A complementary graphical method for reducing and analyzing large data sets. Case studies demonstrating thresholds setting and selection

Methods Inf Med. 2014;53(3):173-85. doi: 10.3414/ME13-01-0075. Epub 2014 Apr 14.


Objectives: Graphical displays can make data more understandable; however, large graphs can challenge human comprehension. We have previously described a filtering method to provide high-level summary views of large data sets. In this paper we demonstrate our method for setting and selecting thresholds to limit graph size while retaining important information by applying it to large single and paired data sets, taken from patient and bibliographic databases.

Methods: Four case studies are used to illustrate our method. The data are either patient discharge diagnoses (coded using the International Classification of Diseases, Clinical Modifications [ICD9-CM]) or Medline citations (coded using the Medical Subject Headings [MeSH]). We use combinations of different thresholds to obtain filtered graphs for detailed analysis. The thresholds setting and selection, such as thresholds for node counts, class counts, ratio values, p values (for diff data sets), and percentiles of selected class count thresholds, are demonstrated with details in case studies. The main steps include: data preparation, data manipulation, computation, and threshold selection and visualization. We also describe the data models for different types of thresholds and the considerations for thresholds selection.

Results: The filtered graphs are 1%-3% of the size of the original graphs. For our case studies, the graphs provide 1) the most heavily used ICD9-CM codes, 2) the codes with most patients in a research hospital in 2011, 3) a profile of publications on "heavily represented topics" in MEDLINE in 2011, and 4) validated knowledge about adverse effects of the medication of rosiglitazone and new interesting areas in the ICD9-CM hierarchy associated with patients taking the medication of pioglitazone.

Conclusions: Our filtering method reduces large graphs to a manageable size by removing relatively unimportant nodes. The graphical method provides summary views based on computation of usage frequency and semantic context of hierarchical terminology. The method is applicable to large data sets (such as a hundred thousand records or more) and can be used to generate new hypotheses from data sets coded with hierarchical terminologies.

Keywords: Data mining method; clinical data repository; data analysis; data filtering method; data visualization; hierarchical terminology; threshold selection; threshold setting.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Algorithms*
  • Clinical Coding
  • Computer Graphics*
  • Data Display
  • Datasets as Topic*
  • Electronic Data Processing*
  • Electronic Health Records / statistics & numerical data*
  • Humans
  • International Classification of Diseases
  • Medical Informatics Computing
  • Patient Discharge
  • Pioglitazone
  • Terminology as Topic
  • Thiazolidinediones / adverse effects
  • Thiazolidinediones / therapeutic use


  • Thiazolidinediones
  • Pioglitazone