About Explicit Variance Minimization: Training Neural Networks for Medical Imaging With Limited Data Annotations

TL;DR

This paper introduces Variance Aware Training (VAT), a novel regularization method for medical imaging neural networks that reduces training time and matches or exceeds state-of-the-art performance by explicitly incorporating variance error into the loss function.

Contribution

The paper proposes VAT, a new regularization technique that leverages the morphological diversity in medical data, with a theoretical foundation and minimal hyper-parameter tuning.

Findings

VAT matches or improves state-of-the-art results

Achieves an order of magnitude reduction in training time

Validated on diverse medical imaging datasets

Abstract

Self-supervised learning methods for computer vision have demonstrated the effectiveness of pre-training feature representations, resulting in well-generalizing Deep Neural Networks, even if the annotated data are limited. However, representation learning techniques require a significant amount of time for model training, with most of the time spent on precise hyper-parameter optimization and selection of augmentation techniques. We hypothesized that if the annotated dataset has enough morphological diversity to capture the diversity of the general population, as is common in medical imaging due to conserved similarities of tissue morphology, the variance error of the trained model is the dominant component of the Bias-Variance Trade-off. Therefore, we proposed the Variance Aware Training (VAT) method that exploits this data property by introducing the variance error into the model loss function, thereby, explicitly regularizing the model. Additionally, we provided a theoretical formulation and proof of the proposed method to aid interpreting the approach. Our method requires selecting only one hyper-parameter and matching or improving the performance of state-of-the-art self-supervised methods while achieving an order of magnitude reduction in the GPU training time. We validated VAT on three medical imaging datasets from diverse domains and for various learning objectives. These included a Magnetic Resonance Imaging (MRI) dataset for the heart semantic segmentation (MICCAI 2017 ACDC challenge), fundus photography dataset for ordinary regression of diabetic retinopathy progression (Kaggle 2019 APTOS Blindness Detection challenge), and classification of histopathologic scans of lymph node sections (PatchCamelyon dataset). Our code is available at https://github.com/DmitriiShubin/Variance-Aware-Training.