Mario Sänger1, Ulf Leser1. 1. Computer Science Department, Knowledge Management in Bioinformatics, Humboldt-Universität zu Berlin, Berlin 10099, Germany.
Abstract
MOTIVATION: The automatic extraction of published relationships between molecular entities has important applications in many biomedical fields, ranging from Systems Biology to Personalized Medicine. Existing works focused on extracting relationships described in single articles or in single sentences. However, a single record is rarely sufficient to judge upon the biological correctness of a relation, as experimental evidence might be weak or only valid in a certain context. Furthermore, statements may be more speculative than confirmative, and different articles often contradict each other. Experts therefore always take the complete literature into account to take a reliable decision upon a relationship. It is an open research question how to do this effectively in an automatic manner. RESULTS: We propose two novel relation extraction approaches which use recent representation learning techniques to create comprehensive models of biomedical entities or entity-pairs, respectively. These representations are learned by considering all publications from PubMed mentioning an entity or a pair. They are used as input for a neural network for classifying relations globally, i.e. the derived predictions are corpus-based, not sentence- or article based as in prior art. Experiments on the extraction of mutation-disease, drug-disease and drug-drug relationships show that the learned embeddings indeed capture semantic information of the entities under study and outperform traditional methods by 4-29% regarding F1 score. AVAILABILITY AND IMPLEMENTATION: Source codes are available at: https://github.com/mariosaenger/bio-re-with-entity-embeddings. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
MOTIVATION: The automatic extraction of published relationships between molecular entities has important applications in many biomedical fields, ranging from Systems Biology to Personalized Medicine. Existing works focused on extracting relationships described in single articles or in single sentences. However, a single record is rarely sufficient to judge upon the biological correctness of a relation, as experimental evidence might be weak or only valid in a certain context. Furthermore, statements may be more speculative than confirmative, and different articles often contradict each other. Experts therefore always take the complete literature into account to take a reliable decision upon a relationship. It is an open research question how to do this effectively in an automatic manner. RESULTS: We propose two novel relation extraction approaches which use recent representation learning techniques to create comprehensive models of biomedical entities or entity-pairs, respectively. These representations are learned by considering all publications from PubMed mentioning an entity or a pair. They are used as input for a neural network for classifying relations globally, i.e. the derived predictions are corpus-based, not sentence- or article based as in prior art. Experiments on the extraction of mutation-disease, drug-disease and drug-drug relationships show that the learned embeddings indeed capture semantic information of the entities under study and outperform traditional methods by 4-29% regarding F1 score. AVAILABILITY AND IMPLEMENTATION: Source codes are available at: https://github.com/mariosaenger/bio-re-with-entity-embeddings. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.