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hoffmangroup / segway

Application for semi-automated genomic annotation.
http://segway.hoffmanlab.org/
GNU General Public License v2.0
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New verb for Segway to test likelihood #98

Open EricR86 opened 7 years ago

EricR86 commented 7 years ago

Original report (BitBucket issue) by Rachel Chan (Bitbucket: rcwchan).

A new verb (ie, 'validate') could be added such that Segway tests likelihood on --include-coords; that is, run gmtKJTwith probE on the specified region(s).

EricR86 commented 7 years ago

Original comment by Michael Hoffman (Bitbucket: hoffman, GitHub: michaelmhoffman).

Probably should be called likelihood.

EricR86 commented 7 years ago

Original comment by Rachel Chan (Bitbucket: rcwchan).

Should minibatch automatically test likelihood on a validation set? If yes, should the region be automatically inferred or should it be required to be specified using something such as --validation-coords?

If automatically inferred, what size should the validation set be? I know we previously said '10x the training set', but what if the minibatch fraction specified is extremely large (ie, 0.10 or greater)?

EricR86 commented 7 years ago

Original comment by Michael Hoffman (Bitbucket: hoffman, GitHub: michaelmhoffman).

How validation works for minibatch is a separate issue than segway likelihood which will essentially be used for test. Please open another enhancement request or discuss on segway-internal.