How to work with scientific literature¶

Nikolay Karelin, PhD

Head of AI, silkdata.ai

Outline¶

• Intro / Motivation
• The way of paper
• Search: Scholar Google and beyond
• Working through paper
• Storage and collaboration
• A bit on economics: Why $15-45 a paper?

Slides and links¶

https://github.com/karelin/sci_papers_talk

Intro¶

Papers, papers, PAPERS ....¶

• ArXiv.org
• NIPS
• ACL
• ACM
• ...

How to select a paper for next product/feature?¶

Goals¶

• Academia
  • New knowledge
  • Grants
• Industry
  • New but settled approaches
  • Algorithms / data / details
• Science is driven by community
  • Papers as main communication media

Innovation risk profile¶

From https://www.slideshare.net/Verhaert/innovation-day-2012-11-luc-van-goethem-frederik-wouters-verhaert-risk-requirements-cooperating-or-counteracting-forces-in-the-process/8

About me¶

• In R&D since 1995
  • Academy: Optics (images), 1995-2008
  • Industry: simulation / HPC, 2008-2017
  • ML
• PhD / optics

Annual number of papers¶

From: Istvan Daruka, Publication dynamics and the proliferation of scientific journals, DOI:10.1051/epn/2014102, 2014

The way of paper¶

Paper types¶

• 'Classical'
  • Letter
  • (Regular / full) article
  • Review
  • Tutorial
  • Conference (extended) abstract
  • Conference proceedings
  • Book chapter
• 'New way'
  • e-print
• Status
  • Invited

Why????¶

• Community
• Habits and traditions
• Slow pace

Peer-review¶

Rejectrion ratio / Time / Bias

Review: variants¶

• Endorsement (arXiv.org)
• Editor's coice (coferences / invited papers)
• Single-round (conferences)
• Post-publication (experimental)

Experiments: https://distill.pub

Review: NIPS¶

• Double blind
• Max 5-6 papers per reviewer
• Criteria
  • Novelty
  • Not submitted elsewhere
  • Quality
  • Significance
  • Clarity
  • Subject area

Details: https://nips.cc/Conferences/2016/PaperInformation/ReviewerInstructions

arXiv.org¶

• Founded in 1991
• Mostly physics
• Initially: pre-print system
• Endorsement system since January 17, 2004, https://arxiv.org/help/endorsement

Stats:¶

From https://arxiv.org/help/stats/2017_by_area/index

arXiv.org: story¶

Why it was banned back in 1990s?

xxx.lanl.gov¶

By Source (WP:NFCC#4), Fair use, https://en.wikipedia.org/w/index.php?curid=55801807

Where to find papers?¶

scholar.google.com¶

scholar.google.com¶

scholar.google.com¶

• Non-commercial project
• Citations
• Free PDFs
• Author profile
• Recommendations (for authors!)

Author profile¶

Source: https://scholar.google.com/citations?user=WLN3QrAAAAAJ&hl=en&oi=ao

Useful browser extensions¶

• Google scholar button
• Unpaywall, https://unpaywall.org/products/extension
• Kopernio, https://kopernio.com/

DOI¶

• Digital Opject Identifier
  • doi.org/10.ddd/xxxxxxx
• Not only papers:
  • Zenodo, https://zenodo.org/
  • GitHub, https://guides.github.com/activities/citable-code/
  • figshare, https://figshare.com/about

arxiv-sanity.com¶

researchgate.net¶

researchgate.net¶

• Subscription
• Reads
• Citations
• Legal status unclear

Open data / APIs¶

• arXiv.org: OAI-PMH, https://arxiv.org/help/oa/index
• Cross-ref, https://www.crossref.org/services/metadata-delivery/
• Unpaywall, https://unpaywall.org/products/api
• Open citations, http://opencitations.net/
• PubMed/PubChem, https://www.ncbi.nlm.nih.gov/home/develop/api/
• ... many closed sources

Working through a paper¶

Possible order¶

• Authors
• Refences
• Figures / tables
• Discussion / conclusion
• Code
• Supplement
• ... read all!

Author order¶

References¶

References - old style¶

Example: https://habrahabr.ru/company/ods/blog/329410/

Abstract: http://naacl2013.naacl.org/abstracts/37.aspx
Paper: https://www.aclweb.org/anthology/N13-1090

Caveats¶

• Style
• Author's goal: new result
• Reference relevance
• No sentiments
• Code updates, ...

From https://www.stm-assoc.org/2009_10_13_MWC_STM_Report.pdf

Storing and collaborationg¶

Why storing?¶

• Notes and comments
• Collaboration
• Access instability

BibTeX¶

• BibTeX-Wikipedia.png
• https://en.wikipedia.org/wiki/BibTeX

BibTeX & JabRef¶

http://www.jabref.org/

Zotero¶

https://www.zotero.org/

Zotero: features and issues¶

• Not only scholar papers (web-pages)
• Export / import
• Community
• Extensions
• Collaborration: paid!

Mendeley¶

Mendeley¶

• Process raw collection
• Mobile client
• Proprietory
• Collaboration: paid!

I, Librarian¶

I'Librarian¶

• https://i-librarian.net/index.php
• https://github.com/mkucej/i-librarian

I'Librarian¶

• Easy setup
• Collaboration
• Almost no sharing of comments
• Low support / rare updates
• Old-style PHP code

A bit on economics¶

Why so expensive?

Publishing process¶

Publishing process¶

• Small circulation
• Complex typography
• Peer-review process
• No self-plagiarism

Classical publishing process: Offprints¶

Source: http://englishcoffeedrinker.blogspot.com.by/2009/12/offprints-and-odd-things.html

Number of scientific journals¶

From https://www.stm-assoc.org/2009_10_13_MWC_STM_Report.pdf

Bell Syst. Tech. J.¶

http://www.alcatel-lucent.com/bstj/

http://netmgt.blogspot.com.by/2012/10/available-in-pdf-bell-system-technical.html

Now: https://ieeexplore.ieee.org/xpl/RecentIssue.jsp?punumber=6731005 (paid!)

Future?¶

• Copyright reform
• New publishing modles
• Data science:
  • Products
  • Automatic analysis
  • ???

We are hiring!¶

• Junior / middle data scientist wanted
• Text / document processing
• Outsource / internal projects

Thank you for attention¶

Nikolay Karelin

Facebook: https://www.facebook.com/nikolay.karelin
Twitter: @nick_karelin
Linked: https://www.linkedin.com/in/nikolay-karelin/

Slides: https://github.com/karelin/sci_papers_talk