Convolutional Gated Recurrent Units for Medical Relation Classification

Convolutional neural networks (CNNs) and recurrent neural networks (RNNs) have become the mainstream architectures for relation classification. We propose a unified architecture, which exploits the advantages of CNN and RNN simultaneously, to identify medical relations in clinical records, with only word embedding features. Our model learns phrase-level features through a CNN layer, and these feature representations are directly fed into a bidirectional gated recurrent unit (GRU) layer to capture long-term feature dependencies. We evaluate our model on two clinical datasets, and experiments demonstrate that our model performs better than previous single-model methods on both datasets.

[1]  Bowen Zhou,et al.  Classifying Relations by Ranking with Convolutional Neural Networks , 2015, ACL.

[2]  Zhiyuan Liu,et al.  A C-LSTM Neural Network for Text Classification , 2015, ArXiv.

[3]  Heng Ji,et al.  A Dependency-Based Neural Network for Relation Classification , 2015, ACL.

[4]  Sanda M. Harabagiu,et al.  Automatic extraction of relations between medical concepts in clinical texts , 2011, J. Am. Medical Informatics Assoc..

[5]  Jimmy Ba,et al.  Adam: A Method for Stochastic Optimization , 2014, ICLR.

[6]  Nitish Srivastava,et al.  Dropout: a simple way to prevent neural networks from overfitting , 2014, J. Mach. Learn. Res..

[7]  Alex Graves,et al.  Supervised Sequence Labelling with Recurrent Neural Networks , 2012, Studies in Computational Intelligence.

[8]  Makoto Miwa,et al.  End-to-End Relation Extraction using LSTMs on Sequences and Tree Structures , 2016, ACL.

[9]  Jürgen Schmidhuber,et al.  Long Short-Term Memory , 1997, Neural Computation.

[10]  Zhiyuan Liu,et al.  Relation Classification via Multi-Level Attention CNNs , 2016, ACL.

[11]  Jong-Hyeok Lee,et al.  Multiple Range-Restricted Bidirectional Gated Recurrent Units with Attention for Relation Classification , 2017, ArXiv.

[12]  Sunil Kumar Sahu,et al.  Learning local and global contexts using a convolutional recurrent network model for relation classification in biomedical text , 2017, CoNLL.

[13]  Bin Dong,et al.  Building a comprehensive syntactic and semantic corpus of Chinese clinical texts , 2016, J. Biomed. Informatics.

[14]  Noah A. Smith,et al.  Proceedings of the 54th Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers) , 2016, ACL 2016.

[15]  Vincent Ng,et al.  Ensemble-Based Medical Relation Classification , 2014, COLING.

[16]  B. Efron,et al.  Bootstrap confidence intervals , 1996 .

[17]  Klaus Mueller,et al.  Extracting Clinical Relations in Electronic Health Records Using Enriched Parse Trees , 2015, INNS Conference on Big Data.

[18]  Razvan C. Bunescu,et al.  A Shortest Path Dependency Kernel for Relation Extraction , 2005, HLT.

[19]  Wei Shi,et al.  Attention-Based Bidirectional Long Short-Term Memory Networks for Relation Classification , 2016, ACL.

[20]  Jun Zhao,et al.  Relation Classification via Convolutional Deep Neural Network , 2014, COLING.

[21]  Sunil Kumar Sahu,et al.  Relation extraction from clinical texts using domain invariant convolutional neural network , 2016, BioNLP@ACL.

[22]  Preslav Nakov,et al.  SemEval-2010 Task 8: Multi-Way Classification of Semantic Relations Between Pairs of Nominals , 2009, SEW@NAACL-HLT.

[23]  Joel D. Martin,et al.  Detecting concept relations in clinical text: Insights from a state-of-the-art model , 2013, J. Biomed. Informatics.

[24]  Ralph Grishman,et al.  Combining Neural Networks and Log-linear Models to Improve Relation Extraction , 2015, ArXiv.

[25]  Sanda M. Harabagiu,et al.  UTD: Classifying Semantic Relations by Combining Lexical and Semantic Resources , 2010, *SEMEVAL.

[26]  Yoshua Bengio,et al.  Neural Machine Translation by Jointly Learning to Align and Translate , 2014, ICLR.

[27]  Dongyan Zhao,et al.  Semantic Relation Classification via Convolutional Neural Networks with Simple Negative Sampling , 2015, EMNLP.

[28]  Andrew Y. Ng,et al.  Semantic Compositionality through Recursive Matrix-Vector Spaces , 2012, EMNLP.

[29]  Peter Szolovits,et al.  MIMIC-III, a freely accessible critical care database , 2016, Scientific Data.

[30]  Shang Gao,et al.  Hierarchical attention networks for information extraction from cancer pathology reports , 2017, J. Am. Medical Informatics Assoc..

[31]  Ting Liu,et al.  Document Modeling with Gated Recurrent Neural Network for Sentiment Classification , 2015, EMNLP.

[32]  Mo Yu Factor-based Compositional Embedding Models , 2014 .

[33]  Ngoc Thang Vu,et al.  Combining Recurrent and Convolutional Neural Networks for Relation Classification , 2016, NAACL.

[34]  Yoshimasa Tsuruoka,et al.  Task-Oriented Learning of Word Embeddings for Semantic Relation Classification , 2015, CoNLL.

[35]  Mark Sandler,et al.  Convolutional recurrent neural networks for music classification , 2016, 2017 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP).

[36]  Zhi Jin,et al.  Improved relation classification by deep recurrent neural networks with data augmentation , 2016, COLING.

[37]  Yoshua Bengio,et al.  Understanding the difficulty of training deep feedforward neural networks , 2010, AISTATS.

[38]  Zhi Jin,et al.  Classifying Relations via Long Short Term Memory Networks along Shortest Dependency Paths , 2015, EMNLP.

[39]  Shuying Shen,et al.  2010 i2b2/VA challenge on concepts, assertions, and relations in clinical text , 2011, J. Am. Medical Informatics Assoc..

[40]  Ming Yang,et al.  Bidirectional Long Short-Term Memory Networks for Relation Classification , 2015, PACLIC.

[41]  Houfeng Wang,et al.  Bidirectional Recurrent Convolutional Neural Network for Relation Classification , 2016, ACL.

[42]  Ani Nenkova,et al.  Proceedings of the 2016 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies , 2016, NAACL 2016.