Invasive or More Direct Measurements Can Provide an Objective Early-Stopping Ceiling for Training Deep Neural Networks on Non-invasive or Less-Direct Biomedical Data.

Early stopping is an extremely common tool to minimize overfitting, which would otherwise be a cause of poor generalization of the model to novel data. However, early stopping is a heuristic that, while effective, primarily relies on ad hoc parameters and metrics. Optimizing when to stop remains a challenge. In this paper, we suggest that for some biomedical applications, a natural dichotomy of invasive/non-invasive measurements, or more generally proximal vs distal measurements of a biological system can be exploited to provide objective advice on early stopping. We discuss the conditions where invasive measurements of a biological process should provide better predictions than non-invasive measurements, or at best offer parity. Hence, if data from an invasive measurement are available locally, or from the literature, that information can be leveraged to know with high certainty whether a model of non-invasive data is overfitted. We present paired invasive/non-invasive cardiac and coronary artery measurements from two mouse strains, one of which spontaneously develops type 2 diabetes, posed as a classification problem. Examination of the various stopping rules shows that generalization is reduced with more training epochs and commonly applied stopping rules give widely different generalization error estimates. The use of an empirically derived training ceiling is demonstrated to be helpful as added information to leverage early stopping in order to reduce overfitting.

Improvement of automated analysis of coronary Doppler echocardiograms.

Coronary artery disease is the leading cause of heart disease, and while it can be assessed through transthoracic Doppler echocardiography (TTDE) by observing changes in coronary flow, manual analysis of TTDE is time consuming and subject to bias. In a previous study, a program was created to automatically analyze coronary flow patterns by parsing Doppler videos into a single continuous image, binarizing and separating the image into cardiac cycles, and extracting data values from each of these cycles. The program significantly reduced variability and time to complete TTDE analysis, but some obstacles such as interfering noise and varying video sizes left room to increase the program's accuracy. The goal of this current study was to refine the existing automation algorithm and heuristics by (1) moving the program to a Python environment, (2) increasing the program's ability to handle challenging cases and video variations, and (3) removing unrepresentative cardiac cycles from the final data set. With this improved analysis, examiners can use the automatic program to easily and accurately identify the early signs of serious heart diseases.