Segmentation with mixed supervision: Confidence maximization helps knowledge distillation

Light mixed-supervised segmentation for 3D medical image data

BACKGROUND

Accurate 3D semantic segmentation models are essential for many clinical applications. To train a model for 3D segmentation, voxel-level annotation is necessary, which is expensive to obtain due to laborious work and privacy protection. To accurately annotate 3D medical data, such as MRI, a common practice is to annotate the volumetric data in a slice-by-slice contouring way along principal axes.

PURPOSE

In order to reduce the annotation effort in slices, weakly supervised learning with a bounding box (Bbox) was proposed to leverage the discriminating information via a tightness prior assumption. Nevertheless, this method requests accurate and tight Bboxes, which will significantly drop the performance when tightness is not held, that is when a relaxed Bbox is applied. Therefore, there is a need to train a stable model based on relaxed Bbox annotation.

METHODS

This paper presents a mixed-supervised training strategy to reduce the annotation effort for 3D segmentation tasks. In the proposed approach, a fully annotated contour is only required for a single slice of the volume. In contrast, the rest of the slices with targets are annotated with relaxed Bboxes. This mixed-supervised method adopts fully supervised learning, relaxed Bbox prior, and contrastive learning during the training, which ensures the network exploits the discriminative information of the training volumes properly. The proposed method was evaluated on two public 3D medical imaging datasets (MRI prostate dataset and Vestibular Schwannoma [VS] dataset).

RESULTS

The proposed method obtained a high segmentation Dice score of 85.3% on an MRI prostate dataset and 83.3% on a VS dataset with relaxed Bbox annotation, which are close to a fully supervised model. Moreover, with the same relaxed Bbox annotations, the proposed method outperforms the state-of-the-art methods. More importantly, the model performance is stable when the accuracy of Bbox annotation varies.

CONCLUSIONS

The presented study proposes a method based on a mixed-supervised learning method in 3D medical imaging. The benefit will be stable segmentation of the target in 3D images with low accurate annotation requirement, which leads to easier model training on large-scale datasets.

Sparse annotation learning for dense volumetric MR image segmentation with uncertainty estimation

Objective.Training neural networks for pixel-wise or voxel-wise image segmentation is a challenging task that requires a considerable amount of training samples with highly accurate and densely delineated ground truth maps. This challenge becomes especially prominent in the medical imaging domain, where obtaining reliable annotations for training samples is a difficult, time-consuming, and expert-dependent process. Therefore, developing models that can perform well under the conditions of limited annotated training data is desirable.Approach.In this study, we propose an innovative framework called the extremely sparse annotation neural network (ESA-Net) that learns with only the single central slice label for 3D volumetric segmentation which explores both intra-slice pixel dependencies and inter-slice image correlations with uncertainty estimation. Specifically, ESA-Net consists of four specially designed distinct components: (1) an intra-slice pixel dependency-guided pseudo-label generation module that exploits uncertainty in network predictions while generating pseudo-labels for unlabeled slices with temporal ensembling; (2) an inter-slice image correlation-constrained pseudo-label propagation module which propagates labels from the labeled central slice to unlabeled slices by self-supervised registration with rotation ensembling; (3) a pseudo-label fusion module that fuses the two sets of generated pseudo-labels with voxel-wise uncertainty guidance; and (4) a final segmentation network optimization module to make final predictions with scoring-based label quantification.Main results.Extensive experimental validations have been performed on two popular yet challenging magnetic resonance image segmentation tasks and compared to five state-of-the-art methods.Significance.Results demonstrate that our proposed ESA-Net can consistently achieve better segmentation performances even under the extremely sparse annotation setting, highlighting its effectiveness in exploiting information from unlabeled data.

MUE-CoT: multi-scale uncertainty entropy-aware co-training framework for left atrial segmentation

Objective.Accurate left atrial segmentation is the basis of the recognition and clinical analysis of atrial fibrillation. Supervised learning has achieved some competitive segmentation results, but the high annotation cost often limits its performance. Semi-supervised learning is implemented from limited labeled data and a large amount of unlabeled data and shows good potential in solving practical medical problems.Approach. In this study, we proposed a collaborative training framework for multi-scale uncertain entropy perception (MUE-CoT) and achieved efficient left atrial segmentation from a small amount of labeled data. Based on the pyramid feature network, learning is implemented from unlabeled data by minimizing the pyramid prediction difference. In addition, novel loss constraints are proposed for co-training in the study. The diversity loss is defined as a soft constraint so as to accelerate the convergence and a novel multi-scale uncertainty entropy calculation method and a consistency regularization term are proposed to measure the consistency between prediction results. The quality of pseudo-labels cannot be guaranteed in the pre-training period, so a confidence-dependent empirical Gaussian function is proposed to weight the pseudo-supervised loss.Main results.The experimental results of a publicly available dataset and an in-house clinical dataset proved that our method outperformed existing semi-supervised methods. For the two datasets with a labeled ratio of 5%, the Dice similarity coefficient scores were 84.94% ± 4.31 and 81.24% ± 2.4, the HD95values were 4.63 mm ± 2.13 and 3.94 mm ± 2.72, and the Jaccard similarity coefficient scores were 74.00% ± 6.20 and 68.49% ± 3.39, respectively.Significance.The proposed model effectively addresses the challenges of limited data samples and high costs associated with manual annotation in the medical field, leading to enhanced segmentation accuracy.