eprintid: 29212
rev_number: 23
userid: 5901
dir: disk0/00/02/92/12
datestamp: 2016-08-09 20:02:43
lastmod: 2021-04-11 05:55:18
status_changed: 2016-08-09 20:02:43
type: article
metadata_visibility: show
eprint_status: archive
creators_name: Gopalakrishnan, V
creators_name: Menon, PG
creators_name: Madan, S
creators_email: 
creators_email: 
creators_email: shm37@pitt.edu
creators_id: 
creators_id: 
creators_id: SHM37
title: cMRI-BED: A novel informatics framework for cardiac MRI biomarker extraction and discovery applied to pediatric cardiomyopathy classification
ispublished: pub
divisions: sch_as_intellsys
divisions: sch_med_biomedicalinformatics
divisions: sch_med_Computational_Systems_Biology
divisions: sch_med_Radiology
divisions: sch_eng_bio
full_text_status: public
abstract: Background: Pediatric cardiomyopathies are a rare, yet heterogeneous group of pathologies of the myocardium that are routinely examined clinically using Cardiovascular Magnetic Resonance Imaging (cMRI). This gold standard powerful non-invasive tool yields high resolution temporal images that characterize myocardial tissue. The complexities associated with the annotation of images and extraction of markers, necessitate the development of efficient workflows to acquire, manage and transform this data into actionable knowledge for patient care to reduce mortality and morbidity. Methods: We develop and test a novel informatics framework called cMRI-BED for biomarker extraction and discovery from such complex pediatric cMRI data that includes the use of a suite of tools for image processing, marker extraction and predictive modeling. We applied our workflow to obtain and analyze a dataset of 83 de-identified cases and controls containing cMRI-derived biomarkers for classifying positive versus negative findings of cardiomyopathy in children. Bayesian rule learning (BRL) methods were applied to derive understandable models in the form of propositional rules with posterior probabilities pertaining to their validity. Popular machine learning methods in the WEKA data mining toolkit were applied using default parameters to assess cross-validation performance of this dataset using accuracy and percentage area under ROC curve (AUC) measures. Results: The best 10-fold cross validation predictive performance obtained on this cMRI-derived biomarker dataset was 80.72% accuracy and 79.6% AUC by a BRL decision tree model, which is promising from this type of rare data. Moreover, we were able to verify that mycocardial delayed enhancement (MDE) status, which is known to be an important qualitative factor in the classification of cardiomyopathies, is picked up by our rule models as an important variable for prediction. Conclusions: Preliminary results show the feasibility of our framework for processing such data while also yielding actionable predictive classification rules that can augment knowledge conveyed in cardiac radiology outcome reports. Interactions between MDE status and other cMRI parameters that are depicted in our rules warrant further investigation and validation. Predictive rules learned from cMRI data to classify positive and negative findings of cardiomyopathy can enhance scientific understanding of the underlying interactions among imaging-derived parameters.
date: 2015-08-13
date_type: published
publication: BioMedical Engineering Online
volume: 14
number: 2
refereed: TRUE
id_number: 10.1186/1475-925X-14-S2-S7
citation:   Gopalakrishnan, V and Menon, PG and Madan, S  (2015) cMRI-BED: A novel informatics framework for cardiac MRI biomarker extraction and discovery applied to pediatric cardiomyopathy classification.  BioMedical Engineering Online, 14 (2).       
document_url: http://d-scholarship-dev.library.pitt.edu/29212/1/art%253A10.1186%252F1475-925X-14-S2-S7.pdf
document_url: http://d-scholarship-dev.library.pitt.edu/29212/7/licence.txt