Thinking About Bioinformatics

Yesterday I talked about applications of potential information to experiment planning, using the example of a robot seeking to discover the principles of genetics from the initial observation of a “mutant” pea plant with white flowers. You can listen to the audio (right click on the audio link, and Save Link As, then listen to the downloaded file using QuickTime player or Real player). I also captured most of the material I wrote on the whiteboard.  Some relevant background material (and detailed exposition of the RoboMendel example) is also available.

Well, I failed to record my seminar audio, but here are some relevant notes for material discussed in the third seminar. This time we discussed the application of information metrics to experiment planning, rather than just model selection. One metric that I emphasized this time is the notion of potential information, which provides a signal for whether the current model needs to be expanded because its fit to the observations is inadequate. The attached material discusses some concrete examples of potential information, for example, for experiment planning.

I gave a talk today on my lab’s work on HIV drug resistance evolution and conditional selection pressure “networks”. The slides and audio are available here (to download the audio right-click the link and select Save Link As…). To listen to the audio you can use the QuickTime player or Real player. For our publications on this topic, see our publications page.

Here are my slides for my second talk at IMA on Feb. 14. I tried to introduce some problems with typical information metrics as they apply to statistical inference problems. Then I describe empirical information, my preferred information metric for statistical inference. The slides are available as a PDF, and the audio of the talk is also available — you can use either RealPlayer or the Quicktime player to listen to this. To download the audio, right-click on this link and choose Save Link As…

I’ve also posted some background material cut from different chapters of my draft textbook as a PDF.

Here are a couple of items relevant to my Feb. 7 intro session at IMA:

• Chapter 1 draft introduction to probabilistic inference.
• Paper on identification of SNPs from EST chromatogram data.