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You're reading from  Bayesian Analysis with Python - Third Edition

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Published inJan 2024
Reading LevelExpert
PublisherPackt
ISBN-139781805127161
Edition3rd Edition
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Osvaldo Martin
Osvaldo Martin
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Osvaldo Martin

Osvaldo Martin is a researcher at CONICET, in Argentina. He has experience using Markov Chain Monte Carlo methods to simulate molecules and perform Bayesian inference. He loves to use Python to solve data analysis problems. He is especially motivated by the development and implementation of software tools for Bayesian statistics and probabilistic modeling. He is an open-source developer, and he contributes to Python libraries like PyMC, ArviZ and Bambi among others. He is interested in all aspects of the Bayesian workflow, including numerical methods for inference, diagnosis of sampling, evaluation and criticism of models, comparison of models and presentation of results.
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10.7 Convergence

Theoretically, MCMC methods are guaranteed to converge once we take infinite samples. In practice, we need to check that we have reasonable finite samples. Usually, we say the sampler has converged once we have collected evidence showing that samples are stable in some sense. A simple test to do is to run the same MCMC simulation multiple times and check whether we get the same result every time. This is the reason why PyMC runs more by default than on chain. For modern computers, this is virtually free as we have multiple cores. Also, they do not create any waste, as we can combine samples from different chains to compute summaries, plots, etc.

There are many ways to check that different chains are practically equivalent, both visually and with formal tests. We are not going to get too technical here; we are just going to show a few examples and hope they are enough for you to develop an intuition for interpreting diagnostics.

10.7.1 Trace plot

One way to check...

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Bayesian Analysis with Python - Third Edition
Published in: Jan 2024Publisher: PacktISBN-13: 9781805127161

Author (1)

author image
Osvaldo Martin

Osvaldo Martin is a researcher at CONICET, in Argentina. He has experience using Markov Chain Monte Carlo methods to simulate molecules and perform Bayesian inference. He loves to use Python to solve data analysis problems. He is especially motivated by the development and implementation of software tools for Bayesian statistics and probabilistic modeling. He is an open-source developer, and he contributes to Python libraries like PyMC, ArviZ and Bambi among others. He is interested in all aspects of the Bayesian workflow, including numerical methods for inference, diagnosis of sampling, evaluation and criticism of models, comparison of models and presentation of results.
Read more about Osvaldo Martin