greenelab/deep-review

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Bare URL used
Open

With this review, we ask the question: what is needed for deep learning to transform how we categorize, study, and treat individuals to maintain or restore health? We choose a high bar for "transform." Andrew Grove, the former CEO of Intel, coined the term Strategic Inflection Point to refer to a change in technologies or environment that requires a business to be fundamentally reshaped [@url:http://www.intel.com/pressroom/archive/speeches/ag080998.htm].
Severity: Info
Found in content/02.intro.md by markdownlint

MD034 - Bare URL used

Tags: links, url

Aliases: no-bare-urls

This rule is triggered whenever a URL is given that isn't surrounded by angle brackets:

For more information, see http://www.example.com/.

To fix this, add angle brackets around the URL:

For more information, see <http:></http:>.

Rationale: Without angle brackets, the URL isn't converted into a link in many markdown parsers.

Note: if you do want a bare URL without it being converted into a link, enclose it in a code block, otherwise in some markdown parsers it will be converted:

`http://www.example.com`

Trailing spaces
Open

1.20. Toyota Technological Institute at Chicago, Chicago, IL  
Severity: Info
Found in content/00.front-matter.md by markdownlint

MD009 - Trailing spaces

Tags: whitespace

Aliases: no-trailing-spaces

Parameters: br_spaces (number; default: 0)

This rule is triggered on any lines that end with whitespace. To fix this, find the line that is triggered and remove any trailing spaces from the end.

The brspaces parameter allows an exception to this rule for a specific amount of trailing spaces used to insert an explicit line break/br element. For example, set brspaces to 2 to allow exactly 2 spaces at the end of a line.

Note: you have to set brspaces to 2 or higher for this exception to take effect - you can't insert a br element with just a single trailing space, so if you set brspaces to 1, the exception will be disabled, just as if it was set to the default of 0.

Trailing spaces
Open

1.30. Institute of Organic Chemistry, Westfälische Wilhelms-Universität Münster, Münster, Germany  
Severity: Info
Found in content/00.front-matter.md by markdownlint

MD009 - Trailing spaces

Tags: whitespace

Aliases: no-trailing-spaces

Parameters: br_spaces (number; default: 0)

This rule is triggered on any lines that end with whitespace. To fix this, find the line that is triggered and remove any trailing spaces from the end.

The brspaces parameter allows an exception to this rule for a specific amount of trailing spaces used to insert an explicit line break/br element. For example, set brspaces to 2 to allow exactly 2 spaces at the end of a line.

Note: you have to set brspaces to 2 or higher for this exception to take effect - you can't insert a br element with just a single trailing space, so if you set brspaces to 1, the exception will be disabled, just as if it was set to the default of 0.

Trailing spaces
Open

1.32. Department of Pathology and Immunology, Washington University in Saint Louis, Saint Louis, MO  
Severity: Info
Found in content/00.front-matter.md by markdownlint

MD009 - Trailing spaces

Tags: whitespace

Aliases: no-trailing-spaces

Parameters: br_spaces (number; default: 0)

This rule is triggered on any lines that end with whitespace. To fix this, find the line that is triggered and remove any trailing spaces from the end.

The brspaces parameter allows an exception to this rule for a specific amount of trailing spaces used to insert an explicit line break/br element. For example, set brspaces to 2 to allow exactly 2 spaces at the end of a line.

Note: you have to set brspaces to 2 or higher for this exception to take effect - you can't insert a br element with just a single trailing space, so if you set brspaces to 1, the exception will be disabled, just as if it was set to the default of 0.

Inline HTML
Open

[]{.fas .fa-info-circle .fa-lg} **Updated Content**<br>
Severity: Info
Found in content/00.front-matter.md by markdownlint

MD033 - Inline HTML

Tags: html

Aliases: no-inline-html

This rule is triggered whenever raw HTML is used in a markdown document:

Inline HTML header

To fix this, use 'pure' markdown instead of including raw HTML:

# Markdown header

Rationale: Raw HTML is allowed in markdown, but this rule is included for those who want their documents to only include "pure" markdown, or for those who are rendering markdown documents in something other than HTML.

Inline HTML
Open

    Srinivas C. Turaga<sup>1.24</sup>,
Severity: Info
Found in content/00.front-matter.md by markdownlint

MD033 - Inline HTML

Tags: html

Aliases: no-inline-html

This rule is triggered whenever raw HTML is used in a markdown document:

Inline HTML header

To fix this, use 'pure' markdown instead of including raw HTML:

# Markdown header

Rationale: Raw HTML is allowed in markdown, but this rule is included for those who want their documents to only include "pure" markdown, or for those who are rendering markdown documents in something other than HTML.

Bare URL used
Open

Federated learning [@url:http://proceedings.mlr.press/v54/mcmahan17a.html] and secure aggregations [@url:https://eprint.iacr.org/2017/281.pdf; @tag:Papernot2017_pate] are complementary approaches that reinforce differential privacy.
Severity: Info
Found in content/03.categorize.md by markdownlint

MD034 - Bare URL used

Tags: links, url

Aliases: no-bare-urls

This rule is triggered whenever a URL is given that isn't surrounded by angle brackets:

For more information, see http://www.example.com/.

To fix this, add angle brackets around the URL:

For more information, see <http:></http:>.

Rationale: Without angle brackets, the URL isn't converted into a link in many markdown parsers.

Note: if you do want a bare URL without it being converted into a link, enclose it in a code block, otherwise in some markdown parsers it will be converted:

`http://www.example.com`

Header levels should only increment by one level at a time
Open

### Statement of Purpose
Severity: Info
Found in LICENSE-CC0.md by markdownlint

MD001 - Header levels should only increment by one level at a time

Tags: headers

Aliases: header-increment

This rule is triggered when you skip header levels in a markdown document, for example:

# Header 1

### Header 3

We skipped out a 2nd level header in this document

When using multiple header levels, nested headers should increase by only one level at a time:

# Header 1

## Header 2

### Header 3

#### Header 4

## Another Header 2

### Another Header 3

Ordered list item prefix
Open

9. For references that do not have any of the above persistent identifiers, the citation key does not need to include a prefix.
Severity: Info
Found in USAGE.md by markdownlint

MD029 - Ordered list item prefix

Tags: ol

Aliases: ol-prefix

Parameters: style ("one", "ordered"; default "one")

This rule is triggered on ordered lists that do not either start with '1.' or do not have a prefix that increases in numerical order (depending on the configured style, which defaults to 'one').

Example valid list if the style is configured as 'one':

1. Do this.
1. Do that.
1. Done.

Example valid list if the style is configured as 'ordered':

1. Do this.
2. Do that.
3. Done.

First header should be a top level header
Open

## Introduction to deep learning
Severity: Info
Found in content/02.intro.md by markdownlint

MD002 - First header should be a top level header

Tags: headers

Aliases: first-header-h1

Parameters: level (number; default 1)

This rule is triggered when the first header in the document isn't a h1 header:

## This isn't a H1 header

### Another header

The first header in the document should be a h1 header:

# Start with a H1 header

## Then use a H2 for subsections

Trailing spaces
Open

1.8. Computational Biology and Stats, Target Sciences, GlaxoSmithKline, Stevenage, United Kingdom  
Severity: Info
Found in content/00.front-matter.md by markdownlint

MD009 - Trailing spaces

Tags: whitespace

Aliases: no-trailing-spaces

Parameters: br_spaces (number; default: 0)

This rule is triggered on any lines that end with whitespace. To fix this, find the line that is triggered and remove any trailing spaces from the end.

The brspaces parameter allows an exception to this rule for a specific amount of trailing spaces used to insert an explicit line break/br element. For example, set brspaces to 2 to allow exactly 2 spaces at the end of a line.

Note: you have to set brspaces to 2 or higher for this exception to take effect - you can't insert a br element with just a single trailing space, so if you set brspaces to 1, the exception will be disabled, just as if it was set to the default of 0.

Trailing spaces
Open

1.24. Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA  
Severity: Info
Found in content/00.front-matter.md by markdownlint

MD009 - Trailing spaces

Tags: whitespace

Aliases: no-trailing-spaces

Parameters: br_spaces (number; default: 0)

This rule is triggered on any lines that end with whitespace. To fix this, find the line that is triggered and remove any trailing spaces from the end.

The brspaces parameter allows an exception to this rule for a specific amount of trailing spaces used to insert an explicit line break/br element. For example, set brspaces to 2 to allow exactly 2 spaces at the end of a line.

Note: you have to set brspaces to 2 or higher for this exception to take effect - you can't insert a br element with just a single trailing space, so if you set brspaces to 1, the exception will be disabled, just as if it was set to the default of 0.

Trailing spaces
Open

1.28. Department of Genetics, Stanford University, Stanford, CA  
Severity: Info
Found in content/00.front-matter.md by markdownlint

MD009 - Trailing spaces

Tags: whitespace

Aliases: no-trailing-spaces

Parameters: br_spaces (number; default: 0)

This rule is triggered on any lines that end with whitespace. To fix this, find the line that is triggered and remove any trailing spaces from the end.

The brspaces parameter allows an exception to this rule for a specific amount of trailing spaces used to insert an explicit line break/br element. For example, set brspaces to 2 to allow exactly 2 spaces at the end of a line.

Note: you have to set brspaces to 2 or higher for this exception to take effect - you can't insert a br element with just a single trailing space, so if you set brspaces to 1, the exception will be disabled, just as if it was set to the default of 0.

Trailing spaces
Open

1.31. Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, DC  
Severity: Info
Found in content/00.front-matter.md by markdownlint

MD009 - Trailing spaces

Tags: whitespace

Aliases: no-trailing-spaces

Parameters: br_spaces (number; default: 0)

This rule is triggered on any lines that end with whitespace. To fix this, find the line that is triggered and remove any trailing spaces from the end.

The brspaces parameter allows an exception to this rule for a specific amount of trailing spaces used to insert an explicit line break/br element. For example, set brspaces to 2 to allow exactly 2 spaces at the end of a line.

Note: you have to set brspaces to 2 or higher for this exception to take effect - you can't insert a br element with just a single trailing space, so if you set brspaces to 1, the exception will be disabled, just as if it was set to the default of 0.

Trailing spaces
Open

1.33. Department of Medicine, Brown University, Providence, RI  
Severity: Info
Found in content/00.front-matter.md by markdownlint

MD009 - Trailing spaces

Tags: whitespace

Aliases: no-trailing-spaces

Parameters: br_spaces (number; default: 0)

This rule is triggered on any lines that end with whitespace. To fix this, find the line that is triggered and remove any trailing spaces from the end.

The brspaces parameter allows an exception to this rule for a specific amount of trailing spaces used to insert an explicit line break/br element. For example, set brspaces to 2 to allow exactly 2 spaces at the end of a line.

Note: you have to set brspaces to 2 or higher for this exception to take effect - you can't insert a br element with just a single trailing space, so if you set brspaces to 1, the exception will be disabled, just as if it was set to the default of 0.

Inline HTML
Open

<sup>†</sup> --- To whom correspondence should be addressed: gitter@biostat.wisc.edu (A.G.) and greenescientist@gmail.com (C.S.G.)
Severity: Info
Found in content/00.front-matter.md by markdownlint

MD033 - Inline HTML

Tags: html

Aliases: no-inline-html

This rule is triggered whenever raw HTML is used in a markdown document:

Inline HTML header

To fix this, use 'pure' markdown instead of including raw HTML:

# Markdown header

Rationale: Raw HTML is allowed in markdown, but this rule is included for those who want their documents to only include "pure" markdown, or for those who are rendering markdown documents in something other than HTML.

Inline HTML
Open

<small>
Severity: Info
Found in content/00.front-matter.md by markdownlint

MD033 - Inline HTML

Tags: html

Aliases: no-inline-html

This rule is triggered whenever raw HTML is used in a markdown document:

Inline HTML header

To fix this, use 'pure' markdown instead of including raw HTML:

# Markdown header

Rationale: Raw HTML is allowed in markdown, but this rule is included for those who want their documents to only include "pure" markdown, or for those who are rendering markdown documents in something other than HTML.

Inline HTML
Open

    Travers Ching<sup>1.1,☯</sup>,
Severity: Info
Found in content/00.front-matter.md by markdownlint

MD033 - Inline HTML

Tags: html

Aliases: no-inline-html

This rule is triggered whenever raw HTML is used in a markdown document:

Inline HTML header

To fix this, use 'pure' markdown instead of including raw HTML:

# Markdown header

Rationale: Raw HTML is allowed in markdown, but this rule is included for those who want their documents to only include "pure" markdown, or for those who are rendering markdown documents in something other than HTML.

Inline HTML
Open

    Anshul Kundaje<sup>1.19,1.28</sup>,
Severity: Info
Found in content/00.front-matter.md by markdownlint

MD033 - Inline HTML

Tags: html

Aliases: no-inline-html

This rule is triggered whenever raw HTML is used in a markdown document:

Inline HTML header

To fix this, use 'pure' markdown instead of including raw HTML:

# Markdown header

Rationale: Raw HTML is allowed in markdown, but this rule is included for those who want their documents to only include "pure" markdown, or for those who are rendering markdown documents in something other than HTML.

Inline HTML
Open

    Austin Huang<sup>1.33</sup>,
Severity: Info
Found in content/00.front-matter.md by markdownlint

MD033 - Inline HTML

Tags: html

Aliases: no-inline-html

This rule is triggered whenever raw HTML is used in a markdown document:

Inline HTML header

To fix this, use 'pure' markdown instead of including raw HTML:

# Markdown header

Rationale: Raw HTML is allowed in markdown, but this rule is included for those who want their documents to only include "pure" markdown, or for those who are rendering markdown documents in something other than HTML.

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