arXiv subjects

Dimitris N. Metaxas

Publications and source records attributed to Dimitris N. Metaxas.

At least 91 records · Page 5Linked to original sources

arXiv2024

The state-of-the-art in Cardiac MRI Reconstruction: Results of the CMRxRecon Challenge in MICCAI 2023

Cardiac MRI, crucial for evaluating heart structure and function, faces limitations like slow imaging and motion artifacts. Undersampling reconstruction, especially data-driven algorithms, has emerged as a promising solution to accelerate scans and enhance imaging performance using highly under-sampled data. Nevertheless, the scarcity of publicly available cardiac k-space datasets and evaluation platform hinder the development of data-driven reconstruction algorithms. To address this issue, we organized the Cardiac MRI Reconstruction Challenge (CMRxRecon) in 2023, in collaboration with the 26th International Conference on MICCAI. CMRxRecon presented an extensive k-space dataset comprising cine and mapping raw data, accompanied by detailed annotations of cardiac anatomical structures. With overwhelming participation, the challenge attracted more than 285 teams and over 600 participants. Among them, 22 teams successfully submitted Docker containers for the testing phase, with 7 teams submitted for both cine and mapping tasks. All teams use deep learning based approaches, indicating that deep learning has predominately become a promising solution for the problem. The first-place winner of both tasks utilizes the E2E-VarNet architecture as backbones. In contrast, U-Net is still the most popular backbone for both multi-coil and single-coil reconstructions. This paper provides a comprehensive overview of the challenge design, presents a summary of the submitted results, reviews the employed methods, and offers an in-depth discussion that aims to inspire future advancements in cardiac MRI reconstruction models. The summary emphasizes the effective strategies observed in Cardiac MRI reconstruction, including backbone architecture, loss function, pre-processing techniques, physical modeling, and model complexity, thereby providing valuable insights for further developments in this field.

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arXiv2024

Taming Self-Training for Open-Vocabulary Object Detection

Recent studies have shown promising performance in open-vocabulary object detection (OVD) by utilizing pseudo labels (PLs) from pretrained vision and language models (VLMs). However, teacher-student self-training, a powerful and widely used paradigm to leverage PLs, is rarely explored for OVD. This work identifies two challenges of using self-training in OVD: noisy PLs from VLMs and frequent distribution changes of PLs. To address these challenges, we propose SAS-Det that tames self-training for OVD from two key perspectives. First, we present a split-and-fusion (SAF) head that splits a standard detection into an open-branch and a closed-branch. This design can reduce noisy supervision from pseudo boxes. Moreover, the two branches learn complementary knowledge from different training data, significantly enhancing performance when fused together. Second, in our view, unlike in closed-set tasks, the PL distributions in OVD are solely determined by the teacher model. We introduce a periodic update strategy to decrease the number of updates to the teacher, thereby decreasing the frequency of changes in PL distributions, which stabilizes the training process. Extensive experiments demonstrate SAS-Det is both efficient and effective. SAS-Det outperforms recent models of the same scale by a clear margin and achieves 37.4 AP50 and 29.1 APr on novel categories of the COCO and LVIS benchmarks, respectively. Code is available at \url{https://github.com/xiaofeng94/SAS-Det}.

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arXiv2024

Generating Enhanced Negatives for Training Language-Based Object Detectors

The recent progress in language-based open-vocabulary object detection can be largely attributed to finding better ways of leveraging large-scale data with free-form text annotations. Training such models with a discriminative objective function has proven successful, but requires good positive and negative samples. However, the free-form nature and the open vocabulary of object descriptions make the space of negatives extremely large. Prior works randomly sample negatives or use rule-based techniques to build them. In contrast, we propose to leverage the vast knowledge built into modern generative models to automatically build negatives that are more relevant to the original data. Specifically, we use large-language-models to generate negative text descriptions, and text-to-image diffusion models to also generate corresponding negative images. Our experimental analysis confirms the relevance of the generated negative data, and its use in language-based detectors improves performance on two complex benchmarks. Code is available at \url{https://github.com/xiaofeng94/Gen-Enhanced-Negs}.

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arXiv2024

DIAGNOSIS: Detecting Unauthorized Data Usages in Text-to-image Diffusion Models

Recent text-to-image diffusion models have shown surprising performance in generating high-quality images. However, concerns have arisen regarding the unauthorized data usage during the training or fine-tuning process. One example is when a model trainer collects a set of images created by a particular artist and attempts to train a model capable of generating similar images without obtaining permission and giving credit to the artist. To address this issue, we propose a method for detecting such unauthorized data usage by planting the injected memorization into the text-to-image diffusion models trained on the protected dataset. Specifically, we modify the protected images by adding unique contents on these images using stealthy image warping functions that are nearly imperceptible to humans but can be captured and memorized by diffusion models. By analyzing whether the model has memorized the injected content (i.e., whether the generated images are processed by the injected post-processing function), we can detect models that had illegally utilized the unauthorized data. Experiments on Stable Diffusion and VQ Diffusion with different model training or fine-tuning methods (i.e, LoRA, DreamBooth, and standard training) demonstrate the effectiveness of our proposed method in detecting unauthorized data usages. Code: https://github.com/ZhentingWang/DIAGNOSIS.

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arXiv2024

Training Like a Medical Resident: Context-Prior Learning Toward Universal Medical Image Segmentation

A major focus of clinical imaging workflow is disease diagnosis and management, leading to medical imaging datasets strongly tied to specific clinical objectives. This scenario has led to the prevailing practice of developing task-specific segmentation models, without gaining insights from widespread imaging cohorts. Inspired by the training program of medical radiology residents, we propose a shift towards universal medical image segmentation, a paradigm aiming to build medical image understanding foundation models by leveraging the diversity and commonality across clinical targets, body regions, and imaging modalities. Towards this goal, we develop Hermes, a novel context-prior learning approach to address the challenges of data heterogeneity and annotation differences in medical image segmentation. In a large collection of eleven diverse datasets (2,438 3D images) across five modalities (CT, PET, T1, T2 and cine MRI) and multiple body regions, we demonstrate the merit of the universal paradigm over the traditional paradigm on addressing multiple tasks within a single model. By exploiting the synergy across tasks, Hermes achieves state-of-the-art performance on all testing datasets and shows superior model scalability. Results on two additional datasets reveals Hermes' strong performance for transfer learning, incremental learning, and generalization to downstream tasks. Hermes's learned priors demonstrate an appealing trait to reflect the intricate relations among tasks and modalities, which aligns with the established anatomical and imaging principles in radiology. The code is available: https://github.com/yhygao/universal-medical-image-segmentation.

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arXiv2023

DiffSLVA: Harnessing Diffusion Models for Sign Language Video Anonymization

Since American Sign Language (ASL) has no standard written form, Deaf signers frequently share videos in order to communicate in their native language. However, since both hands and face convey critical linguistic information in signed languages, sign language videos cannot preserve signer privacy. While signers have expressed interest, for a variety of applications, in sign language video anonymization that would effectively preserve linguistic content, attempts to develop such technology have had limited success, given the complexity of hand movements and facial expressions. Existing approaches rely predominantly on precise pose estimations of the signer in video footage and often require sign language video datasets for training. These requirements prevent them from processing videos 'in the wild,' in part because of the limited diversity present in current sign language video datasets. To address these limitations, our research introduces DiffSLVA, a novel methodology that utilizes pre-trained large-scale diffusion models for zero-shot text-guided sign language video anonymization. We incorporate ControlNet, which leverages low-level image features such as HED (Holistically-Nested Edge Detection) edges, to circumvent the need for pose estimation. Additionally, we develop a specialized module dedicated to capturing facial expressions, which are critical for conveying essential linguistic information in signed languages. We then combine the above methods to achieve anonymization that better preserves the essential linguistic content of the original signer. This innovative methodology makes possible, for the first time, sign language video anonymization that could be used for real-world applications, which would offer significant benefits to the Deaf and Hard-of-Hearing communities. We demonstrate the effectiveness of our approach with a series of signer anonymization experiments.

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arXiv2023

Steering Prototypes with Prompt-tuning for Rehearsal-free Continual Learning

In the context of continual learning, prototypes-as representative class embeddings-offer advantages in memory conservation and the mitigation of catastrophic forgetting. However, challenges related to semantic drift and prototype interference persist. In this study, we introduce the Contrastive Prototypical Prompt (CPP) approach. Through task-specific prompt-tuning, underpinned by a contrastive learning objective, we effectively address both aforementioned challenges. Our evaluations on four challenging class-incremental benchmarks reveal that CPP achieves a significant 4% to 6% improvement over state-of-the-art methods. Importantly, CPP operates without a rehearsal buffer and narrows the performance divergence between continual and offline joint-learning, suggesting an innovative scheme for Transformer-based continual learning systems.

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arXiv2023

DeFormer: Integrating Transformers with Deformable Models for 3D Shape Abstraction from a Single Image

Accurate 3D shape abstraction from a single 2D image is a long-standing problem in computer vision and graphics. By leveraging a set of primitives to represent the target shape, recent methods have achieved promising results. However, these methods either use a relatively large number of primitives or lack geometric flexibility due to the limited expressibility of the primitives. In this paper, we propose a novel bi-channel Transformer architecture, integrated with parameterized deformable models, termed DeFormer, to simultaneously estimate the global and local deformations of primitives. In this way, DeFormer can abstract complex object shapes while using a small number of primitives which offer a broader geometry coverage and finer details. Then, we introduce a force-driven dynamic fitting and a cycle-consistent re-projection loss to optimize the primitive parameters. Extensive experiments on ShapeNet across various settings show that DeFormer achieves better reconstruction accuracy over the state-of-the-art, and visualizes with consistent semantic correspondences for improved interpretability.

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arXiv2023

Fill the K-Space and Refine the Image: Prompting for Dynamic and Multi-Contrast MRI Reconstruction

The key to dynamic or multi-contrast magnetic resonance imaging (MRI) reconstruction lies in exploring inter-frame or inter-contrast information. Currently, the unrolled model, an approach combining iterative MRI reconstruction steps with learnable neural network layers, stands as the best-performing method for MRI reconstruction. However, there are two main limitations to overcome: firstly, the unrolled model structure and GPU memory constraints restrict the capacity of each denoising block in the network, impeding the effective extraction of detailed features for reconstruction; secondly, the existing model lacks the flexibility to adapt to variations in the input, such as different contrasts, resolutions or views, necessitating the training of separate models for each input type, which is inefficient and may lead to insufficient reconstruction. In this paper, we propose a two-stage MRI reconstruction pipeline to address these limitations. The first stage involves filling the missing k-space data, which we approach as a physics-based reconstruction problem. We first propose a simple yet efficient baseline model, which utilizes adjacent frames/contrasts and channel attention to capture the inherent inter-frame/-contrast correlation. Then, we extend the baseline model to a prompt-based learning approach, PromptMR, for all-in-one MRI reconstruction from different views, contrasts, adjacent types, and acceleration factors. The second stage is to refine the reconstruction from the first stage, which we treat as a general video restoration problem to further fuse features from neighboring frames/contrasts in the image domain. Extensive experiments show that our proposed method significantly outperforms previous state-of-the-art accelerated MRI reconstruction methods.

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arXiv2023

Deep Deformable Models: Learning 3D Shape Abstractions with Part Consistency

The task of shape abstraction with semantic part consistency is challenging due to the complex geometries of natural objects. Recent methods learn to represent an object shape using a set of simple primitives to fit the target. \textcolor{black}{However, in these methods, the primitives used do not always correspond to real parts or lack geometric flexibility for semantic interpretation.} In this paper, we investigate salient and efficient primitive descriptors for accurate shape abstractions, and propose \textit{Deep Deformable Models (DDMs)}. DDM employs global deformations and diffeomorphic local deformations. These properties enable DDM to abstract complex object shapes with significantly fewer primitives that offer broader geometry coverage and finer details. DDM is also capable of learning part-level semantic correspondences due to the differentiable and invertible properties of our primitive deformation. Moreover, DDM learning formulation is based on dynamic and kinematic modeling, which enables joint regularization of each sub-transformation during primitive fitting. Extensive experiments on \textit{ShapeNet} demonstrate that DDM outperforms the state-of-the-art in terms of reconstruction and part consistency by a notable margin.

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arXiv2023

DMCVR: Morphology-Guided Diffusion Model for 3D Cardiac Volume Reconstruction

Accurate 3D cardiac reconstruction from cine magnetic resonance imaging (cMRI) is crucial for improved cardiovascular disease diagnosis and understanding of the heart's motion. However, current cardiac MRI-based reconstruction technology used in clinical settings is 2D with limited through-plane resolution, resulting in low-quality reconstructed cardiac volumes. To better reconstruct 3D cardiac volumes from sparse 2D image stacks, we propose a morphology-guided diffusion model for 3D cardiac volume reconstruction, DMCVR, that synthesizes high-resolution 2D images and corresponding 3D reconstructed volumes. Our method outperforms previous approaches by conditioning the cardiac morphology on the generative model, eliminating the time-consuming iterative optimization process of the latent code, and improving generation quality. The learned latent spaces provide global semantics, local cardiac morphology and details of each 2D cMRI slice with highly interpretable value to reconstruct 3D cardiac shape. Our experiments show that DMCVR is highly effective in several aspects, such as 2D generation and 3D reconstruction performance. With DMCVR, we can produce high-resolution 3D cardiac MRI reconstructions, surpassing current techniques. Our proposed framework has great potential for improving the accuracy of cardiac disease diagnosis and treatment planning. Code can be accessed at https://github.com/hexiaoxiao-cs/DMCVR.

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arXiv2023

Classification of lung cancer subtypes on CT images with synthetic pathological priors

The accurate diagnosis on pathological subtypes for lung cancer is of significant importance for the follow-up treatments and prognosis managements. In this paper, we propose self-generating hybrid feature network (SGHF-Net) for accurately classifying lung cancer subtypes on computed tomography (CT) images. Inspired by studies stating that cross-scale associations exist in the image patterns between the same case's CT images and its pathological images, we innovatively developed a pathological feature synthetic module (PFSM), which quantitatively maps cross-modality associations through deep neural networks, to derive the "gold standard" information contained in the corresponding pathological images from CT images. Additionally, we designed a radiological feature extraction module (RFEM) to directly acquire CT image information and integrated it with the pathological priors under an effective feature fusion framework, enabling the entire classification model to generate more indicative and specific pathologically related features and eventually output more accurate predictions. The superiority of the proposed model lies in its ability to self-generate hybrid features that contain multi-modality image information based on a single-modality input. To evaluate the effectiveness, adaptability, and generalization ability of our model, we performed extensive experiments on a large-scale multi-center dataset (i.e., 829 cases from three hospitals) to compare our model and a series of state-of-the-art (SOTA) classification models. The experimental results demonstrated the superiority of our model for lung cancer subtypes classification with significant accuracy improvements in terms of accuracy (ACC), area under the curve (AUC), and F1 score.

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arXiv2023

Pathology-and-genomics Multimodal Transformer for Survival Outcome Prediction

Survival outcome assessment is challenging and inherently associated with multiple clinical factors (e.g., imaging and genomics biomarkers) in cancer. Enabling multimodal analytics promises to reveal novel predictive patterns of patient outcomes. In this study, we propose a multimodal transformer (PathOmics) integrating pathology and genomics insights into colon-related cancer survival prediction. We emphasize the unsupervised pretraining to capture the intrinsic interaction between tissue microenvironments in gigapixel whole slide images (WSIs) and a wide range of genomics data (e.g., mRNA-sequence, copy number variant, and methylation). After the multimodal knowledge aggregation in pretraining, our task-specific model finetuning could expand the scope of data utility applicable to both multi- and single-modal data (e.g., image- or genomics-only). We evaluate our approach on both TCGA colon and rectum cancer cohorts, showing that the proposed approach is competitive and outperforms state-of-the-art studies. Finally, our approach is desirable to utilize the limited number of finetuned samples towards data-efficient analytics for survival outcome prediction. The code is available at https://github.com/Cassie07/PathOmics.

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arXiv2023

A Critical Analysis of the Limitation of Deep Learning based 3D Dental Mesh Segmentation Methods in Segmenting Partial Scans

Tooth segmentation from intraoral scans is a crucial part of digital dentistry. Many Deep Learning based tooth segmentation algorithms have been developed for this task. In most of the cases, high accuracy has been achieved, although, most of the available tooth segmentation techniques make an implicit restrictive assumption of full jaw model and they report accuracy based on full jaw models. Medically, however, in certain cases, full jaw tooth scan is not required or may not be available. Given this practical issue, it is important to understand the robustness of currently available widely used Deep Learning based tooth segmentation techniques. For this purpose, we applied available segmentation techniques on partial intraoral scans and we discovered that the available deep Learning techniques under-perform drastically. The analysis and comparison presented in this work would help us in understanding the severity of the problem and allow us to develop robust tooth segmentation technique without strong assumption of full jaw model.

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arXiv2023

Dealing With Heterogeneous 3D MR Knee Images: A Federated Few-Shot Learning Method With Dual Knowledge Distillation

Federated Learning has gained popularity among medical institutions since it enables collaborative training between clients (e.g., hospitals) without aggregating data. However, due to the high cost associated with creating annotations, especially for large 3D image datasets, clinical institutions do not have enough supervised data for training locally. Thus, the performance of the collaborative model is subpar under limited supervision. On the other hand, large institutions have the resources to compile data repositories with high-resolution images and labels. Therefore, individual clients can utilize the knowledge acquired in the public data repositories to mitigate the shortage of private annotated images. In this paper, we propose a federated few-shot learning method with dual knowledge distillation. This method allows joint training with limited annotations across clients without jeopardizing privacy. The supervised learning of the proposed method extracts features from limited labeled data in each client, while the unsupervised data is used to distill both feature and response-based knowledge from a national data repository to further improve the accuracy of the collaborative model and reduce the communication cost. Extensive evaluations are conducted on 3D magnetic resonance knee images from a private clinical dataset. Our proposed method shows superior performance and less training time than other semi-supervised federated learning methods. Codes and additional visualization results are available at https://github.com/hexiaoxiao-cs/fedml-knee.

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arXiv2023

A Data-scalable Transformer for Medical Image Segmentation: Architecture, Model Efficiency, and Benchmark

Transformers have demonstrated remarkable performance in natural language processing and computer vision. However, existing vision Transformers struggle to learn from limited medical data and are unable to generalize on diverse medical image tasks. To tackle these challenges, we present MedFormer, a data-scalable Transformer designed for generalizable 3D medical image segmentation. Our approach incorporates three key elements: a desirable inductive bias, hierarchical modeling with linear-complexity attention, and multi-scale feature fusion that integrates spatial and semantic information globally. MedFormer can learn across tiny- to large-scale data without pre-training. Comprehensive experiments demonstrate MedFormer's potential as a versatile segmentation backbone, outperforming CNNs and vision Transformers on seven public datasets covering multiple modalities (e.g., CT and MRI) and various medical targets (e.g., healthy organs, diseased tissues, and tumors). We provide public access to our models and evaluation pipeline, offering solid baselines and unbiased comparisons to advance a wide range of downstream clinical applications.

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arXiv2023

Hierarchically Self-Supervised Transformer for Human Skeleton Representation Learning

Despite the success of fully-supervised human skeleton sequence modeling, utilizing self-supervised pre-training for skeleton sequence representation learning has been an active field because acquiring task-specific skeleton annotations at large scales is difficult. Recent studies focus on learning video-level temporal and discriminative information using contrastive learning, but overlook the hierarchical spatial-temporal nature of human skeletons. Different from such superficial supervision at the video level, we propose a self-supervised hierarchical pre-training scheme incorporated into a hierarchical Transformer-based skeleton sequence encoder (Hi-TRS), to explicitly capture spatial, short-term, and long-term temporal dependencies at frame, clip, and video levels, respectively. To evaluate the proposed self-supervised pre-training scheme with Hi-TRS, we conduct extensive experiments covering three skeleton-based downstream tasks including action recognition, action detection, and motion prediction. Under both supervised and semi-supervised evaluation protocols, our method achieves the state-of-the-art performance. Additionally, we demonstrate that the prior knowledge learned by our model in the pre-training stage has strong transfer capability for different downstream tasks.

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arXiv2023

Revisiting Multimodal Representation in Contrastive Learning: From Patch and Token Embeddings to Finite Discrete Tokens

Contrastive learning-based vision-language pre-training approaches, such as CLIP, have demonstrated great success in many vision-language tasks. These methods achieve cross-modal alignment by encoding a matched image-text pair with similar feature embeddings, which are generated by aggregating information from visual patches and language tokens. However, direct aligning cross-modal information using such representations is challenging, as visual patches and text tokens differ in semantic levels and granularities. To alleviate this issue, we propose a Finite Discrete Tokens (FDT) based multimodal representation. FDT is a set of learnable tokens representing certain visual-semantic concepts. Both images and texts are embedded using shared FDT by first grounding multimodal inputs to FDT space and then aggregating the activated FDT representations. The matched visual and semantic concepts are enforced to be represented by the same set of discrete tokens by a sparse activation constraint. As a result, the granularity gap between the two modalities is reduced. Through both quantitative and qualitative analyses, we demonstrate that using FDT representations in CLIP-style models improves cross-modal alignment and performance in visual recognition and vision-language downstream tasks. Furthermore, we show that our method can learn more comprehensive representations, and the learned FDT capture meaningful cross-modal correspondence, ranging from objects to actions and attributes.

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