|
|
Chinese Disease Name Normalization Based on Multi-task Learning and Polymorphic Semantic Features |
Han Pu1,2, Zhang Zhanpeng1, Zhang Wei1 |
1.School of Management, Nanjing University of Posts & Telecommunications, Nanjing 210003 2.Jiangsu Provincial Key Laboratory of Data Engineering and Knowledge Service, Nanjing 210023 |
|
|
Abstract In order to solve the problem of a large number of disease designations in online texts, a Chinese disease name normalization model based on multi-task learning and polymorphic semantic features (multi-task attention-dictionary BERT GRU-CNN, MTAD-BERT-GCNN) is proposed. First, word2vec and Glove were used to generate external semantic feature vectors that integrate local and global semantics. Second, CNN and BERT were used as benchmark models for comparative experimental analysis. Third, GRU, LSTM, BiGRU, and BiLSTM were introduced on CNN to extract semantic relationships between texts. Next, from the perspective of multi-task learning, the above model was combined with BERT to capture static and dynamic semantic information. Finally, the medical dictionary was introduced to calculate the attention matrix as an auxiliary task to adjust the static vector, thereby further improving the model effect. Our experiments were carried out using the self-built Chinese disease name normalization dataset, ChDND. The experimental results found that the MTAD-BERT-GCNN model achieved 89.60% accuracy on the Accuracy@10, which is higher than the basic word-level CNN, and the word-level CNN increased by 12.96% and 5.12%, respectively. This research introduces the concept of multi-task learning in the normalization task of Chinese disease names and optimizes it from the level of the semantic vector and model framework, which has good application value in the construction of Chinese medical knowledge graphs, information extraction, and natural language understanding.
|
Received: 23 November 2020
|
|
|
|
1 Magumba M A, Nabende P, Mwebaze E. Ontology boosted deep learning for disease name extraction from Twitter messages[J]. Journal of Big Data, 2018, 5(1): 1-19. 2 陈美杉, 夏晨曦. 肝癌患者在线提问的命名实体识别研究: 一种基于迁移学习的方法[J]. 数据分析与知识发现, 2019, 3(12): 61-69. 3 Grover S, Aujla G S. Prediction model for influenza epidemic based on Twitter data[J]. International Journal of Advanced Research in Computer and Communication Engineering, 2014, 3(7): 7541-7545. 4 王萍, 牟冬梅, 高和璇, 等. 基于传染病监测数据的危机探测研究[J]. 情报学报, 2019, 38(5): 492-499. 5 Chen L T, Baird A, Straub D. Fostering participant health knowledge and attitudes: an econometric study of a chronic disease-focused online health community[J]. Journal of Management Information Systems, 2019, 36(1): 194-229. 6 Thelwall M, Buckley K. Topic-based sentiment analysis for the social web: the role of mood and issue‐related words[J]. Journal of the American Society for Information Science and Technology, 2013, 64(8): 1608-1617. 7 Li S, Yu C H, Wang Y C, et al. Exploring adverse drug reactions of diabetes medicine using social media analytics and interactive visualizations[J]. International Journal of Information Management, 2019, 48: 228-237. 8 Karimi S, Metke-Jimenez A, Kemp M, et al. CADEC: a corpus of adverse drug event annotations[J]. Journal of Biomedical Informatics, 2015, 55: 73-81. 9 Ching T, Himmelstein D S, Beaulieu-Jones B K, et al. Opportunities and obstacles for deep learning in biology and medicine[J]. Journal of the Royal Society Interface, 2018, 15(141): 20170387. 10 Leaman R, Islamaj Do?an R, Lu Z Y. DNorm: disease name normalization with pairwise learning to rank[J]. Bioinformatics, 2013, 29(22): 2909-2917. 11 韩普, 马健, 张嘉明, 等. 基于多数据源融合的医疗知识图谱框架构建研究[J]. 现代情报, 2019, 39(6): 81-90. 12 林泽斐, 欧石燕. 多特征融合的中文命名实体链接方法研究[J]. 情报学报, 2019, 38(1): 68-78. 13 Luo Y, Song G J, Li P Y, et al. Multi-task medical concept normalization using multi-view convolutional neural network[C]// Proceedings of the AAAI Conference on Artificial Intelligence. Palo Alto: AAAI Press, 2018. 14 Zhang Y Z, Ma X J, Song G J. Chinese medical concept normalization by using text and comorbidity network embedding[C]// Proceedings of the 2018 IEEE International Conference on Data Mining. IEEE, 2018: 777-786. 15 Zhou S J, Li X. Feature engineering vs. deep learning for paper section identification: toward applications in Chinese medical literature[J]. Information Processing & Management, 2020, 57(3): 102206. 16 Ristad E S, Yianilos P N. Learning string-edit distance[J]. IEEE Transactions on Pattern Analysis and Machine Intelligence, 1998, 20(5): 522-532. 17 Aronson A R. Effective mapping of biomedical text to the UMLS metathesaurus: the MetaMap program[J]. Proceedings of the AMIA Symposium, 2001: 17-21. 18 Tsuruoka Y, McNaught J, Tsujii J, et al. Learning string similarity measures for gene/protein name dictionary look-up using logistic regression[J]. Bioinformatics, 2007, 23(20): 2768-2774. 19 Yang H. Automatic extraction of medication information from medical discharge summaries[J]. Journal of the American Medical Informatics Association, 2010, 17(5): 545-548. 20 Khare R, Li J, Lu Z Y. LabeledIn: cataloging labeled indications for human drugs[J]. Journal of Biomedical Informatics, 2014, 52: 448-456. 21 Kate R J. Normalizing clinical terms using learned edit distance patterns[J]. Journal of the American Medical Informatics Association, 2015, 23(2): 380-386. 22 Jonnagaddala J, Jue T R, Chang N W, et al. Improving the dictionary lookup approach for disease normalization using enhanced dictionary and query expansion[J]. Database, 2016, 2016: baw112. 23 Shi H R, Xie P T, Hu Z T, et al. Towards automated ICD coding using deep learning[OL]. (2017-11-30). https://arxiv.org/pdf/1711.04075.pdf. 24 Liu H W, Xu Y. A deep learning way for disease name representation and normalization[C]// Proceedings of the 8th National CCF Conference on Natural Language Processing and Chinese Computing. Cham: Springer, 2017: 151-157. 25 Limsopatham N, Collier N. Normalising medical concepts in social media texts by learning semantic representation[C]// Proceedings of the 54th Annual Meeting of the Association for Computational Linguistics. Stroudsburg: Association for Computational Linguistics, 2016: 1014-1023. 26 Li H D, Chen Q C, Tang B Z, et al. CNN-based ranking for biomedical entity normalization[J]. BMC Bioinformatics, 2017, 18(Suppl 11): 385. 27 Tutubalina E, Miftahutdinov Z, Nikolenko S, et al. Sequence learning with RNNs for medical concept normalization in user-generated texts[OL]. (2018-11-29). https://arxiv.org/pdf/1811.11523. 28 Huang J M, Osorio C, Sy L W. An empirical evaluation of deep learning for ICD-9 code assignment using MIMIC-III clinical notes[J]. Computer Methods and Programs in Biomedicine, 2019, 177: 141-153. 29 Collobert R, Weston J. A unified architecture for natural language processing: deep neural networks with multitask learning[C]// Proceedings of the 25th International Conference on Machine Learning. New York: ACM Press, 2008: 160-167. 30 Liu P F, Qiu X P, Huang X J. Recurrent neural network for text classification with multi-task learning[OL]. (2016-05-17). https://arxiv.org/pdf/1605.05101. 31 Liu P F, Qiu X P, Huang X J. Adversarial multi-task learning for text classification[OL]. (2017-04-19). https://arxiv.org/pdf/1704.05742. 32 Yang J L, Liu Y N, Qian M H, et al. Information extraction from electronic medical records using multitask recurrent neural network with contextual word embedding[J]. Applied Sciences, 2019, 9(18): 3658. 33 Niu J H, Yang Y H, Zhang S H, et al. Multi-task character-level attentional networks for medical concept normalization[J]. Neural Processing Letters, 2019, 49(3): 1239-1256. 34 Devlin J, Chang M W, Lee K, et al. BERT: pre-training of deep bidirectional transformers for language understanding[OL]. (2019-05-24). https://arxiv.org/pdf/1810.04805. 35 陆伟, 李鹏程, 张国标, 等. 学术文本词汇功能识别——基于BERT向量化表示的关键词自动分类研究[J]. 情报学报, 2020, 39(12): 1320-1329. 36 吴俊, 程垚, 郝瀚, 等. 基于BERT嵌入BiLSTM-CRF模型的中文专业术语抽取研究[J]. 情报学报, 2020, 39(4): 409-418. 37 Li F, Jin Y H, Liu W S, et al. Fine-tuning bidirectional encoder representations from transformers (BERT)-based models on large-scale electronic health record notes: an empirical study[J]. JMIR Medical Informatics, 2019, 7(3): e14830. 38 Xu D F, Gopale M, Zhang J C, et al. Unified medical language system resources improve sieve-based generation and bidirectional encoder representations from transformers (BERT)-based ranking for concept normalization[J]. Journal of the American Medical Informatics Association, 2020, 27(10): 1510-1519. 39 Ji Z C, Wei Q, Xu H. BERT-based ranking for biomedical entity normalization[OL]. (2019-08-09). https://arxiv.org/ftp/arxiv/papers/1908/1908.03548.pdf. 40 Kalyan K S, Sangeetha S. BertMCN: mapping colloquial phrases to standard medical concepts using BERT and highway network[J]. Artificial Intelligence in Medicine, 2021, 112: 102008. 41 Lee K, Hasan S A, Farri O, et al. Medical concept normalization for online user-generated texts[C]// Proceedings of the IEEE International Conference on Healthcare Informatics. IEEE, 2017: 462-469. 42 Hochreiter S, Schmidhuber J. Long short-term memory[J]. Neural Computation, 1997, 9(8): 1735-1780. 43 Cho K, van Merri?nboer B, Gulcehre C, et al. Learning phrase representations using RNN encoder-decoder for statistical machine translation[C]// Proceedings of the 2014 Conference on Empirical Methods in Natural Language Processing. Stroudsburg: Association for Computational Linguistics, 2014: 1724-1734. 44 Kim Y. Convolutional neural networks for sentence classification[OL]. (2014-09-03). https://arxiv.org/pdf/1408.5882. 45 Vaswani A, Shazeer N, Parmar N, et al. Attention is all you need[OL]. (2017-12-06). https://arxiv.org/pdf/1706.03762. 46 Dogan R I, Lu Z. An inference method for disease name normalization[C]// Proceedings of the AAAI 2012 Fall Symposium on Information Retrieval and Knowledge Discovery in Biomedical Text. Palo Alto: AAAI Press, 2012: 8-13. 47 Karadeniz ?, ?zgür A. Linking entities through an ontology using word embeddings and syntactic re-ranking[J]. BMC Bioinformatics, 2019, 20(1): 156. |
|
|
|