2016 07-19 gender in computational biology

GENDER DISPARITY IN COMPUTATIONAL BIOLOGY

19 JULY, 2016

2016-07-19

OUTLINE

▸ Gender differences in Publication (background)

▸ Computationally inferring gender

▸ Gender in Biology, Computational Biology and Computer Science

2016-07-19

MEN PUBLISH MORE PAPERS THAN WOMEN

West JD, Jacquet J, King MM, Correll SJ, Bergstrom CT (2013) The Role of Gender in Scholarly Authorship. PLoS ONE 8(7): e66212. doi: 10.1371/journal.pone.0066212

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MEN PUBLISH MORE PAPERS THAN WOMEN

http://fivethirtyeight.com/features/in-science-it-matters-that-women-come-last/

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GENDER DISPARITY VARIES BY FIELD


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GENDER DISPARITY VARIES BY FIELD


http://www.eigenfactor.org/gender/#

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https://commons.wikimedia.org/wiki/File:Matilda_Effect.png

MEN GET MORE CREDIT FOR DISCOVERY THAN WOMEN

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MEN ARE MORE LIKELY TO BE CITED THAN WOMEN

http://www.nature.com/news/bibliometrics-global-gender-disparities-in-science-1.14321

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MEN CITE THEMSELVES MORE OFTEN THAN WOMEN

http://arxiv.org/abs/1607.00376

2016-07-19

INFERRING GENDER FROM FIRST NAMES


We use US Social Security Administration records to determine gender from first names. The US Social Security Administration website (http://www.ssa.gov/oact/babynames/) makes available the top 1000 names annually for each of the 153 million boys and 143 million girls born from 1880–2010. (These data acknowledge only two genders.) We assume we can identify an author's gender if the author's first name is associated with a single gender in social security records at least 95% of the time, as with ‘Mary’, or ‘John’. Otherwise, as with ‘Leslie’ or ‘Sidney’, we are unable to identify the gender and do not include that author in our analysis.

2016-07-19


“To provide the highest possible accuracy, we combine the data of multiple data sources. We use data from publicly available governmental sources and combine them with data we crawl from social networks, which provides you the best possible matches. Each name has to be verified by different sources to be added to our list.”

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BENEFITS:More names available than from census records alone

Androgynous names have probabilities associated

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MAJOR ISSUES:~50% of names have no gender information

Non-western names are less likely to have gender information

BENEFITS:More names available than from census records alone

Androgynous names have probabilities associated

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GUESSES MATCH VERIFIED GENDERS

BMJ 2016; 352 doi: http://dx.doi.org/10.1136/bmj.i847 (Published 02 March 2016)

2016-07-19

GUESSES MATCH VERIFIED GENDERS

BMJ 2016; 352 doi: http://dx.doi.org/10.1136/bmj.i847 (Published 02 March 2016)

Known

Known w/o

NA

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Medical Journal First Authors

P(f

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2016-07-19

OUTLINE

▸ Gender differences in Publication (background)

▸ Computationally inferring gender

▸ Gender in Biology, Computational Biology and Computer Science

2016-07-19

MOTIVATION


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MOTIVATION


COULD BIOLOGY BE A PATH TO COMPUTATIONAL/

QUANTITATIVE SKILLS?

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METHODOLOGY

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METHODOLOGY

▸ Download article info from Pubmed

http://nbviewer.jupyter.org/github/kescobo/gender-comp-bio/blob/name_stats/src/xml_parsing.ipynb

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METHODOLOGY


▸ MeSH Terms: “Biology” and “Computational Biology”


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METHODOLOGY



▸ 1997-2014


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METHODOLOGY



▸ 1997-2014

▸ Parse XML documents for author names, dates etc


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METHODOLOGY



▸ 1997-2014


▸ http://nbviewer.jupyter.org/github/kescobo/gender-comp-bio/blob/name_stats/src/xml_parsing.ipynb


2016-07-19

METHODOLOGY



▸ 1997-2014


▸ http://nbviewer.jupyter.org/github/kescobo/gender-comp-bio/blob/name_stats/src/xml_parsing.ipynb

▸ Use Gender API names to guess genders


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METHODOLOGY

PMID Date Journal Name Position Dataset P(Female) Count26251854 2015/08/06 JEmpirResHum

ResEthics Masaru last bio 0.01 345

26251854 2015/08/06 JEmpirResHumResEthics Ituro second bio NA 0

26251854 2015/08/06 JEmpirResHumResEthics Naoaki penulEmate bio 0 37

26251854 2015/08/06 JEmpirResHumResEthics Mayumi other bio 0.97 654

26152079 2015/07/08 ArchIntHistSci(Paris) Vallori first bio NA 0

26152076 2015/07/08 ArchIntHistSci(Paris) Pierre-Olivier first bio NA 0

26152076 2015/07/08 ArchIntHistSci(Paris) Bernardino last bio 0.02 627

26152075 2015/07/08 ArchIntHistSci(Paris) Dolores first bio 0.98 4438

26152074 2015/07/08 ArchIntHistSci(Paris) Simone first bio 0.33 54976

26031011 2015/06/02 Pak.J.Biol.Sci. Jamuna first bio 0.89 174

26031011 2015/06/02 Pak.J.Biol.Sci. Johanna last bio 0.98 15733

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DATA

▸ Biology (1997-2014)

▸ Publications: 202,818

▸ Authors: 1,111,776

▸ Computational Biology (1997-2014)

▸ Publications: 42882

▸ Authors: 244,141

2016-07-19

DATA

▸ Biology (1997-2014)

▸ Publications: 202,818

▸ Authors: 1,111,776

▸ Computational Biology (1997-2014)

▸ Publications: 42882

▸ Authors: 244,141

▸ Unique Names: 74760

▸ % Names with unknown gender: 43.0%

▸ % Authors with unknown gender: 26.6%

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ARXIV DATA

2006 2008 2010 2012 20140.0

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YearP(female)

Arxiv

Quant BioCS

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Author Position

P(f

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Arxiv Articles 2007-2014

Quant. BioCS

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CONCLUSIONS

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CONCLUSIONS

▸ There are large gender disparities in publishing

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CONCLUSIONS


▸ Computational Biology has larger disparities than Biology as a whole

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CONCLUSIONS


▸ Computational Biology has larger disparities than Biology as a whole

▸ But maybe… better than computer science?