We propose a Deep Variational Clustering (DVC) framework for unsupervised representation learning and clustering of large-scale medical images. DVC simultaneously learns the multivariate Gaussian posterior through the probabilistic convolutional encoder and the likelihood distribution with the probabilistic convolutional decoder; and optimizes cluster labels assignment. Here, the learned multivariate Gaussian posterior captures the latent distribution of a large set of unlabeled images. Then, we perform unsupervised clustering on top of the variational latent space using a clustering loss. In this approach, the probabilistic decoder helps to prevent the distortion of data points in the latent space and to preserve the local structure of data generating distribution. The training process can be considered as a self-training process to refine the latent space and simultaneously optimizing cluster assignments iteratively. We evaluated our proposed framework on three public datasets that represented different medical imaging modalities. Our experimental results show that our proposed framework generalizes better across different datasets. It achieves compelling results on several medical imaging benchmarks. Thus, our approach offers potential advantages over conventional deep unsupervised learning in real-world applications. The source code of the method and all the experiments are available publicly at: //github.com/csfarzin/DVC
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Clustering of hyperspectral images is a fundamental but challenging task. The recent development of hyperspectral image clustering has evolved from shallow models to deep and achieved promising results in many benchmark datasets. However, their poor scalability, robustness, and generalization ability, mainly resulting from their offline clustering scenarios, greatly limit their application to large-scale hyperspectral data. To circumvent these problems, we present a scalable deep online clustering model, named Spectral-Spatial Contrastive Clustering (SSCC), based on self-supervised learning. Specifically, we exploit a symmetric twin neural network comprised of a projection head with a dimensionality of the cluster number to conduct dual contrastive learning from a spectral-spatial augmentation pool. We define the objective function by implicitly encouraging within-cluster similarity and reducing between-cluster redundancy. The resulting approach is trained in an end-to-end fashion by batch-wise optimization, making it robust in large-scale data and resulting in good generalization ability for unseen data. Extensive experiments on three hyperspectral image benchmarks demonstrate the effectiveness of our approach and show that we advance the state-of-the-art approaches by large margins.
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.
Graph Convolutional Networks(GCNs) play a crucial role in graph learning tasks, however, learning graph embedding with few supervised signals is still a difficult problem. In this paper, we propose a novel training algorithm for Graph Convolutional Network, called Multi-Stage Self-Supervised(M3S) Training Algorithm, combined with self-supervised learning approach, focusing on improving the generalization performance of GCNs on graphs with few labeled nodes. Firstly, a Multi-Stage Training Framework is provided as the basis of M3S training method. Then we leverage DeepCluster technique, a popular form of self-supervised learning, and design corresponding aligning mechanism on the embedding space to refine the Multi-Stage Training Framework, resulting in M3S Training Algorithm. Finally, extensive experimental results verify the superior performance of our algorithm on graphs with few labeled nodes under different label rates compared with other state-of-the-art approaches.
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.
3D image segmentation plays an important role in biomedical image analysis. Many 2D and 3D deep learning models have achieved state-of-the-art segmentation performance on 3D biomedical image datasets. Yet, 2D and 3D models have their own strengths and weaknesses, and by unifying them together, one may be able to achieve more accurate results. In this paper, we propose a new ensemble learning framework for 3D biomedical image segmentation that combines the merits of 2D and 3D models. First, we develop a fully convolutional network based meta-learner to learn how to improve the results from 2D and 3D models (base-learners). Then, to minimize over-fitting for our sophisticated meta-learner, we devise a new training method that uses the results of the base-learners as multiple versions of "ground truths". Furthermore, since our new meta-learner training scheme does not depend on manual annotation, it can utilize abundant unlabeled 3D image data to further improve the model. Extensive experiments on two public datasets (the HVSMR 2016 Challenge dataset and the mouse piriform cortex dataset) show that our approach is effective under fully-supervised, semi-supervised, and transductive settings, and attains superior performance over state-of-the-art image segmentation methods.
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
We present a unified framework tackling two problems: class-specific 3D reconstruction from a single image, and generation of new 3D shape samples. These tasks have received considerable attention recently; however, existing approaches rely on 3D supervision, annotation of 2D images with keypoints or poses, and/or training with multiple views of each object instance. Our framework is very general: it can be trained in similar settings to these existing approaches, while also supporting weaker supervision scenarios. Importantly, it can be trained purely from 2D images, without ground-truth pose annotations, and with a single view per instance. We employ meshes as an output representation, instead of voxels used in most prior work. This allows us to exploit shading information during training, which previous 2D-supervised methods cannot. Thus, our method can learn to generate and reconstruct concave object classes. We evaluate our approach on synthetic data in various settings, showing that (i) it learns to disentangle shape from pose; (ii) using shading in the loss improves performance; (iii) our model is comparable or superior to state-of-the-art voxel-based approaches on quantitative metrics, while producing results that are visually more pleasing; (iv) it still performs well when given supervision weaker than in prior works.
Hashing has been a widely-adopted technique for nearest neighbor search in large-scale image retrieval tasks. Recent research has shown that leveraging supervised information can lead to high quality hashing. However, the cost of annotating data is often an obstacle when applying supervised hashing to a new domain. Moreover, the results can suffer from the robustness problem as the data at training and test stage could come from similar but different distributions. This paper studies the exploration of generating synthetic data through semi-supervised generative adversarial networks (GANs), which leverages largely unlabeled and limited labeled training data to produce highly compelling data with intrinsic invariance and global coherence, for better understanding statistical structures of natural data. We demonstrate that the above two limitations can be well mitigated by applying the synthetic data for hashing. Specifically, a novel deep semantic hashing with GANs (DSH-GANs) is presented, which mainly consists of four components: a deep convolution neural networks (CNN) for learning image representations, an adversary stream to distinguish synthetic images from real ones, a hash stream for encoding image representations to hash codes and a classification stream. The whole architecture is trained end-to-end by jointly optimizing three losses, i.e., adversarial loss to correct label of synthetic or real for each sample, triplet ranking loss to preserve the relative similarity ordering in the input real-synthetic triplets and classification loss to classify each sample accurately. Extensive experiments conducted on both CIFAR-10 and NUS-WIDE image benchmarks validate the capability of exploiting synthetic images for hashing. Our framework also achieves superior results when compared to state-of-the-art deep hash models.
Similarity/Distance measures play a key role in many machine learning, pattern recognition, and data mining algorithms, which leads to the emergence of metric learning field. Many metric learning algorithms learn a global distance function from data that satisfy the constraints of the problem. However, in many real-world datasets that the discrimination power of features varies in the different regions of input space, a global metric is often unable to capture the complexity of the task. To address this challenge, local metric learning methods are proposed that learn multiple metrics across the different regions of input space. Some advantages of these methods are high flexibility and the ability to learn a nonlinear mapping but typically achieves at the expense of higher time requirement and overfitting problem. To overcome these challenges, this research presents an online multiple metric learning framework. Each metric in the proposed framework is composed of a global and a local component learned simultaneously. Adding a global component to a local metric efficiently reduce the problem of overfitting. The proposed framework is also scalable with both sample size and the dimension of input data. To the best of our knowledge, this is the first local online similarity/distance learning framework based on PA (Passive/Aggressive). In addition, for scalability with the dimension of input data, DRP (Dual Random Projection) is extended for local online learning in the present work. It enables our methods to be run efficiently on high-dimensional datasets, while maintains their predictive performance. The proposed framework provides a straightforward local extension to any global online similarity/distance learning algorithm based on PA.
Image segmentation is considered to be one of the critical tasks in hyperspectral remote sensing image processing. Recently, convolutional neural network (CNN) has established itself as a powerful model in segmentation and classification by demonstrating excellent performances. The use of a graphical model such as a conditional random field (CRF) contributes further in capturing contextual information and thus improving the segmentation performance. In this paper, we propose a method to segment hyperspectral images by considering both spectral and spatial information via a combined framework consisting of CNN and CRF. We use multiple spectral cubes to learn deep features using CNN, and then formulate deep CRF with CNN-based unary and pairwise potential functions to effectively extract the semantic correlations between patches consisting of three-dimensional data cubes. Effective piecewise training is applied in order to avoid the computationally expensive iterative CRF inference. Furthermore, we introduce a deep deconvolution network that improves the segmentation masks. We also introduce a new dataset and experimented our proposed method on it along with several widely adopted benchmark datasets to evaluate the effectiveness of our method. By comparing our results with those from several state-of-the-art models, we show the promising potential of our method.
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