I'm facing a parameter selection problem, which I would like to solve using Genetic Algorithm (GA). I'm supposed to select not more than 4 parameters out of 3000 possible ones. Using the binary chromosome representation seems like a natural choice. The evaluation function punishes too many "selected" attributes and if the number of attributes is acceptable, it then evaluates the selection.

The problem is that in these sparse conditions the GA can hardly improve the population. Neither the average fitness cost, nor the fitness of the "worst" individual improves over the generations. All I see is slight (even tiny) improvement in the score of the best individual, which, I suppose, is a result of random sampling.

Encoding the problem using indices of the parameters doesn't work either. This is most probably, due to the fact that the chromosomes are directional, while the selection problem isn't (i.e. chromosomes [1, 2, 3, 4]; [4, 3, 2, 1]; [3, 2, 4, 1] etc. are identical)

What problem representation would you suggest?

P.S If this matters, I use [PyEvolve](http://pyevolve.sourceforge.net/).