arXiv subjects

Dimitris Metaxas

Publications and source records attributed to Dimitris Metaxas.

At least 73 records · Page 4Linked to original sources

arXiv2022

Modality Bank: Learn multi-modality images across data centers without sharing medical data

Multi-modality images have been widely used and provide comprehensive information for medical image analysis. However, acquiring all modalities among all institutes is costly and often impossible in clinical settings. To leverage more comprehensive multi-modality information, we propose a privacy secured decentralized multi-modality adaptive learning architecture named ModalityBank. Our method could learn a set of effective domain-specific modulation parameters plugged into a common domain-agnostic network. We demonstrate by switching different sets of configurations, the generator could output high-quality images for a specific modality. Our method could also complete the missing modalities across all data centers, thus could be used for modality completion purposes. The downstream task trained from the synthesized multi-modality samples could achieve higher performance than learning from one real data center and achieve close-to-real performance compare with all real images.

eess.IV↗

arXiv2022

ASL Video Corpora & Sign Bank: Resources Available through the American Sign Language Linguistic Research Project (ASLLRP)

The American Sign Language Linguistic Research Project (ASLLRP) provides Internet access to high-quality ASL video data, generally including front and side views and a close-up of the face. The manual and non-manual components of the signing have been linguistically annotated using SignStream(R). The recently expanded video corpora can be browsed and searched through the Data Access Interface (DAI 2) we have designed; it is possible to carry out complex searches. The data from our corpora can also be downloaded; annotations are available in an XML export format. We have also developed the ASLLRP Sign Bank, which contains almost 6,000 sign entries for lexical signs, with distinct English-based glosses, with a total of 41,830 examples of lexical signs (in addition to about 300 gestures, over 1,000 fingerspelled signs, and 475 classifier examples). The Sign Bank is likewise accessible and searchable on the Internet; it can also be accessed from within SignStream(R) (software to facilitate linguistic annotation and analysis of visual language data) to make annotations more accurate and efficient. Here we describe the available resources. These data have been used for many types of research in linguistics and in computer-based sign language recognition from video; examples of such research are provided in the latter part of this article.

cs.CL↗

arXiv2021

Dual Projection Generative Adversarial Networks for Conditional Image Generation

Conditional Generative Adversarial Networks (cGANs) extend the standard unconditional GAN framework to learning joint data-label distributions from samples, and have been established as powerful generative models capable of generating high-fidelity imagery. A challenge of training such a model lies in properly infusing class information into its generator and discriminator. For the discriminator, class conditioning can be achieved by either (1) directly incorporating labels as input or (2) involving labels in an auxiliary classification loss. In this paper, we show that the former directly aligns the class-conditioned fake-and-real data distributions $P(\text{image}|\text{class})$ ({\em data matching}), while the latter aligns data-conditioned class distributions $P(\text{class}|\text{image})$ ({\em label matching}). Although class separability does not directly translate to sample quality and becomes a burden if classification itself is intrinsically difficult, the discriminator cannot provide useful guidance for the generator if features of distinct classes are mapped to the same point and thus become inseparable. Motivated by this intuition, we propose a Dual Projection GAN (P2GAN) model that learns to balance between {\em data matching} and {\em label matching}. We then propose an improved cGAN model with Auxiliary Classification that directly aligns the fake and real conditionals $P(\text{class}|\text{image})$ by minimizing their $f$-divergence. Experiments on a synthetic Mixture of Gaussian (MoG) dataset and a variety of real-world datasets including CIFAR100, ImageNet, and VGGFace2 demonstrate the efficacy of our proposed models.

cs.CV↗

arXiv2021

AE-StyleGAN: Improved Training of Style-Based Auto-Encoders

StyleGANs have shown impressive results on data generation and manipulation in recent years, thanks to its disentangled style latent space. A lot of efforts have been made in inverting a pretrained generator, where an encoder is trained ad hoc after the generator is trained in a two-stage fashion. In this paper, we focus on style-based generators asking a scientific question: Does forcing such a generator to reconstruct real data lead to more disentangled latent space and make the inversion process from image to latent space easy? We describe a new methodology to train a style-based autoencoder where the encoder and generator are optimized end-to-end. We show that our proposed model consistently outperforms baselines in terms of image inversion and generation quality. Supplementary, code, and pretrained models are available on the project website.

cs.CV↗

arXiv2021

Semi-Supervised Segmentation of Radiation-Induced Pulmonary Fibrosis from Lung CT Scans with Multi-Scale Guided Dense Attention

Computed Tomography (CT) plays an important role in monitoring radiation-induced Pulmonary Fibrosis (PF), where accurate segmentation of the PF lesions is highly desired for diagnosis and treatment follow-up. However, the task is challenged by ambiguous boundary, irregular shape, various position and size of the lesions, as well as the difficulty in acquiring a large set of annotated volumetric images for training. To overcome these problems, we propose a novel convolutional neural network called PF-Net and incorporate it into a semi-supervised learning framework based on Iterative Confidence-based Refinement And Weighting of pseudo Labels (I-CRAWL). Our PF-Net combines 2D and 3D convolutions to deal with CT volumes with large inter-slice spacing, and uses multi-scale guided dense attention to segment complex PF lesions. For semi-supervised learning, our I-CRAWL employs pixel-level uncertainty-based confidence-aware refinement to improve the accuracy of pseudo labels of unannotated images, and uses image-level uncertainty for confidence-based image weighting to suppress low-quality pseudo labels in an iterative training process. Extensive experiments with CT scans of Rhesus Macaques with radiation-induced PF showed that: 1) PF-Net achieved higher segmentation accuracy than existing 2D, 3D and 2.5D neural networks, and 2) I-CRAWL outperformed state-of-the-art semi-supervised learning methods for the PF lesion segmentation task. Our method has a potential to improve the diagnosis of PF and clinical assessment of side effects of radiotherapy for lung cancers.

eess.IV↗

arXiv2021

UTNet: A Hybrid Transformer Architecture for Medical Image Segmentation

Transformer architecture has emerged to be successful in a number of natural language processing tasks. However, its applications to medical vision remain largely unexplored. In this study, we present UTNet, a simple yet powerful hybrid Transformer architecture that integrates self-attention into a convolutional neural network for enhancing medical image segmentation. UTNet applies self-attention modules in both encoder and decoder for capturing long-range dependency at different scales with minimal overhead. To this end, we propose an efficient self-attention mechanism along with relative position encoding that reduces the complexity of self-attention operation significantly from $O(n^2)$ to approximate $O(n)$. A new self-attention decoder is also proposed to recover fine-grained details from the skipped connections in the encoder. Our approach addresses the dilemma that Transformer requires huge amounts of data to learn vision inductive bias. Our hybrid layer design allows the initialization of Transformer into convolutional networks without a need of pre-training. We have evaluated UTNet on the multi-label, multi-vendor cardiac magnetic resonance imaging cohort. UTNet demonstrates superior segmentation performance and robustness against the state-of-the-art approaches, holding the promise to generalize well on other medical image segmentations.

cs.CV↗

arXiv2021

Global and Local Interpretation of black-box Machine Learning models to determine prognostic factors from early COVID-19 data

The COVID-19 corona virus has claimed 4.1 million lives, as of July 24, 2021. A variety of machine learning models have been applied to related data to predict important factors such as the severity of the disease, infection rate and discover important prognostic factors. Often the usefulness of the findings from the use of these techniques is reduced due to lack of method interpretability. Some recent progress made on the interpretability of machine learning models has the potential to unravel more insights while using conventional machine learning models. In this work, we analyze COVID-19 blood work data with some of the popular machine learning models; then we employ state-of-the-art post-hoc local interpretability techniques(e.g.- SHAP, LIME), and global interpretability techniques(e.g. - symbolic metamodeling) to the trained black-box models to draw interpretable conclusions. In the gamut of machine learning algorithms, regressions remain one of the simplest and most explainable models with clear mathematical formulation. We explore one of the most recent techniques called symbolic metamodeling to find the mathematical expression of the machine learning models for COVID-19. We identify Acute Kidney Injury (AKI), initial Albumin level (ALBI), Aspartate aminotransferase (ASTI), Total Bilirubin initial(TBILI) and D-Dimer initial (DIMER) as major prognostic factors of the disease severity. Our contributions are- (i) uncover the underlying mathematical expression for the black-box models on COVID-19 severity prediction task (ii) we are the first to apply symbolic metamodeling to this task, and (iii) discover important features and feature interactions.

cs.LG↗

arXiv2021

CrossNorm and SelfNorm for Generalization under Distribution Shifts

Traditional normalization techniques (e.g., Batch Normalization and Instance Normalization) generally and simplistically assume that training and test data follow the same distribution. As distribution shifts are inevitable in real-world applications, well-trained models with previous normalization methods can perform badly in new environments. Can we develop new normalization methods to improve generalization robustness under distribution shifts? In this paper, we answer the question by proposing CrossNorm and SelfNorm. CrossNorm exchanges channel-wise mean and variance between feature maps to enlarge training distribution, while SelfNorm uses attention to recalibrate the statistics to bridge gaps between training and test distributions. CrossNorm and SelfNorm can complement each other, though exploring different directions in statistics usage. Extensive experiments on different fields (vision and language), tasks (classification and segmentation), settings (supervised and semi-supervised), and distribution shift types (synthetic and natural) show the effectiveness. Code is available at https://github.com/amazon-research/crossnorm-selfnorm

cs.CV↗

arXiv2021

DeepTag: An Unsupervised Deep Learning Method for Motion Tracking on Cardiac Tagging Magnetic Resonance Images

Cardiac tagging magnetic resonance imaging (t-MRI) is the gold standard for regional myocardium deformation and cardiac strain estimation. However, this technique has not been widely used in clinical diagnosis, as a result of the difficulty of motion tracking encountered with t-MRI images. In this paper, we propose a novel deep learning-based fully unsupervised method for in vivo motion tracking on t-MRI images. We first estimate the motion field (INF) between any two consecutive t-MRI frames by a bi-directional generative diffeomorphic registration neural network. Using this result, we then estimate the Lagrangian motion field between the reference frame and any other frame through a differentiable composition layer. By utilizing temporal information to perform reasonable estimations on spatio-temporal motion fields, this novel method provides a useful solution for motion tracking and image registration in dynamic medical imaging. Our method has been validated on a representative clinical t-MRI dataset; the experimental results show that our method is superior to conventional motion tracking methods in terms of landmark tracking accuracy and inference efficiency.

cs.CV↗

arXiv2021

Enabling Data Diversity: Efficient Automatic Augmentation via Regularized Adversarial Training

Data augmentation has proved extremely useful by increasing training data variance to alleviate overfitting and improve deep neural networks' generalization performance. In medical image analysis, a well-designed augmentation policy usually requires much expert knowledge and is difficult to generalize to multiple tasks due to the vast discrepancies among pixel intensities, image appearances, and object shapes in different medical tasks. To automate medical data augmentation, we propose a regularized adversarial training framework via two min-max objectives and three differentiable augmentation models covering affine transformation, deformation, and appearance changes. Our method is more automatic and efficient than previous automatic augmentation methods, which still rely on pre-defined operations with human-specified ranges and costly bi-level optimization. Extensive experiments demonstrated that our approach, with less training overhead, achieves superior performance over state-of-the-art auto-augmentation methods on both tasks of 2D skin cancer classification and 3D organs-at-risk segmentation.

cs.CV↗

arXiv2021

Learning View-Disentangled Human Pose Representation by Contrastive Cross-View Mutual Information Maximization

We introduce a novel representation learning method to disentangle pose-dependent as well as view-dependent factors from 2D human poses. The method trains a network using cross-view mutual information maximization (CV-MIM) which maximizes mutual information of the same pose performed from different viewpoints in a contrastive learning manner. We further propose two regularization terms to ensure disentanglement and smoothness of the learned representations. The resulting pose representations can be used for cross-view action recognition. To evaluate the power of the learned representations, in addition to the conventional fully-supervised action recognition settings, we introduce a novel task called single-shot cross-view action recognition. This task trains models with actions from only one single viewpoint while models are evaluated on poses captured from all possible viewpoints. We evaluate the learned representations on standard benchmarks for action recognition, and show that (i) CV-MIM performs competitively compared with the state-of-the-art models in the fully-supervised scenarios; (ii) CV-MIM outperforms other competing methods by a large margin in the single-shot cross-view setting; (iii) and the learned representations can significantly boost the performance when reducing the amount of supervised training data. Our code is made publicly available at https://github.com/google-research/google-research/tree/master/poem

cs.CV↗

arXiv2021

Liver Fibrosis and NAS scoring from CT images using self-supervised learning and texture encoding

Non-alcoholic fatty liver disease (NAFLD) is one of the most common causes of chronic liver diseases (CLD) which can progress to liver cancer. The severity and treatment of NAFLD is determined by NAFLD Activity Scores (NAS)and liver fibrosis stage, which are usually obtained from liver biopsy. However, biopsy is invasive in nature and involves risk of procedural complications. Current methods to predict the fibrosis and NAS scores from noninvasive CT images rely heavily on either a large annotated dataset or transfer learning using pretrained networks. However, the availability of a large annotated dataset cannot be always ensured andthere can be domain shifts when using transfer learning. In this work, we propose a self-supervised learning method to address both problems. As the NAFLD causes changes in the liver texture, we also propose to use texture encoded inputs to improve the performance of the model. Given a relatively small dataset with 30 patients, we employ a self-supervised network which achieves better performance than a network trained via transfer learning. The code is publicly available at https://github.com/ananyajana/fibrosis_code.

eess.IV↗

arXiv2021

Training Federated GANs with Theoretical Guarantees: A Universal Aggregation Approach

Recently, Generative Adversarial Networks (GANs) have demonstrated their potential in federated learning, i.e., learning a centralized model from data privately hosted by multiple sites. A federatedGAN jointly trains a centralized generator and multiple private discriminators hosted at different sites. A major theoretical challenge for the federated GAN is the heterogeneity of the local data distributions. Traditional approaches cannot guarantee to learn the target distribution, which isa mixture of the highly different local distributions. This paper tackles this theoretical challenge, and for the first time, provides a provably correct framework for federated GAN. We propose a new approach called Universal Aggregation, which simulates a centralized discriminator via carefully aggregating the mixture of all private discriminators. We prove that a generator trained with this simulated centralized discriminator can learn the desired target distribution. Through synthetic and real datasets, we show that our method can learn the mixture of largely different distributions where existing federated GAN methods fail.

cs.LG↗

arXiv2020

Maximum-Entropy Adversarial Data Augmentation for Improved Generalization and Robustness

Adversarial data augmentation has shown promise for training robust deep neural networks against unforeseen data shifts or corruptions. However, it is difficult to define heuristics to generate effective fictitious target distributions containing "hard" adversarial perturbations that are largely different from the source distribution. In this paper, we propose a novel and effective regularization term for adversarial data augmentation. We theoretically derive it from the information bottleneck principle, which results in a maximum-entropy formulation. Intuitively, this regularization term encourages perturbing the underlying source distribution to enlarge predictive uncertainty of the current model, so that the generated "hard" adversarial perturbations can improve the model robustness during training. Experimental results on three standard benchmarks demonstrate that our method consistently outperforms the existing state of the art by a statistically significant margin.

cs.LG↗

arXiv2020

Error-Bounded Correction of Noisy Labels

To collect large scale annotated data, it is inevitable to introduce label noise, i.e., incorrect class labels. To be robust against label noise, many successful methods rely on the noisy classifiers (i.e., models trained on the noisy training data) to determine whether a label is trustworthy. However, it remains unknown why this heuristic works well in practice. In this paper, we provide the first theoretical explanation for these methods. We prove that the prediction of a noisy classifier can indeed be a good indicator of whether the label of a training data is clean. Based on the theoretical result, we propose a novel algorithm that corrects the labels based on the noisy classifier prediction. The corrected labels are consistent with the true Bayesian optimal classifier with high probability. We incorporate our label correction algorithm into the training of deep neural networks and train models that achieve superior testing performance on multiple public datasets.

cs.CV↗

arXiv2020

Deep Learning based NAS Score and Fibrosis Stage Prediction from CT and Pathology Data

Non-Alcoholic Fatty Liver Disease (NAFLD) is becoming increasingly prevalent in the world population. Without diagnosis at the right time, NAFLD can lead to non-alcoholic steatohepatitis (NASH) and subsequent liver damage. The diagnosis and treatment of NAFLD depend on the NAFLD activity score (NAS) and the liver fibrosis stage, which are usually evaluated from liver biopsies by pathologists. In this work, we propose a novel method to automatically predict NAS score and fibrosis stage from CT data that is non-invasive and inexpensive to obtain compared with liver biopsy. We also present a method to combine the information from CT and H\&E stained pathology data to improve the performance of NAS score and fibrosis stage prediction, when both types of data are available. This is of great value to assist the pathologists in computer-aided diagnosis process. Experiments on a 30-patient dataset illustrate the effectiveness of our method.

eess.IV↗

arXiv2020

Oriented Object Detection in Aerial Images with Box Boundary-Aware Vectors

Oriented object detection in aerial images is a challenging task as the objects in aerial images are displayed in arbitrary directions and are usually densely packed. Current oriented object detection methods mainly rely on two-stage anchor-based detectors. However, the anchor-based detectors typically suffer from a severe imbalance issue between the positive and negative anchor boxes. To address this issue, in this work we extend the horizontal keypoint-based object detector to the oriented object detection task. In particular, we first detect the center keypoints of the objects, based on which we then regress the box boundary-aware vectors (BBAVectors) to capture the oriented bounding boxes. The box boundary-aware vectors are distributed in the four quadrants of a Cartesian coordinate system for all arbitrarily oriented objects. To relieve the difficulty of learning the vectors in the corner cases, we further classify the oriented bounding boxes into horizontal and rotational bounding boxes. In the experiment, we show that learning the box boundary-aware vectors is superior to directly predicting the width, height, and angle of an oriented bounding box, as adopted in the baseline method. Besides, the proposed method competes favorably with state-of-the-art methods. Code is available at https://github.com/yijingru/BBAVectors-Oriented-Object-Detection.

cs.CV↗

arXiv2020

Measure Anatomical Thickness from Cardiac MRI with Deep Neural Networks

Accurate estimation of shape thickness from medical images is crucial in clinical applications. For example, the thickness of myocardium is one of the key to cardiac disease diagnosis. While mathematical models are available to obtain accurate dense thickness estimation, they suffer from heavy computational overhead due to iterative solvers. To this end, we propose novel methods for dense thickness estimation, including a fast solver that estimates thickness from binary annular shapes and an end-to-end network that estimates thickness directly from raw cardiac images.We test the proposed models on three cardiac datasets and one synthetic dataset, achieving impressive results and generalizability on all. Thickness estimation is performed without iterative solvers or manual correction, which is 100 times faster than the mathematical model. We also analyze thickness patterns on different cardiac pathologies with a standard clinical model and the results demonstrate the potential clinical value of our method for thickness based cardiac disease diagnosis.

eess.IV↗