Despite achieving promising results in a breadth of medical image segmentation tasks, deep neural networks require large training datasets with pixel-wise annotations. Obtaining these curated datasets is a cumbersome process which limits the applicability in scenarios. Mixed supervision is an appealing alternative for mitigating this obstacle. In this work, we propose a dual-branch architecture, where the upper branch (teacher) receives strong annotations, while the bottom one (student) is driven by limited supervision and guided by the upper branch. Combined with a standard cross-entropy loss over the labeled pixels, our novel formulation integrates two important terms: (i) a Shannon entropy loss defined over the less-supervised images, which encourages confident student predictions in the bottom branch; and (ii) a KL divergence term, which transfers the knowledge (i.e., predictions) of the strongly supervised branch to the less-supervised branch and guides the entropy (student-confidence) term to avoid trivial solutions. We show that the synergy between the entropy and KL divergence yields substantial improvements in performance. We also discuss an interesting link between Shannon-entropy minimization and standard pseudo-mask generation, and argue that the former should be preferred over the latter for leveraging information from unlabeled pixels. We evaluate the effectiveness of the proposed formulation through a series of quantitative and qualitative experiments using two publicly available datasets. Results demonstrate that our method significantly outperforms other strategies for semantic segmentation within a mixed-supervision framework, as well as recent semi-supervised approaches. Our code is publicly available: //github.com/by-liu/ConfKD.
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Despite recent advances in data-independent and deep-learning algorithms, unstained live adherent cell instance segmentation remains a long-standing challenge in cell image processing. Adherent cells' inherent visual characteristics, such as low contrast structures, fading edges, and irregular morphology, have made it difficult to distinguish from one another, even by human experts, let alone computational methods. In this study, we developed a novel deep-learning algorithm called dual-view selective instance segmentation network (DVSISN) for segmenting unstained adherent cells in differential interference contrast (DIC) images. First, we used a dual-view segmentation (DVS) method with pairs of original and rotated images to predict the bounding box and its corresponding mask for each cell instance. Second, we used a mask selection (MS) method to filter the cell instances predicted by the DVS to keep masks closest to the ground truth only. The developed algorithm was trained and validated on our dataset containing 520 images and 12198 cells. Experimental results demonstrate that our algorithm achieves an AP_segm of 0.555, which remarkably overtakes a benchmark by a margin of 23.6%. This study's success opens up a new possibility of using rotated images as input for better prediction in cell images.
This paper proposes a simple method to distill and detect backdoor patterns within an image: \emph{Cognitive Distillation} (CD). The idea is to extract the "minimal essence" from an input image responsible for the model's prediction. CD optimizes an input mask to extract a small pattern from the input image that can lead to the same model output (i.e., logits or deep features). The extracted pattern can help understand the cognitive mechanism of a model on clean vs. backdoor images and is thus called a \emph{Cognitive Pattern} (CP). Using CD and the distilled CPs, we uncover an interesting phenomenon of backdoor attacks: despite the various forms and sizes of trigger patterns used by different attacks, the CPs of backdoor samples are all surprisingly and suspiciously small. One thus can leverage the learned mask to detect and remove backdoor examples from poisoned training datasets. We conduct extensive experiments to show that CD can robustly detect a wide range of advanced backdoor attacks. We also show that CD can potentially be applied to help detect potential biases from face datasets. Code is available at \url{//github.com/HanxunH/CognitiveDistillation}.
In this paper, we propose a one-stage online clustering method called Contrastive Clustering (CC) which explicitly performs the instance- and cluster-level contrastive learning. To be specific, for a given dataset, the positive and negative instance pairs are constructed through data augmentations and then projected into a feature space. Therein, the instance- and cluster-level contrastive learning are respectively conducted in the row and column space by maximizing the similarities of positive pairs while minimizing those of negative ones. Our key observation is that the rows of the feature matrix could be regarded as soft labels of instances, and accordingly the columns could be further regarded as cluster representations. By simultaneously optimizing the instance- and cluster-level contrastive loss, the model jointly learns representations and cluster assignments in an end-to-end manner. Extensive experimental results show that CC remarkably outperforms 17 competitive clustering methods on six challenging image benchmarks. In particular, CC achieves an NMI of 0.705 (0.431) on the CIFAR-10 (CIFAR-100) dataset, which is an up to 19\% (39\%) performance improvement compared with the best baseline.
Deep learning-based semi-supervised learning (SSL) algorithms have led to promising results in medical images segmentation and can alleviate doctors' expensive annotations by leveraging unlabeled data. However, most of the existing SSL algorithms in literature tend to regularize the model training by perturbing networks and/or data. Observing that multi/dual-task learning attends to various levels of information which have inherent prediction perturbation, we ask the question in this work: can we explicitly build task-level regularization rather than implicitly constructing networks- and/or data-level perturbation-and-transformation for SSL? To answer this question, we propose a novel dual-task-consistency semi-supervised framework for the first time. Concretely, we use a dual-task deep network that jointly predicts a pixel-wise segmentation map and a geometry-aware level set representation of the target. The level set representation is converted to an approximated segmentation map through a differentiable task transform layer. Simultaneously, we introduce a dual-task consistency regularization between the level set-derived segmentation maps and directly predicted segmentation maps for both labeled and unlabeled data. Extensive experiments on two public datasets show that our method can largely improve the performance by incorporating the unlabeled data. Meanwhile, our framework outperforms the state-of-the-art semi-supervised medical image segmentation methods. Code is available at: //github.com/Luoxd1996/DTC
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.
Pre-training text representations has recently been shown to significantly improve the state-of-the-art in many natural language processing tasks. The central goal of pre-training is to learn text representations that are useful for subsequent tasks. However, existing approaches are optimized by minimizing a proxy objective, such as the negative log likelihood of language modeling. In this work, we introduce a learning algorithm which directly optimizes model's ability to learn text representations for effective learning of downstream tasks. We show that there is an intrinsic connection between multi-task pre-training and model-agnostic meta-learning with a sequence of meta-train steps. The standard multi-task learning objective adopted in BERT is a special case of our learning algorithm where the depth of meta-train is zero. We study the problem in two settings: unsupervised pre-training and supervised pre-training with different pre-training objects to verify the generality of our approach.Experimental results show that our algorithm brings improvements and learns better initializations for a variety of downstream tasks.
For languages with no annotated resources, transferring knowledge from rich-resource languages is an effective solution for named entity recognition (NER). While all existing methods directly transfer from source-learned model to a target language, in this paper, we propose to fine-tune the learned model with a few similar examples given a test case, which could benefit the prediction by leveraging the structural and semantic information conveyed in such similar examples. To this end, we present a meta-learning algorithm to find a good model parameter initialization that could fast adapt to the given test case and propose to construct multiple pseudo-NER tasks for meta-training by computing sentence similarities. To further improve the model's generalization ability across different languages, we introduce a masking scheme and augment the loss function with an additional maximum term during meta-training. We conduct extensive experiments on cross-lingual named entity recognition with minimal resources over five target languages. The results show that our approach significantly outperforms existing state-of-the-art methods across the board.
The U-Net was presented in 2015. With its straight-forward and successful architecture it quickly evolved to a commonly used benchmark in medical image segmentation. The adaptation of the U-Net to novel problems, however, comprises several degrees of freedom regarding the exact architecture, preprocessing, training and inference. These choices are not independent of each other and substantially impact the overall performance. The present paper introduces the nnU-Net ('no-new-Net'), which refers to a robust and self-adapting framework on the basis of 2D and 3D vanilla U-Nets. We argue the strong case for taking away superfluous bells and whistles of many proposed network designs and instead focus on the remaining aspects that make out the performance and generalizability of a method. We evaluate the nnU-Net in the context of the Medical Segmentation Decathlon challenge, which measures segmentation performance in ten disciplines comprising distinct entities, image modalities, image geometries and dataset sizes, with no manual adjustments between datasets allowed. At the time of manuscript submission, nnU-Net achieves the highest mean dice scores across all classes and seven phase 1 tasks (except class 1 in BrainTumour) in the online leaderboard of the challenge.
Deep neural network architectures have traditionally been designed and explored with human expertise in a long-lasting trial-and-error process. This process requires huge amount of time, expertise, and resources. To address this tedious problem, we propose a novel algorithm to optimally find hyperparameters of a deep network architecture automatically. We specifically focus on designing neural architectures for medical image segmentation task. Our proposed method is based on a policy gradient reinforcement learning for which the reward function is assigned a segmentation evaluation utility (i.e., dice index). We show the efficacy of the proposed method with its low computational cost in comparison with the state-of-the-art medical image segmentation networks. We also present a new architecture design, a densely connected encoder-decoder CNN, as a strong baseline architecture to apply the proposed hyperparameter search algorithm. We apply the proposed algorithm to each layer of the baseline architectures. As an application, we train the proposed system on cine cardiac MR images from Automated Cardiac Diagnosis Challenge (ACDC) MICCAI 2017. Starting from a baseline segmentation architecture, the resulting network architecture obtains the state-of-the-art results in accuracy without performing any trial-and-error based architecture design approaches or close supervision of the hyperparameters changes.
Humans can quickly learn new visual concepts, perhaps because they can easily visualize or imagine what novel objects look like from different views. Incorporating this ability to hallucinate novel instances of new concepts might help machine vision systems perform better low-shot learning, i.e., learning concepts from few examples. We present a novel approach to low-shot learning that uses this idea. Our approach builds on recent progress in meta-learning ("learning to learn") by combining a meta-learner with a "hallucinator" that produces additional training examples, and optimizing both models jointly. Our hallucinator can be incorporated into a variety of meta-learners and provides significant gains: up to a 6 point boost in classification accuracy when only a single training example is available, yielding state-of-the-art performance on the challenging ImageNet low-shot classification benchmark.
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