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J Am Med Inform Assoc 17:528-531 doi:10.1136/jamia.2010.003855
  • Research paper

Integrating existing natural language processing tools for medication extraction from discharge summaries

Table 1

Evaluation results of Vanderbilt's system for 2009 i2b2 challenge

Exact Inexact
F-measure Pre Rec F-measure Pre Rec
Horizontal System-level System 0.821 0.839 0.803 0.822 0.866 0.782
Horizontal Patient-level System 0.810 0.840 0.792 0.807 0.863 0.770
Vertical System-level Dosage 0.855 0.895 0.818 0.880 0.930 0.835
Vertical Patient-level Dosage 0.830 0.878 0.802 0.857 0.915 0.823
Vertical Ssystem-level Frequency 0.868 0.879 0.858 0.859 0.902 0.820
Vertical Patient-level Frequency 0.860 0.881 0.852 0.855 0.900 0.834
Vertical Ssystem-level Mode 0.887 0.918 0.858 0.882 0.926 0.841
Vertical Patient-level Mode 0.842 0.883 0.820 0.839 0.888 0.811
Vertical System-level Medication 0.856 0.842 0.871 0.893 0.895 0.891
Vertical Patient-level Medication 0.855 0.849 0.870 0.884 0.892 0.886
Vertical System-level Reason 0.360 0.459 0.296 0.367 0.517 0.285
Vertical Patient-level Reason 0.344 0.455 0.319 0.360 0.522 0.335
Vertical System-level Duration 0.361 0.364 0.358 0.405 0.458 0.364
Vertical Patient-level Duration 0.369 0.405 0.395 0.423 0.491 0.451

  • ‘Exact’ and ‘inexact’ matching are two different ways to determine whether an extracted textual finding is correct or not.

  • Standard precision, Recall and F-measure were reported for each individual type such as medication names, dosage, and frequency (termed the ‘vertical’ analysis), as well as for all outputs regardless of types (termed the ‘horizontal’ analysis).

  • In addition, those measurements were also calculated at two different levels: patient and system levels.

  • The patient level calculated precision, recall, and F-measure for each note and reported the averages across all notes, while the system level calculated them based on all entries from all notes.

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