Deep learning for extracting protein-protein interactions from biomedical literature

State-of-the-art methods for protein-protein interaction (PPI) extraction are primarily feature-based or kernel-based by leveraging lexical and syntactic information. But how to incorporate such knowledge in the recent deep learning methods remains an open question. In this paper, we propose a multichannel dependency-based convolutional neural network model (McDepCNN). It applies one channel to the embedding vector of each word in the sentence, and another channel to the embedding vector of the head of the corresponding word. Therefore, the model can use richer information obtained from different channels. Experiments on two public benchmarking datasets, AIMed and BioInfer, demonstrate that McDepCNN compares favorably to the state-of-the-art rich-feature and single-kernel based methods. In addition, McDepCNN achieves 24.4% relative improvement in F1-score over the state-of-the-art methods on cross-corpus evaluation and 12% improvement in F1-score over kernel-based methods on "difficult" instances. These results suggest that McDepCNN generalizes more easily over different corpora, and is capable of capturing long distance features in the sentences.Comment: Accepted for publication in Proceedings of the 2017 Workshop on Biomedical Natural Language Processing, 10 pages, 2 figures, 6 table

Jointly Multiple Events Extraction via Attention-based Graph Information Aggregation

Event extraction is of practical utility in natural language processing. In the real world, it is a common phenomenon that multiple events existing in the same sentence, where extracting them are more difficult than extracting a single event. Previous works on modeling the associations between events by sequential modeling methods suffer a lot from the low efficiency in capturing very long-range dependencies. In this paper, we propose a novel Jointly Multiple Events Extraction (JMEE) framework to jointly extract multiple event triggers and arguments by introducing syntactic shortcut arcs to enhance information flow and attention-based graph convolution networks to model graph information. The experiment results demonstrate that our proposed framework achieves competitive results compared with state-of-the-art methods.Comment: accepted by EMNLP 201

When Are Tree Structures Necessary for Deep Learning of Representations?

Recursive neural models, which use syntactic parse trees to recursively generate representations bottom-up, are a popular architecture. But there have not been rigorous evaluations showing for exactly which tasks this syntax-based method is appropriate. In this paper we benchmark {\bf recursive} neural models against sequential {\bf recurrent} neural models (simple recurrent and LSTM models), enforcing apples-to-apples comparison as much as possible. We investigate 4 tasks: (1) sentiment classification at the sentence level and phrase level; (2) matching questions to answer-phrases; (3) discourse parsing; (4) semantic relation extraction (e.g., {\em component-whole} between nouns). Our goal is to understand better when, and why, recursive models can outperform simpler models. We find that recursive models help mainly on tasks (like semantic relation extraction) that require associating headwords across a long distance, particularly on very long sequences. We then introduce a method for allowing recurrent models to achieve similar performance: breaking long sentences into clause-like units at punctuation and processing them separately before combining. Our results thus help understand the limitations of both classes of models, and suggest directions for improving recurrent models