@inproceedings{bhatia-etal-2019-joint,
    title = "Joint Entity Extraction and Assertion Detection for Clinical Text",
    author = "Bhatia, Parminder  and
      Celikkaya, Busra  and
      Khalilia, Mohammed",
    editor = "Korhonen, Anna  and
      Traum, David  and
      M{\`a}rquez, Llu{\'i}s",
    booktitle = "Proceedings of the 57th Annual Meeting of the Association for Computational Linguistics",
    month = jul,
    year = "2019",
    address = "Florence, Italy",
    publisher = "Association for Computational Linguistics",
    url = "https://preview.aclanthology.org/fix-sig-urls/P19-1091/",
    doi = "10.18653/v1/P19-1091",
    pages = "954--959",
    abstract = "Negative medical findings are prevalent in clinical reports, yet discriminating them from positive findings remains a challenging task for in-formation extraction. Most of the existing systems treat this task as a pipeline of two separate tasks, i.e., named entity recognition (NER)and rule-based negation detection. We consider this as a multi-task problem and present a novel end-to-end neural model to jointly extract entities and negations. We extend a standard hierarchical encoder-decoder NER model and first adopt a shared encoder followed by separate decoders for the two tasks. This architecture performs considerably better than the previous rule-based and machine learning-based systems. To overcome the problem of increased parameter size especially for low-resource settings, we propose the Conditional Softmax Shared Decoder architecture which achieves state-of-art results for NER and negation detection on the 2010 i2b2/VA challenge dataset and a proprietary de-identified clinical dataset."
}