Fair Federated Medical Image Segmentation via Client Contribution Estimation

How to ensure fairness is an important topic in federated learning (FL). Recent studies have investigated how to reward clients based on their contribution (collaboration fairness), and how to achieve uniformity of performance across clients (performance fairness). Despite achieving progress on either one, we argue that it is critical to consider them together, in order to engage and motivate more diverse clients joining FL to derive a high-quality global model. In this work, we propose a novel method to optimize both types of fairness simultaneously. Specifically, we propose to estimate client contribution in gradient and data space. In gradient space, we monitor the gradient direction differences of each client with respect to others. And in data space, we measure the prediction error on client data using an auxiliary model. Based on this contribution estimation, we propose a FL method, federated training via contribution estimation (FedCE), i.e., using estimation as global model aggregation weights. We have theoretically analyzed our method and empirically evaluated it on two real-world medical datasets. The effectiveness of our approach has been validated with significant performance improvements, better collaboration fairness, better performance fairness, and comprehensive analytical studies.Comment: Accepted at CVPR 202

COLosSAL: A Benchmark for Cold-start Active Learning for 3D Medical Image Segmentation

Medical image segmentation is a critical task in medical image analysis. In recent years, deep learning based approaches have shown exceptional performance when trained on a fully-annotated dataset. However, data annotation is often a significant bottleneck, especially for 3D medical images. Active learning (AL) is a promising solution for efficient annotation but requires an initial set of labeled samples to start active selection. When the entire data pool is unlabeled, how do we select the samples to annotate as our initial set? This is also known as the cold-start AL, which permits only one chance to request annotations from experts without access to previously annotated data. Cold-start AL is highly relevant in many practical scenarios but has been under-explored, especially for 3D medical segmentation tasks requiring substantial annotation effort. In this paper, we present a benchmark named COLosSAL by evaluating six cold-start AL strategies on five 3D medical image segmentation tasks from the public Medical Segmentation Decathlon collection. We perform a thorough performance analysis and explore important open questions for cold-start AL, such as the impact of budget on different strategies. Our results show that cold-start AL is still an unsolved problem for 3D segmentation tasks but some important trends have been observed. The code repository, data partitions, and baseline results for the complete benchmark are publicly available at https://github.com/MedICL-VU/COLosSAL.Comment: Accepted by MICCAI 202

A Unified Single-stage Learning Model for Estimating Fiber Orientation Distribution Functions on Heterogeneous Multi-shell Diffusion-weighted MRI

Diffusion-weighted (DW) MRI measures the direction and scale of the local diffusion process in every voxel through its spectrum in q-space, typically acquired in one or more shells. Recent developments in micro-structure imaging and multi-tissue decomposition have sparked renewed attention to the radial b-value dependence of the signal. Applications in tissue classification and micro-architecture estimation, therefore, require a signal representation that extends over the radial as well as angular domain. Multiple approaches have been proposed that can model the non-linear relationship between the DW-MRI signal and biological microstructure. In the past few years, many deep learning-based methods have been developed towards faster inference speed and higher inter-scan consistency compared with traditional model-based methods (e.g., multi-shell multi-tissue constrained spherical deconvolution). However, a multi-stage learning strategy is typically required since the learning process relied on various middle representations, such as simple harmonic oscillator reconstruction (SHORE) representation. In this work, we present a unified dynamic network with a single-stage spherical convolutional neural network, which allows efficient fiber orientation distribution function (fODF) estimation through heterogeneous multi-shell diffusion MRI sequences. We study the Human Connectome Project (HCP) young adults with test-retest scans. From the experimental results, the proposed single-stage method outperforms prior multi-stage approaches in repeated fODF estimation with shell dropoff and single-shell DW-MRI sequences

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

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.Comment: Preprin