greenelab / greenelab/netscape

Explore per-algorithm data transformation

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Description

See `1.compress_given_z.py`. Right now, gene expression data is loaded and preprocessed once, then multiple algorithms can be run on the preprocessed data.

With new algorithms being added this isn't always ideal: for example, NMF only works on data with positive values (so z-score preprocessing won't work), but PLIER only works on data with no zero values (so zero-one rescaling won't work)

It would be good to find a performant way to use different preprocessing approaches based on which compression algorithm is being run.

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Research direction

Start with 1.compress_given_z.py and trace where gene expression data is loaded, preprocessed, and passed to each compression algorithm. Compare the preprocessing constraints described for NMF and PLIER, then define a performant per-algorithm transformation flow; done means each algorithm receives compatible data without unnecessary preprocessing work.

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Assessment

Tech stack
python
Domain
data
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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