pwc-archive/papers-with-abstracts huggingface dataset:
Is an Ultra Large Natural Image-Based Foundation Model Superior to a Retina-Specific Model for Detecting Ocular and Systemic Diseases?
Authors: Qingshan Hou, Yukun Zhou, Jocelyn Hui Lin Goh, Ke Zou, Samantha Min Er Yew, Sahana Srinivasan, Meng Wang, Thaddaeus Lo, Xiaofeng Lei, Siegfried K. Wagner, Mark A. Chia, Dawei Yang, Hongyang Jiang, Anran Ran, Rui Santos, Gabor Mark Somfai, Juan Helen Zhou, Haoyu Chen, Qingyu Chen, Carol Yim-Lui Cheung, Pearse A. Keane, Yih Chung Tham
Date: 2025-02-10 00:00:00
Tasks: Disease Prediction

The advent of foundation models (FMs) is transforming medical domain. In ophthalmology, RETFound, a retina-specific FM pre-trained sequentially on 1.4 million natural images and 1.6 million retinal images, has demonstrated high adaptability across clinical applications. Conversely, DINOv2, a general-purpose vision FM pre-trained on 142 million natural images, has shown promise in non-medical domains. However, its applicability to clinical tasks remains underexplored. To address this, we conducted head-to-head evaluations by fine-tuning RETFound and three DINOv2 models (large, base, small) for ocular disease detection and systemic disease prediction tasks, across eight standardized open-source ocular datasets, as well as the Moorfields AlzEye and the UK Biobank datasets. DINOv2-large model outperformed RETFound in detecting diabetic retinopathy (AUROC=0.850-0.952 vs 0.823-0.944, across three datasets, all P<=0.007) and multi-class eye diseases (AUROC=0.892 vs. 0.846, P<0.001). In glaucoma, DINOv2-base model outperformed RETFound (AUROC=0.958 vs 0.940, P<0.001). Conversely, RETFound achieved superior performance over all DINOv2 models in predicting heart failure, myocardial infarction, and ischaemic stroke (AUROC=0.732-0.796 vs 0.663-0.771, all P<0.001). These trends persisted even with 10% of the fine-tuning data. These findings showcase the distinct scenarios where general-purpose and domain-specific FMs excel, highlighting the importance of aligning FM selection with task-specific requirements to optimise clinical performance.
A Data-Efficient Pan-Tumor Foundation Model for Oncology CT Interpretation
Authors: Wenhui Lei, HanYu Chen, Zitian Zhang, Luyang Luo, Qiong Xiao, Yannian Gu, Peng Gao, Yankai Jiang, Ci Wang, Guangtao Wu, Tongjia Xu, Yingjie Zhang, Xiaofan Zhang, Pranav Rajpurkar, Shaoting Zhang, Zhenning Wang
Date: 2025-02-10 00:00:00
Tasks: Lesion Segmentation, Structured Report Generation, Survival Prediction, Transfer Learning

Artificial intelligence-assisted imaging analysis has made substantial strides in tumor diagnosis and management. Here we present PASTA, a pan-tumor CT foundation model that achieves state-of-the-art performance on 45 of 46 representative oncology tasks -- including lesion segmentation, tumor detection in plain CT, tumor staging, survival prediction, structured report generation, and cross-modality transfer learning, significantly outperforming the second-best models on 35 tasks. This remarkable advancement is driven by our development of PASTA-Gen, an innovative synthetic tumor generation framework that produces a comprehensive dataset of 30,000 CT scans with pixel-level annotated lesions and paired structured reports, encompassing malignancies across ten organs and five benign lesion types. By leveraging this rich, high-quality synthetic data, we overcome a longstanding bottleneck in the development of CT foundation models -- specifically, the scarcity of publicly available, high-quality annotated datasets due to privacy constraints and the substantial labor required for scaling precise data annotation. Encouragingly, PASTA demonstrates exceptional data efficiency with promising practical value, markedly improving performance on various tasks with only a small amount of real-world data. The open release of both the synthetic dataset and PASTA foundation model effectively addresses the challenge of data scarcity, thereby advancing oncological research and clinical translation.
Multi-modal Data Fusion and Deep Ensemble Learning for Accurate Crop Yield Prediction
Authors: Akshay Dagadu Yewle, Laman Mirzayeva, Oktay Karakuş
Date: 2025-02-09 00:00:00
Tasks: Crop Yield Prediction, Ensemble Learning

This study introduces RicEns-Net, a novel Deep Ensemble model designed to predict crop yields by integrating diverse data sources through multimodal data fusion techniques. The research focuses specifically on the use of synthetic aperture radar (SAR), optical remote sensing data from Sentinel 1, 2, and 3 satellites, and meteorological measurements such as surface temperature and rainfall. The initial field data for the study were acquired through Ernst & Young's (EY) Open Science Challenge 2023. The primary objective is to enhance the precision of crop yield prediction by developing a machine-learning framework capable of handling complex environmental data. A comprehensive data engineering process was employed to select the most informative features from over 100 potential predictors, reducing the set to 15 features from 5 distinct modalities. This step mitigates the ``curse of dimensionality" and enhances model performance. The RicEns-Net architecture combines multiple machine learning algorithms in a deep ensemble framework, integrating the strengths of each technique to improve predictive accuracy. Experimental results demonstrate that RicEns-Net achieves a mean absolute error (MAE) of 341 kg/Ha (roughly corresponds to 5-6\% of the lowest average yield in the region), significantly exceeding the performance of previous state-of-the-art models, including those developed during the EY challenge.
A Generative Framework for Bidirectional Image-Report Understanding in Chest Radiography
Authors: Nicholas Evans, Stephen Baker, Miles Reed
Date: 2025-02-09 00:00:00
Tasks: Diagnostic, Multimodal Reasoning

The rapid advancements in large language models (LLMs) have unlocked their potential for multimodal tasks, where text and visual data are processed jointly. However, applying LLMs to medical imaging, particularly for chest X-rays (CXR), poses significant challenges due to the need for precise visual-textual alignment and the preservation of critical diagnostic details. In this paper, we propose Multi-Stage Adaptive Vision-Language Tuning (MAViLT), a novel framework designed to enhance multimodal reasoning and generation for CXR understanding. MAViLT incorporates a clinical gradient-weighted tokenization process and a hierarchical fine-tuning strategy, enabling it to generate accurate radiology reports, synthesize realistic CXRs from text, and answer vision-based clinical questions. We evaluate MAViLT on two benchmark datasets, MIMIC-CXR and Indiana University CXR, achieving state-of-the-art results across all tasks. Human evaluations further validate the clinical relevance and utility of MAViLT, making it a robust tool for real-world medical applications. This work demonstrates the feasibility of leveraging LLMs for multimodal medical imaging while addressing key challenges in vision-language integration.
Inverse Problem Sampling in Latent Space Using Sequential Monte Carlo
Authors: Idan Achituve, Hai Victor Habi, Amir Rosenfeld, Arnon Netzer, Idit Diamant, Ethan Fetaya
Date: 2025-02-09 00:00:00
Tasks: Decoder

In image processing, solving inverse problems is the task of finding plausible reconstructions of an image that was corrupted by some (usually known) degradation operator. Commonly, this process is done using a generative image model that can guide the reconstruction towards solutions that appear natural. The success of diffusion models over the last few years has made them a leading candidate for this task. However, the sequential nature of diffusion models makes this conditional sampling process challenging. Furthermore, since diffusion models are often defined in the latent space of an autoencoder, the encoder-decoder transformations introduce additional difficulties. To address these challenges, we suggest a novel sampling method based on sequential Monte Carlo (SMC) in the latent space of diffusion models. We name our method LD-SMC. We define a generative model for the data using additional auxiliary observations and perform posterior inference with SMC sampling based on a backward diffusion process. Empirical evaluations on ImageNet and FFHQ show the benefits of LD-SMC over competing methods in various inverse problem tasks and especially in challenging inpainting tasks.
A Comprehensive Review of U-Net and Its Variants: Advances and Applications in Medical Image Segmentation
Authors: Wang Jiangtao, Nur Intan Raihana Ruhaiyem, Fu Panpan
Date: 2025-02-09 00:00:00
Tasks: Image Segmentation, Medical Image Segmentation, Segmentation, Semantic Segmentation

Medical images often exhibit low and blurred contrast between lesions and surrounding tissues, with considerable variation in lesion edges and shapes even within the same disease, leading to significant challenges in segmentation. Therefore, precise segmentation of lesions has become an essential prerequisite for patient condition assessment and formulation of treatment plans. Significant achievements have been made in research related to the U-Net model in recent years. It improves segmentation performance and is extensively applied in the semantic segmentation of medical images to offer technical support for consistent quantitative lesion analysis methods. First, this paper classifies medical image datasets on the basis of their imaging modalities and then examines U-Net and its various improvement models from the perspective of structural modifications. The research objectives, innovative designs, and limitations of each approach are discussed in detail. Second, we summarize the four central improvement mechanisms of the U-Net and U-Net variant algorithms: the jump-connection mechanism, residual-connection mechanism, 3D-UNet, and transformer mechanism. Finally, we examine the relationships among the four core enhancement mechanisms and commonly utilized medical datasets and propose potential avenues and strategies for future advancements. This paper provides a systematic summary and reference for researchers in related fields, and we look forward to designing more efficient and stable medical image segmentation network models based on the U-Net network.
Image-Based Alzheimer's Disease Detection Using Pretrained Convolutional Neural Network Models
Authors: Nasser A Alsadhan
Date: 2025-02-09 00:00:00
Tasks: Alzheimer's Disease Detection

Alzheimer's disease is an untreatable, progressive brain disorder that slowly robs people of their memory, thinking abilities, and ultimately their capacity to complete even the most basic tasks. Among older adults, it is the most frequent cause of dementia. Although there is presently no treatment for Alzheimer's disease, scientific trials are ongoing to discover drugs to combat the condition. Treatments to slow the signs of dementia are also available. Many researchers throughout the world became interested in developing computer-aided diagnosis systems to aid in the early identification of this deadly disease and assure an accurate diagnosis. In particular, image based approaches have been coupled with machine learning techniques to address the challenges of Alzheimer's disease detection. This study proposes a computer aided diagnosis system to detect Alzheimer's disease from biomarkers captured using neuroimaging techniques. The proposed approach relies on deep learning techniques to extract the relevant visual features from the image collection to accurately predict the Alzheimer's class value. In the experiments, standard datasets and pre-trained deep learning models were investigated. Moreover, standard performance measures were used to assess the models' performances. The obtained results proved that VGG16-based models outperform the state of the art performance.
4D VQ-GAN: Synthesising Medical Scans at Any Time Point for Personalised Disease Progression Modelling of Idiopathic Pulmonary Fibrosis
Authors: An Zhao, MouCheng Xu, Ahmed H. Shahin, Wim Wuyts, Mark G. Jones, Joseph Jacob, Daniel C. Alexander
Date: 2025-02-08 00:00:00
Tasks: Computed Tomography (CT), Diagnostic, Prognosis, Survival Analysis

Understanding the progression trajectories of diseases is crucial for early diagnosis and effective treatment planning. This is especially vital for life-threatening conditions such as Idiopathic Pulmonary Fibrosis (IPF), a chronic, progressive lung disease with a prognosis comparable to many cancers. Computed tomography (CT) imaging has been established as a reliable diagnostic tool for IPF. Accurately predicting future CT scans of early-stage IPF patients can aid in developing better treatment strategies, thereby improving survival outcomes. In this paper, we propose 4D Vector Quantised Generative Adversarial Networks (4D-VQ-GAN), a model capable of generating realistic CT volumes of IPF patients at any time point. The model is trained using a two-stage approach. In the first stage, a 3D-VQ-GAN is trained to reconstruct CT volumes. In the second stage, a Neural Ordinary Differential Equation (ODE) based temporal model is trained to capture the temporal dynamics of the quantised embeddings generated by the encoder in the first stage. We evaluate different configurations of our model for generating longitudinal CT scans and compare the results against ground truth data, both quantitatively and qualitatively. For validation, we conduct survival analysis using imaging biomarkers derived from generated CT scans and achieve a C-index comparable to that of biomarkers derived from the real CT scans. The survival analysis results demonstrate the potential clinical utility inherent to generated longitudinal CT scans, showing that they can reliably predict survival outcomes.
Unsupervised Self-Prior Embedding Neural Representation for Iterative Sparse-View CT Reconstruction
Authors: Xuanyu Tian, Lixuan Chen, Qing Wu, Chenhe Du, Jingjing Shi, Hongjiang Wei, Yuyao Zhang
Date: 2025-02-08 00:00:00
Tasks: CT Reconstruction

Emerging unsupervised implicit neural representation (INR) methods, such as NeRP, NeAT, and SCOPE, have shown great potential to address sparse-view computed tomography (SVCT) inverse problems. Although these INR-based methods perform well in relatively dense SVCT reconstructions, they struggle to achieve comparable performance to supervised methods in sparser SVCT scenarios. They are prone to being affected by noise, limiting their applicability in real clinical settings. Additionally, current methods have not fully explored the use of image domain priors for solving SVCsT inverse problems. In this work, we demonstrate that imperfect reconstruction results can provide effective image domain priors for INRs to enhance performance. To leverage this, we introduce Self-prior embedding neural representation (Spener), a novel unsupervised method for SVCT reconstruction that integrates iterative reconstruction algorithms. During each iteration, Spener extracts local image prior features from the previous iteration and embeds them to constrain the solution space. Experimental results on multiple CT datasets show that our unsupervised Spener method achieves performance comparable to supervised state-of-the-art (SOTA) methods on in-domain data while outperforming them on out-of-domain datasets. Moreover, Spener significantly improves the performance of INR-based methods in handling SVCT with noisy sinograms. Our code is available at https://github.com/MeijiTian/Spener.
Diverse Image Generation with Diffusion Models and Cross Class Label Learning for Polyp Classification
Authors: Vanshali Sharma, Debesh Jha, M. K. Bhuyan, Pradip K. Das, Ulas Bagci
Date: 2025-02-08 00:00:00
Tasks: Image Generation, Medical Procedure

Pathologic diagnosis is a critical phase in deciding the optimal treatment procedure for dealing with colorectal cancer (CRC). Colonic polyps, precursors to CRC, can pathologically be classified into two major types: adenomatous and hyperplastic. For precise classification and early diagnosis of such polyps, the medical procedure of colonoscopy has been widely adopted paired with various imaging techniques, including narrow band imaging and white light imaging. However, the existing classification techniques mainly rely on a single imaging modality and show limited performance due to data scarcity. Recently, generative artificial intelligence has been gaining prominence in overcoming such issues. Additionally, various generation-controlling mechanisms using text prompts and images have been introduced to obtain visually appealing and desired outcomes. However, such mechanisms require class labels to make the model respond efficiently to the provided control input. In the colonoscopy domain, such controlling mechanisms are rarely explored; specifically, the text prompt is a completely uninvestigated area. Moreover, the unavailability of expensive class-wise labels for diverse sets of images limits such explorations. Therefore, we develop a novel model, PathoPolyp-Diff, that generates text-controlled synthetic images with diverse characteristics in terms of pathology, imaging modalities, and quality. We introduce cross-class label learning to make the model learn features from other classes, reducing the burdensome task of data annotation. The experimental results report an improvement of up to 7.91% in balanced accuracy using a publicly available dataset. Moreover, cross-class label learning achieves a statistically significant improvement of up to 18.33% in balanced accuracy during video-level analysis. The code is available at https://github.com/Vanshali/PathoPolyp-Diff.
A Novel Convolutional-Free Method for 3D Medical Imaging Segmentation
Authors: Canxuan Gang
Date: 2025-02-08 00:00:00
Tasks: 3D Medical Imaging Segmentation, Domain Adaptation, Image Segmentation, Medical Image Segmentation, Segmentation, Semantic Segmentation

Segmentation of 3D medical images is a critical task for accurate diagnosis and treatment planning. Convolutional neural networks (CNNs) have dominated the field, achieving significant success in 3D medical image segmentation. However, CNNs struggle with capturing long-range dependencies and global context, limiting their performance, particularly for fine and complex structures. Recent transformer-based models, such as TransUNet and nnFormer, have demonstrated promise in addressing these limitations, though they still rely on hybrid CNN-transformer architectures. This paper introduces a novel, fully convolutional-free model based on transformer architecture and self-attention mechanisms for 3D medical image segmentation. Our approach focuses on improving multi-semantic segmentation accuracy and addressing domain adaptation challenges between thick and thin slice CT images. We propose a joint loss function that facilitates effective segmentation of thin slices based on thick slice annotations, overcoming limitations in dataset availability. Furthermore, we present a benchmark dataset for multi-semantic segmentation on thin slices, addressing a gap in current medical imaging research. Our experiments demonstrate the superiority of the proposed model over traditional and hybrid architectures, offering new insights into the future of convolution-free medical image segmentation.
Multi-Class Segmentation of Aortic Branches and Zones in Computed Tomography Angiography: The AortaSeg24 Challenge
Authors: Muhammad Imran, Jonathan R. Krebs, Vishal Balaji Sivaraman, Teng Zhang, Amarjeet Kumar, Walker R. Ueland, Michael J. Fassler, Jinlong Huang, Xiao Sun, Lisheng Wang, Pengcheng Shi, Maximilian Rokuss, Michael Baumgartner, Yannick Kirchhof, Klaus H. Maier-Hein, Fabian Isensee, Shuolin Liu, Bing Han, Bong Thanh Nguyen, Dong-Jin Shin, Park Ji-Woo, Mathew Choi, Kwang-Hyun Uhm, Sung-Jea Ko, Chanwoong Lee, Jaehee Chun, Jin Sung Kim, Minghui Zhang, Hanxiao Zhang, Xin You, Yun Gu, Zhaohong Pan, Xuan Liu, Xiaokun Liang, Markus Tiefenthaler, Enrique Almar-Munoz, Matthias Schwab, Mikhail Kotyushev, Rostislav Epifanov, Marek Wodzinski, Henning Muller, Abdul Qayyum, Moona Mazher, Steven A. Niederer, Zhiwei Wang, Kaixiang Yang, Jintao Ren, Stine Sofia Korreman, Yuchong Gao, Hongye Zeng, Haoyu Zheng, Rui Zheng, Jinghua Yue, Fugen Zhou, Bo Liu, Alexander Cosman, Muxuan Liang, Chang Zhao, Gilbert R. Upchurch Jr., Jun Ma, Yuyin Zhou, Michol A. Cooper, Wei Shao
Date: 2025-02-07 00:00:00
Tasks: Data Augmentation, Segmentation

Multi-class segmentation of the aorta in computed tomography angiography (CTA) scans is essential for diagnosing and planning complex endovascular treatments for patients with aortic dissections. However, existing methods reduce aortic segmentation to a binary problem, limiting their ability to measure diameters across different branches and zones. Furthermore, no open-source dataset is currently available to support the development of multi-class aortic segmentation methods. To address this gap, we organized the AortaSeg24 MICCAI Challenge, introducing the first dataset of 100 CTA volumes annotated for 23 clinically relevant aortic branches and zones. This dataset was designed to facilitate both model development and validation. The challenge attracted 121 teams worldwide, with participants leveraging state-of-the-art frameworks such as nnU-Net and exploring novel techniques, including cascaded models, data augmentation strategies, and custom loss functions. We evaluated the submitted algorithms using the Dice Similarity Coefficient (DSC) and Normalized Surface Distance (NSD), highlighting the approaches adopted by the top five performing teams. This paper presents the challenge design, dataset details, evaluation metrics, and an in-depth analysis of the top-performing algorithms. The annotated dataset, evaluation code, and implementations of the leading methods are publicly available to support further research. All resources can be accessed at https://aortaseg24.grand-challenge.org.
CoRPA: Adversarial Image Generation for Chest X-rays Using Concept Vector Perturbations and Generative Models
Authors: Amy Rafferty, Rishi Ramaesh, Ajitha Rajan
Date: 2025-02-04 00:00:00
Tasks: Adversarial Attack, Diagnostic, image-classification, Image Classification, Image Generation, Medical Image Classification

Deep learning models for medical image classification tasks are becoming widely implemented in AI-assisted diagnostic tools, aiming to enhance diagnostic accuracy, reduce clinician workloads, and improve patient outcomes. However, their vulnerability to adversarial attacks poses significant risks to patient safety. Current attack methodologies use general techniques such as model querying or pixel value perturbations to generate adversarial examples designed to fool a model. These approaches may not adequately address the unique characteristics of clinical errors stemming from missed or incorrectly identified clinical features. We propose the Concept-based Report Perturbation Attack (CoRPA), a clinically-focused black-box adversarial attack framework tailored to the medical imaging domain. CoRPA leverages clinical concepts to generate adversarial radiological reports and images that closely mirror realistic clinical misdiagnosis scenarios. We demonstrate the utility of CoRPA using the MIMIC-CXR-JPG dataset of chest X-rays and radiological reports. Our evaluation reveals that deep learning models exhibiting strong resilience to conventional adversarial attacks are significantly less robust when subjected to CoRPA's clinically-focused perturbations. This underscores the importance of addressing domain-specific vulnerabilities in medical AI systems. By introducing a specialized adversarial attack framework, this study provides a foundation for developing robust, real-world-ready AI models in healthcare, ensuring their safe and reliable deployment in high-stakes clinical environments.