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prototype selection benchmark #14

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sjanssen2 opened this issue May 12, 2017 · 4 comments
Closed

prototype selection benchmark #14

sjanssen2 opened this issue May 12, 2017 · 4 comments
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@sjanssen2
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are we ready for a 1 million genome tree?
Runtime, Memory?, Accuracy with #genomes and #selected genomes
@sjanssen2 sjanssen2 self-assigned this May 12, 2017
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sjanssen2 commented May 12, 2017 •
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Can we simulate distance matrices where we know the best prototypes?
Low noise background for total matrix + high noise for prototypes?!

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sjanssen2 commented May 12, 2017 •
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@wasade any idea if skbio distance matrix objects are able to load a 1m x 1m matrix into memory?

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@sjanssen2 If the prototypes mean genomes, I believe we can. Just do MinHash. But maybe you meant something else?

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I think this issue has been addressed. Benchmarking notebook is now in.

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