jaybee84 / ml-in-rd

Manuscript for perspective on machine learning in rare disease
Other
2 stars 1 forks source link

porting justin's edits into GH #253

Closed jaybee84 closed 1 year ago

jaybee84 commented 1 year ago

Purpose

This PR ports Justin's edits and comments into GH.

Directions for reviewers

Please review the edits and comments. in-line edits that accompany Justin's comments are jaybee84's edits in response to comments. Additional edits have been provided by allawayr and jaybee84 in form of code suggestions.

Issues highlighted by Justin: Among them are that many of the cited examples of different ML applications seem gratuitous, and don't illuminate how the approach was used to help solve a particular problem. Stylistically, there is the too frequent use of parenthetical statements, as well as sentences that are too vague or don't contribute much to the paper. I have attempted to make corrections along these lines, and have also added a number of comments that should be addressed.

Are there ways to address these issues in the different sections?

Which areas should receive a particularly close look?

  1. Do the edits preserve the intent of the section?
  2. Are there specific references that can be removed without taking away from the text?

Is there anything that you want to discuss further?

Is the pull request ready for review?

Yes

Manuscript checklist

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

AppVeyorBot commented 1 year ago

AppVeyor build 1.0.699 for commit 2fe6cf3c34ac45e53830e3a0f19473fda6448fd4 is now complete.

Found 24 potential spelling error(s). Preview:content/02.intro.md:21:modelsthey content/03.combining-datasets.md:3:transcriptome content/03.combining-datasets.md:5:missingness content/03.combining-datasets.md:7:hoc content/03.combining-datasets.md:13:ontologies content/05.model-complexity.md:32:ALS content/05.model-complexity.md:32:amyotrophic content/09. ethics_declaration.md:3:Tempus content/11. author_contributions.md:3:ICMJE content/11. author_contributions.md:5:...
The rendered manuscript from this build is temporarily available for download at:

AppVeyorBot commented 1 year ago

AppVeyor build 1.0.702 for commit 5fa011a212f8fad7ea8afc76e08cbac60f11c91b is now complete.

Found 26 potential spelling error(s). Preview:content/02.intro.md:21:modelsthey content/03.combining-datasets.md:3:transcriptome content/03.combining-datasets.md:5:missingness content/03.combining-datasets.md:7:hoc content/03.combining-datasets.md:13:ontologies content/05.model-complexity.md:32:ALS content/05.model-complexity.md:32:amyotrophic content/08.outlook.md:35:explainability content/09. ethics_declaration.md:3:Tempus content/09. ethics_declaration.md:4:funder...
The rendered manuscript from this build is temporarily available for download at:

AppVeyorBot commented 1 year ago

AppVeyor build 1.0.703 for commit ca870a1a09c999e30145cedec9d5f2c2866d76fc is now complete.

Found 26 potential spelling error(s). Preview:content/02.intro.md:21:modelsthey content/03.combining-datasets.md:3:transcriptome content/03.combining-datasets.md:5:missingness content/03.combining-datasets.md:7:hoc content/03.combining-datasets.md:13:ontologies content/05.model-complexity.md:32:ALS content/05.model-complexity.md:32:amyotrophic content/08.outlook.md:35:explainability content/09. ethics_declaration.md:3:Tempus content/09. ethics_declaration.md:4:funder...
The rendered manuscript from this build is temporarily available for download at:

AppVeyorBot commented 1 year ago

AppVeyor build 1.0.704 for commit d358866d05302d4fb4c859e9b2c018e023dcdef1 is now complete.

Found 25 potential spelling error(s). Preview:content/03.combining-datasets.md:3:transcriptome content/03.combining-datasets.md:5:missingness content/03.combining-datasets.md:7:hoc content/03.combining-datasets.md:13:ontologies content/05.model-complexity.md:32:ALS content/05.model-complexity.md:32:amyotrophic content/08.outlook.md:35:explainability content/09. ethics_declaration.md:3:Tempus content/09. ethics_declaration.md:4:funder content/11. author_contributions....
The rendered manuscript from this build is temporarily available for download at:

AppVeyorBot commented 1 year ago

AppVeyor build 1.0.705 for commit 2c3da1068c6d676e346e8d1389d4a6aafaf9e58f is now complete.

Found 25 potential spelling error(s). Preview:content/03.combining-datasets.md:3:transcriptome content/03.combining-datasets.md:5:missingness content/03.combining-datasets.md:7:hoc content/03.combining-datasets.md:13:ontologies content/05.model-complexity.md:31:ALS content/05.model-complexity.md:31:amyotrophic content/08.outlook.md:35:explainability content/09. ethics_declaration.md:3:Tempus content/09. ethics_declaration.md:4:funder content/11. author_contributions....
The rendered manuscript from this build is temporarily available for download at:

AppVeyorBot commented 1 year ago

AppVeyor build 1.0.706 for commit 6bd81767d2778cd02e8e908647357dff7b210869 is now complete.

Found 25 potential spelling error(s). Preview:content/03.combining-datasets.md:3:transcriptome content/03.combining-datasets.md:5:missingness content/03.combining-datasets.md:7:hoc content/03.combining-datasets.md:13:ontologies content/05.model-complexity.md:31:ALS content/05.model-complexity.md:31:amyotrophic content/08.outlook.md:35:explainability content/09. ethics_declaration.md:3:Tempus content/09. ethics_declaration.md:4:funder content/11. author_contributions....
The rendered manuscript from this build is temporarily available for download at:

AppVeyorBot commented 1 year ago

AppVeyor build 1.0.707 for commit 09cbe1c4af6d21ef63eaeab9422172327652d13e is now complete.

Found 25 potential spelling error(s). Preview:content/03.combining-datasets.md:3:transcriptome content/03.combining-datasets.md:5:missingness content/03.combining-datasets.md:7:hoc content/03.combining-datasets.md:13:ontologies content/05.model-complexity.md:31:ALS content/05.model-complexity.md:31:amyotrophic content/08.outlook.md:35:explainability content/09. ethics_declaration.md:3:Tempus content/09. ethics_declaration.md:4:funder content/11. author_contributions....
The rendered manuscript from this build is temporarily available for download at:

AppVeyorBot commented 1 year ago

AppVeyor build 1.0.708 for commit 52397399764ae440210c1f6325c475e76a6e461a is now complete.

Found 25 potential spelling error(s). Preview:content/03.combining-datasets.md:3:transcriptome content/03.combining-datasets.md:5:missingness content/03.combining-datasets.md:7:hoc content/03.combining-datasets.md:13:ontologies content/05.model-complexity.md:31:ALS content/05.model-complexity.md:31:amyotrophic content/08.outlook.md:35:explainability content/09. ethics_declaration.md:3:Tempus content/09. ethics_declaration.md:4:funder content/11. author_contributions....
The rendered manuscript from this build is temporarily available for download at: