Deformable shapes provide important and complex geometric features of objects presented in images. However, such information is oftentimes missing or underutilized as implicit knowledge in many image analysis tasks. This paper presents Geo-SIC, the first deep learning model to learn deformable shapes in a deformation space for an improved performance of image classification. We introduce a newly designed framework that (i) simultaneously derives features from both image and latent shape spaces with large intra-class variations; and (ii) gains increased model interpretability by allowing direct access to the underlying geometric features of image data. In particular, we develop a boosted classification network, equipped with an unsupervised learning of geometric shape representations characterized by diffeomorphic transformations within each class. In contrast to previous approaches using pre-extracted shapes, our model provides a more fundamental approach by naturally learning the most relevant shape features jointly with an image classifier. We demonstrate the effectiveness of our method on both simulated 2D images and real 3D brain magnetic resonance (MR) images. Experimental results show that our model substantially improves the image classification accuracy with an additional benefit of increased model interpretability. Our code is publicly available at //github.com/jw4hv/Geo-SIC
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Recent years have seen rapid progress at the intersection between causality and machine learning. Motivated by scientific applications involving high-dimensional data, in particular in biomedicine, we propose a deep neural architecture for learning causal relationships between variables from a combination of empirical data and prior causal knowledge. We combine convolutional and graph neural networks within a causal risk framework to provide a flexible and scalable approach. Empirical results include linear and nonlinear simulations (where the underlying causal structures are known and can be directly compared against), as well as a real biological example where the models are applied to high-dimensional molecular data and their output compared against entirely unseen validation experiments. These results demonstrate the feasibility of using deep learning approaches to learn causal networks in large-scale problems spanning thousands of variables.
Node classification for graph-structured data aims to classify nodes whose labels are unknown. While studies on static graphs are prevalent, few studies have focused on dynamic graph node classification. Node classification on dynamic graphs is challenging for two reasons. First, the model needs to capture both structural and temporal information, particularly on dynamic graphs with a long history and require large receptive fields. Second, model scalability becomes a significant concern as the size of the dynamic graph increases. To address these problems, we propose the Time Augmented Dynamic Graph Neural Network (TADGNN) framework. TADGNN consists of two modules: 1) a time augmentation module that captures the temporal evolution of nodes across time structurally, creating a time-augmented spatio-temporal graph, and 2) an information propagation module that learns the dynamic representations for each node across time using the constructed time-augmented graph. We perform node classification experiments on four dynamic graph benchmarks. Experimental results demonstrate that TADGNN framework outperforms several static and dynamic state-of-the-art (SOTA) GNN models while demonstrating superior scalability. We also conduct theoretical and empirical analyses to validate the efficiency of the proposed method. Our code is available at //sites.google.com/view/tadgnn.
Deformable image registration, i.e., the task of aligning multiple images into one coordinate system by non-linear transformation, serves as an essential preprocessing step for neuroimaging data. Recent research on deformable image registration is mainly focused on improving the registration accuracy using multi-stage alignment methods, where the source image is repeatedly deformed in stages by a same neural network until it is well-aligned with the target image. Conventional methods for multi-stage registration can often blur the source image as the pixel/voxel values are repeatedly interpolated from the image generated by the previous stage. However, maintaining image quality such as sharpness during image registration is crucial to medical data analysis. In this paper, we study the problem of anti-blur deformable image registration and propose a novel solution, called Anti-Blur Network (ABN), for multi-stage image registration. Specifically, we use a pair of short-term registration and long-term memory networks to learn the nonlinear deformations at each stage, where the short-term registration network learns how to improve the registration accuracy incrementally and the long-term memory network combines all the previous deformations to allow an interpolation to perform on the raw image directly and preserve image sharpness. Extensive experiments on both natural and medical image datasets demonstrated that ABN can accurately register images while preserving their sharpness. Our code and data can be found at //github.com/anonymous3214/ABN
Deep neural networks have achieved remarkable success in computer vision tasks. Existing neural networks mainly operate in the spatial domain with fixed input sizes. For practical applications, images are usually large and have to be downsampled to the predetermined input size of neural networks. Even though the downsampling operations reduce computation and the required communication bandwidth, it removes both redundant and salient information obliviously, which results in accuracy degradation. Inspired by digital signal processing theories, we analyze the spectral bias from the frequency perspective and propose a learning-based frequency selection method to identify the trivial frequency components which can be removed without accuracy loss. The proposed method of learning in the frequency domain leverages identical structures of the well-known neural networks, such as ResNet-50, MobileNetV2, and Mask R-CNN, while accepting the frequency-domain information as the input. Experiment results show that learning in the frequency domain with static channel selection can achieve higher accuracy than the conventional spatial downsampling approach and meanwhile further reduce the input data size. Specifically for ImageNet classification with the same input size, the proposed method achieves 1.41% and 0.66% top-1 accuracy improvements on ResNet-50 and MobileNetV2, respectively. Even with half input size, the proposed method still improves the top-1 accuracy on ResNet-50 by 1%. In addition, we observe a 0.8% average precision improvement on Mask R-CNN for instance segmentation on the COCO dataset.
We present a new method to learn video representations from large-scale unlabeled video data. Ideally, this representation will be generic and transferable, directly usable for new tasks such as action recognition and zero or few-shot learning. We formulate unsupervised representation learning as a multi-modal, multi-task learning problem, where the representations are shared across different modalities via distillation. Further, we introduce the concept of loss function evolution by using an evolutionary search algorithm to automatically find optimal combination of loss functions capturing many (self-supervised) tasks and modalities. Thirdly, we propose an unsupervised representation evaluation metric using distribution matching to a large unlabeled dataset as a prior constraint, based on Zipf's law. This unsupervised constraint, which is not guided by any labeling, produces similar results to weakly-supervised, task-specific ones. The proposed unsupervised representation learning results in a single RGB network and outperforms previous methods. Notably, it is also more effective than several label-based methods (e.g., ImageNet), with the exception of large, fully labeled video datasets.
Modern neural network training relies heavily on data augmentation for improved generalization. After the initial success of label-preserving augmentations, there has been a recent surge of interest in label-perturbing approaches, which combine features and labels across training samples to smooth the learned decision surface. In this paper, we propose a new augmentation method that leverages the first and second moments extracted and re-injected by feature normalization. We replace the moments of the learned features of one training image by those of another, and also interpolate the target labels. As our approach is fast, operates entirely in feature space, and mixes different signals than prior methods, one can effectively combine it with existing augmentation methods. We demonstrate its efficacy across benchmark data sets in computer vision, speech, and natural language processing, where it consistently improves the generalization performance of highly competitive baseline networks.
Time Series Classification (TSC) is an important and challenging problem in data mining. With the increase of time series data availability, hundreds of TSC algorithms have been proposed. Among these methods, only a few have considered Deep Neural Networks (DNNs) to perform this task. This is surprising as deep learning has seen very successful applications in the last years. DNNs have indeed revolutionized the field of computer vision especially with the advent of novel deeper architectures such as Residual and Convolutional Neural Networks. Apart from images, sequential data such as text and audio can also be processed with DNNs to reach state-of-the-art performance for document classification and speech recognition. In this article, we study the current state-of-the-art performance of deep learning algorithms for TSC by presenting an empirical study of the most recent DNN architectures for TSC. We give an overview of the most successful deep learning applications in various time series domains under a unified taxonomy of DNNs for TSC. We also provide an open source deep learning framework to the TSC community where we implemented each of the compared approaches and evaluated them on a univariate TSC benchmark (the UCR/UEA archive) and 12 multivariate time series datasets. By training 8,730 deep learning models on 97 time series datasets, we propose the most exhaustive study of DNNs for TSC to date.
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.
Convolutional networks (ConvNets) have achieved great successes in various challenging vision tasks. However, the performance of ConvNets would degrade when encountering the domain shift. The domain adaptation is more significant while challenging in the field of biomedical image analysis, where cross-modality data have largely different distributions. Given that annotating the medical data is especially expensive, the supervised transfer learning approaches are not quite optimal. In this paper, we propose an unsupervised domain adaptation framework with adversarial learning for cross-modality biomedical image segmentations. Specifically, our model is based on a dilated fully convolutional network for pixel-wise prediction. Moreover, we build a plug-and-play domain adaptation module (DAM) to map the target input to features which are aligned with source domain feature space. A domain critic module (DCM) is set up for discriminating the feature space of both domains. We optimize the DAM and DCM via an adversarial loss without using any target domain label. Our proposed method is validated by adapting a ConvNet trained with MRI images to unpaired CT data for cardiac structures segmentations, and achieved very promising results.
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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