{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,8,23]],"date-time":"2025-08-23T19:10:07Z","timestamp":1755976207895,"version":"3.44.0"},"publisher-location":"New York, NY, USA","reference-count":23,"publisher":"ACM","license":[{"start":{"date-parts":[[2024,1,12]],"date-time":"2024-01-12T00:00:00Z","timestamp":1705017600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"content-domain":{"domain":["dl.acm.org"],"crossmark-restriction":true},"short-container-title":[],"published-print":{"date-parts":[[2024,1,12]]},"DOI":"10.1145\/3640900.3640901","type":"proceedings-article","created":{"date-parts":[[2024,3,1]],"date-time":"2024-03-01T12:04:59Z","timestamp":1709294699000},"page":"48-54","update-policy":"https:\/\/doi.org\/10.1145\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Temporal Name Entity Recognition and Relation Extraction in Clinical Electronic Health Records with Span-based Entity and Relation Transformer"],"prefix":"10.1145","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9093-4680","authenticated-orcid":false,"given":"Nuria","family":"Lebe\u00f1a","sequence":"first","affiliation":[{"name":"Department of Electricity and Electronics, University of the Basque Country, Spain and Ixa research group, Computer science faculty EHU, Spain"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4248-8182","authenticated-orcid":false,"given":"Arantza","family":"Casillas","sequence":"additional","affiliation":[{"name":"Department of Electricity and Electronics, University of the Basque Country, Spain and Ixa research group, Computer science faculty EHU, Spain"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2638-9598","authenticated-orcid":false,"given":"Alicia","family":"P\u00e9rez","sequence":"additional","affiliation":[{"name":"Computer Languages and Systems, University of the Basque Country, Spain and Ixa research group, Computer science faculty EHU, Spain"}]}],"member":"320","published-online":{"date-parts":[[2024,3]]},"reference":[{"key":"e_1_3_2_1_1_1","volume-title":"Contextual String Embeddings for Sequence Labeling. In COLING 2018, 27th International Conference on Computational Linguistics. 1638\u20131649","author":"Akbik Alan","year":"2018","unstructured":"Alan Akbik, Duncan Blythe, and Roland Vollgraf. 2018. Contextual String Embeddings for Sequence Labeling. In COLING 2018, 27th International Conference on Computational Linguistics. 1638\u20131649."},{"key":"e_1_3_2_1_2_1","volume-title":"Transformer-xl: Attentive language models beyond a fixed-length context. arXiv preprint arXiv:1901.02860","author":"Dai Zihang","year":"2019","unstructured":"Zihang Dai, Zhilin Yang, Yiming Yang, Jaime Carbonell, Quoc\u00a0V Le, and Ruslan Salakhutdinov. 2019. Transformer-xl: Attentive language models beyond a fixed-length context. arXiv preprint arXiv:1901.02860 (2019)."},{"key":"e_1_3_2_1_3_1","volume-title":"Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805","author":"Devlin Jacob","year":"2018","unstructured":"Jacob Devlin, Ming-Wei Chang, Kenton Lee, and Kristina Toutanova. 2018. Bert: Pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018)."},{"key":"e_1_3_2_1_4_1","volume-title":"Span-based joint entity and relation extraction with transformer pre-training. arXiv preprint arXiv:1909.07755","author":"Eberts Markus","year":"2019","unstructured":"Markus Eberts and Adrian Ulges. 2019. Span-based joint entity and relation extraction with transformer pre-training. arXiv preprint arXiv:1909.07755 (2019)."},{"key":"e_1_3_2_1_5_1","volume-title":"a freely accessible critical care database. Scientific data 3, 1","author":"Johnson EW","year":"2016","unstructured":"Alistair\u00a0EW Johnson, Tom\u00a0J Pollard, Lu Shen, H\u00a0Lehman Li-Wei, Mengling Feng, Mohammad Ghassemi, Benjamin Moody, Peter Szolovits, Leo\u00a0Anthony Celi, and Roger\u00a0G Mark. 2016. MIMIC-III, a freely accessible critical care database. Scientific data 3, 1 (2016), 1\u20139."},{"key":"e_1_3_2_1_6_1","volume-title":"Transfer learning for named-entity recognition with neural networks. arXiv preprint arXiv:1705.06273","author":"Lee Ji\u00a0Young","year":"2017","unstructured":"Ji\u00a0Young Lee, Franck Dernoncourt, and Peter Szolovits. 2017. Transfer learning for named-entity recognition with neural networks. arXiv preprint arXiv:1705.06273 (2017)."},{"key":"e_1_3_2_1_7_1","doi-asserted-by":"publisher","DOI":"10.18653\/v1\/E17-1108"},{"key":"e_1_3_2_1_8_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ins.2021.09.028"},{"key":"e_1_3_2_1_9_1","doi-asserted-by":"crossref","unstructured":"Chen Lin Timothy Miller Dmitriy Dligach Farig Sadeque Steven Bethard and Guergana Savova. 2020. A BERT-based one-pass multi-task model for clinical temporal relation extraction. (2020).","DOI":"10.18653\/v1\/2020.bionlp-1.7"},{"key":"e_1_3_2_1_10_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0218942"},{"key":"e_1_3_2_1_11_1","volume-title":"Roberta: A robustly optimized bert pretraining approach. arXiv preprint arXiv:1907.11692","author":"Liu Yinhan","year":"2019","unstructured":"Yinhan Liu, Myle Ott, Naman Goyal, Jingfei Du, Mandar Joshi, Danqi Chen, Omer Levy, Mike Lewis, Luke Zettlemoyer, and Veselin Stoyanov. 2019. Roberta: A robustly optimized bert pretraining approach. arXiv preprint arXiv:1907.11692 (2019)."},{"key":"e_1_3_2_1_12_1","volume-title":"A general framework for information extraction using dynamic span graphs. arXiv preprint arXiv:1904.03296","author":"Luan Yi","year":"2019","unstructured":"Yi Luan, Dave Wadden, Luheng He, Amy Shah, Mari Ostendorf, and Hannaneh Hajishirzi. 2019. A general framework for information extraction using dynamic span graphs. arXiv preprint arXiv:1904.03296 (2019)."},{"key":"e_1_3_2_1_13_1","unstructured":"Bernardo Magnini Bego\u00f1a Altuna Alberto Lavelli Manuela Speranza and Roberto Zanoli. [n. d.]. E3C: European Clinical Case Corpus. ([n. d.])."},{"key":"e_1_3_2_1_14_1","doi-asserted-by":"publisher","DOI":"10.1080\/0952813X.2020.1744198"},{"key":"e_1_3_2_1_15_1","volume-title":"End-to-end relation extraction using lstms on sequences and tree structures. arXiv preprint arXiv:1601.00770","author":"Miwa Makoto","year":"2016","unstructured":"Makoto Miwa and Mohit Bansal. 2016. End-to-end relation extraction using lstms on sequences and tree structures. arXiv preprint arXiv:1601.00770 (2016)."},{"key":"e_1_3_2_1_16_1","unstructured":"Alec Radford Karthik Narasimhan Tim Salimans and Ilya Sutskever. 2018. Improving language understanding by generative pre-training. (2018)."},{"key":"e_1_3_2_1_17_1","doi-asserted-by":"publisher","DOI":"10.1186\/s12911-023-02117-3"},{"key":"e_1_3_2_1_18_1","volume-title":"Relation extraction from clinical texts using domain invariant convolutional neural network. arXiv preprint arXiv:1606.09370","author":"Sahu Sunil\u00a0Kumar","year":"2016","unstructured":"Sunil\u00a0Kumar Sahu, Ashish Anand, Krishnadev Oruganty, and Mahanandeeshwar Gattu. 2016. Relation extraction from clinical texts using domain invariant convolutional neural network. arXiv preprint arXiv:1606.09370 (2016)."},{"key":"e_1_3_2_1_19_1","volume-title":"BioFLAIR: Pretrained Pooled Contextualized Embeddings for Biomedical Sequence Labeling Tasks. arXiv preprint arXiv:1908.05760","author":"Sharma Shreyas","year":"2019","unstructured":"Shreyas Sharma and Ron Daniel\u00a0Jr. 2019. BioFLAIR: Pretrained Pooled Contextualized Embeddings for Biomedical Sequence Labeling Tasks. arXiv preprint arXiv:1908.05760 (2019)."},{"key":"e_1_3_2_1_20_1","doi-asserted-by":"publisher","DOI":"10.1145\/3442381.3449895"},{"key":"e_1_3_2_1_21_1","volume-title":"Mass: Masked sequence to sequence pre-training for language generation. arXiv preprint arXiv:1905.02450","author":"Song Kaitao","year":"2019","unstructured":"Kaitao Song, Xu Tan, Tao Qin, Jianfeng Lu, and Tie-Yan Liu. 2019. Mass: Masked sequence to sequence pre-training for language generation. arXiv preprint arXiv:1905.02450 (2019)."},{"key":"e_1_3_2_1_22_1","doi-asserted-by":"publisher","DOI":"10.1162\/tacl_a_00172"},{"key":"e_1_3_2_1_23_1","doi-asserted-by":"publisher","DOI":"10.18653\/v1\/S17-2098"}],"event":{"name":"ICBBB 2024: 2024 14th International Conference on Bioscience, Biochemistry and Bioinformatics","acronym":"ICBBB 2024","location":"Kyoto Japan"},"container-title":["Proceedings of the 2024 14th International Conference on Bioscience, Biochemistry and Bioinformatics"],"original-title":[],"link":[{"URL":"https:\/\/dl.acm.org\/doi\/10.1145\/3640900.3640901","content-type":"unspecified","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/dl.acm.org\/doi\/pdf\/10.1145\/3640900.3640901","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,8,23]],"date-time":"2025-08-23T18:36:34Z","timestamp":1755974194000},"score":1,"resource":{"primary":{"URL":"https:\/\/dl.acm.org\/doi\/10.1145\/3640900.3640901"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,1,12]]},"references-count":23,"alternative-id":["10.1145\/3640900.3640901","10.1145\/3640900"],"URL":"https:\/\/doi.org\/10.1145\/3640900.3640901","relation":{},"subject":[],"published":{"date-parts":[[2024,1,12]]},"assertion":[{"value":"2024-03-01","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}