@inproceedings{c5333ba097b64e2a8df281e530c553ad,
title = "PENNER: Pattern-enhanced Nested Named Entity Recognition in Biomedical Literature",
abstract = "Many biomedical entity mentions contain other entity mentions nested inside. Most current named entity recognition (NER) systems deal with only flat entities and ignore such nested entities, which may introduce errors to subsequent tasks such as relation extraction and knowledge base completion. Recently, fully supervised methods are proposed for nested named entity recognition. Despite their success on benchmark datasets, supervised methods rely on human annotation and lead to highly specialized systems that cannot be easily adapted to new entity types. In this study, we propose PENNER, a novel and effective pattern-enhanced nested named entity recognition method that relies on massive corpora plus only very weak supervision. We compare PENNER with a state-of-the-art BioNER system, PubTator, and observe great improvement at recognizing genes, chemicals, diseases and species. PENNER can also accurately extract new types of entities, such as biological process and treatment, that are not annotated by PubTator.",
keywords = "meta-pattern discovery, multi-set expansion, nested named entity recognition, pattern mining",
author = "Xuan Wang and Yu Zhang and Qi Li and Wu, {Cathy H.} and Jiawei Han",
note = "Publisher Copyright: {\textcopyright} 2018 IEEE.; 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018 ; Conference date: 03-12-2018 Through 06-12-2018",
year = "2019",
month = jan,
day = "21",
doi = "10.1109/BIBM.2018.8621485",
language = "English (US)",
series = "Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018",
publisher = "Institute of Electrical and Electronics Engineers Inc.",
pages = "540--547",
editor = "Harald Schmidt and David Griol and Haiying Wang and Jan Baumbach and Huiru Zheng and Zoraida Callejas and Xiaohua Hu and Julie Dickerson and Le Zhang",
booktitle = "Proceedings - 2018 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2018",
address = "United States",
}