Sunday, 29 August 2010

ALIFE-XII Proceedings

Are available as a 95MB pdf file. Sample chapters and the Table of Contents are also available.

Our own work, Using Meta-Genetic Algorithms to tune parameters of Genetic Algorithms to fi nd lowest energy Molecular Conformers by Brain and Addicoat Proc. of the Alife XII Conference 2010 pp 378-385 is available as an 11 Mb pdf.
Determining the electronic structure of long chain molecules is essential to the understanding of many biological processes, notably those involving molecular receptors in cells. Finding minimum energy conformers and thus electronic structure of long-chain molecules by exhaustive search quickly becomes infeasible as the chain length increases. Typically, resources required are proportional to the number of possible conformers (shapes), which scales as O(3^L) where L is the length. An optimized genetic algorithm that can determine the minimum energy conformer of an arbitrary long-chain molecule in a feasible time is described, using the tool, PyEvolve. The method is to first solve a generic problem for a long chain by exhaustive search, then by using the pre-determined results in a look-up table, to make use of a Meta-GA to optimize parameters of a simple GA through an evolutionary process to solve that same problem. By comparing the results using the tuned parameters obtained by this method with the results from exhaustive search on several molecules of comparable chain length we have obtained quantitative measurements of an increase in speed by a factor of three over standard parameter settings, and a factor of ten over exhaustive search.
It's not written for a general audience, but parts may not be too heavy going for some of my readers.


athel said...

Amazing. I first learned of the existence of your blog today (from your posts at Jack of Kent), and on visiting it for the first time I see that we both had papers at ALIFE XII. I didn't go myself, but my Chilean colleagues did.

Zimbel said...

Thank you. I've been curious about this work for a while, and this paper has answered my questions.

Zoe Brain said...

Hi Athel - what was your paper?

Maybe I should have let more people there know about my unusual biology - but I try not to let it dominate my life.

Also, there are limits on acceptance, even amongst the most highly educated. I try not to test them.

One day, there will be no difference between the way IS and TS people are treated regardless of whether their medical history is known or not. One day, the whole concept of "Stealth" will be obsolete.

That day is not yet upon us.

athel said...

Hi Athel - what was your paper?

pp. 94-100: "(M,R) systems and RAF sets: common ideas, tools and projections". Quite a lot different from yours, but then I'm not a rocket scientist.

Maybe I should have let more people there know about my unusual biology - but I try not to let it dominate my life.

You have the same right as anyone else to keep quiet about things that are no one else's business. However, I've been educated quite a lot by things you say in your blog, and I'm glad to have read it. I don't think I've knowingly ever met a transgendered person, and I've only once knowingly seen one (other than in magazines, television, etc.)