Monthly Archives: January 2017

Vaccine Delivery, the case of HPV prevention

Tough choices are when and how much. http://jamanetwork.com/journals/jama/fullarticle/2588253

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Filed under global health

Write-up of my SIAM Tutorial

That was nice of them to do: https://sinews.siam.org/Details-Page/machine-learnings-impact-on-global-public-health

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Filed under global health

So cool–nbtutor

The first release of nbtutor (“Visualize Python code execution (line-by-line) in Jupyter Notebook cells.”) is available on pypi:

pip install nbtutor
jupyter nbextension install --sys-prefix --overwrite --py nbtutor
jupyter nbextension enable --sys-prefix --py nbtutor

https://github.com/lgpage/nbtutor

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Filed under education

Pretty good alphabet book

This was not designed for kids, but it seems to have captured my 4 year old’s attention for the moring: https://www.cdc.gov/dpdx/az.html

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Point/Polygon Pubs

Some additional papers on the point/polygon problem:

Click to access 1505.06891v1.pdf


Click to access 1608.03769.pdf

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Filed under statistics

Named Entity Resolution in Python

http://textminingonline.com/how-to-use-stanford-named-entity-recognizer-ner-in-python-nltk-and-other-programming-languages

https://github.com/aboSamoor/polyglot

http://nlp.stanford.edu/software/CRF-NER.shtml#Download

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GATHER

Did I not yet blog about the GATHER guidelines? I know I sent some excited emails about them when they were released. GATHER mandates reproducible research for descriptive epidemiology. Full details: http://www.thelancet.com/journals/lancet/article/PIIS0140-6736(16)30388-9/fulltext

Summary image [replace with a prettier version]: http://www.thelancet.com/cms/attachment/2061463589/2063015189/si1.gif

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Global Health and the US Election

Heidi Larson | November 19, 2016

Donald Trump could be the biggest single threat to vaccine confidence ever faced.

The confidence levels required to maintain vaccination at a sufficient level to ensure herd immunity are high. Currently 83% of Americans think that vaccines are safe – but, only a small drop in that number could lower vaccine confidence and uptake to unacceptable levels and risk disease outbreaks. In Texas, Wakefield’s current home state, the trend in vaccine exemptions is already accelerating with the number of exemptions up to 44,716 in 2016, from only 2,314 in 2003.

http://www.vaccineconfidence.org/dangerous-liaisons

May I suggest that the term “herd immunity” should be replaced? To me, it sounds disrespectful to the children the vaccines are intended to protect. I think “group immunity” could be an alternative amenable to the editor’s find-and-replace feature.

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Measures of Interdisciplinarity Summary

Interesting email from SCISIP mailing list: Re: [scisip] Looking for statistics about state of interdisciplinary research
Tue 11/22/2016 8:10 AM

Hi, all:

Thank you to those who helped me pull some numbers on the status interdisciplinary research. Here is what I found just from these two listservs. It’s simply a summary of the replies I received, not a comprehensive literature review. Hope it’s helpful. Full references are below my signature.

Interdisciplinary Research (IDR) Statistics
Funding:
• Bethany Laursen (22 November 2016) did a keyword search for “interdisciplinary” of the active, forecasted, closed, and archived grants posted at http://www.grants.gov. This search returned $15.6 trillion earmarked for IDR and programs from 2007-2019 by all US agencies. Active and forecasted grants from this search total nearly $1.3 trillion.

Publications:
Authorship
• Porter and Rafols (2009) reported an approximately 75% increase in the number of co-authors across 6 topic domains from 1975-2005
• The National Research Council publication Enhancing the Effectiveness of Team Science (2015, p.1) reported that 90% of all publications are now authored by two or more people.

Topics/Subject Matter
• Van Noorden (2015) illustrated a slight increase in the % of papers citing other disciplines over recent decades, and a slight decrease in the % of papers citing the same discipline
• Porter and Rafols (2009) report an approximately 50% increase in the # of cited disciplines per article across 6 topic domains from 1975-2005.
• Porter and Rafols (2009) also report that the disciplines that are cited tend to be near each other (i.e., narrow IDR). However, this might be due to the dominance of the quantity of articles coming from the USA in 1975-2005. A report from Elsevier (2015) showed that USA articles tend to be narrowly interdisciplinary. Interestingly, as of 2013, China now produces as many (perhaps more) IDR articles as the USA, and their articles are much more broadly interdisciplinary.

Citation Impact
• Van Noorden (2015) showed that in the short term (3 years post-publication) the more interdisciplinary an article is, the fewer citations it gets compared to other articles. However, that trend reverses over the long term (13 years post-publication).

Titles of Articles
• Van Noorden (2015) showed there has been a dramatic increase in the number of social science and humanities articles that include the word “interdisciplin*” in their titles over recent decades. This increase has been less dramatic for the natural sciences and engineering.

Dissertations:
• Bowman et al (2014) demonstrate that 2.3 million dissertations in ProQuest are better classified by topic than by subject category, indicating an emerging “post-disciplinary” research space.

How to Measure IDR:
• Wagner et al (2010) discuss principles for choosing measures of IDR
• Sugimoto and Weingart (2015) clearly and comprehensively review how the word “discipline” developed across the world and how we now operationalize it in terms of journals, founding “great men,” and other social phenomena.
• Porter and Rafols (2009) describe and apply the Rao-Stirling diversity index
• Guevara et al (2016) demonstrate a new method for mapping the “research space” in terms of fields in which the same author publishes.

Thanks, all! Hope to see many of you at SciTS next year.

Bethany

______________
Bethany Laursen
Ph.D. student, Community Sustainability
M.A. student, Philosophy
Michigan State University

References
Bowman, T. D., Tsou, A., Ni, C., & Sugimoto, C. R. (2014). Post-interdisciplinary frames of reference: exploring permeability and perceptions of disciplinarity in the social sciences. Scientometrics, 101(3), 1695–1714. http://doi.org/10.1007/s11192-014-1338-z

Elsevier. (2015). A Review of the UK’s Interdisciplinary Research Using a Citation-Based Approach (pp. 1–102).

Guevara, M. R., Hartmann, D., Aristarán, M., Mendoza, M., & Hidalgo, C. A. (2016). The research space: using career paths to predict the evolution of the research output of individuals, institutions, and nations. Scientometrics, 1–22. http://doi.org/10.1007/s11192-016-2125-9

National Research Council. (2015). Enhancing the Effectiveness of Team Science. (N. J. Cooke & M. L. Hilton, Eds.) (pp. 1–256). Washington, D.C.: National Academies Press. http://doi.org/10.17226/19007

Porter, A. L., & Rafols, I. (2009). Is science becoming more interdisciplinary? Measuring and mapping six research fields over time. Scientometrics, 81(3), 719–745. http://doi.org/10.1007/s11192-008-2197-2

Sugimoto, C. R., & Weingart, S. (2015). The kaleidoscope of disciplinarity. Journal of Documentation, 71(4), 775–794. http://doi.org/10.1108/JD-06-2014-0082

Van Noorden, R. (2015). Interdisciplinary research by the numbers. Nature, 525(7569), 306–307. http://doi.org/10.1038/525306a

Wagner, C. S., Roessner, J. D., Bobb, K., Klein, J. T., Boyack, K. W., Keyton, J., et al. (2011). Approaches to understanding and measuring interdisciplinary scientific research (IDR): A review of the literature. Journal of Informetrics, 5(1), 14–26. http://doi.org/10.1016/j.joi.2010.06.004

On Nov 11, 2016, at 10:38 AM, Bethany Laursen wrote:

Hi, everyone:

My work in this field tends to be qualitative and philosophical. Does anyone have some recent statistics that might summarize the state of interdisciplinary research, in the USA or beyond? For example,

• $$ spent on interdisciplinary research annually by NSF, NIH
• Trending average # of fields per publication per the Web of Science taxonomy
• Trend in # of interdisciplinary journals
• etc.

Thanks in advance for filling in a gap in my knowledge!

Bethany

______________
Bethany Laursen
Ph.D. student, Community Sustainability
M.A. student, Philosophy
Michigan State University

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Perfect Timing

This may be just what I needed:

Dear Abraham,

I am pleased to announce that Foundations and Trends in Machine Learning (www.nowpublishers.com/mal) has published the following issue:

Volume 9, Issue 2-3
Patterns of Scalable Bayesian Inference
By Elaine Angelino (University of California, Berkeley, USA), Matthew James Johnson (Harvard University, USA) and
Ryan P. Adams (Harvard University and Twitter, USA)
http://dx.doi.org/10.1561/2200000052

The link will take you to the article abstract. If your library has a subscription, you will be able to download the PDF of the article.
If you do not have access, download the free preview here: http://www.nowpublishers.com/article/DownloadSummary/MAL-052

To purchase the book version of this issue, go to the secure Order Form:
http://www.nowpublishers.com/Order/BuyBook?isbn=978-1-68083-218-1
You will receive the alert member discount price of $40 (includes shipping) by quoting the Promotion Code: 318306

This issue is also available for purchase at this year’s NIPS conference. Visit our booth to view all of the latest FnT ML titles.

Best Regards,

Tanya Capawana
now publishers

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