pwc-archive/papers-with-abstracts huggingface dataset:
Efficient Multi-disparity Transformer for Light Field Image Super-resolution
Authors: Zeke Zexi Hu, Haodong Chen, Yuk Ying Chung, Xiaoming Chen
Date: 2024-07-22 00:00:00
Tasks: Image Super-Resolution, Super-Resolution

This paper presents the Multi-scale Disparity Transformer (MDT), a novel Transformer tailored for light field image super-resolution (LFSR) that addresses the issues of computational redundancy and disparity entanglement caused by the indiscriminate processing of sub-aperture images inherent in conventional methods. MDT features a multi-branch structure, with each branch utilising independent disparity self-attention (DSA) to target specific disparity ranges, effectively reducing computational complexity and disentangling disparities. Building on this architecture, we present LF-MDTNet, an efficient LFSR network. Experimental results demonstrate that LF-MDTNet outperforms existing state-of-the-art methods by 0.37 dB and 0.41 dB PSNR at the 2x and 4x scales, achieving superior performance with fewer parameters and higher speed.
Hierarchical Homogeneity-Based Superpixel Segmentation: Application to Hyperspectral Image Analysis
Authors: Luciano Carvalho Ayres, Sérgio José Melo de Almeida, José Carlos Moreira Bermudez, Ricardo Augusto Borsoi
Date: 2024-07-22 00:00:00
Tasks: Hyperspectral image analysis, Superpixels

Hyperspectral image (HI) analysis approaches have recently become increasingly complex and sophisticated. Recently, the combination of spectral-spatial information and superpixel techniques have addressed some hyperspectral data issues, such as the higher spatial variability of spectral signatures and dimensionality of the data. However, most existing superpixel approaches do not account for specific HI characteristics resulting from its high spectral dimension. In this work, we propose a multiscale superpixel method that is computationally efficient for processing hyperspectral data. The Simple Linear Iterative Clustering (SLIC) oversegmentation algorithm, on which the technique is based, has been extended hierarchically. Using a novel robust homogeneity testing, the proposed hierarchical approach leads to superpixels of variable sizes but with higher spectral homogeneity when compared to the classical SLIC segmentation. For validation, the proposed homogeneity-based hierarchical method was applied as a preprocessing step in the spectral unmixing and classification tasks carried out using, respectively, the Multiscale sparse Unmixing Algorithm (MUA) and the CNN-Enhanced Graph Convolutional Network (CEGCN) methods. Simulation results with both synthetic and real data show that the technique is competitive with state-of-the-art solutions.
MedEdit: Counterfactual Diffusion-based Image Editing on Brain MRI
Authors: Malek Ben Alaya, Daniel M. Lang, Benedikt Wiestler, Julia A. Schnabel, Cosmin I. Bercea
Date: 2024-07-21 00:00:00
Tasks: counterfactual, Denoising, Image Generation

Denoising diffusion probabilistic models enable high-fidelity image synthesis and editing. In biomedicine, these models facilitate counterfactual image editing, producing pairs of images where one is edited to simulate hypothetical conditions. For example, they can model the progression of specific diseases, such as stroke lesions. However, current image editing techniques often fail to generate realistic biomedical counterfactuals, either by inadequately modeling indirect pathological effects like brain atrophy or by excessively altering the scan, which disrupts correspondence to the original images. Here, we propose MedEdit, a conditional diffusion model for medical image editing. MedEdit induces pathology in specific areas while balancing the modeling of disease effects and preserving the integrity of the original scan. We evaluated MedEdit on the Atlas v2.0 stroke dataset using Frechet Inception Distance and Dice scores, outperforming state-of-the-art diffusion-based methods such as Palette (by 45%) and SDEdit (by 61%). Additionally, clinical evaluations by a board-certified neuroradiologist confirmed that MedEdit generated realistic stroke scans indistinguishable from real ones. We believe this work will enable counterfactual image editing research to further advance the development of realistic and clinically useful imaging tools.
Diffusion Models for Unsupervised Anomaly Detection in Fetal Brain Ultrasound
Authors: Hanna Mykula, Lisa Gasser, Silvia Lobmaier, Julia A. Schnabel, Veronika Zimmer, Cosmin I. Bercea
Date: 2024-07-21 00:00:00
Tasks: Anomaly Detection, Denoising, Diagnostic, Unsupervised Anomaly Detection

Ultrasonography is an essential tool in mid-pregnancy for assessing fetal development, appreciated for its non-invasive and real-time imaging capabilities. Yet, the interpretation of ultrasound images is often complicated by acoustic shadows, speckle noise, and other artifacts that obscure crucial diagnostic details. To address these challenges, our study presents a novel unsupervised anomaly detection framework specifically designed for fetal ultrasound imaging. This framework incorporates gestational age filtering, precise identification of fetal standard planes, and targeted segmentation of brain regions to enhance diagnostic accuracy. Furthermore, we introduce the use of denoising diffusion probabilistic models in this context, marking a significant innovation in detecting previously unrecognized anomalies. We rigorously evaluated the framework using various diffusion-based anomaly detection methods, noise types, and noise levels. Notably, AutoDDPM emerged as the most effective, achieving an area under the precision-recall curve of 79.8\% in detecting anomalies. This advancement holds promise for improving the tools available for nuanced and effective prenatal diagnostics.
Non-Reference Quality Assessment for Medical Imaging: Application to Synthetic Brain MRIs
Authors: Karl Van Eeden Risager, Torkan Gholamalizadeh, Mostafa Mehdipour Ghazi
Date: 2024-07-20 00:00:00
Tasks: Benchmarking, Domain Adaptation

Generating high-quality synthetic data is crucial for addressing challenges in medical imaging, such as domain adaptation, data scarcity, and privacy concerns. Existing image quality metrics often rely on reference images, are tailored for group comparisons, or are intended for 2D natural images, limiting their efficacy in complex domains like medical imaging. This study introduces a novel deep learning-based non-reference approach to assess brain MRI quality by training a 3D ResNet. The network is designed to estimate quality across six distinct artifacts commonly encountered in MRI scans. Additionally, a diffusion model is trained on diverse datasets to generate synthetic 3D images of high fidelity. The approach leverages several datasets for training and comprehensive quality assessment, benchmarking against state-of-the-art metrics for real and synthetic images. Results demonstrate superior performance in accurately estimating distortions and reflecting image quality from multiple perspectives. Notably, the method operates without reference images, indicating its applicability for evaluating deep generative models. Besides, the quality scores in the [0, 1] range provide an intuitive assessment of image quality across heterogeneous datasets. Evaluation of generated images offers detailed insights into specific artifacts, guiding strategies for improving generative models to produce high-quality synthetic images. This study presents the first comprehensive method for assessing the quality of real and synthetic 3D medical images in MRI contexts without reliance on reference images.
Large-vocabulary forensic pathological analyses via prototypical cross-modal contrastive learning
Authors: Chen Shen, Chunfeng Lian, Wanqing Zhang, Fan Wang, Jianhua Zhang, Shuanliang Fan, Xin Wei, Gongji Wang, Kehan Li, Hongshu Mu, Hao Wu, Xinggong Liang, Jianhua Ma, Zhenyuan Wang
Date: 2024-07-20 00:00:00
Tasks: Contrastive Learning, Diagnostic, Language Modeling, Language Modelling, whole slide images

Forensic pathology is critical in determining the cause and manner of death through post-mortem examinations, both macroscopic and microscopic. The field, however, grapples with issues such as outcome variability, laborious processes, and a scarcity of trained professionals. This paper presents SongCi, an innovative visual-language model (VLM) designed specifically for forensic pathology. SongCi utilizes advanced prototypical cross-modal self-supervised contrastive learning to enhance the accuracy, efficiency, and generalizability of forensic analyses. It was pre-trained and evaluated on a comprehensive multi-center dataset, which includes over 16 million high-resolution image patches, 2,228 vision-language pairs of post-mortem whole slide images (WSIs), and corresponding gross key findings, along with 471 distinct diagnostic outcomes. Our findings indicate that SongCi surpasses existing multi-modal AI models in many forensic pathology tasks, performs comparably to experienced forensic pathologists and significantly better than less experienced ones, and provides detailed multi-modal explainability, offering critical assistance in forensic investigations. To the best of our knowledge, SongCi is the first VLM specifically developed for forensic pathological analysis and the first large-vocabulary computational pathology (CPath) model that directly processes gigapixel WSIs in forensic science.
MedMAE: A Self-Supervised Backbone for Medical Imaging Tasks
Authors: Anubhav Gupta, Islam Osman, Mohamed S. Shehata, John W. Braun
Date: 2024-07-20 00:00:00
Tasks: Self-Supervised Learning

Medical imaging tasks are very challenging due to the lack of publicly available labeled datasets. Hence, it is difficult to achieve high performance with existing deep-learning models as they require a massive labeled dataset to be trained effectively. An alternative solution is to use pre-trained models and fine-tune them using the medical imaging dataset. However, all existing models are pre-trained using natural images, which is a completely different domain from that of medical imaging, which leads to poor performance due to domain shift. To overcome these problems, we propose a large-scale unlabeled dataset of medical images and a backbone pre-trained using the proposed dataset with a self-supervised learning technique called Masked autoencoder. This backbone can be used as a pre-trained model for any medical imaging task, as it is trained to learn a visual representation of different types of medical images. To evaluate the performance of the proposed backbone, we used four different medical imaging tasks. The results are compared with existing pre-trained models. These experiments show the superiority of our proposed backbone in medical imaging tasks.
Representing Topological Self-Similarity Using Fractal Feature Maps for Accurate Segmentation of Tubular Structures
Authors: Jiaxing Huang, Yanfeng Zhou, Yaoru Luo, Guole Liu, Heng Guo, Ge Yang
Date: 2024-07-20 00:00:00
Tasks: Decoder, Segmentation

Accurate segmentation of long and thin tubular structures is required in a wide variety of areas such as biology, medicine, and remote sensing. The complex topology and geometry of such structures often pose significant technical challenges. A fundamental property of such structures is their topological self-similarity, which can be quantified by fractal features such as fractal dimension (FD). In this study, we incorporate fractal features into a deep learning model by extending FD to the pixel-level using a sliding window technique. The resulting fractal feature maps (FFMs) are then incorporated as additional input to the model and additional weight in the loss function to enhance segmentation performance by utilizing the topological self-similarity. Moreover, we extend the U-Net architecture by incorporating an edge decoder and a skeleton decoder to improve boundary accuracy and skeletal continuity of segmentation, respectively. Extensive experiments on five tubular structure datasets validate the effectiveness and robustness of our approach. Furthermore, the integration of FFMs with other popular segmentation models such as HR-Net also yields performance enhancement, suggesting FFM can be incorporated as a plug-in module with different model architectures. Code and data are openly accessible at https://github.com/cbmi-group/FFM-Multi-Decoder-Network.
Universal Medical Imaging Model for Domain Generalization with Data Privacy
Authors: Ahmed Radwan, Islam Osman, Mohamed S. Shehata
Date: 2024-07-20 00:00:00
Tasks: Domain Generalization, Federated Learning

Achieving domain generalization in medical imaging poses a significant challenge, primarily due to the limited availability of publicly labeled datasets in this domain. This limitation arises from concerns related to data privacy and the necessity for medical expertise to accurately label the data. In this paper, we propose a federated learning approach to transfer knowledge from multiple local models to a global model, eliminating the need for direct access to the local datasets used to train each model. The primary objective is to train a global model capable of performing a wide variety of medical imaging tasks. This is done while ensuring the confidentiality of the private datasets utilized during the training of these models. To validate the effectiveness of our approach, extensive experiments were conducted on eight datasets, each corresponding to a different medical imaging application. The client's data distribution in our experiments varies significantly as they originate from diverse domains. Despite this variation, we demonstrate a statistically significant improvement over a state-of-the-art baseline utilizing masked image modeling over a diverse pre-training dataset that spans different body parts and scanning types. This improvement is achieved by curating information learned from clients without accessing any labeled dataset on the server.
Improving Representation of High-frequency Components for Medical Visual Foundation Models
Authors: Yuetan Chu, Yilan Zhang, Zhongyi Han, Changchun Yang, Longxi Zhou, Gongning Luo, Chao Huang, Xin Gao
Date: 2024-07-19 00:00:00
Tasks: Lung Nodule Detection

Foundation models have recently attracted significant attention for their impressive generalizability across diverse downstream tasks. However, these models are demonstrated to exhibit great limitations in representing high-frequency components and fine-grained details. In many medical imaging tasks, the precise representation of such information is crucial due to the inherently intricate anatomical structures, sub-visual features, and complex boundaries involved. Consequently, the limited representation of prevalent foundation models can result in significant performance degradation or even failure in these tasks. To address these challenges, we propose a novel pretraining strategy, named Frequency-advanced Representation Autoencoder (Frepa). Through high-frequency masking and low-frequency perturbation combined with adversarial learning, Frepa encourages the encoder to effectively represent and preserve high-frequency components in the image embeddings. Additionally, we introduce an innovative histogram-equalized image masking strategy, extending the Masked Autoencoder approach beyond ViT to other architectures such as Swin Transformer and convolutional networks. We develop Frepa across nine medical modalities and validate it on 32 downstream tasks for both 2D images and 3D volume data. Without fine-tuning, Frepa can outperform other self-supervised pretraining methods and, in some cases, even surpasses task-specific trained models. This improvement is particularly significant for tasks involving fine-grained details, such as achieving up to a +15% increase in DSC for retina vessel segmentation and a +7% increase in IoU for lung nodule detection. Further experiments quantitatively reveal that Frepa enables superior high-frequency representations and preservation in the embeddings, underscoring its potential for developing more generalized and universal medical image foundation models.
DeepCA: Deep Learning-based 3D Coronary Artery Tree Reconstruction from Two 2D Non-simultaneous X-ray Angiography Projections
Authors: Yiying Wang, Abhirup Banerjee, Robin P. Choudhury, Vicente Grau
Date: 2024-07-19 00:00:00
Tasks: 3D geometry, Generative Adversarial Network

Cardiovascular diseases (CVDs) are the most common cause of death worldwide. Invasive x-ray coronary angiography (ICA) is one of the most important imaging modalities for the diagnosis of CVDs. ICA typically acquires only two 2D projections, which makes the 3D geometry of coronary vessels difficult to interpret, thus requiring 3D coronary artery tree reconstruction from two projections. State-of-the-art approaches require significant manual interactions and cannot correct the non-rigid cardiac and respiratory motions between non-simultaneous projections. In this study, we propose a novel deep learning pipeline named \emph{DeepCA}. We leverage the Wasserstein conditional generative adversarial network with gradient penalty, latent convolutional transformer layers, and a dynamic snake convolutional critic to implicitly compensate for the non-rigid motion and provide 3D coronary artery tree reconstruction. Through simulating projections from coronary computed tomography angiography (CCTA), we achieve the generalisation of 3D coronary tree reconstruction on real non-simultaneous ICA projections. We incorporate an application-specific evaluation metric to validate our proposed model on both a CCTA dataset and a real ICA dataset, together with Chamfer $\ell_2$ distance. The results demonstrate promising performance of our DeepCA model in vessel topology preservation, recovery of missing features, and generalisation ability to real ICA data. To the best of our knowledge, this is the first study that leverages deep learning to achieve 3D coronary tree reconstruction from two real non-simultaneous x-ray angiographic projections.
Segmentation of Brain Metastases in MRI: A Two-Stage Deep Learning Approach with Modality Impact Study
Authors: Yousef Sadegheih, Dorit Merhof
Date: 2024-07-19 00:00:00
Tasks: Segmentation

Brain metastasis segmentation poses a significant challenge in medical imaging due to the complex presentation and variability in size and location of metastases. In this study, we first investigate the impact of different imaging modalities on segmentation performance using a 3D U-Net. Through a comprehensive analysis, we determine that combining all available modalities does not necessarily enhance performance. Instead, the combination of T1-weighted with contrast enhancement (T1c), T1-weighted (T1), and FLAIR modalities yields superior results. Building on these findings, we propose a two-stage detection and segmentation model specifically designed to accurately segment brain metastases. Our approach demonstrates that leveraging three key modalities (T1c, T1, and FLAIR) achieves significantly higher accuracy compared to single-pass deep learning models. This targeted combination allows for precise segmentation, capturing even small metastases that other models often miss. Our model sets a new benchmark in brain metastasis segmentation, highlighting the importance of strategic modality selection and multi-stage processing in medical imaging. Our implementation is freely accessible to the research community on \href{https://github.com/xmindflow/Met-Seg}{GitHub}.
Semantic Communications for 3D Human Face Transmission with Neural Radiance Fields
Authors: Guanlin Wu, Zhonghao Lyu, Juyong Zhang, Jie Xu
Date: 2024-07-19 00:00:00
Tasks: Face Model, NeRF

This paper investigates the transmission of three-dimensional (3D) human face content for immersive communication over a rate-constrained transmitter-receiver link. We propose a new framework named NeRF-SeCom, which leverages neural radiance fields (NeRF) and semantic communications to improve the quality of 3D visualizations while minimizing the communication overhead. In the NeRF-SeCom framework, we first train a NeRF face model based on the NeRFBlendShape method, which is pre-shared between the transmitter and receiver as the semantic knowledge base to facilitate the real-time transmission. Next, with knowledge base, the transmitter extracts and sends only the essential semantic features for the receiver to reconstruct 3D face in real time. To optimize the transmission efficiency, we classify the expression features into static and dynamic types. Over each video chunk, static features are transmitted once for all frames, whereas dynamic features are transmitted over a portion of frames to adhere to rate constraints. Additionally, we propose a feature prediction mechanism, which allows the receiver to predict the dynamic features for frames that are not transmitted. Experiments show that our proposed NeRF-SeCom framework significantly outperforms benchmark methods in delivering high-quality 3D visualizations of human faces.
APS-USCT: Ultrasound Computed Tomography on Sparse Data via AI-Physic Synergy
Authors: Yi Sheng, Hanchen Wang, Yipei Liu, Junhuan Yang, Weiwen Jiang, Youzuo Lin, Lei Yang
Date: 2024-07-18 00:00:00
Tasks: Decoder, Image Reconstruction, SSIM

Ultrasound computed tomography (USCT) is a promising technique that achieves superior medical imaging reconstruction resolution by fully leveraging waveform information, outperforming conventional ultrasound methods. Despite its advantages, high-quality USCT reconstruction relies on extensive data acquisition by a large number of transducers, leading to increased costs, computational demands, extended patient scanning times, and manufacturing complexities. To mitigate these issues, we propose a new USCT method called APS-USCT, which facilitates imaging with sparse data, substantially reducing dependence on high-cost dense data acquisition. Our APS-USCT method consists of two primary components: APS-wave and APS-FWI. The APS-wave component, an encoder-decoder system, preprocesses the waveform data, converting sparse data into dense waveforms to augment sample density prior to reconstruction. The APS-FWI component, utilizing the InversionNet, directly reconstructs the speed of sound (SOS) from the ultrasound waveform data. We further improve the model's performance by incorporating Squeeze-and-Excitation (SE) Blocks and source encoding techniques. Testing our method on a breast cancer dataset yielded promising results. It demonstrated outstanding performance with an average Structural Similarity Index (SSIM) of 0.8431. Notably, over 82% of samples achieved an SSIM above 0.8, with nearly 61% exceeding 0.85, highlighting the significant potential of our approach in improving USCT image reconstruction by efficiently utilizing sparse data.