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Register a new userTowards Robust Medical Image Segmentation on Small-Scale Data with Incomplete Labels
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Nanqing Dong
Publication date
2020
fields
Informatics Engineering
and research's language is
English
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The data-driven nature of deep learning models for semantic segmentation requires a large number of pixel-level annotations. However, large-scale and fully labeled medical datasets are often unavailable for practical tasks. Recently, partially supervised methods have been proposed to utilize images with incomplete labels to mitigate the data scarcity problem in the medical domain. As an emerging research area, the breakthroughs made by existing methods rely on either large-scale data or complex model design, which makes them 1) less practical for certain real-life tasks and 2) less robust for small-scale data. It is time to step back and think about the robustness of partially supervised methods and how to maximally utilize small-scale and partially labeled data for medical image segmentation tasks. To bridge the methodological gaps in label-efficient deep learning with partial supervision, we propose RAMP, a simple yet efficient data augmentation framework for partially supervised medical image segmentation by exploiting the assumption that patients share anatomical similarities. We systematically evaluate RAMP and the previous methods in various controlled multi-structure segmentation tasks. Compared to the mainstream approaches, RAMP consistently improves the performance of traditional segmentation networks on small-scale partially labeled data and utilize additional image-wise weak annotations.
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Accurately and globally mapping human infrastructure is an important and challenging task with applications in routing, regulation compliance monitoring, and natural disaster response management etc.. In this paper we present progress in developing an algorithmic pipeline and distributed compute system that automates the process of map creation using high resolution aerial images. Unlike previous studies, most of which use datasets that are available only in a few cities across the world, we utilizes publicly available imagery and map data, both of which cover the contiguous United States (CONUS). We approach the technical challenge of inaccurate and incomplete training data adopting state-of-the-art convolutional neural network architectures such as the U-Net and the CycleGAN to incrementally generate maps with increasingly more accurate and more complete labels of man-made infrastructure such as roads and houses. Since scaling the mapping task to CONUS calls for parallelization, we then adopted an asynchronous distributed stochastic parallel gradient descent training scheme to distribute the computational workload onto a cluster of GPUs with nearly linear speed-up.
Despite the success of deep learning methods in medical image segmentation tasks, the human-level performance relies on massive training data with high-quality annotations, which are expensive and time-consuming to collect. The fact is that there exist low-quality annotations with label noise, which leads to suboptimal performance of learned models. Two prominent directions for segmentation learning with noisy labels include pixel-wise noise robust training and image-level noise robust training. In this work, we propose a novel framework to address segmenting with noisy labels by distilling effective supervision information from both pixel and image levels. In particular, we explicitly estimate the uncertainty of every pixel as pixel-wise noise estimation, and propose pixel-wise robust learning by using both the original labels and pseudo labels. Furthermore, we present an image-level robust learning method to accommodate more information as the complements to pixel-level learning. We conduct extensive experiments on both simulated and real-world noisy datasets. The results demonstrate the advantageous performance of our method compared to state-of-the-art baselines for medical image segmentation with noisy labels.
To mitigate the radiologists workload, computer-aided diagnosis with the capability to review and analyze medical images is gradually deployed. Deep learning-based region of interest segmentation is among the most exciting use cases. However, this paradigm is restricted in real-world clinical applications due to poor robustness and generalization. The issue is more sinister with a lack of training data. In this paper, we address the challenge from the representation learning point of view. We investigate that the collapsed representations, as one of the main reasons which caused poor robustness and generalization, could be avoided through transfer learning. Therefore, we propose a novel two-stage framework for robust generalized segmentation. In particular, an unsupervised Tile-wise AutoEncoder (T-AE) pretraining architecture is coined to learn meaningful representation for improving the generalization and robustness of the downstream tasks. Furthermore, the learned knowledge is transferred to the segmentation benchmark. Coupled with an image reconstruction network, the representation keeps to be decoded, encouraging the model to capture more semantic features. Experiments of lung segmentation on multi chest X-ray datasets are conducted. Empirically, the related experimental results demonstrate the superior generalization capability of the proposed framework on unseen domains in terms of high performance and robustness to corruption, especially under the scenario of the limited training data.
Deep learning models usually require a large amount of labeled data to achieve satisfactory performance. In multimedia analysis, domain adaptation studies the problem of cross-domain knowledge transfer from a label rich source domain to a label scarce target domain, thus potentially alleviates the annotation requirement for deep learning models. However, we find that contemporary domain adaptation methods for cross-domain image understanding perform poorly when source domain is noisy. Weakly Supervised Domain Adaptation (WSDA) studies the domain adaptation problem under the scenario where source data can be noisy. Prior methods on WSDA remove noisy source data and align the marginal distribution across domains without considering the fine-grained semantic structure in the embedding space, which have the problem of class misalignment, e.g., features of cats in the target domain might be mapped near features of dogs in the source domain. In this paper, we propose a novel method, termed Noise Tolerant Domain Adaptation, for WSDA. Specifically, we adopt the cluster assumption and learn cluster discriminatively with class prototypes in the embedding space. We propose to leverage the location information of the data points in the embedding space and model the location information with a Gaussian mixture model to identify noisy source data. We then design a network which incorporates the Gaussian mixture noise model as a sub-module for unsupervised noise removal and propose a novel cluster-level adversarial adaptation method which aligns unlabeled target data with the less noisy class prototypes for mapping the semantic structure across domains. We conduct extensive experiments to evaluate the effectiveness of our method on both general images and medical images from COVID-19 and e-commerce datasets. The results show that our method significantly outperforms state-of-the-art WSDA methods.
Deep learning-based segmentation methods are vulnerable to unforeseen data distribution shifts during deployment, e.g. change of image appearances or contrasts caused by different scanners, unexpected imaging artifacts etc. In this paper, we present a cooperative framework for training image segmentation models and a latent space augmentation method for generating hard examples. Both contributions improve model generalization and robustness with limited data. The cooperative training framework consists of a fast-thinking network (FTN) and a slow-thinking network (STN). The FTN learns decoupled image features and shape features for image reconstruction and segmentation tasks. The STN learns shape priors for segmentation correction and refinement. The two networks are trained in a cooperative manner. The latent space augmentation generates challenging examples for training by masking the decoupled latent space in both channel-wise and spatial-wise manners. We performed extensive experiments on public cardiac imaging datasets. Using only 10 subjects from a single site for training, we demonstrated improved cross-site segmentation performance and increased robustness against various unforeseen imaging artifacts compared to strong baseline methods. Particularly, cooperative training with latent space data augmentation yields 15% improvement in terms of average Dice score when compared to a standard training method.
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