BackgroundFamily history (FH) information, including family members, side of family of family members (i.e., maternal or paternal), living status of family members, observations (diseases) of family members, etc., is very important in the decision-making process of disorder diagnosis and treatment. However FH information cannot be used directly by computers as it is always embedded in unstructured text in electronic health records (EHRs). In order to extract FH information form clinical text, there is a need of natural language processing (NLP). In the BioCreative/OHNLP2018 challenge, there is a task regarding FH extraction (i.e., task1), including two subtasks: (1) entity identification, identifying family members and their observations (diseases) mentioned in clinical text; (2) family history extraction, extracting side of family of family members, living status of family members, and observations of family members. For this task, we propose a system based on deep joint learning methods to extract FH information. Our system achieves the highest F1- scores of 0.8901 on subtask1 and 0.6359 on subtask2, respectively.
This is the system description of the Harbin Institute of Technology Shenzhen (HITSZ) team for the first and second subtasks of the fourth Social Media Mining for Health Applications (SMM4H) shared task in 2019. The two subtasks are automatic classification and extraction of adverse effect mentions in tweets. The systems for the two subtasks are based on bidirectional encoder representations from transformers (BERT), and achieves promising results. Among the systems we developed for subtask1, the best F1-score was 0.6457, for subtask2, the best relaxed F1-score and the best strict F1-score were 0.614 and 0.407 respectively. Our system ranks first among all systems on subtask1.
The Biological Text Mining Unit at BSC and CNIO organized the first shared task on chemical & drug mention recognition from Spanish medical texts called PharmaCoNER (Pharmacological Substances, Compounds and proteins and Named Entity Recognition track) in 2019. The shared task includes two tracks: one for NER offset and entity classification (track 1) and the other one for concept indexing (track 2). We developed a pipeline system based on deep learning methods for this shared task, specifically, a subsystem based on BERT (Bidirectional Encoder Representations from Transformers) for NER offset and entity classification and a subsystem based on Bpool (Bi-LSTM with max/mean pooling) for concept indexing. Evaluation conducted on the shared task data showed that our system achieves a micro-average F1-score of 0.9105 on track 1 and a microaverage F1-score of 0.8391 on track 2.
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