No abstract

No abstract

No abstract

Identifying interactions between proteins is important to understand underlying biological processes. Extracting a protein-protein interaction (PPI) from the raw text is often very difficult. Previous supervised learning methods have used handcrafted features on human-annotated data sets. In this paper, we propose a novel tree recurrent neural network with structured attention architecture for doing PPI. Our architecture achieves state of the art results (precision, recall, and F1-score) on the AIMed and BioInfer benchmark data sets. Moreover, our models achieve a significant improvement over previous best models without any explicit feature extraction. Our experimental results show that traditional recurrent networks have inferior performance compared to tree recurrent networks for the supervised PPI problem.

In recent NLP research, a topic of interest is universal sentence encoding, sentence representations that can be used in any supervised task. At the word sequence level, fully attention-based models suffer from two problems: a quadratic increase in memory consumption with respect to the sentence length and an inability to capture and use syntactic information. Recursive neural nets can extract very good syntactic information by traversing a tree structure. To this end, we propose Tree Transformer, a model that captures phrase level syntax for constituency trees as well as word-level dependencies for dependency trees by doing recursive traversal only with attention. Evaluation of this model on four tasks gets noteworthy results compared to the standard transformer and LSTM-based models as well as tree-structured LSTMs. Ablation studies to find whether positional information is inherently encoded in the trees and which type of attention is suitable for doing the recursive traversal are provided.