Article (Scientific journals)
Machine Learning to Support the Presentation of Complex Pathway Graphs.
Nielsen, Sune Steinbjorn; Ostaszewski, Marek; McGee, Fintan et al.
2019In IEEE/ACM Transactions on Computational Biology and Bioinformatics
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Keywords :
Network visualization; Bioinformatics; Machine learning
Abstract :
[en] Visualization of biological mechanisms by means of pathway graphs is necessary to better understand the often complex underlying system. Manual layout of such pathways or maps of knowledge is a difficult and time consuming process. Node duplication is a technique that makes layouts with improved readability possible by reducing edge crossings and shortening edge lengths in drawn diagrams. In this article we propose an approach using Machine Learning (ML) to facilitate parts of this task by training a Support Vector Machine (SVM) with actions taken during manual biocuration. Our training input is a series of incremental snapshots of a diagram describing mechanisms of a disease, progressively curated by a human expert employing node duplication in the process. As a test of the trained SVM models, they are applied to a single large instance and 25 medium-sized instances of hand-curated biological pathways. Finally, in a user validation study, we compare the model predictions to the outcome of a node duplication questionnaire answered by users of biological pathways with varying experience. We successfully predicted nodes for duplication and emulated human choices, demonstrating that our approach can effectively learn human-like node duplication preferences to support curation of pathway diagrams in various contexts.
Research center :
- Luxembourg Centre for Systems Biomedicine (LCSB): Bioinformatics Core (R. Schneider Group)
Disciplines :
Computer science
Author, co-author :
Nielsen, Sune Steinbjorn ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB) ; Luxembourg Institute of Science & Technology - LIST > Environmental Research and Innovation (ERIN) Department
Ostaszewski, Marek  ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)
McGee, Fintan;  Luxembourg Institute of Science & Technology - LIST > Environmental Research and Innovation (ERIN) Department
Hoksza, David ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)
Zorzan, Simone;  Luxembourg Institute of Science & Technology - LIST > Environmental Research and Innovation (ERIN) Department
External co-authors :
no
Language :
English
Title :
Machine Learning to Support the Presentation of Complex Pathway Graphs.
Publication date :
2019
Journal title :
IEEE/ACM Transactions on Computational Biology and Bioinformatics
ISSN :
1557-9964
Publisher :
IEEE Computer Society, United States - New York
Peer reviewed :
Peer Reviewed verified by ORBi
Focus Area :
Systems Biomedicine
Available on ORBilu :
since 09 October 2019

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