Well-known shortcomings, advantages and computational challenges in Bayesian modelling: a few case stories
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.
| 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 |
Lecture rating
| People found this lecture: | ||
| Worth seeing | ||
| because it is: | ||
| Valuable and informative | ||
| Well presented | ||
| Easily understandable | ||
| Acceptably recorded | ||
| You need to login to cast your vote. | ||
Report a problem or upload files
If you have found a problem with this lecture or would like to send us extra material, articles, exercises, etc., please use our ticket system to describe your request and upload the data.Enter your e-mail into the 'Cc' field, and we will keep you updated with your request's status.
Related content
Link this page
Would you like to put a link to this lecture on your homepage?Go ahead! Copy the HTML snippet !





