Biomedical Event Trigger Identification Using Bidirectional Recurrent Neural Network Based Models

Biomedical events describe complex interactions between various biomedical entities. Event trigger is a word or a phrase which typically signifies the occurrence of an event. Event trigger identification is an important first step in all event extraction methods. However many of the current approaches either rely on complex hand-crafted features or consider features only within a window. In this paper we propose a method that takes the advantage of recurrent neural network (RNN) to extract higher level features present across the sentence. Thus hidden state representation of RNN along with word and entity type embedding as features avoid relying on the complex hand-crafted features generated using various NLP toolkits. Our experiments have shown to achieve state-of-art F1-score on Multi Level Event Extraction (MLEE) corpus. We have also performed category-wise analysis of the result and discussed the importance of various features in trigger identification task.Comment: The work has been accepted in BioNLP at ACL-201

Discovering Power Laws in Entity Length

This paper presents a discovery that the length of the entities in various datasets follows a family of scale-free power law distributions. The concept of entity here broadly includes the named entity, entity mention, time expression, aspect term, and domain-specific entity that are well investigated in natural language processing and related areas. The entity length denotes the number of words in an entity. The power law distributions in entity length possess the scale-free property and have well-defined means and finite variances. We explain the phenomenon of power laws in entity length by the principle of least effort in communication and the preferential mechanism

External Evaluation of Event Extraction Classifiers for Automatic Pathway Curation: An extended study of the mTOR pathway

This paper evaluates the impact of various event extraction systems on automatic pathway curation using the popular mTOR pathway. We quantify the impact of training data sets as well as different machine learning classifiers and show that some improve the quality of automatically extracted pathways