Learning robust medical image segmentation from multi-source annotations

Abstract

Collecting annotations from multiple independent sources could mitigate the impact of potential noises and biases from a single source, which is a common practice in medical image segmentation. However, learning segmentation networks from multi-source annotations remains a challenge due to the uncertainties brought by the variance of the annotations. In this paper, we proposed an Uncertainty-guided Multi-source Annotation Network (UMA-Net), which guided the training process by uncertainty estimation at both the pixel and the image levels. First, we developed an annotation uncertainty estimation module (AUEM) to estimate the pixel-wise uncertainty of each annotation, which then guided the network to learn from reliable pixels by a weighted segmentation loss. Second, a quality assessment module (QAM) was proposed to assess the image-level quality of the input samples based on the former estimated annotation uncertainties. Furthermore, instead of discarding the low-quality samples, we introduced an auxiliary predictor to learn from them and thus ensured the preservation of their representation knowledge in the backbone without directly accumulating errors within the primary predictor. Extensive experiments demonstrated the effectiveness and feasibility of our proposed UMA-Net on various datasets, including 2D chest X-ray segmentation dataset, 2D fundus image segmentation dataset, 3D breast DCE-MRI segmentation dataset, and the QUBIQ multi-task segmentation dataset. Code will be released at https://github.com/wangjin2945/UMA-Net.