Using ILP to identify pathway activation patterns in systems biology

Neaves, Samuel ORCID: https://orcid.org/0000-0002-4064-3794, Millard, Louise A.C. and Tsoka, Sophia 2016. Using ILP to identify pathway activation patterns in systems biology. Presented at: 25th International Conference, ILP 2015, Kyoto, Japan, 20–22 August 2015. Inductive Logic Programming. ILP 2015. Lecture Notes in Computer Science , vol.9575 Springer, pp. 137-151. 10.1007/978-3-319-40566-7_10

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Abstract

We show a logical aggregation method that, combined with propositionalization methods, can construct novel structured biological features from gene expression data. We do this to gain understanding of pathway mechanisms, for instance, those associated with a particular disease. We illustrate this method on the task of distinguishing between two types of lung cancer; Squamous Cell Carcinoma (SCC) and Adenocarcinoma (AC). We identify pathway activation patterns in pathways previously implicated in the development of cancers. Our method identified a model with comparable predictive performance to the winning algorithm of a recent challenge, while providing biologically relevant explanations that may be useful to a biologist.

Item Type:	Conference or Workshop Item (Paper)
Date Type:	Published Online
Status:	Published
Schools:	Schools > Medicine
Publisher:	Springer
ISBN:	9783319405650
Last Modified:	19 Nov 2024 16:01
URI:	https://orca.cardiff.ac.uk/id/eprint/172256

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