We introduce a family of deep-learning architectures for inter-sentence relation extraction, i.e., relations where the participants are not necessarily in the same sentence. We apply these architectures to an important use case in the biomedical domain: assigning biological context to biochemical events. In this work, biological context is defined as the type of biological system within which the biochemical event is observed. The neural architectures encode and aggregate multiple occurrences of the same candidate context mentions to determine whether it is the correct context for a particular event mention. We propose two broad types of architectures: the first type aggregates multiple instances that correspond to the same candidate context with respect to event mention before emitting a classification; the second type independently classifies each instance and uses the results to vote for the final class, akin to an ensemble approach. Our experiments show that the proposed neural classifiers are competitive and some achieve better performance than previous state of the art traditional machine learning methods without the need for feature engineering. Our analysis shows that the neural methods particularly improve precision compared to traditional machine learning classifiers and also demonstrates how the difficulty of inter-sentence relation extraction increases as the distance between the event and context mentions increase.

Mutations in oncogenes are much more likely to lead to cancer in some tissue types than others, because some tissues express other proteins that counteract the oncogene. For example, in mice, the G12D activating mutation in K-ras causes lung tumors but not muscle-derived sarcomas, because muscle cells express two proteins (Arf and Ink4a) that cause cell division to halt when Ras is overactive. An automated event extraction system might extract the biochemical event "G12D activates mutation in K-ras", but without understanding the biological context - of whether this event occurs in lung or muscle tissue - the reader will not understand why the event does or does not lead to cancer. Biological context is not only important, it also comes in many varieties. Here we focus on biological container context, where a biological "container" may be specified at various levels of granularity, but each level serves to further specify the type of biological system in which an event might occur.