Source Code or pseudo code for MED

[Craig Mclean]

Good Morning,

I really admire the algorithm you developed with the MED paper. Is the source code available anywhere? I'm still a bit unclear how the selection of high entropy features takes place during box one of the flow diagram. Also, is pseudo code available for this algorithm? 

Thank you,

Craig McLean 

[A. Murat Eren]

Thank you for the e-mail, Craig.

The source code is available here:

https://github.com/merenlab/oligotyping

The loop in which high-entropy positions are selected every iteration and used to decompose nodes in the topology is described here (which itself is like a pseudo code):

https://github.com/merenlab/oligotyping/blob/master/Oligotyping/lib/decomposer.py#L391

While reading it you will probably jump from here to here and come back to see here how is the `node.discriminants` is determined and used later to decompose data.

I hope the comments in the code also help.

Best wishes,

--

A. Murat Eren (Meren)
http://merenlab.org :: twitter :: gpg

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[Craig Mclean]

Meren,

Thanks for getting back to me so quickly. I really appreciate you passing on this info to me. 

Craig