title: Disorder recognition in clinical texts using multi-label structured SVM.
abstract: BACKGROUND
  Information extraction in clinical texts enables medical workers to find out problems of patients faster as well as makes intelligent diagnosis possible in the future. There has been a lot of work about disorder mention recognition in clinical narratives. But recognition of some more complicated disorder mentions like overlapping ones is still an open issue. This paper proposes a multi-label structured Support Vector Machine (SVM) based method for disorder mention recognition. We present a multi-label scheme which could be used in complicated entity recognition tasks.
  
  
  RESULTS
  We performed three sets of experiments to evaluate our model. Our best F1-Score on the 2013 Conference and Labs of the Evaluation Forum data set is 0.7343. There are six types of labels in our multi-label scheme, all of which are represented by 24-bit binary numbers. The binary digits of each label contain information about different disorder mentions. Our multi-label method can recognize not only disorder mentions in the form of contiguous or discontiguous words but also mentions whose spans overlap with each other. The experiments indicate that our multi-label structured SVM model outperforms the condition random field (CRF) model for this disorder mention recognition task. The experiments show that our multi-label scheme surpasses the baseline. Especially for overlapping disorder mentions, the F1-Score of our multi-label scheme is 0.1428 higher than the baseline BIOHD1234 scheme.
  
  
  CONCLUSIONS
  This multi-label structured SVM based approach is demonstrated to work well with this disorder recognition task. The novel multi-label scheme we presented is superior to the baseline and it can be used in other models to solve various types of complicated entity recognition tasks as well.
authors.affiliation: School of Electronics Engineering and Computer Science, Peking University, Beijing, 100871, China.
authors.forename: Wutao
authors.initials: W
authors.lastname: Lin
authors.affiliation: School of Computer, Wuhan University, Wuhan, 430072, China. dhji@whu.edu.cn.
authors.forename: Donghong
authors.initials: D
authors.lastname: Ji
authors.affiliation: School of Computer, Wuhan University, Wuhan, 430072, China.
authors.forename: Yanan
authors.initials: Y
authors.lastname: Lu
mesh_terms: D057225:Data Mining / Q000379:methods*; D004194:Disease; D006801:Humans; D060388:Support Vector Machine
keywords: Clinical text; Information extraction; Multi-label; Structured support vector machine