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].
1.14. Ecological and Evolutionary Signal-processing and Informatics Laboratory, Department of Electrical and Computer Engineering, Drexel University, Philadelphia, PA
Blindly tested in the latest CASP competition (i.e. CASP12 [@url:http://www.predictioncenter.org/casp12/rrc_avrg_results.cgi]), RaptorX-Contact ranked first in F₁ score on free-modeling targets as well as the whole set of targets.
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`
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.
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.
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.
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:
This rule is triggered on any header that has a punctuation character as the
last character in the line:
# This is a header.
To fix this, remove any trailing punctuation:
# This is a header
Note: The punctuation parameter can be used to specify what characters class
as punctuation at the end of the header. For example, you can set it to
'.,;:!' to allow headers with question marks in them, such as might be used
in an FAQ.
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.
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.
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.
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.
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.
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.
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:
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':
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.
MD031 - Fenced code blocks should be surrounded by blank lines
Tags: code, blank_lines
Aliases: blanks-around-fences
This rule is triggered when fenced code blocks are either not preceded or not
followed by a blank line:
Some text
```
Code block
```
```
Another code block
```
Some more text
To fix this, ensure that all fenced code blocks have a blank line both before
and after (except where the block is at the beginning or end of the document):
Some text
```
Code block
```
```
Another code block
```
Some more text
Rationale: Aside from aesthetic reasons, some parsers, including kramdown, will
not parse fenced code blocks that don't have blank lines before and after them.
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.
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.
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.