Dependency And Amr Embeddings For Drug-Drug Interaction Extraction From Biomedical Literature

Keywords

Abstract Meaning Representation; Deep learning; Dependency; Drug-drug interaction; Embeddings

Abstract

Drug-drug interaction (DDI) is an unexpected change in a drug's effect on the human body when the drug and a second drug are co-prescribed and taken together. As many DDIs are frequently reported in biomedical literature, it is important to mine DDI information from literature to keep DDI knowledge up to date. One of the SemEval challenges in the year 2011 and 2013 was designed to tackle the task where the best system achieved an F1 score of 0.80. In this paper, we propose to utilize dependency embeddings and Abstract Meaning Representation (AMR) embeddings as features for extracting DDIs. Our contribution is two-fold. First, we employed dependency embeddings, previously shown effective for sentence classification, for DDI extraction. The dependency embeddings incorporated structural syntactic contexts into the embeddings, which were not present in the conventional word embeddings. Second, we proposed a novel syntactic embedding approach using AMR. AMR aims to abstract away from syntactic idiosyncrasies and attempts to capture only the core meaning of a sentence, which could potentially improve DDI extraction from sentences. Two classifiers (Support Vector Machine and Random Forest) taking these embedding features as input were evaluated on the DDIExtraction 2013 challenge corpus. The experimental results show the effectiveness of dependency and AMR embeddings in the DDI extraction task. The best performance was obtained by combining word, dependency and AMR embeddings (F1 score=0.84).

Publication Date

8-20-2017

Publication Title

ACM-BCB 2017 - Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics

Number of Pages

36-43

Document Type

Article; Proceedings Paper

Personal Identifier

scopus

DOI Link

https://doi.org/10.1145/3107411.3107426

Socpus ID

85031316038 (Scopus)

Source API URL

https://api.elsevier.com/content/abstract/scopus_id/85031316038

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