[BioPython] Bio.kNN documentation

[Bruce Southey]

On Tue, Oct 7, 2008 at 6:10 PM, Michiel de Hoon <mjldehoon at yahoo.com> wrote:
>> Bruce wrote:
>> > (I guess I am volunteering myself to provide some
>> material on
>> > machine learning with BioPython. So this is a start.)
>>
>> Michiel has suggested adding a whole chapter to the
>> tutorial about
>> supervised learning, presumably incorporating his logistic
>> regression
>> example as part of this.  Have a look at thread
>> "Bio.MarkovModel;
>> Bio.Popgen, Bio.PDB documentation" on the dev mailing
>> list.  I'm sure
>> you can contribute (even if just by proof reading).
>
> Some more documentation on machine learning would definitely be useful. Recently I started a chapter on supervised learning methods in the tutorial. Right now it only covers logistic regression, but it should also include Bio.MarkovModel, Bio.MaxEntropy, Bio.NaiveBayes, and Bio.kNN. If you are planning to write some documentation on any of these, please let us know so we can avoid duplicated efforts. The new tutorial is in CVS; I put a copy of the HTML output of the latest version at
> http://biopython.org/DIST/docs/tutorial/Tutorial.new.html.
>
> Thanks!
>
> --Michiel
>

Hi,
I have not given it too much thought at present but this reflects some
of the work I have been doing or involved with. I do not know enough
about Bio.MarkovModel, Bio.MaxEntropy and Bio.NaiveBayes to really
help. But I did think to start with trying to extend the supervised
learning material to be more general.  One aspect is to get provide
working code using different methodologies for different examples.

Regards
Bruce