|
|
Bacteria Biotope Relation Extraction Based on a Fusion Neural Network |
LI Mengying1, WANG Jian1, WANG Yan1, LIN Hongfei1, YANG Zhihao1 |
1.School of Computer Science and Technology, Dalian University of Technology, Dalian 116024 |
|
|
Abstract To build a complete bacteria biotope relation database, a relation extraction system based on a convolutional neural network(CNN)-long short-term memory(LSTM) model is proposed. Combining CNN and LSTM, the deep learning of hidden features are realized, and the distributed word vector feature and entity position feature are extracted as feature input of the model.Comparative experiments verify the advantages of CNN-LSTM model after the addition of features.The feature output of the CNN model is taken as the feature input of the LSTM model, and the best result is obtained on the BB-event corpus published by the Bio-NLP 2016 shared task.
|
Received: 20 October 2018
|
|
Fund:Supported by National Key R&D Program of China(No.2016YFB1001103), National Natural Science Foundation of China(No.61572098) |
About author:: (LI Mengying, master student. Her research interests include natural language processing.)(WANG Jan(Corresponding author), Ph.D., professor. Her research interests include natural language processing.)(WANG Yan, Ph.D. candidate. His research interests include natural language processing.)(LIN Hongfei, Ph.D., professor. His research interests include natural language processing.) (YANG Zhihao, Ph.D., professor. His research interests include natural language processing.) |
|
|
|
[1] NÉDELLEC C, BOSSY R, KIM J D, et al. Overview of BioNLP Shared Task 2013 // Proc of the BioNLP Shared Task 2013 Workshop. Berlin, Germany: Springer, 2013: 1-7. [2] 王健,李虹磊,林鸿飞,等.基于神经网络的微生物生长环境关系抽取方法.华南理工大学学报(自然科学版), 2017, 45(3):76-81. (WANG J, LI H L, LIN H F, et al. Bacteria Biotope Extraction on the Basis of Neural Network. Journal of South China University of Technology(Natural Science Edition), 2017, 45(3): 76-81.) [3] BJÖRNE J, HEIMONEN J, GINTER F, et al. Extracting Complex Biological Events with Rich Graph-Based Feature Sets // Proc of the Workshop on BioNLP: Shared Task. Berlin, Germany: Springer, 2009: 10-18. [4] RATKOVIC Z, GOLIK W, WARNIER P, et al. BioNLP 2011 Task Bacteria Biotope: The Alvis System // Proc of the BioNLP Shared Task 2011 Workshop. Stroudsburg, USA: ACL, 2011: 102-111. [5] KARADENIZ I, ÖZGÜR A. Bacteria Biotope Detection, Ontology-Based Normalization, and Relation Extraction Using Syntactic Rules // Proc of the BioNLP Shared Task 2013 Workshop. Berlin, Germany: Springer, 2013: 170-177. [6] LI L S, LIU S S, QIN M Y, et al. Extracting Biomedical Event with Dual Decomposition Integrating Word Embeddings. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2016, 13(4): 669-677. [7] LEVER J, JONES S J.VERSE: Event and Relation Extraction in the BioNLP 2016 Shared Task // Proc of the 4th BioNLP Shared Task Workshop. Berlin, Germany: Springer, 2016: 42-49. [8] LECUN Y, BENGIO Y, HINTON G. Deep Learning. Nature, 2015, 521(7553): 436-444. [9] COLLOBERT R, WESTON J, KARLEN M,et al. Natural Language Processing(Almost) from Scratch. Journal of Machine Lear-ning Research, 2011, 12: 2493-2537. [10] BOSSY R, GOLIK W, RATKOVIC Z, et al. BioNLP Shared Task 2013-An Overview of the Bacteria Biotope Task // Proc of the Bionlp Shared Task 2013 Workshop. Berlin, Germany: Springer, 2013: 161-169. [11] MIKOLOV T, YIH W T, ZWEIG G.Linguistic Regularities in Continuous Space Word Representations // Proc of the Conference of the North American Chapter of the Association for Computational Linguistics-Human Language Technologies. Berlin, Germany: Springer, 2013: 746-751. [12] GOODFELLOW I, BENGIO Y, COURVILLE A. Deep Learning.Cambridge, USA: The MIT Press, 2016. [13] HOCHREITER S, SCHMIDHUBER J.Long Short-Term Memory. Neural Computation, 1997, 9(8): 1735-1780. [14] RAVURI S, STOLOCKE A.A Comparative Study of Recurrent Neural Network Models for Lexical Domain Classification // Proc of the IEEE International Conference on Acoustics, Speech and Signal Processing. Washington, USA: IEEE, 2016: 6075-6079. |
|
|
|