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Register a new userPoissonSeg: Semi-Supervised Few-Shot Medical Image Segmentation via Poisson Learning
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Xiaoang Shen
Publication date
2021
fields
Informatics Engineering
and research's language is
English
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The application of deep learning to medical image segmentation has been hampered due to the lack of abundant pixel-level annotated data. Few-shot Semantic Segmentation (FSS) is a promising strategy for breaking the deadlock. However, a high-performing FSS model still requires sufficient pixel-level annotated classes for training to avoid overfitting, which leads to its performance bottleneck in medical image segmentation due to the unmet need for annotations. Thus, semi-supervised FSS for medical images is accordingly proposed to utilize unlabeled data for further performance improvement. Nevertheless, existing semi-supervised FSS methods has two obvious defects: (1) neglecting the relationship between the labeled and unlabeled data; (2) using unlabeled data directly for end-to-end training leads to degenerated representation learning. To address these problems, we propose a novel semi-supervised FSS framework for medical image segmentation. The proposed framework employs Poisson learning for modeling data relationship and propagating supervision signals, and Spatial Consistency Calibration for encouraging the model to learn more coherent representations. In this process, unlabeled samples do not involve in end-to-end training, but provide supervisory information for query image segmentation through graph-based learning. We conduct extensive experiments on three medical image segmentation datasets (i.e. ISIC skin lesion segmentation, abdominal organs segmentation for MRI and abdominal organs segmentation for CT) to demonstrate the state-of-the-art performance and broad applicability of the proposed framework.
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The predicament in semi-supervised few-shot learning (SSFSL) is to maximize the value of the extra unlabeled data to boost the few-shot learner. In this paper, we propose a Poisson Transfer Network (PTN) to mine the unlabeled information for SSFSL from two aspects. First, the Poisson Merriman Bence Osher (MBO) model builds a bridge for the communications between labeled and unlabeled examples. This model serves as a more stable and informative classifier than traditional graph-based SSFSL methods in the message-passing process of the labels. Second, the extra unlabeled samples are employed to transfer the knowledge from base classes to novel classes through contrastive learning. Specifically, we force the augmented positive pairs close while push the negative ones distant. Our contrastive transfer scheme implicitly learns the novel-class embeddings to alleviate the over-fitting problem on the few labeled data. Thus, we can mitigate the degeneration of embedding generality in novel classes. Extensive experiments indicate that PTN outperforms the state-of-the-art few-shot and SSFSL models on miniImageNet and tieredImageNet benchmark datasets.
Automated segmentation in medical image analysis is a challenging task that requires a large amount of manually labeled data. However, manually annotating medical data is often laborious, and most existing learning-based approaches fail to accurately delineate object boundaries without effective geometric constraints. Contrastive learning, a sub-area of self-supervised learning, has recently been noted as a promising direction in multiple application fields. In this work, we present a novel Contrastive Voxel-wise Representation Learning (CVRL) method with geometric constraints to learn global-local visual representations for volumetric medical image segmentation with limited annotations. Our framework can effectively learn global and local features by capturing 3D spatial context and rich anatomical information. Specifically, we introduce a voxel-to-volume contrastive algorithm to learn global information from 3D images, and propose to perform local voxel-to-voxel contrast to explicitly make use of local cues in the embedding space. Moreover, we integrate an elastic interaction-based active contour model as a geometric regularization term to enable fast and reliable object delineations in an end-to-end learning manner. Results on the Atrial Segmentation Challenge dataset demonstrate superiority of our proposed scheme, especially in a setting with a very limited number of annotated data.
Deep learning has demonstrated significant improvements in medical image segmentation using a sufficiently large amount of training data with manual labels. Acquiring well-representative labels requires expert knowledge and exhaustive labors. In this paper, we aim to boost the performance of semi-supervised learning for medical image segmentation with limited labels using a self-ensembling contrastive learning technique. To this end, we propose to train an encoder-decoder network at image-level with small amounts of labeled images, and more importantly, we learn latent representations directly at feature-level by imposing contrastive loss on unlabeled images. This method strengthens intra-class compactness and inter-class separability, so as to get a better pixel classifier. Moreover, we devise a student encoder for online learning and an exponential moving average version of it, called teacher encoder, to improve the performance iteratively in a self-ensembling manner. To construct contrastive samples with unlabeled images, two sampling strategies that exploit structure similarity across medical images and utilize pseudo-labels for construction, termed region-aware and anatomical-aware contrastive sampling, are investigated. We conduct extensive experiments on an MRI and a CT segmentation dataset and demonstrate that in a limited label setting, the proposed method achieves state-of-the-art performance. Moreover, the anatomical-aware strategy that prepares contrastive samples on-the-fly using pseudo-labels realizes better contrastive regularization on feature representations.
The success of deep learning methods in medical image segmentation tasks heavily depends on a large amount of labeled data to supervise the training. On the other hand, the annotation of biomedical images requires domain knowledge and can be laborious. Recently, contrastive learning has demonstrated great potential in learning latent representation of images even without any label. Existing works have explored its application to biomedical image segmentation where only a small portion of data is labeled, through a pre-training phase based on self-supervised contrastive learning without using any labels followed by a supervised fine-tuning phase on the labeled portion of data only. In this paper, we establish that by including the limited label in formation in the pre-training phase, it is possible to boost the performance of contrastive learning. We propose a supervised local contrastive loss that leverages limited pixel-wise annotation to force pixels with the same label to gather around in the embedding space. Such loss needs pixel-wise computation which can be expensive for large images, and we further propose two strategies, downsampling and block division, to address the issue. We evaluate our methods on two public biomedical image datasets of different modalities. With different amounts of labeled data, our methods consistently outperform the state-of-the-art contrast-based methods and other semi-supervised learning techniques.
Although having achieved great success in medical image segmentation, deep convolutional neural networks usually require a large dataset with manual annotations for training and are difficult to generalize to unseen classes. Few-shot learning has the potential to address these challenges by learning new classes from only a few labeled examples. In this work, we propose a new framework for few-shot medical image segmentation based on prototypical networks. Our innovation lies in the design of two key modules: 1) a context relation encoder (CRE) that uses correlation to capture local relation features between foreground and background regions; and 2) a recurrent mask refinement module that repeatedly uses the CRE and a prototypical network to recapture the change of context relationship and refine the segmentation mask iteratively. Experiments on two abdomen CT datasets and an abdomen MRI dataset show the proposed method obtains substantial improvement over the state-of-the-art methods by an average of 16.32%, 8.45% and 6.24% in terms of DSC, respectively. Code is publicly available.
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