to the locally-balanced proposal distributions of Zanella (2020), thus yielding MTM algorithms that do not exhibit those pathological behaviours. To theoretically analyse these algorithms, we study the high-dimensional performance of ideal schemes that can be thought of as MTM algorithms which sample an infinite number of candidates at each iteration, as well as the discrepancy between such schemes and the MTM algorithms which sample a finite number of candidates. Our analysis unveils a strong distinction between the convergence and stationary phases: in the former, local balancing is crucial and effective to achieve fast convergence, while in the latter, the canonical and novel weight functions yield similar performance. Numerical experiments include an application in precision medicine involving a computationally-expensive forward model, which makes the use of parallel computing within MTM iterations beneficial.