I found an interesting paper that claims to improve predictive models on
genomes by exploiting the fact that genes tend to clump together on a
chromosome ("linkage disequilibrium").
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0093379#s2
In their data, they order the genes (technically single-nucleotide
polymorphisms, or "SNPs") according to their physical location on a
chromosome and organize these features into disjoint "blocks" of contiguous
SNPs. They then modify the Random Forest to select only from the SNPs in a
randomly selected "block" at each node, instead of the normal RF which
picks randomly from all the features at each node.
Anyway, I was wondering how to adapt the scikit RF algorithm to do
something like this. I'm working with some plant biologists who would find
this useful. (Also, I'm not a biologist, so please feel free to correct me
if I got anything wrong.)
Thanks
DG
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