TEMPTING system: a hybrid method of rule and machine learning for temporal relation extraction in patient discharge summaries.
Patient discharge summaries provide detailed medical information about individuals who have been hospitalized. To make a precise and legitimate assessment of the abundant data, a proper time layout of the sequence of relevant events should be compiled and used to drive a patient-specific timeline, which could further assist medical personnel in making clinical decisions. The process of identifying the chronological order of entities is called temporal relation extraction. In this paper, we propose a hybrid method to identify appropriate temporal links between a pair of entities. The method combines two approaches: one is rule-based and the other is based on the maximum entropy model. We develop an integration algorithm to fuse the results of the two approaches. All rules and the integration algorithm are formally stated so that one can easily reproduce the system and results. To optimize the system's configuration, we used the 2012 i2b2 challenge TLINK track dataset and applied threefold cross validation to the training set. Then, we evaluated its performance on the training and test datasets. The experiment results show that the proposed TEMPTING (TEMPoral relaTion extractING) system (ranked seventh) achieved an F-score of 0.563, which was at least 30% better than that of the baseline system, which randomly selects TLINK candidates from all pairs and assigns the TLINK types. The TEMPTING system using the hybrid method also outperformed the stage-based TEMPTING system. Its F-scores were 3.51% and 0.97% better than those of the stage-based system on the training set and test set, respectively.
Institute of Information Science, Academia Sinica, Nankang, Taipei, Taiwan, ROC; Department of Information Management, National Taiwan University, Taipei, Taiwan, ROC.
Yung-Chun
YC
Chang
Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan, ROC. Electronic address: hjdai@tmu.edu.tw.
Hong-Jie
HJ
Dai
Institute of Information Science, Academia Sinica, Nankang, Taipei, Taiwan, ROC.
Johnny Chi-Yang
JC
Wu
Institute of Information Science, Academia Sinica, Nankang, Taipei, Taiwan, ROC.
Jian-Ming
JM
Chen
Department of Computer Science and Information Engineering, National Central University, Taoyuan, Taiwan, ROC.
Richard Tzong-Han
RT
Tsai
Institute of Information Science, Academia Sinica, Nankang, Taipei, Taiwan, ROC.
Wen-Lian
WL
Hsu
D000465:Algorithms; D057225:Data Mining / Q000379:methods; D016208:Databases, Factual; D057286:Electronic Health Records; D006801:Humans; D008490:Medical Informatics / Q000379:methods*; D009323:Natural Language Processing; D063886:Patient Discharge Summaries; D015203:Reproducibility of Results; D013997:Time Factors
Hybrid method; Maximum entropy; Natural language processing; Temporal relation extraction; Text mining