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Osvaldo A. Martin

Publications and source records attributed to Osvaldo A. Martin.

4 recordsLinked to original sources

Recommendations for visual predictive checks in Bayesian workflow

A key step in the Bayesian workflow for model building is the graphical assessment of model predictions, whether these are drawn from the prior or posterior predictive distribution. The goal of these assessments is to identify whether the model is a reasonable (and ideally accurate) representation of the domain knowledge and/or observed data. There are many commonly used visual predictive checks which can be misleading if their implicit assumptions do not match the reality. Thus, there is a need for more guidance for selecting, interpreting, and diagnosing appropriate visualizations. As a visual predictive check itself can be viewed as a model fit to data, assessing when this model fails to represent the data is important for drawing well-informed conclusions. We present recommendations and diagnostic tools to mitigate ad-hoc decision-making in visual predictive checks. These contributions aim to improve the robustness and interpretability of Bayesian model criticism practices. We offer recommendations for appropriate visual predictive checks for observations that are: continuous, discrete, or a mixture of the two. We also discuss diagnostics to aid in the selection of visual methods. Specifically, in the detection of an incorrect assumption of continuously-distributed data: identifying when data is likely to be discrete or contain discrete components, detecting and estimating possible bounds in data, and a diagnostic of the goodness-of-fit to data for density plots made through kernel density estimates.

stat.ME↗

Prior knowledge elicitation: The past, present, and future

Specification of the prior distribution for a Bayesian model is a central part of the Bayesian workflow for data analysis, but it is often difficult even for statistical experts. In principle, prior elicitation transforms domain knowledge of various kinds into well-defined prior distributions, and offers a solution to the prior specification problem. In practice, however, we are still fairly far from having usable prior elicitation tools that could significantly influence the way we build probabilistic models in academia and industry. We lack elicitation methods that integrate well into the Bayesian workflow and perform elicitation efficiently in terms of costs of time and effort. We even lack a comprehensive theoretical framework for understanding different facets of the prior elicitation problem. Why are we not widely using prior elicitation? We analyse the state of the art by identifying a range of key aspects of prior knowledge elicitation, from properties of the modelling task and the nature of the priors to the form of interaction with the expert. The existing prior elicitation literature is reviewed and categorized in these terms. This allows recognizing under-studied directions in prior elicitation research, finally leading to a proposal of several new avenues to improve prior elicitation methodology.

stat.ME↗

Bambi: A simple interface for fitting Bayesian linear models in Python

The popularity of Bayesian statistical methods has increased dramatically in recent years across many research areas and industrial applications. This is the result of a variety of methodological advances with faster and cheaper hardware as well as the development of new software tools. Here we introduce an open source Python package named Bambi (BAyesian Model Building Interface) that is built on top of the PyMC probabilistic programming framework and the ArviZ package for exploratory analysis of Bayesian models. Bambi makes it easy to specify complex generalized linear hierarchical models using a formula notation similar to those found in R. We demonstrate Bambi's versatility and ease of use with a few examples spanning a range of common statistical models including multiple regression, logistic regression, and mixed-effects modeling with crossed group specific effects. Additionally we discuss how automatic priors are constructed. Finally, we conclude with a discussion of our plans for the future development of Bambi.

stat.CO↗

The Marginal Stability of Proteins: How Jiggling and Wiggling of Atoms are Connected to Neutral Evolution

Here we propose that the upper bound marginal stability of proteins (7.4 kcal/mol) is a universal property that includes macro-molecular complexes and is not affected by molecular changes such as mutations and Post-Translational Modifications. Its existence is, essentially, a consequence of the Anfinsen thermodynamic hypothesis rather than a result of an evolutive process. This result enables us to conjecture that neutral evolution should also be, with respect to protein stability, a universal phenomenon.

q-bio.BM↗