jaybee84 / ml-in-rd

Manuscript for perspective on machine learning in rare disease
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Putting it all together section #120

Closed jaclyn-taroni closed 3 years ago

jaclyn-taroni commented 3 years ago

Purpose

Addresses #111.

In an earlier pull request, I moved the coverage of DeepProfile and MultiPLIER into their own section (currently) titled "Multiple approaches are required." (Alternative title suggestions are most welcome!)

The goal of this section is to emphasize that you are most likely not going to employ one of the approaches we cover in isolation; you're going to need multiple techniques "woven together." A secondary goal of this section is to unify the regularization, other data and knowledge, and representation learning sections. Transfer learning is covered in the section immediately preceding this one and the main point of difference I'm trying to make is how putting some constraints on the representation the model learns can be helpful.

Directions for reviewers

I would like to probably take another pass through this before it goes in, but figured we could collect comments in parallel!

Which areas should receive a particularly close look?

Manuscript checklist

Unless otherwise noted above, this PR will be considered ready for review when all four items have been checked.

AppVeyorBot commented 3 years ago

AppVeyor build 1.0.249 for commit 0b590a39ef1cf53d5009e11bdd758e69322d185c is now complete.

Found 9 potential spelling error(s). Preview:content/01.synopsis.md:6:TODO content/02.intro.md:3:TODO content/03.heterogeneity.md:51:TODO content/05.prior-knowledge.md:14:TODO content/05.prior-knowledge.md:21:TODO content/05.prior-knowledge.md:35:TODO content/06.multiple-approaches-required.md:14:autoencoders content/06.multiple-approaches-required.md:14:TODO content/06.multiple-approaches-required.md:14:VAEs...
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AppVeyorBot commented 3 years ago

AppVeyor build 1.0.250 for commit 1b0fd354345bc76c256a837211f71ccdcae676ec is now complete.

Found 9 potential spelling error(s). Preview:content/01.synopsis.md:6:TODO content/02.intro.md:3:TODO content/03.heterogeneity.md:51:TODO content/05.prior-knowledge.md:14:TODO content/05.prior-knowledge.md:21:TODO content/05.prior-knowledge.md:35:TODO content/06.multiple-approaches-required.md:15:autoencoders content/06.multiple-approaches-required.md:15:TODO content/06.multiple-approaches-required.md:15:VAEs...
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allaway commented 3 years ago

"Multiple approaches are required." (Alternative title suggestions are most welcome!)

How about "Using composite approaches can be a powerful strategy"?

AppVeyorBot commented 3 years ago

AppVeyor build 1.0.251 for commit 6974cb3462d1bb46544b2fd969dce2c2b9569d98 is now complete.

Found 9 potential spelling error(s). Preview:content/01.synopsis.md:6:TODO content/02.intro.md:3:TODO content/03.heterogeneity.md:51:TODO content/05.prior-knowledge.md:14:TODO content/05.prior-knowledge.md:21:TODO content/05.prior-knowledge.md:35:TODO content/06.multiple-approaches-required.md:15:autoencoders content/06.multiple-approaches-required.md:15:TODO content/06.multiple-approaches-required.md:15:VAEs...
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AppVeyorBot commented 3 years ago

AppVeyor build 1.0.252 for commit 22084e518cd16872390fedab20ebfe9f6a00a904 is now complete.

Found 9 potential spelling error(s). Preview:content/01.synopsis.md:6:TODO content/02.intro.md:3:TODO content/03.heterogeneity.md:51:TODO content/05.prior-knowledge.md:14:TODO content/05.prior-knowledge.md:21:TODO content/05.prior-knowledge.md:35:TODO content/06.multiple-approaches-required.md:15:autoencoders content/06.multiple-approaches-required.md:15:TODO content/06.multiple-approaches-required.md:15:VAEs...
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AppVeyorBot commented 3 years ago

AppVeyor build 1.0.253 for commit f1c2504d7187a05157bedcaab51feb5b824f39c6 is now complete.

Found 2 potential spelling error(s). Preview:content/06.multiple-approaches-required.md:15:autoencoders content/06.multiple-approaches-required.md:15:VAEs...
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jaybee84 commented 3 years ago

@jaclyn-taroni: would you like to address #128 in this PR, or should I merge this in as-is before you start working on #128 in a new PR?

jaclyn-taroni commented 3 years ago

So long as merging this doesn't "undo" any edits that happened on the Google Doc, I say go for it and I'll open up a new one later.

jaybee84 commented 3 years ago

Sounds good. I will merge this in to reflect the "before google doc" version.. after that the google doc edits will be reflected in #129

AppVeyorBot commented 3 years ago

AppVeyor build 1.0.278 for commit a2788b2eb84bb184df00607f2b7f2a0d39590340 is now complete.

Found 2 potential spelling error(s). Preview:content/06.multiple-approaches-required.md:15:autoencoders content/06.multiple-approaches-required.md:15:VAEs...
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