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Bayesian Research Kitchen

Well-known shortcomings, advantages and computational challenges in Bayesian modelling: a few case stories

author: Ole Winther, Technical University of Denmark

Description

Bayesian inference can be used to judge the data fit quantitatively through the marginal likelihood. In many practical cases only one model is considered and parameter averaging is simply used to avoid overfitting. I show such an example for a large data set of genomic sequence tags where we want to predict how many new unique tags we will find if we perform new sequencing. The two parameter Yor-Pitman process is used and the results illustrate a few well-known facts: parameter averaging can be crucial and large data sets will expose the inadequacy of the model as seen by unrealistically narrow error-bars on (cross-validated) predictions. This indicates that we should come up with better models and being able to calculate the marginal likelihood for these models to perform model selection. In the second part of the talk I will discuss some of the computational challenges of calculating marginal likelihoods. Gaussian process classification is used as an example to illustrate that this is hard even for a uni-modal posterior.

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Slides
0:00 Well-known shortcomings, advantages and computational challenges in Bayesian modelling: a few case stories
0:24 Overview
3:05 How many species?
3:28 DNA sequence tags - CAGE
6:50 Look at the data - cerebellum
8:08 Look at the data - embryo
8:14 Chinese restaurant process - Yor-Pitman sampling formula
11:38 Inference and prediction
11:43 Chinese restaurant process - Yor-Pitman sampling formula
11:59 Inference and prediction
13:52 Averaging versus max. likelihood
15:12 Chinese restaurant process - Yor-Pitman sampling formula
15:42 Averaging versus max. likelihood
16:18 Notice anything funny?
19:25 Notice anything funny? Example 2
19:30 (Well-known) take home messages
21:22 Notice anything funny? Example 2
21:49 (Well-known) take home messages
28:50 Calculating the marginal likelihood
31:19 Motivation: validating EP corrections
34:04 Marginal likelihood from importance sampling
35:11 Marginal likelihood from thermodynamic integration
38:30 The trouble with Gibbs sampling
38:32 Marginal likelihood from thermodynamic integration
38:45 The trouble with Gibbs sampling
38:59 Marginal likelihood from thermodynamic integration
40:13 The trouble with Gibbs sampling
41:08 A trivial cure for N(f |0, C)
42:07 Gaussian process classification (GPC)
43:58 MCMC for GPC - related work
45:27 Gibbs sampling - pos/neg covariance
46:20 Efficient Gibbs sampling I
47:16 Determine limits of conditionals
48:36 Gibbs sampling positive covariance
49:03 Gibbs sampling negative covariance
49:22 Kuss+Rasmussen set-up
50:31 Summary
51:56 - Questions

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