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