arXiv subjects

Hayit Greenspan

Publications and source records attributed to Hayit Greenspan.

At least 19 recordsLinked to original sources

arXiv2026

SymmAdapt: Symmetrical Flow Matching for Source-Free Domain Adaptation in Medical Image Segmentation

Domain shift across imaging modalities and acquisition sites remains a significant barrier to the clinical deployment of segmentation models. Source-free unsupervised domain adaptation (SFUDA) addresses this by adapting a pretrained model to an unlabeled target domain without requiring access to sensitive source data. We introduce a novel SFUDA framework built on Symmetrical Flow Matching, a unified generative model that segments an input image and synthesizes a source-like image from a mask within the same learned flow. By initializing inference from a domain-agnostic Gaussian origin, the model preserves structural consistency across domains and grounds predictions in learned anatomy rather than shifted texture statistics. Our pipeline leverages this symmetry to generate reliable pseudo-labels and corresponding source-like synthetic images from unlabeled target data, creating a generative replay buffer that anchors source knowledge during a generative self-training stage that fine-tunes on a joint set of real target and synthetic source-like images. We evaluate on abdominal multi-organ and cardiac segmentation, covering cross-modality MRI<->CT shifts, and multi-site prostate segmentation. Our approach outperforms SFUDA baselines and is competitive with conventional UDA methods.

cs.CV↗

arXiv2026

DiffuSAM: Diffusion-Based Prompt-Free SAM2 for Few-Shot and Source-Free Medical Image Segmentation

Segmentation models such as Segment Anything Model (SAM) and SAM2 achieve strong prompt-driven zero-shot performance. However, their training on natural images limits domain transfer to medical data. Consequently, accurate segmentation typically requires extensive fine-tuning and expert-designed prompts. We propose DiffuSAM, a diffusion-based adaptation of SAM2 for prompt-free medical image segmentation. Our framework synthesizes SAM2-compatible segmentation mask-like embeddings via a lightweight diffusion-prior from off-the-shelf frozen SAM2 image features. The generated embeddings are integrated into SAM2's mask decoder to produce accurate segmentations, thereby eliminating the need for user prompts. The diffusion prior is further conditioned on previously segmented slices, enforcing spatial consistency across volumes. Evaluated on the BTCV and CHAOS datasets for CT and MRI under Source-Free Unsupervised Domain Adaptation (SF-UDA) and Few-Shot settings, DiffuSAM achieves competitive performance with efficient training and inference. Code is available upon request from the corresponding author.

cs.CV↗

arXiv2026

Anatomical Token Uncertainty for Transformer-Guided Active MRI Acquisition

Full data acquisition in MRI is inherently slow, which limits clinical throughput and increases patient discomfort. Compressed Sensing MRI (CS-MRI) seeks to accelerate acquisition by reconstructing images from under-sampled k-space data, requiring both an optimal sampling trajectory and a high-fidelity reconstruction model. In this work, we propose a novel active sampling framework that leverages the inherent discrete structure of a pretrained medical image tokenizer and a latent transformer. By representing anatomy through a dictionary of quantized visual tokens, the model provides a well-defined probability distribution over the latent space. We utilize this distribution to derive a principled uncertainty measure via token entropy, which guides the active sampling process. We introduce two strategies to exploit this latent uncertainty: (1) Latent Entropy Selection (LES), projecting patch-wise token entropy into the $k$-space domain to identify informative sampling lines, and (2) Gradient-based Entropy Optimization (GEO), which identifies regions of maximum uncertainty reduction via the $k$-space gradient of a total latent entropy loss. We evaluate our framework on the fastMRI singlecoil Knee and Brain datasets at $\times 8$ and $\times 16$ acceleration. Our results demonstrate that our active policies outperform state-of-the-art baselines in perceptual metrics, and feature-based distances. Our code is available at https://github.com/levayz/TRUST-MRI.

cs.CV↗

arXiv2024

ProtoSAM: One-Shot Medical Image Segmentation With Foundational Models

This work introduces a new framework, ProtoSAM, for one-shot medical image segmentation. It combines the use of prototypical networks, known for few-shot segmentation, with SAM - a natural image foundation model. The method proposed creates an initial coarse segmentation mask using the ALPnet prototypical network, augmented with a DINOv2 encoder. Following the extraction of an initial mask, prompts are extracted, such as points and bounding boxes, which are then input into the Segment Anything Model (SAM). State-of-the-art results are shown on several medical image datasets and demonstrate automated segmentation capabilities using a single image example (one shot) with no need for fine-tuning of the foundation model. Our code is available at: https://github.com/levayz/ProtoSAM

cs.CV↗

arXiv2024

X-ray2CTPA: Leveraging Diffusion Models to Enhance Pulmonary Embolism Classification

Chest X-rays or chest radiography (CXR), commonly used for medical diagnostics, typically enables limited imaging compared to computed tomography (CT) scans, which offer more detailed and accurate three-dimensional data, particularly contrast-enhanced scans like CT Pulmonary Angiography (CTPA). However, CT scans entail higher costs, greater radiation exposure, and are less accessible than CXRs. In this work we explore cross-modal translation from a 2D low contrast-resolution X-ray input to a 3D high contrast and spatial-resolution CTPA scan. Driven by recent advances in generative AI, we introduce a novel diffusion-based approach to this task. We evaluate the models performance using both quantitative metrics and qualitative feedback from radiologists, ensuring diagnostic relevance of the generated images. Furthermore, we employ the synthesized 3D images in a classification framework and show improved AUC in a PE categorization task, using the initial CXR input. The proposed method is generalizable and capable of performing additional cross-modality translations in medical imaging. It may pave the way for more accessible and cost-effective advanced diagnostic tools. The code for this project is available: https://github.com/NoaCahan/X-ray2CTPA .

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arXiv2024

DINOv2 based Self Supervised Learning For Few Shot Medical Image Segmentation

Deep learning models have emerged as the cornerstone of medical image segmentation, but their efficacy hinges on the availability of extensive manually labeled datasets and their adaptability to unforeseen categories remains a challenge. Few-shot segmentation (FSS) offers a promising solution by endowing models with the capacity to learn novel classes from limited labeled examples. A leading method for FSS is ALPNet, which compares features between the query image and the few available support segmented images. A key question about using ALPNet is how to design its features. In this work, we delve into the potential of using features from DINOv2, which is a foundational self-supervised learning model in computer vision. Leveraging the strengths of ALPNet and harnessing the feature extraction capabilities of DINOv2, we present a novel approach to few-shot segmentation that not only enhances performance but also paves the way for more robust and adaptable medical image analysis.

cs.CV↗

arXiv2023

A Self Supervised StyleGAN for Image Annotation and Classification with Extremely Limited Labels

The recent success of learning-based algorithms can be greatly attributed to the immense amount of annotated data used for training. Yet, many datasets lack annotations due to the high costs associated with labeling, resulting in degraded performances of deep learning methods. Self-supervised learning is frequently adopted to mitigate the reliance on massive labeled datasets since it exploits unlabeled data to learn relevant feature representations. In this work, we propose SS-StyleGAN, a self-supervised approach for image annotation and classification suitable for extremely small annotated datasets. This novel framework adds self-supervision to the StyleGAN architecture by integrating an encoder that learns the embedding to the StyleGAN latent space, which is well-known for its disentangled properties. The learned latent space enables the smart selection of representatives from the data to be labeled for improved classification performance. We show that the proposed method attains strong classification results using small labeled datasets of sizes 50 and even 10. We demonstrate the superiority of our approach for the tasks of COVID-19 and liver tumor pathology identification.

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arXiv2023

Neural Network Reconstruction of the Left Atrium using Sparse Catheter Paths

Catheter based radiofrequency ablation for pulmonary vein isolation has become the first line of treatment for atrial fibrillation in recent years. This requires a rather accurate map of the left atrial sub-endocardial surface including the ostia of the pulmonary veins, which requires dense sampling of the surface and takes more than 10 minutes. The focus of this work is to provide left atrial visualization early in the procedure to ease procedure complexity and enable further workflows, such as using catheters that have difficulty sampling the surface. We propose a dense encoder-decoder network with a novel regularization term to reconstruct the shape of the left atrium from partial data which is derived from simple catheter maneuvers. To train the network, we acquire a large dataset of 3D atria shapes and generate corresponding catheter trajectories. Once trained, we show that the suggested network can sufficiently approximate the atrium shape based on a given trajectory. We compare several network solutions for the 3D atrium reconstruction. We demonstrate that the solution proposed produces realistic visualization using partial acquisition within a 3-minute time interval. Synthetic and human clinical cases are shown.

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arXiv2022

HeartBEiT: Vision Transformer for Electrocardiogram Data Improves Diagnostic Performance at Low Sample Sizes

The electrocardiogram (ECG) is a ubiquitous diagnostic modality. Convolutional neural networks (CNNs) applied towards ECG analysis require large sample sizes, and transfer learning approaches result in suboptimal performance when pre-training is done on natural images. We leveraged masked image modeling to create the first vision-based transformer model, HeartBEiT, for electrocardiogram waveform analysis. We pre-trained this model on 8.5 million ECGs and then compared performance vs. standard CNN architectures for diagnosis of hypertrophic cardiomyopathy, low left ventricular ejection fraction and ST elevation myocardial infarction using differing training sample sizes and independent validation datasets. We show that HeartBEiT has significantly higher performance at lower sample sizes compared to other models. Finally, we also show that HeartBEiT improves explainability of diagnosis by highlighting biologically relevant regions of the EKG vs. standard CNNs. Thus, we present the first vision-based waveform transformer that can be used to develop specialized models for ECG analysis especially at low sample sizes.

eess.SP↗

arXiv2021

Weakly Supervised Attention Model for RV StrainClassification from volumetric CTPA Scans

Pulmonary embolus (PE) refers to obstruction of pulmonary arteries by blood clots. PE accounts for approximately 100,000 deaths per year in the United States alone. The clinical presentation of PE is often nonspecific, making the diagnosis challenging. Thus, rapid and accurate risk stratification is of paramount importance. High-risk PE is caused by right ventricular (RV) dysfunction from acute pressure overload, which in return can help identify which patients require more aggressive therapy. Reconstructed four-chamber views of the heart on chest CT can detect right ventricular enlargement. CT pulmonary angiography (CTPA) is the golden standard in the diagnostic workup of suspected PE. Therefore, it can link between diagnosis and risk stratification strategies. We developed a weakly supervised deep learning algorithm, with an emphasis on a novel attention mechanism, to automatically classify RV strain on CTPA. Our method is a 3D DenseNet model with integrated 3D residual attention blocks. We evaluated our model on a dataset of CTPAs of emergency department (ED) PE patients. This model achieved an area under the receiver operating characteristic curve (AUC) of 0.88 for classifying RV strain. The model showed a sensitivity of 87% and specificity of 83.7%. Our solution outperforms state-of-the-art 3D CNN networks. The proposed design allows for a fully automated network that can be trained easily in an end-to-end manner without requiring computationally intensive and time-consuming preprocessing or strenuous labeling of the data.We infer that unmarked CTPAs can be used for effective RV strain classification. This could be used as a second reader, alerting for high-risk PE patients. To the best of our knowledge, there are no previous deep learning-based studies that attempted to solve this problem.

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arXiv2021

COVID-19 in CXR: from Detection and Severity Scoring to Patient Disease Monitoring

In this work, we estimate the severity of pneumonia in COVID-19 patients and conduct a longitudinal study of disease progression. To achieve this goal, we developed a deep learning model for simultaneous detection and segmentation of pneumonia in chest Xray (CXR) images and generalized to COVID-19 pneumonia. The segmentations were utilized to calculate a "Pneumonia Ratio" which indicates the disease severity. The measurement of disease severity enables to build a disease extent profile over time for hospitalized patients. To validate the model relevance to the patient monitoring task, we developed a validation strategy which involves a synthesis of Digital Reconstructed Radiographs (DRRs - synthetic Xray) from serial CT scans; we then compared the disease progression profiles that were generated from the DRRs to those that were generated from CT volumes.

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arXiv2021

A review of deep learning in medical imaging: Imaging traits, technology trends, case studies with progress highlights, and future promises

Since its renaissance, deep learning has been widely used in various medical imaging tasks and has achieved remarkable success in many medical imaging applications, thereby propelling us into the so-called artificial intelligence (AI) era. It is known that the success of AI is mostly attributed to the availability of big data with annotations for a single task and the advances in high performance computing. However, medical imaging presents unique challenges that confront deep learning approaches. In this survey paper, we first present traits of medical imaging, highlight both clinical needs and technical challenges in medical imaging, and describe how emerging trends in deep learning are addressing these issues. We cover the topics of network architecture, sparse and noisy labels, federating learning, interpretability, uncertainty quantification, etc. Then, we present several case studies that are commonly found in clinical practice, including digital pathology and chest, brain, cardiovascular, and abdominal imaging. Rather than presenting an exhaustive literature survey, we instead describe some prominent research highlights related to these case study applications. We conclude with a discussion and presentation of promising future directions.

cs.CV↗

arXiv2021

Learning Rotation Invariant Features for Cryogenic Electron Microscopy Image Reconstruction

Cryo-Electron Microscopy (Cryo-EM) is a Nobel prize-winning technology for determining the 3D structure of particles at near-atomic resolution. A fundamental step in the recovering of the 3D single-particle structure is to align its 2D projections; thus, the construction of a canonical representation with a fixed rotation angle is required. Most approaches use discrete clustering which fails to capture the continuous nature of image rotation, others suffer from low-quality image reconstruction. We propose a novel method that leverages the recent development in the generative adversarial networks. We introduce an encoder-decoder with a rotation angle classifier. In addition, we utilize a discriminator on the decoder output to minimize the reconstruction error. We demonstrate our approach with the Cryo-EM 5HDB and the rotated MNIST datasets showing substantial improvement over recent methods.

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arXiv2020

Automated triage of COVID-19 from various lung abnormalities using chest CT features

The outbreak of COVID-19 has lead to a global effort to decelerate the pandemic spread. For this purpose chest computed-tomography (CT) based screening and diagnosis of COVID-19 suspected patients is utilized, either as a support or replacement to reverse transcription-polymerase chain reaction (RT-PCR) test. In this paper, we propose a fully automated AI based system that takes as input chest CT scans and triages COVID-19 cases. More specifically, we produce multiple descriptive features, including lung and infections statistics, texture, shape and location, to train a machine learning based classifier that distinguishes between COVID-19 and other lung abnormalities (including community acquired pneumonia). We evaluated our system on a dataset of 2191 CT cases and demonstrated a robust solution with 90.8% sensitivity at 85.4% specificity with 94.0% ROC-AUC. In addition, we present an elaborated feature analysis and ablation study to explore the importance of each feature.

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arXiv2020

Nodule2vec: a 3D Deep Learning System for Pulmonary Nodule Retrieval Using Semantic Representation

Content-based retrieval supports a radiologist decision making process by presenting the doctor the most similar cases from the database containing both historical diagnosis and further disease development history. We present a deep learning system that transforms a 3D image of a pulmonary nodule from a CT scan into a low-dimensional embedding vector. We demonstrate that such a vector representation preserves semantic information about the nodule and offers a viable approach for content-based image retrieval (CBIR). We discuss the theoretical limitations of the available datasets and overcome them by applying transfer learning of the state-of-the-art lung nodule detection model. We evaluate the system using the LIDC-IDRI dataset of thoracic CT scans. We devise a similarity score and show that it can be utilized to measure similarity 1) between annotations of the same nodule by different radiologists and 2) between the query nodule and the top four CBIR results. A comparison between doctors and algorithm scores suggests that the benefit provided by the system to the radiologist end-user is comparable to obtaining a second radiologist's opinion.

cs.IR↗

arXiv2020

Joint Liver Lesion Segmentation and Classification via Transfer Learning

Transfer learning and joint learning approaches are extensively used to improve the performance of Convolutional Neural Networks (CNNs). In medical imaging applications in which the target dataset is typically very small, transfer learning improves feature learning while joint learning has shown effectiveness in improving the network's generalization and robustness. In this work, we study the combination of these two approaches for the problem of liver lesion segmentation and classification. For this purpose, 332 abdominal CT slices containing lesion segmentation and classification of three lesion types are evaluated. For feature learning, the dataset of MICCAI 2017 Liver Tumor Segmentation (LiTS) Challenge is used. Joint learning shows improvement in both segmentation and classification results. We show that a simple joint framework outperforms the commonly used multi-task architecture (Y-Net), achieving an improvement of 10% in classification accuracy, compared to a 3% improvement with Y-Net.

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arXiv2020

Semi-supervised lung nodule retrieval

Content based image retrieval (CBIR) provides the clinician with visual information that can support, and hopefully improve, his or her decision making process. Given an input query image, a CBIR system provides as its output a set of images, ranked by similarity to the query image. Retrieved images may come with relevant information, such as biopsy-based malignancy labeling, or categorization. Ground truth on similarity between dataset elements (e.g. between nodules) is not readily available, thus greatly challenging machine learning methods. Such annotations are particularly difficult to obtain, due to the subjective nature of the task, with high inter-observer variability requiring multiple expert annotators. Consequently, past approaches have focused on manual feature extraction, while current approaches use auxiliary tasks, such as a binary classification task (e.g. malignancy), for which ground-true is more readily accessible. However, in a previous study, we have shown that binary auxiliary tasks are inferior to the usage of a rough similarity estimate that are derived from data annotations. The current study suggests a semi-supervised approach that involves two steps: 1) Automatic annotation of a given partially labeled dataset; 2) Learning a semantic similarity metric space based on the predicated annotations. The proposed system is demonstrated in lung nodule retrieval using the LIDC dataset, and shows that it is feasible to learn embedding from predicted ratings. The semi-supervised approach has demonstrated a significantly higher discriminative ability than the fully-unsupervised reference.

cs.IR↗

arXiv2020

Coronavirus Detection and Analysis on Chest CT with Deep Learning

The outbreak of the novel coronavirus, officially declared a global pandemic, has a severe impact on our daily lives. As of this writing there are approximately 197,188 confirmed cases of which 80,881 are in "Mainland China" with 7,949 deaths, a mortality rate of 3.4%. In order to support radiologists in this overwhelming challenge, we develop a deep learning based algorithm that can detect, localize and quantify severity of COVID-19 manifestation from chest CT scans. The algorithm is comprised of a pipeline of image processing algorithms which includes lung segmentation, 2D slice classification and fine grain localization. In order to further understand the manifestations of the disease, we perform unsupervised clustering of abnormal slices. We present our results on a dataset comprised of 110 confirmed COVID-19 patients from Zhejiang province, China.

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