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awesome-relation-extraction-biomedical-literature

A curated list of awesome resources dedicated to Relation Extraction especially for biomedical literature. I dedicate it for those interested in this topic

Supervised Learnings

Unsupervised Learnings

Feature Representation by Deep Learning

CNN

  • Liu, S., Tang, B., Chen, Q., & Wang, X. (2016). Drug-Drug Interaction Extraction via Convolutional Neural Networks. Computational and Mathematical Methods in Medicine, 2016. https://doi.org/10.1155/2016/6918381

  • Suárez-Paniagua, V., Segura-Bedmar, I. Evaluation of pooling operations in convolutional architectures for drug-drug interaction extraction. BMC Bioinformatics 19, 209 (2018).

RNN

LSTM

Hybrid Model

  • Yi Z. et al. (2017) Drug-Drug Interaction Extraction via Recurrent Neural Network with Multiple Attention Layers. In: Cong G., Peng WC., Zhang W., Li C., Sun A. (eds) Advanced Data Mining and Applications. ADMA 2017. Lecture Notes in Computer Science, vol 10604. Springer, Cham. https://doi.org/10.1007/978-3-319-69179-4_39
  • Zheng, W., Lin, H., Luo, L., Zhao, Z., Li, Z., Zhang, Y., Yang, Z., & Wang, J. (2017). An attention-based effective neural model for drug-drug interactions extraction. BMC Bioinformatics, 18(1), 1–11. https://doi.org/10.1186/s12859-017-1855-x
  • Zhou, D., Miao, L., & He, Y. (2018). Position-aware deep multi-task learning for drug–drug interaction extraction. Artificial Intelligence in Medicine, 87, 1–8. https://doi.org/10.1016/j.artmed.2018.03.001
  • Liu, J., Huang, Z., Ren, F., & Hua, L. (2019). Drug-drug interaction extraction based on transfer weight matrix and memory network. IEEE Access, 7, 101260–101268. https://doi.org/10.1109/ACCESS.2019.2930641
  • Sahu, S. K., & Anand, A. (2018). Drug-drug interaction extraction from biomedical texts using long short-term memory network. Journal of Biomedical Informatics, 86(August), 15–24. https://doi.org/10.1016/j.jbi.2018.08.005
  • Sun, X., Dong, K., Ma, L., Sutcliffe, R., He, F., Chen, S., & Feng, J. (2019). Drug-drug interaction extraction via recurrent hybrid convolutional neural networks with an improved focal loss. Entropy, 21(1). https://doi.org/10.3390/e21010037
  • Ren, Y., Fei, H., & Ji, D. (2019). Drug-Drug Interaction Extraction Using a Span-based Neural Network Model. Proceedings - 2019 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2019, 1237–1239. https://doi.org/10.1109/BIBM47256.2019.8983248
  • Wu, H., Xing, Y., Ge, W., Liu, X., Zou, J., Zhou, C., & Liao, J. (2020). Drug-drug interaction extraction via hybrid neural networks on biomedical literature. Journal of Biomedical Informatics, 106(November 2019), 103432. https://doi.org/10.1016/j.jbi.2020.103432
  • Zaikis, D., & Vlahavas, I. (2020). Drug-drug interaction classification using attention based neural networks. PervasiveHealth: Pervasive Computing Technologies for Healthcare, 34–40. https://doi.org/10.1145/3411408.3411461
  • Fatehifar, M., & Karshenas, H. (2021). Drug-Drug interaction extraction using a position and similarity fusion-based attention mechanism. Journal of Biomedical Informatics, 115(December 2020), 103707. https://doi.org/10.1016/j.jbi.2021.103707

Pre-trained Model

  • Nguyen, D. P., & Bao Ho, T. (2020). Drug-Drug Interaction Extraction from Biomedical Texts via Relation BERT. Proceedings - 2020 RIVF International Conference on Computing and Communication Technologies, RIVF 2020. https://doi.org/10.1109/RIVF48685.2020.9140783
  • Wen, A., Sun, X., Yu, K., Wu, Y., Zhang, J., & Yuan, Z. (2020). Drug-Drug Interaction Extraction using Pre-training Model of Enhanced Entity Information. Proceedings - IEEE Congress on Cybermatics: 2020 IEEE International Conferences on Internet of Things, IThings 2020, IEEE Green Computing and Communications, GreenCom 2020, IEEE Cyber, Physical and Social Computing, CPSCom 2020 and IEEE Smart Data, SmartD, 527–532. https://doi.org/10.1109/iThings-GreenCom-CPSCom-SmartData-Cybermatics50389.2020.00094