[Biojava-dev] bits of information

[Lachlan Coin]

Hi,

I guess it all depends on your intuition about what information actually
means, but sticking to standard definitions, the low bits of information
reflects the fact that there is not much  uncertainty in this
distribution.  If the distribution was 100% A, then  there
would be no  uncertainty, and bits of information should return 0.  On the other
hand, information (or uncertainty) is maximised with 25% A,C,G,T.

Lachlan


On Sun, 1 Jun 2003, Schreiber, Mark wrote:

> Hi -
>
> The bitsOfInformation() method from DistributionTools seems to be returning only the average weighted entropy not the actual information.
>
> Eg for a distribution made thus:
>
>       //set the weight of a to 0.97
>       dist.setWeight(DNATools.a(), 0.97);
>       //set the others to 0.01
>       dist.setWeight(DNATools.c(), 0.01);
>       dist.setWeight(DNATools.g(), 0.01);
>       dist.setWeight(DNATools.t(), 0.01);
>
> The bits of information is calculated to be: 0.24194073285321088 bits
>
> This strikes me as a bit low (excuse the pun). Possibly there should be a method called totalEntropy and bits of information should return log2(alpha size) - totalEntropy.
>
> - Mark
>
>
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-------------------------------------------------------------
Lachlan Coin
Wellcome Trust Sanger Institute		Magdalene College
Cambridge  CB10 1SA			Cambridge CB30AG
Ph: +44 1223 494 820
Fax: +44 1223 494 919
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