Revisiting Fine-Tuning Strategies for Self-supervised Medical Imaging Analysis

TL;DR

This paper systematically investigates fine-tuning strategies for self-supervised learning in medical imaging, revealing that intermediate layer fine-tuning outperforms end-to-end approaches and combining multiple SSL models yields significant performance gains.

Contribution

It introduces a comprehensive analysis of fine-tuning layers for SSL in medical imaging and proposes strategies that outperform standard end-to-end fine-tuning.

Findings

Fine-tuning the second quarter of the network is optimal for contrastive SSL.

Fine-tuning the third quarter is best for restorative SSL.

Combining multiple SSL models improves performance by up to 3.57%.

Abstract

Despite the rapid progress in self-supervised learning (SSL), end-to-end fine-tuning still remains the dominant fine-tuning strategy for medical imaging analysis. However, it remains unclear whether this approach is truly optimal for effectively utilizing the pre-trained knowledge, especially considering the diverse categories of SSL that capture different types of features. In this paper, we present the first comprehensive study that discovers effective fine-tuning strategies for self-supervised learning in medical imaging. After developing strong contrastive and restorative SSL baselines that outperform SOTA methods across four diverse downstream tasks, we conduct an extensive fine-tuning analysis across multiple pre-training and fine-tuning datasets, as well as various fine-tuning dataset sizes. Contrary to the conventional wisdom of fine-tuning only the last few layers of a pre-trained network, we show that fine-tuning intermediate layers is more effective, with fine-tuning the second quarter (25-50%) of the network being optimal for contrastive SSL whereas fine-tuning the third quarter (50-75%) of the network being optimal for restorative SSL. Compared to the de-facto standard of end-to-end fine-tuning, our best fine-tuning strategy, which fine-tunes a shallower network consisting of the first three quarters (0-75%) of the pre-trained network, yields improvements of as much as 5.48%. Additionally, using these insights, we propose a simple yet effective method to leverage the complementary strengths of multiple SSL models, resulting in enhancements of up to 3.57% compared to using the best model alone. Hence, our fine-tuning strategies not only enhance the performance of individual SSL models, but also enable effective utilization of the complementary strengths offered by multiple SSL models, leading to significant improvements in self-supervised medical imaging analysis.