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findThreshold is slow

Issue #75 resolved
Jason Vander Heiden created an issue

A user reports that findThreshold is very slow (hours). Can we improve this?

Comments (6)

  2. nima nouri

    We are working on a new methodology to resolve this issue. Very close to the end, but needs more investigations...

  3. Steven Kleinstein

    @namita1025, can you update your threshold method with a parameter on # sequences to downsample the data. The default value should be something reasonable so that the method runs in reasonable time.

  4. Namita Gupta

    This parameter exists already but I didn't want to make a default value to subsample in case people didn't notice the parameter.

  5. Namita Gupta

    Documentation notes that subsampling to 15000 is robust, but that still takes time. I haven't tested subsampling further down.

  6. Jason Vander Heiden reporter

    Doesn't seem to be a fix for the density fit method, but the new method has been integrated and it's faster and set default.

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Type
enhancement
Priority
major
Status
resolved
Milestone
–
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0
Watchers
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