Abstract
Human-induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) provide an excellent platform for potential clinical and research applications. Identifying abnormal Ca2+ transients is crucial for evaluating cardiomyocyte function that requires labor-intensive manual effort. Therefore, we develop an analytical pipeline for automatic assessment of Ca2+ transient abnormality, by employing advanced machine learning methods together with an Analytical Algorithm. First, we adapt an existing Analytical Algorithm to identify Ca2+ transient peaks and determine peak abnormality based on quantified peak characteristics. Second, we train a peak-level Support Vector Machine (SVM) classifier by using human-expert assessment of peak abnormality as outcome and profiled peak variables as predictive features. Third, we train another cell-level SVM classifier by using human-expert assessment of cell abnormality as outcome and quantified cell-level variables as predictive features. This cell-level SVM classifier can be used to assess additional Ca2+ transient signals. By applying this pipeline to our Ca2+ transient data, we trained a cell-level SVM classifier using 200 cells as training data, then tested its accuracy in an independent dataset of 54 cells. As a result, we obtained 88% training accuracy and 87% test accuracy. Further, we provide a free R package to implement our pipeline for high-throughput CM Ca2+ analysis.
Highlights
Human-induced pluripotent stem cell-derived cardiomyocytes provide an excellent platform for potential clinical and research applications
With a set of C a2+ signals as the training data, our pipeline first trains a peak-level Support Vector Machine (SVM) classifier by taking peak assessments by human experts as responses and 14 peak variables as predicting features
Cell abnormality assessment based on those two types of peak assessments along with other cell variables are taken as predictors to train a signal-level SVM classifier for predicting signal abnormality
Summary
Human-induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) provide an excellent platform for potential clinical and research applications. We adapt an existing Analytical Algorithm to identify Ca2+ transient peaks and determine peak abnormality based on quantified peak characteristics. We train a peak-level Support Vector Machine (SVM) classifier by using human-expert assessment of peak abnormality as outcome and profiled peak variables as predictive features. We train another cell-level SVM classifier by using humanexpert assessment of cell abnormality as outcome and quantified cell-level variables as predictive features This cell-level SVM classifier can be used to assess additional Ca2+ transient signals. Manual identification of abnormal Ca2+ transients by human experts becomes a bottleneck hindering its application to high-throughput analysis. The analytical algorithm fails to account for the valuable manual assessment results about existing data
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