arXiv subjects

Dimitris N. Metaxas

Publications and source records attributed to Dimitris N. Metaxas.

At least 109 records · Page 6Linked to original sources

arXiv2023

WORD: A large scale dataset, benchmark and clinical applicable study for abdominal organ segmentation from CT image

Whole abdominal organ segmentation is important in diagnosing abdomen lesions, radiotherapy, and follow-up. However, oncologists' delineating all abdominal organs from 3D volumes is time-consuming and very expensive. Deep learning-based medical image segmentation has shown the potential to reduce manual delineation efforts, but it still requires a large-scale fine annotated dataset for training, and there is a lack of large-scale datasets covering the whole abdomen region with accurate and detailed annotations for the whole abdominal organ segmentation. In this work, we establish a new large-scale \textit{W}hole abdominal \textit{OR}gan \textit{D}ataset (\textit{WORD}) for algorithm research and clinical application development. This dataset contains 150 abdominal CT volumes (30495 slices). Each volume has 16 organs with fine pixel-level annotations and scribble-based sparse annotations, which may be the largest dataset with whole abdominal organ annotation. Several state-of-the-art segmentation methods are evaluated on this dataset. And we also invited three experienced oncologists to revise the model predictions to measure the gap between the deep learning method and oncologists. Afterwards, we investigate the inference-efficient learning on the WORD, as the high-resolution image requires large GPU memory and a long inference time in the test stage. We further evaluate the scribble-based annotation-efficient learning on this dataset, as the pixel-wise manual annotation is time-consuming and expensive. The work provided a new benchmark for the abdominal multi-organ segmentation task, and these experiments can serve as the baseline for future research and clinical application development.

eess.IV↗

arXiv2023

3D Tooth Mesh Segmentation with Simplified Mesh Cell Representation

Manual tooth segmentation of 3D tooth meshes is tedious and there is variations among dentists. %Manual tooth annotation of 3D tooth meshes is a tedious task. Several deep learning based methods have been proposed to perform automatic tooth mesh segmentation. Many of the proposed tooth mesh segmentation algorithms summarize the mesh cell as - the cell center or barycenter, the normal at barycenter, the cell vertices and the normals at the cell vertices. Summarizing of the mesh cell/triangle in this manner imposes an implicit structural constraint and makes it difficult to work with multiple resolutions which is done in many point cloud based deep learning algorithms. We propose a novel segmentation method which utilizes only the barycenter and the normal at the barycenter information of the mesh cell and yet achieves competitive performance. We are the first to demonstrate that it is possible to relax the implicit structural constraint and yet achieve superior segmentation performance

cs.CV↗

arXiv2022

Visual Prompt Tuning for Test-time Domain Adaptation

Models should be able to adapt to unseen data during test-time to avoid performance drops caused by inevitable distribution shifts in real-world deployment scenarios. In this work, we tackle the practical yet challenging test-time adaptation (TTA) problem, where a model adapts to the target domain without accessing the source data. We propose a simple recipe called \textit{Data-efficient Prompt Tuning} (DePT) with two key ingredients. First, DePT plugs visual prompts into the vision Transformer and only tunes these source-initialized prompts during adaptation. We find such parameter-efficient finetuning can efficiently adapt the model representation to the target domain without overfitting to the noise in the learning objective. Second, DePT bootstraps the source representation to the target domain by memory bank-based online pseudo-labeling. A hierarchical self-supervised regularization specially designed for prompts is jointly optimized to alleviate error accumulation during self-training. With much fewer tunable parameters, DePT demonstrates not only state-of-the-art performance on major adaptation benchmarks VisDA-C, ImageNet-C, and DomainNet-126, but also superior data efficiency, i.e., adaptation with only 1\% or 10\% data without much performance degradation compared to 100\% data. In addition, DePT is also versatile to be extended to online or multi-source TTA settings.

cs.CV↗

arXiv2022

CDDSA: Contrastive Domain Disentanglement and Style Augmentation for Generalizable Medical Image Segmentation

Generalization to previously unseen images with potential domain shifts and different styles is essential for clinically applicable medical image segmentation, and the ability to disentangle domain-specific and domain-invariant features is key for achieving Domain Generalization (DG). However, existing DG methods can hardly achieve effective disentanglement to get high generalizability. To deal with this problem, we propose an efficient Contrastive Domain Disentanglement and Style Augmentation (CDDSA) framework for generalizable medical image segmentation. First, a disentangle network is proposed to decompose an image into a domain-invariant anatomical representation and a domain-specific style code, where the former is sent to a segmentation model that is not affected by the domain shift, and the disentangle network is regularized by a decoder that combines the anatomical and style codes to reconstruct the input image. Second, to achieve better disentanglement, a contrastive loss is proposed to encourage the style codes from the same domain and different domains to be compact and divergent, respectively. Thirdly, to further improve generalizability, we propose a style augmentation method based on the disentanglement representation to synthesize images in various unseen styles with shared anatomical structures. Our method was validated on a public multi-site fundus image dataset for optic cup and disc segmentation and an in-house multi-site Nasopharyngeal Carcinoma Magnetic Resonance Image (NPC-MRI) dataset for nasopharynx Gross Tumor Volume (GTVnx) segmentation. Experimental results showed that the proposed CDDSA achieved remarkable generalizability across different domains, and it outperformed several state-of-the-art methods in domain-generalizable segmentation.

cs.CV↗

arXiv2022

More Than Just Attention: Improving Cross-Modal Attentions with Contrastive Constraints for Image-Text Matching

Cross-modal attention mechanisms have been widely applied to the image-text matching task and have achieved remarkable improvements thanks to its capability of learning fine-grained relevance across different modalities. However, the cross-modal attention models of existing methods could be sub-optimal and inaccurate because there is no direct supervision provided during the training process. In this work, we propose two novel training strategies, namely Contrastive Content Re-sourcing (CCR) and Contrastive Content Swapping (CCS) constraints, to address such limitations. These constraints supervise the training of cross-modal attention models in a contrastive learning manner without requiring explicit attention annotations. They are plug-in training strategies and can be easily integrated into existing cross-modal attention models. Additionally, we introduce three metrics including Attention Precision, Recall, and F1-Score to quantitatively measure the quality of learned attention models. We evaluate the proposed constraints by incorporating them into four state-of-the-art cross-modal attention-based image-text matching models. Experimental results on both Flickr30k and MS-COCO datasets demonstrate that integrating these constraints improves the model performance in terms of both retrieval performance and attention metrics.

cs.CV↗

arXiv2022

Learned Half-Quadratic Splitting Network for MR Image Reconstruction

Magnetic Resonance (MR) image reconstruction from highly undersampled $k$-space data is critical in accelerated MR imaging (MRI) techniques. In recent years, deep learning-based methods have shown great potential in this task. This paper proposes a learned half-quadratic splitting algorithm for MR image reconstruction and implements the algorithm in an unrolled deep learning network architecture. We compare the performance of our proposed method on a public cardiac MR dataset against DC-CNN and LPDNet, and our method outperforms other methods in both quantitative results and qualitative results with fewer model parameters and faster reconstruction speed. Finally, we enlarge our model to achieve superior reconstruction quality, and the improvement is $1.76$ dB and $2.74$ dB over LPDNet in peak signal-to-noise ratio on $5\times$ and $10\times$ acceleration, respectively. Code for our method is publicly available at https://github.com/hellopipu/HQS-Net.

eess.IV↗

arXiv2022

Towards Self-supervised and Weight-preserving Neural Architecture Search

Neural architecture search (NAS) algorithms save tremendous labor from human experts. Recent advancements further reduce the computational overhead to an affordable level. However, it is still cumbersome to deploy the NAS techniques in real-world applications due to the fussy procedures and the supervised learning paradigm. In this work, we propose the self-supervised and weight-preserving neural architecture search (SSWP-NAS) as an extension of the current NAS framework by allowing the self-supervision and retaining the concomitant weights discovered during the search stage. As such, we simplify the workflow of NAS to a one-stage and proxy-free procedure. Experiments show that the architectures searched by the proposed framework achieve state-of-the-art accuracy on CIFAR-10, CIFAR-100, and ImageNet datasets without using manual labels. Moreover, we show that employing the concomitant weights as initialization consistently outperforms the random initialization and the two-stage weight pre-training method by a clear margin under semi-supervised learning scenarios. Codes are publicly available at https://github.com/LzVv123456/SSWP-NAS.

cs.CV↗

arXiv2022

Learning Transferable Reward for Query Object Localization with Policy Adaptation

We propose a reinforcement learning based approach to query object localization, for which an agent is trained to localize objects of interest specified by a small exemplary set. We learn a transferable reward signal formulated using the exemplary set by ordinal metric learning. Our proposed method enables test-time policy adaptation to new environments where the reward signals are not readily available, and outperforms fine-tuning approaches that are limited to annotated images. In addition, the transferable reward allows repurposing the trained agent from one specific class to another class. Experiments on corrupted MNIST, CU-Birds, and COCO datasets demonstrate the effectiveness of our approach.

cs.CV↗

arXiv2022

SCPM-Net: An Anchor-free 3D Lung Nodule Detection Network using Sphere Representation and Center Points Matching

Lung nodule detection from 3D Computed Tomography scans plays a vital role in efficient lung cancer screening. Despite the SOTA performance obtained by recent anchor-based detectors using CNNs for this task, they require predetermined anchor parameters such as the size, number, and aspect ratio of anchors, and have limited robustness when dealing with lung nodules with a massive variety of sizes. To overcome these problems, we propose a 3D sphere representation-based center-points matching detection network that is anchor-free and automatically predicts the position, radius, and offset of nodules without the manual design of nodule/anchor parameters. The SCPM-Net consists of two novel components: sphere representation and center points matching. First, to match the nodule annotation in clinical practice, we replace the commonly used bounding box with our proposed bounding sphere to represent nodules with the centroid, radius, and local offset in 3D space. A compatible sphere-based intersection over-union loss function is introduced to train the lung nodule detection network stably and efficiently. Second, we empower the network anchor-free by designing a positive center-points selection and matching process, which naturally discards pre-determined anchor boxes. An online hard example mining and re-focal loss subsequently enable the CPM process to be more robust, resulting in more accurate point assignment and mitigation of class imbalance. In addition, to better capture spatial information and 3D context for the detection, we propose to fuse multi-level spatial coordinate maps with the feature extractor and combine them with 3D squeeze-and-excitation attention modules. Experimental results on the LUNA16 dataset showed that our proposed framework achieves superior performance compared with existing anchor-based and anchor-free methods for lung nodule detection.

cs.CV↗

arXiv2021

Improved Transformer for High-Resolution GANs

Attention-based models, exemplified by the Transformer, can effectively model long range dependency, but suffer from the quadratic complexity of self-attention operation, making them difficult to be adopted for high-resolution image generation based on Generative Adversarial Networks (GANs). In this paper, we introduce two key ingredients to Transformer to address this challenge. First, in low-resolution stages of the generative process, standard global self-attention is replaced with the proposed multi-axis blocked self-attention which allows efficient mixing of local and global attention. Second, in high-resolution stages, we drop self-attention while only keeping multi-layer perceptrons reminiscent of the implicit neural function. To further improve the performance, we introduce an additional self-modulation component based on cross-attention. The resulting model, denoted as HiT, has a nearly linear computational complexity with respect to the image size and thus directly scales to synthesizing high definition images. We show in the experiments that the proposed HiT achieves state-of-the-art FID scores of 30.83 and 2.95 on unconditional ImageNet $128 \times 128$ and FFHQ $256 \times 256$, respectively, with a reasonable throughput. We believe the proposed HiT is an important milestone for generators in GANs which are completely free of convolutions. Our code is made publicly available at https://github.com/google-research/hit-gan

cs.CV↗

arXiv2021

Hybrid Supervision Learning for Pathology Whole Slide Image Classification

Weak supervision learning on classification labels has demonstrated high performance in various tasks, while a few pixel-level fine annotations are also affordable. Naturally a question comes to us that whether the combination of pixel-level (e.g., segmentation) and image level (e.g., classification) annotation can introduce further improvement. However in computational pathology this is a difficult task for this reason: High resolution of whole slide images makes it difficult to do end-to-end classification model training, which is challenging to research of weak or hybrid supervision learning in the past. To handle this problem, we propose a hybrid supervision learning framework for this kind of high resolution images with sufficient image-level coarse annotations and a few pixel-level fine labels. This framework, when applied in training patch model, can carefully make use of coarse image-level labels to refine generated pixel-level pseudo labels. Complete strategy is proposed to suppress pixel-level false positives and false negatives. A large hybrid annotated dataset is used to evaluate the effectiveness of hybrid supervision learning. By extracting pixel-level pseudo labels in initially image-level labeled samples, we achieve 5.2% higher specificity than purely training on existing labels while retaining 100% sensitivity, in the task of image-level classification to be positive or negative.

cs.CV↗

arXiv2021

Stochastic Transformer Networks with Linear Competing Units: Application to end-to-end SL Translation

Automating sign language translation (SLT) is a challenging real world application. Despite its societal importance, though, research progress in the field remains rather poor. Crucially, existing methods that yield viable performance necessitate the availability of laborious to obtain gloss sequence groundtruth. In this paper, we attenuate this need, by introducing an end-to-end SLT model that does not entail explicit use of glosses; the model only needs text groundtruth. This is in stark contrast to existing end-to-end models that use gloss sequence groundtruth, either in the form of a modality that is recognized at an intermediate model stage, or in the form of a parallel output process, jointly trained with the SLT model. Our approach constitutes a Transformer network with a novel type of layers that combines: (i) local winner-takes-all (LWTA) layers with stochastic winner sampling, instead of conventional ReLU layers, (ii) stochastic weights with posterior distributions estimated via variational inference, and (iii) a weight compression technique at inference time that exploits estimated posterior variance to perform massive, almost lossless compression. We demonstrate that our approach can reach the currently best reported BLEU-4 score on the PHOENIX 2014T benchmark, but without making use of glosses for model training, and with a memory footprint reduced by more than 70%.

cs.CL↗

arXiv2021

Object-Guided Instance Segmentation With Auxiliary Feature Refinement for Biological Images

Instance segmentation is of great importance for many biological applications, such as study of neural cell interactions, plant phenotyping, and quantitatively measuring how cells react to drug treatment. In this paper, we propose a novel box-based instance segmentation method. Box-based instance segmentation methods capture objects via bounding boxes and then perform individual segmentation within each bounding box region. However, existing methods can hardly differentiate the target from its neighboring objects within the same bounding box region due to their similar textures and low-contrast boundaries. To deal with this problem, in this paper, we propose an object-guided instance segmentation method. Our method first detects the center points of the objects, from which the bounding box parameters are then predicted. To perform segmentation, an object-guided coarse-to-fine segmentation branch is built along with the detection branch. The segmentation branch reuses the object features as guidance to separate target object from the neighboring ones within the same bounding box region. To further improve the segmentation quality, we design an auxiliary feature refinement module that densely samples and refines point-wise features in the boundary regions. Experimental results on three biological image datasets demonstrate the advantages of our method. The code will be available at https://github.com/yijingru/ObjGuided-Instance-Segmentation.

cs.CV↗

arXiv2021

A Good Image Generator Is What You Need for High-Resolution Video Synthesis

Image and video synthesis are closely related areas aiming at generating content from noise. While rapid progress has been demonstrated in improving image-based models to handle large resolutions, high-quality renderings, and wide variations in image content, achieving comparable video generation results remains problematic. We present a framework that leverages contemporary image generators to render high-resolution videos. We frame the video synthesis problem as discovering a trajectory in the latent space of a pre-trained and fixed image generator. Not only does such a framework render high-resolution videos, but it also is an order of magnitude more computationally efficient. We introduce a motion generator that discovers the desired trajectory, in which content and motion are disentangled. With such a representation, our framework allows for a broad range of applications, including content and motion manipulation. Furthermore, we introduce a new task, which we call cross-domain video synthesis, in which the image and motion generators are trained on disjoint datasets belonging to different domains. This allows for generating moving objects for which the desired video data is not available. Extensive experiments on various datasets demonstrate the advantages of our methods over existing video generation techniques. Code will be released at https://github.com/snap-research/MoCoGAN-HD.

cs.CV↗

arXiv2021

Deep Animation Video Interpolation in the Wild

In the animation industry, cartoon videos are usually produced at low frame rate since hand drawing of such frames is costly and time-consuming. Therefore, it is desirable to develop computational models that can automatically interpolate the in-between animation frames. However, existing video interpolation methods fail to produce satisfying results on animation data. Compared to natural videos, animation videos possess two unique characteristics that make frame interpolation difficult: 1) cartoons comprise lines and smooth color pieces. The smooth areas lack textures and make it difficult to estimate accurate motions on animation videos. 2) cartoons express stories via exaggeration. Some of the motions are non-linear and extremely large. In this work, we formally define and study the animation video interpolation problem for the first time. To address the aforementioned challenges, we propose an effective framework, AnimeInterp, with two dedicated modules in a coarse-to-fine manner. Specifically, 1) Segment-Guided Matching resolves the "lack of textures" challenge by exploiting global matching among color pieces that are piece-wise coherent. 2) Recurrent Flow Refinement resolves the "non-linear and extremely large motion" challenge by recurrent predictions using a transformer-like architecture. To facilitate comprehensive training and evaluations, we build a large-scale animation triplet dataset, ATD-12K, which comprises 12,000 triplets with rich annotations. Extensive experiments demonstrate that our approach outperforms existing state-of-the-art interpolation methods for animation videos. Notably, AnimeInterp shows favorable perceptual quality and robustness for animation scenarios in the wild. The proposed dataset and code are available at https://github.com/lisiyao21/AnimeInterp/.

cs.CV↗

arXiv2021

FocusNetv2: Imbalanced Large and Small Organ Segmentation with Adversarial Shape Constraint for Head and Neck CT Images

Radiotherapy is a treatment where radiation is used to eliminate cancer cells. The delineation of organs-at-risk (OARs) is a vital step in radiotherapy treatment planning to avoid damage to healthy organs. For nasopharyngeal cancer, more than 20 OARs are needed to be precisely segmented in advance. The challenge of this task lies in complex anatomical structure, low-contrast organ contours, and the extremely imbalanced size between large and small organs. Common segmentation methods that treat them equally would generally lead to inaccurate small-organ labeling. We propose a novel two-stage deep neural network, FocusNetv2, to solve this challenging problem by automatically locating, ROI-pooling, and segmenting small organs with specifically designed small-organ localization and segmentation sub-networks while maintaining the accuracy of large organ segmentation. In addition to our original FocusNet, we employ a novel adversarial shape constraint on small organs to ensure the consistency between estimated small-organ shapes and organ shape prior knowledge. Our proposed framework is extensively tested on both self-collected dataset of 1,164 CT scans and the MICCAI Head and Neck Auto Segmentation Challenge 2015 dataset, which shows superior performance compared with state-of-the-art head and neck OAR segmentation methods.

eess.IV↗

arXiv2021

Variational Bayesian Sequence-to-Sequence Networks for Memory-Efficient Sign Language Translation

Memory-efficient continuous Sign Language Translation is a significant challenge for the development of assisted technologies with real-time applicability for the deaf. In this work, we introduce a paradigm of designing recurrent deep networks whereby the output of the recurrent layer is derived from appropriate arguments from nonparametric statistics. A novel variational Bayesian sequence-to-sequence network architecture is proposed that consists of a) a full Gaussian posterior distribution for data-driven memory compression and b) a nonparametric Indian Buffet Process prior for regularization applied on the Gated Recurrent Unit non-gate weights. We dub our approach Stick-Breaking Recurrent network and show that it can achieve a substantial weight compression without diminishing modeling performance.

stat.ML↗

arXiv2020

Multi-modal AsynDGAN: Learn From Distributed Medical Image Data without Sharing Private Information

As deep learning technologies advance, increasingly more data is necessary to generate general and robust models for various tasks. In the medical domain, however, large-scale and multi-parties data training and analyses are infeasible due to the privacy and data security concerns. In this paper, we propose an extendable and elastic learning framework to preserve privacy and security while enabling collaborative learning with efficient communication. The proposed framework is named distributed Asynchronized Discriminator Generative Adversarial Networks (AsynDGAN), which consists of a centralized generator and multiple distributed discriminators. The advantages of our proposed framework are five-fold: 1) the central generator could learn the real data distribution from multiple datasets implicitly without sharing the image data; 2) the framework is applicable for single-modality or multi-modality data; 3) the learned generator can be used to synthesize samples for down-stream learning tasks to achieve close-to-real performance as using actual samples collected from multiple data centers; 4) the synthetic samples can also be used to augment data or complete missing modalities for one single data center; 5) the learning process is more efficient and requires lower bandwidth than other distributed deep learning methods.

cs.LG↗