Multiscale Laplacian graph kernel combined with lexico-syntactic patterns for biomedical event extraction from literature

Abstract

Bio-event extraction is an extensive research area in the field of biomedical text mining, this focuses on elaborating relationships between biomolecules and can provide various aspects of their nature. Bio-event extraction plays a vital role in biomedical literature mining applications such as biological network construction, pathway curation, and drug repurposing. Extracting biological events automatically is a difficult task because of the uncertainty and assortment of natural language processing such as negations and speculations, which provides further room for the development of feasible methodologies. This paper presents a hybrid approach that integrates an ensemble-learning framework by combining a Multiscale Laplacian Graph kernel and a feature-based linear kernel, using a pattern-matching engine to identify biomedical events with arguments. This graph-based kernel not only captures the topological relationships between the individual event nodes but also identifies the associations among the subgraphs for complex events. In addition, the lexico-syntactic patterns were used to automatically discover the semantic role of each word in the sentence. For performance evaluation, we used the gold standard corpora, namely BioNLP-ST (2009, 2011, and 2013) and GENIA-MK. Experimental results show that our approach achieved better performance than other state-of-the-art systems.