title: Automated Classification of Selected Data Elements from Free-text Diagnostic Reports for Clinical Research.
abstract: OBJECTIVE
  In the Multiple Myeloma clinical registry at Heidelberg University Hospital, most data are extracted from discharge letters. Our aim was to analyze if it is possible to make the manual documentation process more efficient by using methods of natural language processing for multiclass classification of free-text diagnostic reports to automatically document the diagnosis and state of disease of myeloma patients. The first objective was to create a corpus consisting of free-text diagnosis paragraphs of patients with multiple myeloma from German diagnostic reports, and its manual annotation of relevant data elements by documentation specialists. The second objective was to construct and evaluate a framework using different NLP methods to enable automatic multiclass classification of relevant data elements from free-text diagnostic reports.
  
  
  METHODS
  The main diagnoses paragraph was extracted from the clinical report of one third randomly selected patients of the multiple myeloma research database from Heidelberg University Hospital (in total 737 selected patients). An EDC system was setup and two data entry specialists performed independently a manual documentation of at least nine specific data elements for multiple myeloma characterization. Both data entries were compared and assessed by a third specialist and an annotated text corpus was created. A framework was constructed, consisting of a self-developed package to split multiple diagnosis sequences into several subsequences, four different preprocessing steps to normalize the input data and two classifiers: a maximum entropy classifier (MEC) and a support vector machine (SVM). In total 15 different pipelines were examined and assessed by a ten-fold cross-validation, reiterated 100 times. For quality indication the average error rate and the average F1-score were conducted. For significance testing the approximate randomization test was used.
  
  
  RESULTS
  The created annotated corpus consists of 737 different diagnoses paragraphs with a total number of 865 coded diagnosis. The dataset is publicly available in the supplementary online files for training and testing of further NLP methods. Both classifiers showed low average error rates (MEC: 1.05; SVM: 0.84) and high F1-scores (MEC: 0.89; SVM: 0.92). However the results varied widely depending on the classified data element. Preprocessing methods increased this effect and had significant impact on the classification, both positive and negative. The automatic diagnosis splitter increased the average error rate significantly, even if the F1-score decreased only slightly.
  
  
  CONCLUSIONS
  The low average error rates and high average F1-scores of each pipeline demonstrate the suitability of the investigated NPL methods. However, it was also shown that there is no best practice for an automatic classification of data elements from free-text diagnostic reports.
authors.affiliation: Martin Löpprich, Heidelberg University, Institute of Medical Biometry and Informatics, Im Neuenheimer Feld 130.3, 69120 Heidelberg, Germany, E-mail: martin.loepprich@med.uni-heidelberg.de.
authors.forename: Martin
authors.initials: M
authors.lastname: Löpprich
authors.forename: Felix
authors.initials: F
authors.lastname: Krauss
authors.forename: Matthias
authors.initials: M
authors.lastname: Ganzinger
authors.forename: Karsten
authors.initials: K
authors.lastname: Senghas
authors.forename: Stefan
authors.initials: S
authors.lastname: Riezler
authors.forename: Petra
authors.initials: P
authors.lastname: Knaup
mesh_terms: D001331:Automation; D035843:Biomedical Research; D057225:Data Mining; D016208:Databases, Factual; D006801:Humans; D009101:Multiple Myeloma / Q000175:diagnosis; D009323:Natural Language Processing; D058028:Research Report; D060388:Support Vector Machine
keywords: Medical informatics; classification; medical writing; multiple myeloma; natural language processing