Entries in "status reports"
February 15, 2007
Matlab code working
It took me longer than I had intended, partly because I was re-learning to use Matlab and partly because I've written something more general than I had originally set out to, but my attempt at replicating a GRN model from literature is up and running. I've written some code that makes it easy for me to convert a list of "Node A activates Node B and Node C inhibits it" type interactions into a fully-specified GRN, and I'm using that to try and replicate Li et al's yeast cell cycle network.
So far, the network I have isn't behaving the same as the one reported in their paper, but I haven't done anywhere near enough debugging yet. I'll be spending tomorrow doing just that, because the chances are the lack of correspondence between my results and theirs stems from a logic error in my code.
Oh, and it's been really nice interacting with Matlab again. I had forgotten quite how much I liked it as a development environment.
October 20, 2006
Timing problems
The trip to Bloomington was very fruitful in terms of getting to meet a few people I'd previously only heard from over email, going to interesting talks, and getting feedback from my advisor. Unfortunately, the most important single thing I found out represented a substantial setback, and this is why it's taken me a while to get around to blogging about where I'm at with research.
Continue reading "Timing problems"
August 10, 2006
What to try next with coevolution
I'm waiting for a lot of experiments to finish, but interim results from the coevolutionary runs continue to look as unimpressive as those I described at the end of my last post. I'll let the current crop run out for another day, but meanwhile I need to come up with some hypotheses about why these runs are doing so badly, and tests for those hypotheses. This can guide the experiments I set up tomorrow and leave running over the weekend. Ideas after the cut.
Continue reading "What to try next with coevolution"
July 17, 2006
Continuous-sensory experiments
As I set out almost a month ago, I'm now running experiments in which the agents receive sensory input on a continuous scale, and must respond appropriately to that in order to perform well. So far I've found one good agent among a general background of unsuccessful runs, but I'm still tinkering with parameters to try and make the process more reliable. Detailed method and a brief overview of results so far are behind the cut.