Visualizing the topical structure of the medical sciences: a self-organizing map approach.

<h4>Background</h4>We implement a high-resolution visualization of the medical knowledge domain using the self-organizing map (SOM) method, based on a corpus of over two million publications. While self-organizing maps have been used for document visualization for some time, (1) little i...

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Autores principales:	André Skupin, Joseph R Biberstine, Katy Börner
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/463a78a1ce244a388c64fadd27d70b25
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spelling	oai:doaj.org-article:463a78a1ce244a388c64fadd27d70b252021-11-18T07:53:49ZVisualizing the topical structure of the medical sciences: a self-organizing map approach.1932-620310.1371/journal.pone.0058779https://doaj.org/article/463a78a1ce244a388c64fadd27d70b252013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23554924/?tool=EBIhttps://doaj.org/toc/1932-6203<h4>Background</h4>We implement a high-resolution visualization of the medical knowledge domain using the self-organizing map (SOM) method, based on a corpus of over two million publications. While self-organizing maps have been used for document visualization for some time, (1) little is known about how to deal with truly large document collections in conjunction with a large number of SOM neurons, (2) post-training geometric and semiotic transformations of the SOM tend to be limited, and (3) no user studies have been conducted with domain experts to validate the utility and readability of the resulting visualizations. Our study makes key contributions to all of these issues.<h4>Methodology</h4>Documents extracted from Medline and Scopus are analyzed on the basis of indexer-assigned MeSH terms. Initial dimensionality is reduced to include only the top 10% most frequent terms and the resulting document vectors are then used to train a large SOM consisting of over 75,000 neurons. The resulting two-dimensional model of the high-dimensional input space is then transformed into a large-format map by using geographic information system (GIS) techniques and cartographic design principles. This map is then annotated and evaluated by ten experts stemming from the biomedical and other domains.<h4>Conclusions</h4>Study results demonstrate that it is possible to transform a very large document corpus into a map that is visually engaging and conceptually stimulating to subject experts from both inside and outside of the particular knowledge domain. The challenges of dealing with a truly large corpus come to the fore and require embracing parallelization and use of supercomputing resources to solve otherwise intractable computational tasks. Among the envisaged future efforts are the creation of a highly interactive interface and the elaboration of the notion of this map of medicine acting as a base map, onto which other knowledge artifacts could be overlaid.André SkupinJoseph R BiberstineKaty BörnerPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 3, p e58779 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q André Skupin Joseph R Biberstine Katy Börner Visualizing the topical structure of the medical sciences: a self-organizing map approach.
description	<h4>Background</h4>We implement a high-resolution visualization of the medical knowledge domain using the self-organizing map (SOM) method, based on a corpus of over two million publications. While self-organizing maps have been used for document visualization for some time, (1) little is known about how to deal with truly large document collections in conjunction with a large number of SOM neurons, (2) post-training geometric and semiotic transformations of the SOM tend to be limited, and (3) no user studies have been conducted with domain experts to validate the utility and readability of the resulting visualizations. Our study makes key contributions to all of these issues.<h4>Methodology</h4>Documents extracted from Medline and Scopus are analyzed on the basis of indexer-assigned MeSH terms. Initial dimensionality is reduced to include only the top 10% most frequent terms and the resulting document vectors are then used to train a large SOM consisting of over 75,000 neurons. The resulting two-dimensional model of the high-dimensional input space is then transformed into a large-format map by using geographic information system (GIS) techniques and cartographic design principles. This map is then annotated and evaluated by ten experts stemming from the biomedical and other domains.<h4>Conclusions</h4>Study results demonstrate that it is possible to transform a very large document corpus into a map that is visually engaging and conceptually stimulating to subject experts from both inside and outside of the particular knowledge domain. The challenges of dealing with a truly large corpus come to the fore and require embracing parallelization and use of supercomputing resources to solve otherwise intractable computational tasks. Among the envisaged future efforts are the creation of a highly interactive interface and the elaboration of the notion of this map of medicine acting as a base map, onto which other knowledge artifacts could be overlaid.
format	article
author	André Skupin Joseph R Biberstine Katy Börner
author_facet	André Skupin Joseph R Biberstine Katy Börner
author_sort	André Skupin
title	Visualizing the topical structure of the medical sciences: a self-organizing map approach.
title_short	Visualizing the topical structure of the medical sciences: a self-organizing map approach.
title_full	Visualizing the topical structure of the medical sciences: a self-organizing map approach.
title_fullStr	Visualizing the topical structure of the medical sciences: a self-organizing map approach.
title_full_unstemmed	Visualizing the topical structure of the medical sciences: a self-organizing map approach.
title_sort	visualizing the topical structure of the medical sciences: a self-organizing map approach.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/463a78a1ce244a388c64fadd27d70b25
work_keys_str_mv	AT andreskupin visualizingthetopicalstructureofthemedicalsciencesaselforganizingmapapproach AT josephrbiberstine visualizingthetopicalstructureofthemedicalsciencesaselforganizingmapapproach AT katyborner visualizingthetopicalstructureofthemedicalsciencesaselforganizingmapapproach
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Visualizing the topical structure of the medical sciences: a self-organizing map approach.

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