Comparing Published Scientific Journal Articles to Their Pre-print Versions

Comparing Published Scientific
Journal Articles
to Their Pre-print Versions
Martin Klein Peter Broadwell
@mart1nkle1n @peterbroadwell
with Sharon E. Farb and Todd Grappone
@farbthink, @liber8er
{martinklein,broadwell,farb,grappone}@library.ucla.edu
University of California Los Angeles

Comparing Published Scientific Journal Articles
@mart1nkle1n #jcdl2016, Newark, NJ, 06/21/2016
2
Scientific Output in Numbers
Global STM publishing market > $25 billion
• 55% of this from USA
• 28% from Europe, Middle East
• Journals core part of scholarly communication process
• English language journal revenue: ~ $10 billion
• ~ 70% of that out of libraries’ budget
• > 28k scholarly peer-reviewed journals (+3.5% p.a.)
• ~ 2.5 million articles per year (+3% p.a.)
• 21% of research papers from USA
“STM Report: An Overview of Scientific and Scholarly Publishing”, Mark Ware and Michael Mabe, March 2015

3
University of California Publication Impact
“Research Performance of the UC System,” Elsevier, March 2015

4
Open Access by Disciplines
“Open Access to the Scientific Journal Literature: Situation 2009”, Björk B-C et al. 2010
http://dx.doi.org/10.1371/journal.pone.0011273

5
Open Access Rate Overall
2010
“Open Access to the Scientific Journal Literature: Situation 2009”, Björk B-C et al.
(http://dx.doi.org/10.1371/journal.pone.0011273)

6
2010
 20.4% OA rate

7
2010
 20.4% OA rate
2015
“Open Access and Sources of Full-Text Articles in Google Scholar in Different
Subject Fields”, Hammid et al.
(http://dx.doi.org/10.1007/s11192-015-1642-2)

8
2010
 20.4% OA rate
2015
“Open Access and Sources of Full-Text Articles in Google Scholar in Different
Subject Fields”, Hammid et al.
(http://dx.doi.org/10.1007/s11192-015-1642-2)
 61.1% OA rate

9
Pre-print v. Final Published
arXiv.org
• Average annual operating cost for 2013 - 2017:
$826,000
Final Published
• English language STM journals: $10 billion in 2013
http://arxiv.org/help/support/faq#3D
“STM Report: An Overview of Scientific and Scholarly Publishing”, Mark Ware and Michael Mabe, March 2015

10
Role of Publisher
• Entrepreneur
• Copyediting
• Tagging
• Marketer
• Distributor
• E-Host

11
Value of Publisher
“Once you’ve gone through the peer review process, if you look
at the article that is actually published in a journal, it looks
radically different [to the one submitted due to] that process of
transformation, the copy-editing, the database linking, the data
visualisation tools, making sure that the metadata for the article
is all right, so when people come to [Elsevier database]
ScienceDirect or type a search into Google, they can actually
find what they are looking for on their platforms.”
Gemma Hersh
http://www.thebookseller.com/news/elsevier-defends-its-value-after-open-access-disputes-328037

12
Working Assumptions
1. If the publishers’ argument is valid, the text of a
pre-print paper should vary significantly from its
corresponding post-print version.
1. By applying standard similarity measures, we
should be able to detect and quantify such
differences.

13
Assembling a pre-print corpus
Source: arXiv.org
• 1.1 million publication records
• Metadata (typical DC, including DOI) obtained
via OAI-PMH interface
• PDF versions of articles available via Amazon’s
S3 service (using “requester pays” option)

14
Finding a matching post-print corpus
1. Extract DOIs from arXiv metadata
• 44.5% or articles have DOI
2. CrossRef’s Metadata Search API
• Match by DOI
• Download article & metadata in XML/PDF
 Results in:
• 11,017 full text articles
• Majority published by Elsevier between 2003 and
2015

15
Text Comparison Methods
1. Length ratio
2. Levenshtein ratio
3. Cosine similarity
4. Jaccard coefficient
5. Sorensen similarity

16
Comparison of Sections
“Analyzing News Events in Non-Traditional Digital Library Collections” M.Klein, P.Broadwell, 2015
http://dx.doi.org/10.1145/2756406.2756948

17

18
Title Comparison
Explore our findings at http://sologlo.library.ucla.edu/prepost
Papers
Similarity (1 = most similar)
%ofallpapers
1 ... 0.9 0.9 ... 0.8 0.8 ... 0.7 0.7 ... 0.6 0.6 ... 0.5 0.5 ... 0.4 0.4 ... 0.3 0.3 ... 0.2 0.2 ... 0.1 0.1 ... 0
1100020003000400050006000700080009000
0102030405060708090100
Length
Levenshtein
Cosine
Sorensen
Jaccard
Percentage

19

20
Abstract Comparison
Papers
%ofallpapers
1 ... 0.9 0.9 ... 0.8 0.8 ... 0.7 0.7 ... 0.6 0.6 ... 0.5 0.5 ... 0.4 0.4 ... 0.3 0.3 ... 0.2 0.2 ... 0.1 0.1 ... 0
1100020003000400050006000700080009000
0102030405060708090100
Length
Levenshtein
Cosine
Sorensen
Jaccard
Percentage

21
10.1016/j.physletb.2006.10.068
Physics Letters B

22

23
Body Comparison
Papers
%ofallpapers
1 ... 0.9 0.9 ... 0.8 0.8 ... 0.7 0.7 ... 0.6 0.6 ... 0.5 0.5 ... 0.4 0.4 ... 0.3 0.3 ... 0.2 0.2 ... 0.1 0.1 ... 0
110002000300040005000600070008000
0102030405060708090100
Length
Levenshtein
Cosine
Sorensen
Jaccard
Percentage

24
Publication Dates
Papers
0100030005000
1−90
91−180
181−270
271−360
361−450
451−540
541−630
631−720
>720
Pre−print first
Final published first
Number of days

25
Assembling a pre-print corpus
Source: arXiv.org
• 1.1 million publication records
• metadata (typical DC, including DOI) obtained
via OAI-PMH interface
• PDF versions of articles available via Amazon’s
S3 service (using “requester pays” option)
• *Latest version used if multiple available*
• 35% of all arXiv papers have > 1 version
• 58% of our matched papers have > 1 version
• Repeat experiment with *earliest version*

26
Publication Dates of Earliest Versions
Papers
Number of days
01000200030004000
1−90
91−180
181−270
271−360
361−450
451−540
541−630
631−720
>720
Pre−print first
Final published first

27
Title Deltas
Papers
%ofallpapers
1 ... 0.9 0.9 ... 0.8 0.8 ... 0.7 0.7 ... 0.6 0.6 ... 0.5 0.5 ... 0.4 0.4 ... 0.3 0.3 ... 0.2 0.2 ... 0.1 0.1 ... 0
−1000−800−600−400−2000200
1009080706050403020100
Length
Levenshtein
Cosine
Sorensen
Jaccard
Percentage

28
Title Deltas
Papers
%ofallpapers
1 ... 0.9 0.9 ... 0.8 0.8 ... 0.7 0.7 ... 0.6 0.6 ... 0.5 0.5 ... 0.4 0.4 ... 0.3 0.3 ... 0.2 0.2 ... 0.1 0.1 ... 0
−1000−800−600−400−2000200
1009080706050403020100
Length
Levenshtein
Cosine
Sorensen
Jaccard
Percentage

29
Title Deltas
Papers
%ofallpapers
1 ... 0.9 0.9 ... 0.8 0.8 ... 0.7 0.7 ... 0.6 0.6 ... 0.5 0.5 ... 0.4 0.4 ... 0.3 0.3 ... 0.2 0.2 ... 0.1 0.1 ... 0
−1000−800−600−400−2000200
1009080706050403020100
Length
Levenshtein
Cosine
Sorensen
Jaccard
Percentage

30
Abstract Deltas
Papers
%ofallpapers
1 ... 0.9 0.9 ... 0.8 0.8 ... 0.7 0.7 ... 0.6 0.6 ... 0.5 0.5 ... 0.4 0.4 ... 0.3 0.3 ... 0.2 0.2 ... 0.1 0.1 ... 0
−1500−1000−5000500
1009080706050403020100
Length
Levenshtein
Cosine
Sorensen
Jaccard
Percentage

31
Body Deltas
Papers
%ofallpapers
1 ... 0.9 0.9 ... 0.8 0.8 ... 0.7 0.7 ... 0.6 0.6 ... 0.5 0.5 ... 0.4 0.4 ... 0.3 0.3 ... 0.2 0.2 ... 0.1 0.1 ... 0
−1500−1000−50005001000
100806040200
Length
Levenshtein
Cosine
Sorensen
Jaccard
Percentage

32
Discussion & Future Work
• Single corpus experiment
• Pre-print/final published matches based on:
• DOIs
• CrossRef API results
• UCLA serial subscriptions (majority Elsevier
publications)
• Expand to other disciplines/publishers
• Overlay with ISI Impact factor and usage statistics
• Refine extraction/comparison of authors and
references
• Operate at scale

Comparing Published Scientific Journal Articles to Their Pre-print Versions

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