[Discussion] Proposed restructuring

[jaclyn-taroni]

⚠️ This is ready to be looked at and discussed, but, if folks agree with the restructuring plan, it should not be merged until we have a plan for those next steps! ⚠️

Purpose

I thought I was going to quickly address the rewrite of the transfer learning and multi-task learning sections (#110) and then move onto the putting it all together section (#111), but as I was editing 05.prior-knowledge.md the representation learning section felt out of place. It occurred to me we talk about dimensionality reduction in the first section (03.heterogeneity.md).

I propose that we make the section that is about "Managing disparities in data generation is required for robust analysis" more general – let's talk about issues related to features >> samples, characterizing structure in your data, feature selection and feature learning. By first talking about dimension reduction more generally, we can then focus in on how that can reveal structure that's not of particular scientific interest (batch effects) as a specific motivation or use case. I also think talking about feature selection (the why) in the first section could be a helpful bit of set up for some of the points in 04.model-complexity.md.

To this end, I've done the following in this pull request:

• Rearranged 03.heterogeneity.md (no renaming, yet) such that
  • Some of the ideas expressed above are included as TODOs/HTML comments
  • The text around dimensionality reduction that was specifically about heterogeneity is broken out under the tentative section header Dimensionality reduction and representation learning
  • The other text about assessing batch effect (anecdote #113; correction) is in it's own section with the placeholder title Visualization and correction of technical effects
• Moved representation learning from 05.prior-knowledge.md to the section of 03.heterogeneity.md that also covers dimensionality reduction
• Moved the Dincer et al. and Taroni et al. text that was in 05.prior-knowledge.md to a new file 06.multiple-approaches-required.md
• Renumbered subsequent sections. (Side note: Does "putting it all together" belong in conclusions? I guess we'll find out.)

Directions for reviewers

The diff for this is not going to be particularly useful. For the most part, no small scale text changes of particular consequence have been made. (You will find that the flow is absolutely bonkers as a result 😀 ) Instead, I thought we should discuss this proposed restructuring and then track and split up work such that I am not blocking everyone else.

As such, please focus on the big picture 🖼️ and if you agree with these changes to the structure in principal. If you do agree, do you think the new first section could use its own figure?

Manuscript checklist

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

• [ 🤞 with all the cutting and pasting ] All changes to text follow "one sentence per line" [Manubot instructions]
• [x] All citations follow the Manubot citation instructions
• [x] All changes or additions to tables follow the Manubot table instructions
• [x] All figures follow the Manubot figure instructions
• [ ] All terms that need to be added to glossary have been added to #50
• [ ] There are no new spelling errors identified by the Manubot spellchecker

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[allaway]

I too support this proposal. :) :shipit:

I think the first section could use a figure, though might run the risk of veering into "review" territory

[jaclyn-taroni]

Everything we wanted to track is now tracked, so I will go ahead and merge this!