Disruptive Autoencoders: Leveraging Low-level features for 3D Medical Image Pre-training

TL;DR

This paper introduces Disruptive Autoencoders, a novel pre-training framework for 3D medical images that leverages local masking, low-level perturbations, and cross-modal contrastive learning to improve representation and achieve state-of-the-art results.

Contribution

It proposes a new pre-training method combining local masking, low-level perturbations, and cross-modal contrastive loss for 3D medical images, addressing modality-specific challenges.

Findings

Achieves state-of-the-art performance on multiple downstream tasks.

Top of the BTCV multi-organ segmentation challenge leaderboard.

Effective learning of local and low-level features in 3D medical images.

Abstract

Harnessing the power of pre-training on large-scale datasets like ImageNet forms a fundamental building block for the progress of representation learning-driven solutions in computer vision. Medical images are inherently different from natural images as they are acquired in the form of many modalities (CT, MR, PET, Ultrasound etc.) and contain granulated information like tissue, lesion, organs etc. These characteristics of medical images require special attention towards learning features representative of local context. In this work, we focus on designing an effective pre-training framework for 3D radiology images. First, we propose a new masking strategy called local masking where the masking is performed across channel embeddings instead of tokens to improve the learning of local feature representations. We combine this with classical low-level perturbations like adding noise and downsampling to further enable low-level representation learning. To this end, we introduce Disruptive Autoencoders, a pre-training framework that attempts to reconstruct the original image from disruptions created by a combination of local masking and low-level perturbations. Additionally, we also devise a cross-modal contrastive loss (CMCL) to accommodate the pre-training of multiple modalities in a single framework. We curate a large-scale dataset to enable pre-training of 3D medical radiology images (MRI and CT). The proposed pre-training framework is tested across multiple downstream tasks and achieves state-of-the-art performance. Notably, our proposed method tops the public test leaderboard of BTCV multi-organ segmentation challenge.