Pseudo-labels are widely employed in weakly supervised 3D segmentation tasks where only sparse ground-truth labels are available for learning. Existing methods often rely on empirical label selection strategies, such as confidence thresholding, to generate beneficial pseudo-labels for model training. This approach may, however, hinder the comprehensive exploitation of unlabeled data points. We hypothesize that this selective usage arises from the noise in pseudo-labels generated on unlabeled data. The noise in pseudo-labels may result in significant discrepancies between pseudo-labels and model predictions, thus confusing and affecting the model training greatly. To address this issue, we propose a novel learning strategy to regularize the generated pseudo-labels and effectively narrow the gaps between pseudo-labels and model predictions. More specifically, our method introduces an Entropy Regularization loss and a Distribution Alignment loss for weakly supervised learning in 3D segmentation tasks, resulting in an ERDA learning strategy. Interestingly, by using KL distance to formulate the distribution alignment loss, it reduces to a deceptively simple cross-entropy-based loss which optimizes both the pseudo-label generation network and the 3D segmentation network simultaneously. Despite the simplicity, our method promisingly improves the performance. We validate the effectiveness through extensive experiments on various baselines and large-scale datasets. Results show that ERDA effectively enables the effective usage of all unlabeled data points for learning and achieves state-of-the-art performance under different settings. Remarkably, our method can outperform fully-supervised baselines using only 1% of true annotations. Code and model will be made publicly available.
相關內容
In the context of label-efficient learning on video data, the distillation method and the structural design of the teacher-student architecture have a significant impact on knowledge distillation. However, the relationship between these factors has been overlooked in previous research. To address this gap, we propose a new weakly supervised learning framework for knowledge distillation in video classification that is designed to improve the efficiency and accuracy of the student model. Our approach leverages the concept of substage-based learning to distill knowledge based on the combination of student substages and the correlation of corresponding substages. We also employ the progressive cascade training method to address the accuracy loss caused by the large capacity gap between the teacher and the student. Additionally, we propose a pseudo-label optimization strategy to improve the initial data label. To optimize the loss functions of different distillation substages during the training process, we introduce a new loss method based on feature distribution. We conduct extensive experiments on both real and simulated data sets, demonstrating that our proposed approach outperforms existing distillation methods in terms of knowledge distillation for video classification tasks. Our proposed substage-based distillation approach has the potential to inform future research on label-efficient learning for video data.
Improving Segmentation and Detection of Lesions in CT Scans Using Intensity Distribution Supervision
We propose a method to incorporate the intensity information of a target lesion on CT scans in training segmentation and detection networks. We first build an intensity-based lesion probability (ILP) function from an intensity histogram of the target lesion. It is used to compute the probability of being the lesion for each voxel based on its intensity. Finally, the computed ILP map of each input CT scan is provided as additional supervision for network training, which aims to inform the network about possible lesion locations in terms of intensity values at no additional labeling cost. The method was applied to improve the segmentation of three different lesion types, namely, small bowel carcinoid tumor, kidney tumor, and lung nodule. The effectiveness of the proposed method on a detection task was also investigated. We observed improvements of 41.3% -> 47.8%, 74.2% -> 76.0%, and 26.4% -> 32.7% in segmenting small bowel carcinoid tumor, kidney tumor, and lung nodule, respectively, in terms of per case Dice scores. An improvement of 64.6% -> 75.5% was achieved in detecting kidney tumors in terms of average precision. The results of different usages of the ILP map and the effect of varied amount of training data are also presented.
The optimal prediction strategy for out-of-distribution (OOD) setups is a fundamental question in machine learning. In this paper, we address this question and present several contributions. We propose three reject option models for OOD setups: the Cost-based model, the Bounded TPR-FPR model, and the Bounded Precision-Recall model. These models extend the standard reject option models used in non-OOD setups and define the notion of an optimal OOD selective classifier. We establish that all the proposed models, despite their different formulations, share a common class of optimal strategies. Motivated by the optimal strategy, we introduce double-score OOD methods that leverage uncertainty scores from two chosen OOD detectors: one focused on OOD/ID discrimination and the other on misclassification detection. The experimental results consistently demonstrate the superior performance of this simple strategy compared to state-of-the-art methods. Additionally, we propose novel evaluation metrics derived from the definition of the optimal strategy under the proposed OOD rejection models. These new metrics provide a comprehensive and reliable assessment of OOD methods without the deficiencies observed in existing evaluation approaches.
Statistical shape models (SSM) have been well-established as an excellent tool for identifying variations in the morphology of anatomy across the underlying population. Shape models use consistent shape representation across all the samples in a given cohort, which helps to compare shapes and identify the variations that can detect pathologies and help in formulating treatment plans. In medical imaging, computing these shape representations from CT/MRI scans requires time-intensive preprocessing operations, including but not limited to anatomy segmentation annotations, registration, and texture denoising. Deep learning models have demonstrated exceptional capabilities in learning shape representations directly from volumetric images, giving rise to highly effective and efficient Image-to-SSM. Nevertheless, these models are data-hungry and due to the limited availability of medical data, deep learning models tend to overfit. Offline data augmentation techniques, that use kernel density estimation based (KDE) methods for generating shape-augmented samples, have successfully aided Image-to-SSM networks in achieving comparable accuracy to traditional SSM methods. However, these augmentation methods focus on shape augmentation, whereas deep learning models exhibit image-based texture bias results in sub-optimal models. This paper introduces a novel strategy for on-the-fly data augmentation for the Image-to-SSM framework by leveraging data-dependent noise generation or texture augmentation. The proposed framework is trained as an adversary to the Image-to-SSM network, augmenting diverse and challenging noisy samples. Our approach achieves improved accuracy by encouraging the model to focus on the underlying geometry rather than relying solely on pixel values.
A mainstream type of current self-supervised learning methods pursues a general-purpose representation that can be well transferred to downstream tasks, typically by optimizing on a given pretext task such as instance discrimination. In this work, we argue that existing pretext tasks inevitably introduce biases into the learned representation, which in turn leads to biased transfer performance on various downstream tasks. To cope with this issue, we propose Maximum Entropy Coding (MEC), a more principled objective that explicitly optimizes on the structure of the representation, so that the learned representation is less biased and thus generalizes better to unseen downstream tasks. Inspired by the principle of maximum entropy in information theory, we hypothesize that a generalizable representation should be the one that admits the maximum entropy among all plausible representations. To make the objective end-to-end trainable, we propose to leverage the minimal coding length in lossy data coding as a computationally tractable surrogate for the entropy, and further derive a scalable reformulation of the objective that allows fast computation. Extensive experiments demonstrate that MEC learns a more generalizable representation than previous methods based on specific pretext tasks. It achieves state-of-the-art performance consistently on various downstream tasks, including not only ImageNet linear probe, but also semi-supervised classification, object detection, instance segmentation, and object tracking. Interestingly, we show that existing batch-wise and feature-wise self-supervised objectives could be seen equivalent to low-order approximations of MEC. Code and pre-trained models are available at //github.com/xinliu20/MEC.
While recent studies on semi-supervised learning have shown remarkable progress in leveraging both labeled and unlabeled data, most of them presume a basic setting of the model is randomly initialized. In this work, we consider semi-supervised learning and transfer learning jointly, leading to a more practical and competitive paradigm that can utilize both powerful pre-trained models from source domain as well as labeled/unlabeled data in the target domain. To better exploit the value of both pre-trained weights and unlabeled target examples, we introduce adaptive consistency regularization that consists of two complementary components: Adaptive Knowledge Consistency (AKC) on the examples between the source and target model, and Adaptive Representation Consistency (ARC) on the target model between labeled and unlabeled examples. Examples involved in the consistency regularization are adaptively selected according to their potential contributions to the target task. We conduct extensive experiments on several popular benchmarks including CUB-200-2011, MIT Indoor-67, MURA, by fine-tuning the ImageNet pre-trained ResNet-50 model. Results show that our proposed adaptive consistency regularization outperforms state-of-the-art semi-supervised learning techniques such as Pseudo Label, Mean Teacher, and MixMatch. Moreover, our algorithm is orthogonal to existing methods and thus able to gain additional improvements on top of MixMatch and FixMatch. Our code is available at //github.com/SHI-Labs/Semi-Supervised-Transfer-Learning.
Object detectors usually achieve promising results with the supervision of complete instance annotations. However, their performance is far from satisfactory with sparse instance annotations. Most existing methods for sparsely annotated object detection either re-weight the loss of hard negative samples or convert the unlabeled instances into ignored regions to reduce the interference of false negatives. We argue that these strategies are insufficient since they can at most alleviate the negative effect caused by missing annotations. In this paper, we propose a simple but effective mechanism, called Co-mining, for sparsely annotated object detection. In our Co-mining, two branches of a Siamese network predict the pseudo-label sets for each other. To enhance multi-view learning and better mine unlabeled instances, the original image and corresponding augmented image are used as the inputs of two branches of the Siamese network, respectively. Co-mining can serve as a general training mechanism applied to most of modern object detectors. Experiments are performed on MS COCO dataset with three different sparsely annotated settings using two typical frameworks: anchor-based detector RetinaNet and anchor-free detector FCOS. Experimental results show that our Co-mining with RetinaNet achieves 1.4%~2.1% improvements compared with different baselines and surpasses existing methods under the same sparsely annotated setting.
A key requirement for the success of supervised deep learning is a large labeled dataset - a condition that is difficult to meet in medical image analysis. Self-supervised learning (SSL) can help in this regard by providing a strategy to pre-train a neural network with unlabeled data, followed by fine-tuning for a downstream task with limited annotations. Contrastive learning, a particular variant of SSL, is a powerful technique for learning image-level representations. In this work, we propose strategies for extending the contrastive learning framework for segmentation of volumetric medical images in the semi-supervised setting with limited annotations, by leveraging domain-specific and problem-specific cues. Specifically, we propose (1) novel contrasting strategies that leverage structural similarity across volumetric medical images (domain-specific cue) and (2) a local version of the contrastive loss to learn distinctive representations of local regions that are useful for per-pixel segmentation (problem-specific cue). We carry out an extensive evaluation on three Magnetic Resonance Imaging (MRI) datasets. In the limited annotation setting, the proposed method yields substantial improvements compared to other self-supervision and semi-supervised learning techniques. When combined with a simple data augmentation technique, the proposed method reaches within 8% of benchmark performance using only two labeled MRI volumes for training, corresponding to only 4% (for ACDC) of the training data used to train the benchmark.
In this paper, we adopt 3D Convolutional Neural Networks to segment volumetric medical images. Although deep neural networks have been proven to be very effective on many 2D vision tasks, it is still challenging to apply them to 3D tasks due to the limited amount of annotated 3D data and limited computational resources. We propose a novel 3D-based coarse-to-fine framework to effectively and efficiently tackle these challenges. The proposed 3D-based framework outperforms the 2D counterpart to a large margin since it can leverage the rich spatial infor- mation along all three axes. We conduct experiments on two datasets which include healthy and pathological pancreases respectively, and achieve the current state-of-the-art in terms of Dice-S{\o}rensen Coefficient (DSC). On the NIH pancreas segmentation dataset, we outperform the previous best by an average of over 2%, and the worst case is improved by 7% to reach almost 70%, which indicates the reliability of our framework in clinical applications.
Recent advances in 3D fully convolutional networks (FCN) have made it feasible to produce dense voxel-wise predictions of volumetric images. In this work, we show that a multi-class 3D FCN trained on manually labeled CT scans of several anatomical structures (ranging from the large organs to thin vessels) can achieve competitive segmentation results, while avoiding the need for handcrafting features or training class-specific models. To this end, we propose a two-stage, coarse-to-fine approach that will first use a 3D FCN to roughly define a candidate region, which will then be used as input to a second 3D FCN. This reduces the number of voxels the second FCN has to classify to ~10% and allows it to focus on more detailed segmentation of the organs and vessels. We utilize training and validation sets consisting of 331 clinical CT images and test our models on a completely unseen data collection acquired at a different hospital that includes 150 CT scans, targeting three anatomical organs (liver, spleen, and pancreas). In challenging organs such as the pancreas, our cascaded approach improves the mean Dice score from 68.5 to 82.2%, achieving the highest reported average score on this dataset. We compare with a 2D FCN method on a separate dataset of 240 CT scans with 18 classes and achieve a significantly higher performance in small organs and vessels. Furthermore, we explore fine-tuning our models to different datasets. Our experiments illustrate the promise and robustness of current 3D FCN based semantic segmentation of medical images, achieving state-of-the-art results. Our code and trained models are available for download: //github.com/holgerroth/3Dunet_abdomen_cascade.
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