Volume 9, Number 9, July 2019

Attribute Reduction and Decision Tree Pruning to Simplify Liver Fibrosis Prediction Algorithms
A Cohort Study

  Authors

Mahasen Mabrouk¹, Abubakr Awad², Hend Shousha¹, Wafaa Alakel^1,3, Ahmed Salama¹ and Tahany Awad¹, ¹Cairo University, Egypt, ²University of Aberdeen, UK and ³National Hepatology and Tropical Medicine Research Institute, Cairo, Egypt

  Abstract

Background: Assessment of liver fibrosis is a vital need for enabling therapeutic decisions and prognostic evaluations of chronic hepatitis. Liver biopsy is considered the definitive investigation for assessing the stage of liver fibrosis but it carries several limitations. FIB-4 and APRI also have a limited accuracy. The National Committee for Control of Viral Hepatitis (NCCVH) in Egypt has supplied a valuable pool of electronic patients’ data that data mining techniques can analyze to disclose hidden patterns, trends leading to the evolution of predictive algorithms.

Aim: to collaborate with physicians to develop a novel reliable, easy to comprehend noninvasive model to predict the stage of liver fibrosis utilizing routine workup, without imposing extra costs for additional examinations especially in areas with limited resources like Egypt.

Methods: This multi-centered retrospective study included baseline demographic, laboratory, and histopathological data of 69106 patients with chronic hepatitis C. We started by data collection preprocessing, cleansing and formatting for knowledge discovery of useful information from Electronic Health Records EHRs. Data mining has been used to build a decision tree (Reduced Error Pruning tree (REP tree)) with 10-fold internal cross-validation. Histopathology results were used to assess accuracy for fibrosis stages. Machine learning feature selection and reduction (CfsSubseteval / best first) reduced the initial number of input features (N=15) to the most relevant ones (N=6) for developing the prediction model.

Results: In this study, 32419 patients had F(0-1), 25073 had F(2) and 11615 had F(3-4). FIB-4 and APRI revalidation in our study showed low accuracy and high discordance with biopsy results, with overall AUC 0.68 and 0.58 respectively. Out of 15 attributes machine learning selected Age, AFP, AST, glucose, albumin, and platelet as the most relevant attributes. Results for REP tree indicated an overall classification accuracy up to 70% and ROC Area 0.74 which was not nearly affected by attribute reduction, and pruning . However attribute reduction, and tree pruning were associated with simpler model easy to understand by physician with less time for execution.

Conclusion: This study we had the chance to study a large cohort of 69106 chronic hepatitis patients with available liver biopsy results to revise and validate the accuracy of FIB-4 and APRI. This study represents the collaboration between computer scientist and hepatologists to provide clinicians with an accurate novel and reliable, noninvasive model to predict the stage of liver fibrosis.

  Keywords

Liver Fibrosis, Data Mining, Weka, Decision Tree, Attribute Reduction, Tree Pruning

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