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Parsing bibliographies / style predictor

Sylvester Keil
Dear all,

I've recently completed a long-term project of mine by writing a web
application that exposes the AnyStyle parser library for ML-powered
parsing of bibliographies. The web application (and API) is available at
http://anystyle.io (SSL available too) and is very exciting (if I may
say so myself) for mainly two reasons:

1. The parsing process is split into two steps, showing you the output
of the ML-driven step in an editor that allows you to make changes to
the parse result.

2. These changes can be recorded and used directly to train the ML
model.

This is exciting, because so far it required a lot of effort and
know-how to prepare training data. Now there is a single public model
that everyone can help improve. Obviously, this part is still very
experimental — it will be interesting to see if the model starts to
deteriorate at some point if fed too much training data. Meanwhile, we
now have a publicly available parser that should be fairly easy to train
to recognize, for example new styles or languages. Please do take a look
if you're interested! I imagine most of you will be interested in the
'CiteProc' output format (the 'JSON' format is less interesting, because
it does not apply as much post-processing to individual fields).

The parser is also accessible via a JSON API; I wrote a very quick
prototype for a style-predictor (Rintze's idea!) similar to the one in
the CSL editor. You can give the predictor a reference, the reference
will be parsed and the parsed result rendered in all independent CSL
styles; these formatted references are then compared with the original
one using the Levenshtein distance and the best matches reported. It's
just a quick prototype; you can take a look at it here:

https://gist.github.com/inukshuk/f1d47aeab1f778bca8ce

The parsing is very fast, but the rendering using citeproc-ruby takes
quite some time :) But since the parsing API is so simple, it should be
very easy to recast this example in JavaScript, Haskell or Python.

I thought this might be of interest to some of you on this list. Just
let me know if you have any questions!

Sylvester



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Re: Parsing bibliographies / style predictor

Bruce D'Arcus-3

Cool!

So does this get us one step closer to the magic style finder and generator?

Bruce

On May 17, 2014 4:07 PM, "Sylvester Keil" <[hidden email]> wrote:
Dear all,

I've recently completed a long-term project of mine by writing a web
application that exposes the AnyStyle parser library for ML-powered
parsing of bibliographies. The web application (and API) is available at
http://anystyle.io (SSL available too) and is very exciting (if I may
say so myself) for mainly two reasons:

1. The parsing process is split into two steps, showing you the output
of the ML-driven step in an editor that allows you to make changes to
the parse result.

2. These changes can be recorded and used directly to train the ML
model.

This is exciting, because so far it required a lot of effort and
know-how to prepare training data. Now there is a single public model
that everyone can help improve. Obviously, this part is still very
experimental — it will be interesting to see if the model starts to
deteriorate at some point if fed too much training data. Meanwhile, we
now have a publicly available parser that should be fairly easy to train
to recognize, for example new styles or languages. Please do take a look
if you're interested! I imagine most of you will be interested in the
'CiteProc' output format (the 'JSON' format is less interesting, because
it does not apply as much post-processing to individual fields).

The parser is also accessible via a JSON API; I wrote a very quick
prototype for a style-predictor (Rintze's idea!) similar to the one in
the CSL editor. You can give the predictor a reference, the reference
will be parsed and the parsed result rendered in all independent CSL
styles; these formatted references are then compared with the original
one using the Levenshtein distance and the best matches reported. It's
just a quick prototype; you can take a look at it here:

https://gist.github.com/inukshuk/f1d47aeab1f778bca8ce

The parsing is very fast, but the rendering using citeproc-ruby takes
quite some time :) But since the parsing API is so simple, it should be
very easy to recast this example in JavaScript, Haskell or Python.

I thought this might be of interest to some of you on this list. Just
let me know if you have any questions!

Sylvester



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Re: Parsing bibliographies / style predictor

rmzelle
Administrator
A more short term goal would be to incorporate this into Mendeley's
CSL editor. It's probably more user-friendly if users no longer have
to reformat a fixed predefined set of item metadata (as currently is
required for http://editor.citationstyles.org/searchByExample/ ), but
instead can just copy and paste some references that already exist in
the desired format, and have the tool show CSL styles that give
similar output.

Rintze

On Sun, May 18, 2014 at 8:27 PM, Bruce D'Arcus <[hidden email]> wrote:

> So does this get us one step closer to the magic style finder and generator?
>
> Bruce
>
> On May 17, 2014 4:07 PM, "Sylvester Keil" <[hidden email]> wrote:
>>
>> Dear all,
>>
>> I've recently completed a long-term project of mine by writing a web
>> application that exposes the AnyStyle parser library for ML-powered
>> parsing of bibliographies. The web application (and API) is available at
>> http://anystyle.io (SSL available too) and is very exciting (if I may
>> say so myself) for mainly two reasons:
>>
>> 1. The parsing process is split into two steps, showing you the output
>> of the ML-driven step in an editor that allows you to make changes to
>> the parse result.
>>
>> 2. These changes can be recorded and used directly to train the ML
>> model.
>>
>> This is exciting, because so far it required a lot of effort and
>> know-how to prepare training data. Now there is a single public model
>> that everyone can help improve. Obviously, this part is still very
>> experimental — it will be interesting to see if the model starts to
>> deteriorate at some point if fed too much training data. Meanwhile, we
>> now have a publicly available parser that should be fairly easy to train
>> to recognize, for example new styles or languages. Please do take a look
>> if you're interested! I imagine most of you will be interested in the
>> 'CiteProc' output format (the 'JSON' format is less interesting, because
>> it does not apply as much post-processing to individual fields).
>>
>> The parser is also accessible via a JSON API; I wrote a very quick
>> prototype for a style-predictor (Rintze's idea!) similar to the one in
>> the CSL editor. You can give the predictor a reference, the reference
>> will be parsed and the parsed result rendered in all independent CSL
>> styles; these formatted references are then compared with the original
>> one using the Levenshtein distance and the best matches reported. It's
>> just a quick prototype; you can take a look at it here:
>>
>> https://gist.github.com/inukshuk/f1d47aeab1f778bca8ce
>>
>> The parsing is very fast, but the rendering using citeproc-ruby takes
>> quite some time :) But since the parsing API is so simple, it should be
>> very easy to recast this example in JavaScript, Haskell or Python.
>>
>> I thought this might be of interest to some of you on this list. Just
>> let me know if you have any questions!
>>
>> Sylvester

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Re: Parsing bibliographies / style predictor

Robert Knight
> So does this get us one step closer to the magic style finder and generator?

I think Rintze is more on the mark about making it easy to find an
existing style. Reducing the overall hassle for users I think is more
about
reducing the unnecessary proliferation of styles. Within Elsevier one
of the outcomes of trying to ensure that CSL styles are available for
all their journals is the consolidation of existing styles into only a
handful - which becomes much easier when you have better visibility (
a journal name -> style URI mapping) on how many different styles
there really are.

Regards,
Rob.


On 19 May 2014 01:47, Rintze Zelle <[hidden email]> wrote:

> A more short term goal would be to incorporate this into Mendeley's
> CSL editor. It's probably more user-friendly if users no longer have
> to reformat a fixed predefined set of item metadata (as currently is
> required for http://editor.citationstyles.org/searchByExample/ ), but
> instead can just copy and paste some references that already exist in
> the desired format, and have the tool show CSL styles that give
> similar output.
>
> Rintze
>
> On Sun, May 18, 2014 at 8:27 PM, Bruce D'Arcus <[hidden email]> wrote:
>> So does this get us one step closer to the magic style finder and generator?
>>
>> Bruce
>>
>> On May 17, 2014 4:07 PM, "Sylvester Keil" <[hidden email]> wrote:
>>>
>>> Dear all,
>>>
>>> I've recently completed a long-term project of mine by writing a web
>>> application that exposes the AnyStyle parser library for ML-powered
>>> parsing of bibliographies. The web application (and API) is available at
>>> http://anystyle.io (SSL available too) and is very exciting (if I may
>>> say so myself) for mainly two reasons:
>>>
>>> 1. The parsing process is split into two steps, showing you the output
>>> of the ML-driven step in an editor that allows you to make changes to
>>> the parse result.
>>>
>>> 2. These changes can be recorded and used directly to train the ML
>>> model.
>>>
>>> This is exciting, because so far it required a lot of effort and
>>> know-how to prepare training data. Now there is a single public model
>>> that everyone can help improve. Obviously, this part is still very
>>> experimental — it will be interesting to see if the model starts to
>>> deteriorate at some point if fed too much training data. Meanwhile, we
>>> now have a publicly available parser that should be fairly easy to train
>>> to recognize, for example new styles or languages. Please do take a look
>>> if you're interested! I imagine most of you will be interested in the
>>> 'CiteProc' output format (the 'JSON' format is less interesting, because
>>> it does not apply as much post-processing to individual fields).
>>>
>>> The parser is also accessible via a JSON API; I wrote a very quick
>>> prototype for a style-predictor (Rintze's idea!) similar to the one in
>>> the CSL editor. You can give the predictor a reference, the reference
>>> will be parsed and the parsed result rendered in all independent CSL
>>> styles; these formatted references are then compared with the original
>>> one using the Levenshtein distance and the best matches reported. It's
>>> just a quick prototype; you can take a look at it here:
>>>
>>> https://gist.github.com/inukshuk/f1d47aeab1f778bca8ce
>>>
>>> The parsing is very fast, but the rendering using citeproc-ruby takes
>>> quite some time :) But since the parsing API is so simple, it should be
>>> very easy to recast this example in JavaScript, Haskell or Python.
>>>
>>> I thought this might be of interest to some of you on this list. Just
>>> let me know if you have any questions!
>>>
>>> Sylvester
>
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Re: Parsing bibliographies / style predictor

Carles Pina
In reply to this post by Sylvester Keil
Hi,

On 17 May 2014 21:06, Sylvester Keil <[hidden email]> wrote:
> Dear all,
>
> I've recently completed a long-term project of mine by writing a web
> application that exposes the AnyStyle parser library for ML-powered
> parsing of bibliographies. The web application (and API) is available at
> http://anystyle.io (SSL available too) and is very exciting (if I may
> say so myself) for mainly two reasons:

As Rintze said: this is very cool! Thank you very much for doing it!

I'll send to you some feedback off-list.

The CSL Editor would be an obvious point of improvement, I'll also
forward this to some colleagues that might be interested.

Regards,

--
Carles Pina | Software Engineer
http://www.mendeley.com/profiles/Carles-Pina/

Mendeley Limited | London, UK | www.mendeley.com
Registered in England and Wales | Company Number 6419015

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Re: Parsing bibliographies / style predictor

Sebastian Karcher
In reply to this post by Robert Knight
> but instead can just copy and paste some references that already exist in the desired format, and have the tool show CSL styles that give similar output.

I talked to Steve about this back when he wrote the tool - I suggested
at a more basic level to allow using items supplied via citation data
supplied as CSL-JSON or RIS, but the main bottleneck isn't actually
getting the data in (the task that Sylvester's tool would make very
simple). The problem is that it takes a significant time (5-10mins?)
to generate citations in all styles for new data and those new
citations are needed to generate the set of closest matches.
It may still be possible to use a similar approach to do this,
especially if Sylvester's tool could be extended to more quickly
identify similar styles, but that's going to be a lot more advanced
than simply plugging it into the existing CSL editor, unfortunately.

> Reducing the overall hassle for users I think is more about reducing the unnecessary proliferation of styles.
on an ideological level I couldn't agree more. On a pragmatic level, I
see only very little movement in that direction, especially once we
look beyond the US-centric market with the big publishers that are
able to unify journal styles and a small set of major style guides
that students are required to use. Every university in the UK seems to
think they need their own citation style and in Germany it's even
worse—many _departments_ have their own custom style and at times even
individual professors. We can and should definitely lobby for fewer
styles - but realistically I wouldn't expect much to change on this
front in the medium term.

Sebastian


On Mon, May 19, 2014 at 3:09 AM, Robert Knight
<[hidden email]> wrote:

>> So does this get us one step closer to the magic style finder and generator?
>
> I think Rintze is more on the mark about making it easy to find an
> existing style. Reducing the overall hassle for users I think is more
> about
> reducing the unnecessary proliferation of styles. Within Elsevier one
> of the outcomes of trying to ensure that CSL styles are available for
> all their journals is the consolidation of existing styles into only a
> handful - which becomes much easier when you have better visibility (
> a journal name -> style URI mapping) on how many different styles
> there really are.
>
> Regards,
> Rob.
>
>
> On 19 May 2014 01:47, Rintze Zelle <[hidden email]> wrote:
>> A more short term goal would be to incorporate this into Mendeley's
>> CSL editor. It's probably more user-friendly if users no longer have
>> to reformat a fixed predefined set of item metadata (as currently is
>> required for http://editor.citationstyles.org/searchByExample/ ), but
>> instead can just copy and paste some references that already exist in
>> the desired format, and have the tool show CSL styles that give
>> similar output.
>>
>> Rintze
>>
>> On Sun, May 18, 2014 at 8:27 PM, Bruce D'Arcus <[hidden email]> wrote:
>>> So does this get us one step closer to the magic style finder and generator?
>>>
>>> Bruce
>>>
>>> On May 17, 2014 4:07 PM, "Sylvester Keil" <[hidden email]> wrote:
>>>>
>>>> Dear all,
>>>>
>>>> I've recently completed a long-term project of mine by writing a web
>>>> application that exposes the AnyStyle parser library for ML-powered
>>>> parsing of bibliographies. The web application (and API) is available at
>>>> http://anystyle.io (SSL available too) and is very exciting (if I may
>>>> say so myself) for mainly two reasons:
>>>>
>>>> 1. The parsing process is split into two steps, showing you the output
>>>> of the ML-driven step in an editor that allows you to make changes to
>>>> the parse result.
>>>>
>>>> 2. These changes can be recorded and used directly to train the ML
>>>> model.
>>>>
>>>> This is exciting, because so far it required a lot of effort and
>>>> know-how to prepare training data. Now there is a single public model
>>>> that everyone can help improve. Obviously, this part is still very
>>>> experimental — it will be interesting to see if the model starts to
>>>> deteriorate at some point if fed too much training data. Meanwhile, we
>>>> now have a publicly available parser that should be fairly easy to train
>>>> to recognize, for example new styles or languages. Please do take a look
>>>> if you're interested! I imagine most of you will be interested in the
>>>> 'CiteProc' output format (the 'JSON' format is less interesting, because
>>>> it does not apply as much post-processing to individual fields).
>>>>
>>>> The parser is also accessible via a JSON API; I wrote a very quick
>>>> prototype for a style-predictor (Rintze's idea!) similar to the one in
>>>> the CSL editor. You can give the predictor a reference, the reference
>>>> will be parsed and the parsed result rendered in all independent CSL
>>>> styles; these formatted references are then compared with the original
>>>> one using the Levenshtein distance and the best matches reported. It's
>>>> just a quick prototype; you can take a look at it here:
>>>>
>>>> https://gist.github.com/inukshuk/f1d47aeab1f778bca8ce
>>>>
>>>> The parsing is very fast, but the rendering using citeproc-ruby takes
>>>> quite some time :) But since the parsing API is so simple, it should be
>>>> very easy to recast this example in JavaScript, Haskell or Python.
>>>>
>>>> I thought this might be of interest to some of you on this list. Just
>>>> let me know if you have any questions!
>>>>
>>>> Sylvester
>>
>> ------------------------------------------------------------------------------
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>
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--
Sebastian Karcher
Ph.D. Candidate
Department of Political Science
Northwestern University

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Re: Parsing bibliographies / style predictor

rmzelle
Administrator
On Mon, May 19, 2014 at 12:17 PM, Sebastian Karcher
<[hidden email]> wrote:

>> but instead can just copy and paste some references that already exist in the desired format, and have the tool show CSL styles that give similar output.
>
> I talked to Steve about this back when he wrote the tool - I suggested
> at a more basic level to allow using items supplied via citation data
> supplied as CSL-JSON or RIS, but the main bottleneck isn't actually
> getting the data in (the task that Sylvester's tool would make very
> simple). The problem is that it takes a significant time (5-10mins?)
> to generate citations in all styles for new data and those new
> citations are needed to generate the set of closest matches.
> It may still be possible to use a similar approach to do this,
> especially if Sylvester's tool could be extended to more quickly
> identify similar styles, but that's going to be a lot more advanced
> than simply plugging it into the existing CSL editor, unfortunately.

I'm wondering how citeproc-ruby, citeproc-js, and citeproc-hs compare,
performance wise. And even if a user needs to wait a few minutes, that
might still be a better experience than the current setup.

Rintze

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Re: Parsing bibliographies / style predictor

Robert Knight
> We can and should definitely lobby for
> fewer styles - but realistically I wouldn't expect much to
> change on this front in the medium term.

I don't think it is so much a matter of "lobbying" as maximizing the
convenience to librarians,
departments or whoever else makes the decisions of picking an existing style.

But yes, I take your point.

On 19 May 2014 17:25, Rintze Zelle <[hidden email]> wrote:

> On Mon, May 19, 2014 at 12:17 PM, Sebastian Karcher
> <[hidden email]> wrote:
>>> but instead can just copy and paste some references that already exist in the desired format, and have the tool show CSL styles that give similar output.
>>
>> I talked to Steve about this back when he wrote the tool - I suggested
>> at a more basic level to allow using items supplied via citation data
>> supplied as CSL-JSON or RIS, but the main bottleneck isn't actually
>> getting the data in (the task that Sylvester's tool would make very
>> simple). The problem is that it takes a significant time (5-10mins?)
>> to generate citations in all styles for new data and those new
>> citations are needed to generate the set of closest matches.
>> It may still be possible to use a similar approach to do this,
>> especially if Sylvester's tool could be extended to more quickly
>> identify similar styles, but that's going to be a lot more advanced
>> than simply plugging it into the existing CSL editor, unfortunately.
>
> I'm wondering how citeproc-ruby, citeproc-js, and citeproc-hs compare,
> performance wise. And even if a user needs to wait a few minutes, that
> might still be a better experience than the current setup.
>
> Rintze
>
> ------------------------------------------------------------------------------
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Re: Parsing bibliographies / style predictor

rmzelle
Administrator
It's off-topic, but getting Wiley on board would help quite a bit with
trimming down the number of independent styles. I never got any
further in their bureaucracy than a single dysfunctional reply:

"Unfortunately, I regret to inform you that we already have our own
way of standardizing and handling journal citation/reference styles.
Nonetheless, we would like to thank you for your offer."

when I asked them whether they use a limited set of citation formats
for their journals. If any of you have good contacts at Wiley, let me
know.

Rintze

On Mon, May 19, 2014 at 1:24 PM, Robert Knight
<[hidden email]> wrote:
>> We can and should definitely lobby for
>> fewer styles - but realistically I wouldn't expect much to
>> change on this front in the medium term.
>
> I don't think it is so much a matter of "lobbying" as maximizing the
> convenience to librarians,
> departments or whoever else makes the decisions of picking an existing style.
>
> But yes, I take your point.

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