Jonny: Undo revision 472 by Jonny (talk)

2022-10-26T21:12:18Z

Undo revision 472 by Jonny (talk)

← Older revision		Revision as of 21:12, 26 October 2022
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	{{Participant		{{Participant
	\|Timezone=~~CET~~ (~~GMT+01~~:00/~~GMT+02~~:00)		\|Timezone=America/Chicago (GMT−06:00/GMT−05:00)
	~~\|Affiliation=Deep Science Ventures~~
	\|Projects=SoftCite		\|Projects=SoftCite
	\|Table Assignment=Table 2		\|Table Assignment=Table 2

Jonny at 20:50, 26 October 2022

2022-10-26T20:50:02Z

← Older revision		Revision as of 20:50, 26 October 2022
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	{{Participant		{{Participant
	\|Timezone=~~America/Chicago~~ (~~GMT−06~~:00/~~GMT−05~~:00)		\|Timezone=CET (GMT+01:00/GMT+02:00)
			\|Affiliation=Deep Science Ventures
	\|Projects=SoftCite		\|Projects=SoftCite
			\|Table Assignment=Table 2
	}}		}}
	{{Workshop Submission		{{Workshop Submission

Jonny: Created page with "{{Participant |Timezone=America/Chicago (GMT−06:00/GMT−05:00) |Projects=SoftCite }} {{Workshop Submission |Interest=We are working to make software visible in the scholarly record, where it matters most to incentivizing high quality software work, and so that researchers, disciplines, and funders of science can all better discuss, analyze, coordinate, and improve our software dependent scientific work. I am interested in the workshop to explore understanding two asp..."

2022-10-26T20:08:05Z

Created page with "{{Participant |Timezone=America/Chicago (GMT−06:00/GMT−05:00) |Projects=SoftCite }} {{Workshop Submission |Interest=We are working to make software visible in the scholarly record, where it matters most to incentivizing high quality software work, and so that researchers, disciplines, and funders of science can all better discuss, analyze, coordinate, and improve our software dependent scientific work. I am interested in the workshop to explore understanding two asp..."

New page

{{Participant
|Timezone=America/Chicago (GMT−06:00/GMT−05:00)
|Projects=SoftCite
}}
{{Workshop Submission
|Interest=We are working to make software visible in the scholarly record, where it matters most to incentivizing high quality software work, and so that researchers, disciplines, and funders of science can all better discuss, analyze, coordinate, and improve our software dependent scientific work. I am interested in the workshop to explore understanding two aspects. 1. How entity extraction from scholarly documents can help synthesis, 2. Understanding how software, and collaboration on software, can change how science is done.

In particular I think that the work done to synthesize knowledge in software, and then make it available to communities of practice/scholarship, is an area that could be studied here. For example, the way that tidyverse in the R world has reshaped the way that people think about tabular data formats and their relationship to research methodology. Or the way that AtlasTi in its interface encodes particular understandings of grounded theory.

Tool use by scholars could also be an interesting way to identify potential cross-disciplinary opportunities, if otherwise unlinked communities are using similar tools.

I'm also interested in how infrastructures like protocols.io or research pre-registration could emerge synthesis and collaboraitons.
|Frame=Tool-builder
|Materials=We have created and published:
A gold-standard human annotation dataset, called SoftCite, consisting of just under 5,000 annotated academic PDFs (in biomedicine and economics) https://github.com/howisonlab/softcite-dataset/
A machine learning model for software entity extraction pipeline which processes scholarly PDFs directly and recognizes software mentions as good levels of performance with real distribution (F-scores ~0.80) https://github.com/softcite/software_mentions_client
Published new method approaches for machine learning on unbalanced datasets (Lopez et al., 2021)
A dataset of extractions from the CORD-19 paper collection (Du et al., 2021), which we have used to manually sample and describe current progress on software citation https://zenodo.org/record/5140437 and https://peerj.com/articles/cs-1022/

A prototype knowledge base which links software mentions and bibliometric data, allowing location of publications mentioning specific packages. https://github.com/softcite/softcite_kb

I have also bee part of ground studying the connection between "Theory" and "Code": https://arxiv.org/abs/1910.09902
|Organizer Topics=Machine Learning, Credit Assignment, Bibliometrics
}}

Patrice Lopez - Revision history

Jonny: Undo revision 472 by Jonny (talk)

Jonny at 20:50, 26 October 2022