Papers

Goodness of Fit for Bayesian Generative Models with Applications in Population Genetics

GL Mailloux, P Bastide, JM Marin, A Estoup - arXiv preprint arXiv …, 2025 - arxiv.org
Computer Science paper stat.ME Suggest

… fields, inferences about models with intractable likelihoods rely on simulation-based methods, such as Approximate Bayesian Computation and SimulationBased Inference…

Link to paper

BibTeX

@article{2501.17107v1,
Author        = {Guillaume Le Mailloux and Paul Bastide and Jean-Michel Marin and Arnaud Estoup},
Title         = {Goodness of Fit for Bayesian Generative Models with Applications in
  Population Genetics},
Eprint        = {2501.17107v1},
ArchivePrefix = {arXiv},
PrimaryClass  = {stat.ME},
Abstract      = {In population genetics and other application fields, models with intractable
likelihood are common. Approximate Bayesian Computation (ABC) or more generally
Simulation-Based Inference (SBI) methods work by simulating instrumental data
sets from the models under study and comparing them with the observed data set,
using advanced machine learning tools for tasks such as model selection and
parameter inference. The present work focuses on model criticism, and more
specifically on Goodness of fit (GoF) tests, for intractable likelihood models.
We introduce two new GoF tests: the pre-inference \gof tests whether the
observed dataset is distributed from the prior predictive distribution, while
the post-inference GoF tests whether there is a parameter value such that the
observed dataset is distributed from the likelihood with that value. The
pre-inference test can be used to prune a large set of models using a limited
amount of simulations, while the post-inference test is used to assess the fit
of a selected model. Both tests are based on the Local Outlier Factor (LOF,
Breunig et al., 2000). This indicator was initially defined for outlier and
novelty detection. It is able to quantify local density deviations, capturing
subtleties that a more traditional k-NN-based approach may miss. We evaluated
the performance of our two GoF tests on simulated datasets from three different
model settings of varying complexity. We then illustrate the utility of these
approaches on a dataset of single nucleotide polymorphism (SNP) markers for the
evaluation of complex evolutionary scenarios of modern human populations. Our
dual-test GoF approach highlights the flexibility of our method: the
pre-inference \gof test provides insight into model validity from a Bayesian
perspective, while the post-inference test provides a more general and
traditional view of assessing goodness of fit},
Year          = {2025},
Month         = {Jan},
Url           = {http://arxiv.org/abs/2501.17107v1},
File          = {2501.17107v1.pdf}
}

Share