Since things are still chugging slowly on the servers, started looking at ideas on how to make everything faster. After all, there’s more than a couple CPUs sitting around twiddling their fingers – I ought to think of ways to have them all play. That and making the solution more scalable – too many [...]
Archive for February, 2008
Moar Speed
Posted in MeSH, PubMed on February 20, 2008 | Leave a Comment »
More ball drawing (hypergeometric distribution-related)
Posted in Uncategorized on February 8, 2008 | Leave a Comment »
Thinking a bit about rearranging the hypergeometric distribution also yields another way of getting a p-value combining the gene-mesh and disease-mesh links. Rather than computing the p-values separately, we can instead ask whether the marked ball draw rate in the gene is equal to higher than the rate we see for the disease. Is the [...]
Nailing down the profile comparison
Posted in Uncategorized on February 7, 2008 | Leave a Comment »
Okay, went to thinking about combining the p-values last night, and hashed out a prototype – or rather, rederived the equations I was hoping to use. And starting to wonder if there are other ways of doing this…maybe a bit too convenient
First, we do a term-term combination of the p-values. If we multiply them, it’s [...]
Drawing balls out of bags
Posted in Uncategorized on February 6, 2008 | Leave a Comment »
Thinking in terms of drawing coloured marbles from bags, the standby for the hypergeometric distribution, and how to extend this to the more ephemeral gene profiles vs disease profiles.
The gene profile tells us, for each term, how unlikely it was to find X number of articles annotated with the term given that you looked at [...]
Co-occurrence numbers
Posted in MeSH, PubMed on February 1, 2008 | Leave a Comment »
I’ll probably have to re-run the MeSH co-occurrence numbers, due to errors (blech!) – looks like single quotes are no good, I’ll have to go to double quotes. Actually, I can probably resubset it so that I do disease MeSH-MeSH co-occurrence, since this is to compute disease profiles. That should speed things up dramatically (by [...]
Presentation Update Ideas
Posted in presentation on February 1, 2008 | Leave a Comment »
Working on making my work more accessible for the “first-off” audience. One great idea was to use examples, and show screenshots/logos to reinforce ideas. The idea that pictures > words. I should also see if I can get a picture (or else draw) the MeSH hierarchy (or part of it)
I should also update my motivation [...]
