Improving Span, or Span 2 #10
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Add external weights, ConstantRegressionEmissionScheme and ZeroPoissonMixture
Some problems with sampling
Add external weights, ConstantRegressionEmissionScheme and ZeroPoissonMixture
Some problems with sampling
…l fit time reduced twice
- Regenerated Span model for track view testing - Fixed "id" problems in SpanFitInformation - Fixed wrong FQNs in SpanFitInformationTest
olegs
approved these changes
Sep 27, 2019
| @@ -14,7 +14,7 @@ import org.jetbrains.bio.viktor._I | |||
| object MixtureInternals { | |||
| @JvmStatic | |||
| fun predict(logGammas: F64Array): IntArray { | |||
| return IntArray(logGammas.shape[0]) { logGammas.V[_I, it].argMax() } | |||
| return IntArray(logGammas.shape[1]) { logGammas.V[_I, it].argMax() } | |||
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Was this this a bug-fix, why dimension is changed here?
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It was, I even commented on it, and you asked me to provide a test. Since this is a really hard-to-miss bug (shape is usually something like 3 x 15_000_000), I'd say that the integration and sample-and-fit tests that we have cover this issue pretty well.
(That reminds me, though, that I've recently killed argMax in viktor. I have to either bring it back or work around this.)
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A companion PR for JetBrains-Research/epigenome#1436.
Introduces:
RegessionEmissonScheme,IntegerRegressionEmissionSchemeandPoissonRegressionEmissionScheme;2bitfiles for custom genome builds if they're in the same folder as thechrom.sizesfile.Also minor code style improvements.