Granularity-aware fusion of biological networks for information extraction

Sean West, Hesham H Ali

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Current biomedical research approaches capture multiple data sources, fusing and integrating them to extract accurate information. While the purpose of fusion in the biomedical domain is to create a more holistic picture of biological reality, latent sensitivities of the fusion process often result in information loss. It has been shown that biomedical data fusion is sensitive to granularity dimensions, scales of semantic relationships across specificity and mereology. Low granularity data casts a wide net, while high granularity data has focus. When data fusion occurs between low and high granularities, these benefits counteract each other. In this study, we reexamine the union function as a basis for biomedical data fusions, via comparison to a granularity-aware function. This granularity-aware approach uses domain knowledge (low granularity) as a filter for expression relationships (high granularity). We use pancreatic cancer expression data and domain knowledge networks to test the fusion approaches. We support previous findings that granularity-unaware fusion allows domain knowledge to eclipse condition-specific data. In addition, we find that the granularity-aware approach tends to outperform both the union and non-fusion networks, resulting in higher information extraction scores. Further, the granularity-aware approach increases the network information extraction effect size between disease and normal networks, allowing for a more distinctive delineation between the two conditions.

Original languageEnglish (US)
Title of host publicationProceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017
EditorsIllhoi Yoo, Jane Huiru Zheng, Yang Gong, Xiaohua Tony Hu, Chi-Ren Shyu, Yana Bromberg, Jean Gao, Dmitry Korkin
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages638-642
Number of pages5
ISBN (Electronic)9781509030491
DOIs
StatePublished - Dec 15 2017
Event2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017 - Kansas City, United States
Duration: Nov 13 2017Nov 16 2017

Publication series

NameProceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017
Volume2017-January

Other

Other2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017
CountryUnited States
CityKansas City
Period11/13/1711/16/17

Fingerprint

Information Storage and Retrieval
Data fusion
Pancreatic Neoplasms
Semantics
Biomedical Research

Keywords

  • data fusion
  • granularity
  • information extraction
  • information loss

ASJC Scopus subject areas

  • Biomedical Engineering
  • Health Informatics

Cite this

West, S., & Ali, H. H. (2017). Granularity-aware fusion of biological networks for information extraction. In I. Yoo, J. H. Zheng, Y. Gong, X. T. Hu, C-R. Shyu, Y. Bromberg, J. Gao, ... D. Korkin (Eds.), Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017 (pp. 638-642). (Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017; Vol. 2017-January). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/BIBM.2017.8217728

Granularity-aware fusion of biological networks for information extraction. / West, Sean; Ali, Hesham H.

Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017. ed. / Illhoi Yoo; Jane Huiru Zheng; Yang Gong; Xiaohua Tony Hu; Chi-Ren Shyu; Yana Bromberg; Jean Gao; Dmitry Korkin. Institute of Electrical and Electronics Engineers Inc., 2017. p. 638-642 (Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017; Vol. 2017-January).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

West, S & Ali, HH 2017, Granularity-aware fusion of biological networks for information extraction. in I Yoo, JH Zheng, Y Gong, XT Hu, C-R Shyu, Y Bromberg, J Gao & D Korkin (eds), Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017. Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017, vol. 2017-January, Institute of Electrical and Electronics Engineers Inc., pp. 638-642, 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017, Kansas City, United States, 11/13/17. https://doi.org/10.1109/BIBM.2017.8217728
West S, Ali HH. Granularity-aware fusion of biological networks for information extraction. In Yoo I, Zheng JH, Gong Y, Hu XT, Shyu C-R, Bromberg Y, Gao J, Korkin D, editors, Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017. Institute of Electrical and Electronics Engineers Inc. 2017. p. 638-642. (Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017). https://doi.org/10.1109/BIBM.2017.8217728
West, Sean ; Ali, Hesham H. / Granularity-aware fusion of biological networks for information extraction. Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017. editor / Illhoi Yoo ; Jane Huiru Zheng ; Yang Gong ; Xiaohua Tony Hu ; Chi-Ren Shyu ; Yana Bromberg ; Jean Gao ; Dmitry Korkin. Institute of Electrical and Electronics Engineers Inc., 2017. pp. 638-642 (Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017).
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