In medical image segmentation, supervised deep networks' success comes at the cost of requiring abundant labeled data. While asking domain experts to annotate only one or a few of the cohort's images is feasible, annotating all available images is impractical. This issue is further exacerbated when pre-trained deep networks are exposed to a new image dataset from an unfamiliar distribution. Using available open-source data for ad-hoc transfer learning or hand-tuned techniques for data augmentation only provides suboptimal solutions. Motivated by atlas-based segmentation, we propose a novel volumetric self-supervised learning for data augmentation capable of synthesizing volumetric image-segmentation pairs via learning transformations from a single labeled atlas to the unlabeled data. Our work's central tenet benefits from a combined view of one-shot generative learning and the proposed self-supervised training strategy that cluster unlabeled volumetric images with similar styles together. Unlike previous methods, our method does not require input volumes at inference time to synthesize new images. Instead, it can generate diversified volumetric image-segmentation pairs from a prior distribution given a single or multi-site dataset. Augmented data generated by our method used to train the segmentation network provide significant improvements over state-of-the-art deep one-shot learning methods on the task of brain MRI segmentation. Ablation studies further exemplified that the proposed appearance model and joint training are crucial to synthesize realistic examples compared to existing medical registration methods. The code, data, and models are available at //github.com/devavratTomar/SST.
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The development of deep segmentation models for computational pathology (CPath) can help foster the investigation of interpretable morphological biomarkers. Yet, there is a major bottleneck in the success of such approaches because supervised deep learning models require an abundance of accurately labelled data. This issue is exacerbated in the field of CPath because the generation of detailed annotations usually demands the input of a pathologist to be able to distinguish between different tissue constructs and nuclei. Manually labelling nuclei may not be a feasible approach for collecting large-scale annotated datasets, especially when a single image region can contain thousands of different cells. However, solely relying on automatic generation of annotations will limit the accuracy and reliability of ground truth. Therefore, to help overcome the above challenges, we propose a multi-stage annotation pipeline to enable the collection of large-scale datasets for histology image analysis, with pathologist-in-the-loop refinement steps. Using this pipeline, we generate the largest known nuclear instance segmentation and classification dataset, containing nearly half a million labelled nuclei in H&E stained colon tissue. We have released the dataset and encourage the research community to utilise it to drive forward the development of downstream cell-based models in CPath.
Person image generation aims to perform non-rigid deformation on source images, which generally requires unaligned data pairs for training. Recently, self-supervised methods express great prospects in this task by merging the disentangled representations for self-reconstruction. However, such methods fail to exploit the spatial correlation between the disentangled features. In this paper, we propose a Self-supervised Correlation Mining Network (SCM-Net) to rearrange the source images in the feature space, in which two collaborative modules are integrated, Decomposed Style Encoder (DSE) and Correlation Mining Module (CMM). Specifically, the DSE first creates unaligned pairs at the feature level. Then, the CMM establishes the spatial correlation field for feature rearrangement. Eventually, a translation module transforms the rearranged features to realistic results. Meanwhile, for improving the fidelity of cross-scale pose transformation, we propose a graph based Body Structure Retaining Loss (BSR Loss) to preserve reasonable body structures on half body to full body generation. Extensive experiments conducted on DeepFashion dataset demonstrate the superiority of our method compared with other supervised and unsupervised approaches. Furthermore, satisfactory results on face generation show the versatility of our method in other deformation tasks.
We aim at the problem named One-Shot Unsupervised Domain Adaptation. Unlike traditional Unsupervised Domain Adaptation, it assumes that only one unlabeled target sample can be available when learning to adapt. This setting is realistic but more challenging, in which conventional adaptation approaches are prone to failure due to the scarce of unlabeled target data. To this end, we propose a novel Adversarial Style Mining approach, which combines the style transfer module and task-specific module into an adversarial manner. Specifically, the style transfer module iteratively searches for harder stylized images around the one-shot target sample according to the current learning state, leading the task model to explore the potential styles that are difficult to solve in the almost unseen target domain, thus boosting the adaptation performance in a data-scarce scenario. The adversarial learning framework makes the style transfer module and task-specific module benefit each other during the competition. Extensive experiments on both cross-domain classification and segmentation benchmarks verify that ASM achieves state-of-the-art adaptation performance under the challenging one-shot setting.
In this paper, we aim to improve the performance of semantic image segmentation in a semi-supervised setting in which training is effectuated with a reduced set of annotated images and additional non-annotated images. We present a method based on an ensemble of deep segmentation models. Each model is trained on a subset of the annotated data, and uses the non-annotated images to exchange information with the other models, similar to co-training. Even if each model learns on the same non-annotated images, diversity is preserved with the use of adversarial samples. Our results show that this ability to simultaneously train models, which exchange knowledge while preserving diversity, leads to state-of-the-art results on two challenging medical image datasets.
Biomedical image segmentation is an important task in many medical applications. Segmentation methods based on convolutional neural networks attain state-of-the-art accuracy; however, they typically rely on supervised training with large labeled datasets. Labeling datasets of medical images requires significant expertise and time, and is infeasible at large scales. To tackle the lack of labeled data, researchers use techniques such as hand-engineered preprocessing steps, hand-tuned architectures, and data augmentation. However, these techniques involve costly engineering efforts, and are typically dataset-specific. We present an automated data augmentation method for medical images. We demonstrate our method on the task of segmenting magnetic resonance imaging (MRI) brain scans, focusing on the one-shot segmentation scenario -- a practical challenge in many medical applications. Our method requires only a single segmented scan, and leverages other unlabeled scans in a semi-supervised approach. We learn a model of transforms from the images, and use the model along with the labeled example to synthesize additional labeled training examples for supervised segmentation. Each transform is comprised of a spatial deformation field and an intensity change, enabling the synthesis of complex effects such as variations in anatomy and image acquisition procedures. Augmenting the training of a supervised segmenter with these new examples provides significant improvements over state-of-the-art methods for one-shot biomedical image segmentation. Our code is available at //github.com/xamyzhao/brainstorm.
Semantic segmentation is one of the basic topics in computer vision, it aims to assign semantic labels to every pixel of an image. Unbalanced semantic label distribution could have a negative influence on segmentation accuracy. In this paper, we investigate using data augmentation approach to balance the semantic label distribution in order to improve segmentation performance. We propose using generative adversarial networks (GANs) to generate realistic images for improving the performance of semantic segmentation networks. Experimental results show that the proposed method can not only improve segmentation performance on those classes with low accuracy, but also obtain 1.3% to 2.1% increase in average segmentation accuracy. It shows that this augmentation method can boost accuracy and be easily applicable to any other segmentation models.
Generative Adversarial Networks (GAN) boast impressive capacity to generate realistic images. However, like much of the field of deep learning, they require an inordinate amount of data to produce results, thereby limiting their usefulness in generating novelty. In the same vein, recent advances in meta-learning have opened the door to many few-shot learning applications. In the present work, we propose Few-shot Image Generation using Reptile (FIGR), a GAN meta-trained with Reptile. Our model successfully generates novel images on both MNIST and Omniglot with as little as 4 images from an unseen class. We further contribute FIGR-8, a new dataset for few-shot image generation, which contains 1,548,944 icons categorized in over 18,409 classes. Trained on FIGR-8, initial results show that our model can generalize to more advanced concepts (such as "bird" and "knife") from as few as 8 samples from a previously unseen class of images and as little as 10 training steps through those 8 images. This work demonstrates the potential of training a GAN for few-shot image generation and aims to set a new benchmark for future work in the domain.
Deep neural networks have achieved great successes on the image captioning task. However, most of the existing models depend heavily on paired image-sentence datasets, which are very expensive to acquire. In this paper, we make the first attempt to train an image captioning model in an unsupervised manner. Instead of relying on manually labeled image-sentence pairs, our proposed model merely requires an image set, a sentence corpus, and an existing visual concept detector. The sentence corpus is used to teach the captioning model how to generate plausible sentences. Meanwhile, the knowledge in the visual concept detector is distilled into the captioning model to guide the model to recognize the visual concepts in an image. In order to further encourage the generated captions to be semantically consistent with the image, the image and caption are projected into a common latent space so that they can be used to reconstruct each other. Given that the existing sentence corpora are mainly designed for linguistic research and thus with little reference to image contents, we crawl a large-scale image description corpus of 2 million natural sentences to facilitate the unsupervised image captioning scenario. Experimental results show that our proposed model is able to produce quite promising results without using any labeled training pairs.
We address the problem of segmenting 3D multi-modal medical images in scenarios where very few labeled examples are available for training. Leveraging the recent success of adversarial learning for semi-supervised segmentation, we propose a novel method based on Generative Adversarial Networks (GANs) to train a segmentation model with both labeled and unlabeled images. The proposed method prevents over-fitting by learning to discriminate between true and fake patches obtained by a generator network. Our work extends current adversarial learning approaches, which focus on 2D single-modality images, to the more challenging context of 3D volumes of multiple modalities. The proposed method is evaluated on the problem of segmenting brain MRI from the iSEG-2017 and MRBrainS 2013 datasets. Significant performance improvement is reported, compared to state-of-art segmentation networks trained in a fully-supervised manner. In addition, our work presents a comprehensive analysis of different GAN architectures for semi-supervised segmentation, showing recent techniques like feature matching to yield a higher performance than conventional adversarial training approaches. Our code is publicly available at //github.com/arnab39/FewShot_GAN-Unet3D
Deep Convolutional Neural Networks have pushed the state-of-the art for semantic segmentation provided that a large amount of images together with pixel-wise annotations is available. Data collection is expensive and a solution to alleviate it is to use transfer learning. This reduces the amount of annotated data required for the network training but it does not get rid of this heavy processing step. We propose a method of transfer learning without annotations on the target task for datasets with redundant content and distinct pixel distributions. Our method takes advantage of the approximate content alignment of the images between two datasets when the approximation error prevents the reuse of annotation from one dataset to another. Given the annotations for only one dataset, we train a first network in a supervised manner. This network autonomously learns to generate deep data representations relevant to the semantic segmentation. Then the images in the new dataset, we train a new network to generate a deep data representation that matches the one from the first network on the previous dataset. The training consists in a regression between feature maps and does not require any annotations on the new dataset. We show that this method reaches performances similar to a classic transfer learning on the PASCAL VOC dataset with synthetic transformations.
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