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Publication - Dr Louise Millard

    Using ILP to Identify Pathway Activation Patterns in Systems Biology


    Neaves, S, Millard, L & Tsoka, S, 2016, ‘Using ILP to Identify Pathway Activation Patterns in Systems Biology’. in: Katsumi Inoue, Hayato Ohwada, Akihiro Yamamoto (eds) Inductive Logic Programming: 25th International Conference, ILP 2015, Kyoto, Japan, August 20-22, 2015, Revised Selected Papers. Springer Verlag, pp. 137-151


    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.

    Full details in the University publications repository