arXiv subjects

Ehsan Samei

Publications and source records attributed to Ehsan Samei.

15 recordsLinked to original sources

arXiv2025

NodMAISI: Nodule-Oriented Medical AI for Synthetic Imaging

Objective: Although medical imaging datasets are increasingly available, abnormal and annotation-intensive findings critical to lung cancer screening, particularly small pulmonary nodules, remain underrepresented and inconsistently curated. Methods: We introduce NodMAISI, an anatomically constrained, nodule-oriented CT synthesis and augmentation framework trained on a unified multi-source cohort (7,042 patients, 8,841 CTs, 14,444 nodules). The framework integrates: (i) a standardized curation and annotation pipeline linking each CT with organ masks and nodule-level annotations, (ii) a ControlNet-conditioned rectified-flow generator built on MAISI-v2's foundational blocks to enforce anatomy- and lesion-consistent synthesis, and (iii) lesion-aware augmentation that perturbs nodule masks (controlled shrinkage) while preserving surrounding anatomy to generate paired CT variants. Results: Across six public test datasets, NodMAISI improved distributional fidelity relative to MAISI-v2 (real-to-synthetic FID range 1.18 to 2.99 vs 1.69 to 5.21). In lesion detectability analysis using a MONAI nodule detector, NodMAISI substantially increased average sensitivity and more closely matched clinical scans (IMD-CT: 0.69 vs 0.39; DLCS24: 0.63 vs 0.20), with the largest gains for sub-centimeter nodules where MAISI-v2 frequently failed to reproduce the conditioned lesion. In downstream nodule-level malignancy classification trained on LUNA25 and externally evaluated on LUNA16, LNDbv4, and DLCS24, NodMAISI augmentation improved AUC by 0.07 to 0.11 at <=20% clinical data and by 0.12 to 0.21 at 10%, consistently narrowing the performance gap under data scarcity.

cs.CV↗

arXiv2025

Reinforcement Learning-Based Optimization of CT Acquisition and Reconstruction Parameters Through Virtual Imaging Trials

Protocol optimization is critical in Computed Tomography (CT) to achieve high diagnostic image quality while minimizing radiation dose. However, due to the complex interdependencies among CT acquisition and reconstruction parameters, traditional optimization methods rely on exhaustive testing of combinations of these parameters, which is often impractical. This study introduces a novel methodology that combines virtual imaging tools with reinforcement learning to optimize CT protocols more efficiently. Human models with liver lesions were imaged using a validated CT simulator and reconstructed with a novel CT reconstruction toolkit. The optimization parameter space included tube voltage, tube current, reconstruction kernel, slice thickness, and pixel size. The optimization process was performed using a Proximal Policy Optimization (PPO) agent, which was trained to maximize an image quality objective, specifically the detectability index (d') of liver lesions in the reconstructed images. Optimization performance was compared against an exhaustive search performed on a supercomputer. The proposed reinforcement learning approach achieved the global maximum d' across test cases while requiring 79.7% fewer steps than the exhaustive search, demonstrating both accuracy and computational efficiency. The proposed framework is flexible and can accommodate various image quality objectives. The findings highlight the potential of integrating virtual imaging tools with reinforcement learning for CT protocol management.

cs.LG↗

arXiv2025

Demographic Distribution Matching between real world and virtual phantom population

Virtual imaging trials (VITs) offer scalable and cost-effective tools for evaluating imaging systems and protocols. However, their translational impact depends on rigorous comparability between virtual and real-world populations. This study introduces DISTINCT (Distributional Subsampling for Covariate-Targeted Alignment), a statistical framework for selecting demographically aligned subsamples from large clinical datasets to support robust comparisons with virtual cohorts. We applied DISTINCT to the National Lung Screening Trial (NLST) and a companion virtual trial dataset (VLST). The algorithm jointly aligned typical continuous (age, BMI) and categorical (sex, race, ethnicity) variables by constructing multidimensional bins based on discretized covariates. For a given target size, DISTINCT samples individuals to match the joint demographic distribution of the reference population. We evaluated the demographic similarity between VLST and progressively larger NLST subsamples using Wasserstein and Kolmogorov-Smirnov (K-S) distances to identify the maximal subsample size with acceptable alignment. The algorithm identified a maximal aligned NLST subsample of 9,974 participants, preserving demographic similarity to the VLST population. Receiver operating characteristic (ROC) analysis using risk scores for lung cancer detection showed that area under the curve (AUC) estimates stabilized beyond 6,000 participants, confirming the sufficiency of aligned subsamples for virtual imaging trial evaluation. Stratified AUC analysis revealed substantial performance variation across demographic subgroups, reinforcing the importance of covariate alignment in comparative studies.

stat.AP↗

arXiv2024

XCAT-3.0: A Comprehensive Library of Personalized Digital Twins Derived from CT Scans

Virtual Imaging Trials (VIT) offer a cost-effective and scalable approach for evaluating medical imaging technologies. Computational phantoms, which mimic real patient anatomy and physiology, play a central role in VITs. However, the current libraries of computational phantoms face limitations, particularly in terms of sample size and diversity. Insufficient representation of the population hampers accurate assessment of imaging technologies across different patient groups. Traditionally, the more realistic computational phantoms were created by manual segmentation, which is a laborious and time-consuming task, impeding the expansion of phantom libraries. This study presents a framework for creating realistic computational phantoms using a suite of automatic segmentation models and performing three forms of automated quality control on the segmented organ masks. The result is the release of over 2500 new computational phantoms, so-named XCAT3.0 after the ubiquitous XCAT computational construct. This new formation embodies 140 structures and represents a comprehensive approach to detailed anatomical modeling. The developed computational phantoms are formatted in both voxelized and surface mesh formats. The framework is combined with an in-house CT scanner simulator to produce realistic CT images. The framework has the potential to advance virtual imaging trials, facilitating comprehensive and reliable evaluations of medical imaging technologies. Phantoms may be requested at https://cvit.duke.edu/resources/. Code, model weights, and sample CT images are available at https://xcat-3.github.io/.

eess.IV↗

arXiv2024

Proceedings Virtual Imaging Trials in Medicine 2024

This submission comprises the proceedings of the 1st Virtual Imaging Trials in Medicine conference, organized by Duke University on April 22-24, 2024. The listed authors serve as the program directors for this conference. The VITM conference is a pioneering summit uniting experts from academia, industry and government in the fields of medical imaging and therapy to explore the transformative potential of in silico virtual trials and digital twins in revolutionizing healthcare. The proceedings are categorized by the respective days of the conference: Monday presentations, Tuesday presentations, Wednesday presentations, followed by the abstracts for the posters presented on Monday and Tuesday.

physics.med-ph↗

arXiv2024

Reproducible Benchmarking for Lung Nodule Detection and Malignancy Classification Across Multiple Low-Dose CT Datasets

Evaluation of artificial intelligence (AI) models for low-dose CT lung cancer screening is limited by heterogeneous datasets, annotation standards, and evaluation protocols, making performance difficult to compare and translate across clinical settings. We establish a public, reproducible multi-dataset benchmark for lung nodule detection and nodule-level cancer classification and quantify cross-dataset generalizability. Using the Duke Lung Cancer Screening (DLCS) dataset as a clinically curated development set, we evaluate performance across LUNA16/LIDC-IDRI, NLST-3D, and LUNA25. Detection models trained on DLCS and LUNA16 were evaluated externally on NLST-3D using free-response ROC analysis. For malignancy classification, we compared five strategies: randomly initialized ResNet50, Models Genesis, Med3D, a Foundation Model for Cancer Biomarkers, and a Strategic Warm-Start (ResNet50-SWS) approach pretrained using detection-derived candidate patches stratified by confidence. Performance was summarized using AUC with 95% confidence intervals and DeLong tests. Detection performance varied substantially by training dataset, with DLCS-trained models outperforming LUNA16-trained models on external NLST-3D evaluation (sensitivity at 2 false positives per scan: 0.72 vs. 0.64; p < 0.001). For malignancy classification, ResNet50-SWS achieved AUCs of 0.71 (DLCS), 0.90 (LUNA16), 0.81 (NLST-3D), and 0.80 (LUNA25), consistently matching or exceeding alternative pretraining strategies. These results demonstrate that dataset characteristics strongly influence lung cancer AI performance and highlight the need for transparent, multi-dataset benchmarking.

cs.CV↗

arXiv2024

Virtual Lung Screening Trial (VLST): An In Silico Study Inspired by the National Lung Screening Trial for Lung Cancer Detection

Clinical imaging trials play a crucial role in advancing medical innovation but are often costly, inefficient, and ethically constrained. Virtual Imaging Trials (VITs) present a solution by simulating clinical trial components in a controlled, risk-free environment. The Virtual Lung Screening Trial (VLST), an in silico study inspired by the National Lung Screening Trial (NLST), illustrates the potential of VITs to expedite clinical trials, minimize risks to participants, and promote optimal use of imaging technologies in healthcare. This study aimed to show that a virtual imaging trial platform could investigate some key elements of a major clinical trial, specifically the NLST, which compared Computed tomography (CT) and chest radiography (CXR) for lung cancer screening. With simulated cancerous lung nodules, a virtual patient cohort of 294 subjects was created using XCAT human models. Each virtual patient underwent both CT and CXR imaging, with deep learning models, the AI CT-Reader and AI CXR-Reader, acting as virtual readers to perform recall patients with suspicion of lung cancer. The primary outcome was the difference in diagnostic performance between CT and CXR, measured by the Area Under the Curve (AUC). The AI CT-Reader showed superior diagnostic accuracy, achieving an AUC of 0.92 (95% CI: 0.90-0.95) compared to the AI CXR-Reader's AUC of 0.72 (95% CI: 0.67-0.77). Furthermore, at the same 94% CT sensitivity reported by the NLST, the VLST specificity of 73% was similar to the NLST specificity of 73.4%. This CT performance highlights the potential of VITs to replicate certain aspects of clinical trials effectively, paving the way toward a safe and efficient method for advancing imaging-based diagnostics.

eess.IV↗

arXiv2023

Large Intestine 3D Shape Refinement Using Point Diffusion Models for Digital Phantom Generation

Accurate 3D modeling of human organs is critical for constructing digital phantoms in virtual imaging trials. However, organs such as the large intestine remain particularly challenging due to their complex geometry and shape variability. We propose CLAP, a novel Conditional LAtent Point-diffusion model that combines geometric deep learning with denoising diffusion models to enhance 3D representations of the large intestine. Given point clouds sampled from segmentation masks, we employ a hierarchical variational autoencoder to learn both global and local latent shape representations. Two conditional diffusion models operate within this latent space to refine the organ shape. A pretrained surface reconstruction model is then used to convert the refined point clouds into meshes. CLAP achieves substantial improvements in shape modeling accuracy, reducing Chamfer distance by 26% and Hausdorff distance by 36% relative to the initial suboptimal shapes. This approach offers a robust and extensible solution for high-fidelity organ modeling, with potential applicability to a wide range of anatomical structures.

cs.CV↗

arXiv2023

The Utility of the Virtual Imaging Trials Methodology for Objective Characterization of AI Systems and Training Data

Purpose: The credibility of Artificial Intelligence (AI) models for medical imaging continues to be a challenge, affected by the diversity of models, the data used to train the models, and applicability of their combination to produce reproducible results for new data. In this work, we aimed to explore whether emerging Virtual Imaging Trials (VIT) methodologies can provide an objective resource to approach this challenge. Approach: The study was conducted for the case example of COVID-19 diagnosis using clinical and virtual computed tomography (CT) and chest radiography (CXR) processed with convolutional neural networks. Multiple AI models were developed and tested using 3D ResNet-like and 2D EfficientNetv2 architectures across diverse datasets. Results: Model performance was evaluated using the area under the curve (AUC) and the DeLong method for AUC confidence intervals. The models trained on the most diverse datasets showed the highest external testing performance, with AUC values ranging from 0.73-0.76 for CT and 0.70-0.73 for CXR. Internal testing yielded higher AUC values (0.77-0.85 for CT and 0.77-1.0 for CXR), highlighting a substantial drop in performance during external validation, which underscores the importance of diverse and comprehensive training and testing data. Most notably, the VIT approach provided objective assessment of the utility of diverse models and datasets, while offering insight into the influence of dataset characteristics, patient factors, and imaging physics on AI efficacy. Conclusions: The VIT approach enhances model transparency and reliability, offering nuanced insights into the factors driving AI performance and bridging the gap between experimental and clinical settings.

eess.IV↗

arXiv2022

Virtual vs. Reality: External Validation of COVID-19 Classifiers using XCAT Phantoms for Chest Computed Tomography

Research studies of artificial intelligence models in medical imaging have been hampered by poor generalization. This problem has been especially concerning over the last year with numerous applications of deep learning for COVID-19 diagnosis. Virtual imaging trials (VITs) could provide a solution for objective evaluation of these models. In this work utilizing the VITs, we created the CVIT-COVID dataset including 180 virtually imaged computed tomography (CT) images from simulated COVID-19 and normal phantom models under different COVID-19 morphology and imaging properties. We evaluated the performance of an open-source, deep-learning model from the University of Waterloo trained with multi-institutional data and an in-house model trained with the open clinical dataset called MosMed. We further validated the model's performance against open clinical data of 305 CT images to understand virtual vs. real clinical data performance. The open-source model was published with nearly perfect performance on the original Waterloo dataset but showed a consistent performance drop in external testing on another clinical dataset (AUC=0.77) and our simulated CVIT-COVID dataset (AUC=0.55). The in-house model achieved an AUC of 0.87 while testing on the internal test set (MosMed test set). However, performance dropped to an AUC of 0.65 and 0.69 when evaluated on clinical and our simulated CVIT-COVID dataset. The VIT framework offered control over imaging conditions, allowing us to show there was no change in performance as CT exposure was changed from 28.5 to 57 mAs. The VIT framework also provided voxel-level ground truth, revealing that performance of in-house model was much higher at AUC=0.87 for diffuse COVID-19 infection size >2.65% lung volume versus AUC=0.52 for focal disease with <2.65% volume. The virtual imaging framework enabled these uniquely rigorous analyses of model performance.

eess.IV↗

arXiv2022

Quality or Quantity: Toward a Unified Approach for Multi-organ Segmentation in Body CT

Organ segmentation of medical images is a key step in virtual imaging trials. However, organ segmentation datasets are limited in terms of quality (because labels cover only a few organs) and quantity (since case numbers are limited). In this study, we explored the tradeoffs between quality and quantity. Our goal is to create a unified approach for multi-organ segmentation of body CT, which will facilitate the creation of large numbers of accurate virtual phantoms. Initially, we compared two segmentation architectures, 3D-Unet and DenseVNet, which were trained using XCAT data that is fully labeled with 22 organs, and chose the 3D-Unet as the better performing model. We used the XCAT-trained model to generate pseudo-labels for the CT-ORG dataset that has only 7 organs segmented. We performed two experiments: First, we trained 3D-UNet model on the XCAT dataset, representing quality data, and tested it on both XCAT and CT-ORG datasets. Second, we trained 3D-UNet after including the CT-ORG dataset into the training set to have more quantity. Performance improved for segmentation in the organs where we have true labels in both datasets and degraded when relying on pseudo-labels. When organs were labeled in both datasets, Exp-2 improved Average DSC in XCAT and CT-ORG by 1. This demonstrates that quality data is the key to improving the model's performance.

eess.IV↗

arXiv2022

Co-occurring Diseases Heavily Influence the Performance of Weakly Supervised Learning Models for Classification of Chest CT

Despite the potential of weakly supervised learning to automatically annotate massive amounts of data, little is known about its limitations for use in computer-aided diagnosis (CAD). For CT specifically, interpreting the performance of CAD algorithms can be challenging given the large number of co-occurring diseases. This paper examines the effect of co-occurring diseases when training classification models by weakly supervised learning, specifically by comparing multi-label and multiple binary classifiers using the same training data. Our results demonstrated that the binary model outperformed the multi-label classification in every disease category in terms of AUC. However, this performance was heavily influenced by co-occurring diseases in the binary model, suggesting it did not always learn the correct appearance of the specific disease. For example, binary classification of lung nodules resulted in an AUC of < 0.65 when there were no other co-occurring diseases, but when lung nodules co-occurred with emphysema, the performance reached AUC > 0.80. We hope this paper revealed the complexity of interpreting disease classification performance in weakly supervised models and will encourage researchers to examine the effect of co-occurring diseases on classification performance in the future.

eess.IV↗

arXiv2021

Classification of Multiple Diseases on Body CT Scans using Weakly Supervised Deep Learning

Purpose: To design multi-disease classifiers for body CT scans for three different organ systems using automatically extracted labels from radiology text reports.Materials & Methods: This retrospective study included a total of 12,092 patients (mean age 57 +- 18; 6,172 women) for model development and testing (from 2012-2017). Rule-based algorithms were used to extract 19,225 disease labels from 13,667 body CT scans from 12,092 patients. Using a three-dimensional DenseVNet, three organ systems were segmented: lungs and pleura; liver and gallbladder; and kidneys and ureters. For each organ, a three-dimensional convolutional neural network classified no apparent disease versus four common diseases for a total of 15 different labels across all three models. Testing was performed on a subset of 2,158 CT volumes relative to 2,875 manually derived reference labels from 2133 patients (mean age 58 +- 18;1079 women). Performance was reported as receiver operating characteristic area under the curve (AUC) with 95% confidence intervals by the DeLong method. Results: Manual validation of the extracted labels confirmed 91% to 99% accuracy across the 15 different labels. AUCs for lungs and pleura labels were: atelectasis 0.77 (95% CI: 0.74, 0.81), nodule 0.65 (0.61, 0.69), emphysema 0.89 (0.86, 0.92), effusion 0.97 (0.96, 0.98), and no apparent disease 0.89 (0.87, 0.91). AUCs for liver and gallbladder were: hepatobiliary calcification 0.62 (95% CI: 0.56, 0.67), lesion 0.73 (0.69, 0.77), dilation 0.87 (0.84, 0.90), fatty 0.89 (0.86, 0.92), and no apparent disease 0.82 (0.78, 0.85). AUCs for kidneys and ureters were: stone 0.83 (95% CI: 0.79, 0.87), atrophy 0.92 (0.89, 0.94), lesion 0.68 (0.64, 0.72), cyst 0.70 (0.66, 0.73), and no apparent disease 0.79 (0.75, 0.83). Conclusion: Weakly-supervised deep learning models were able to classify diverse diseases in multiple organ systems.

cs.CV↗

arXiv2020

iPhantom: a framework for automated creation of individualized computational phantoms and its application to CT organ dosimetry

Objective: This study aims to develop and validate a novel framework, iPhantom, for automated creation of patient-specific phantoms or digital-twins (DT) using patient medical images. The framework is applied to assess radiation dose to radiosensitive organs in CT imaging of individual patients. Method: From patient CT images, iPhantom segments selected anchor organs (e.g. liver, bones, pancreas) using a learning-based model developed for multi-organ CT segmentation. Organs challenging to segment (e.g. intestines) are incorporated from a matched phantom template, using a diffeomorphic registration model developed for multi-organ phantom-voxels. The resulting full-patient phantoms are used to assess organ doses during routine CT exams. Result: iPhantom was validated on both the XCAT (n=50) and an independent clinical (n=10) dataset with similar accuracy. iPhantom precisely predicted all organ locations with good accuracy of Dice Similarity Coefficients (DSC) >0.6 for anchor organs and DSC of 0.3-0.9 for all other organs. iPhantom showed less than 10% dose errors for the majority of organs, which was notably superior to the state-of-the-art baseline method (20-35% dose errors). Conclusion: iPhantom enables automated and accurate creation of patient-specific phantoms and, for the first time, provides sufficient and automated patient-specific dose estimates for CT dosimetry. Significance: The new framework brings the creation and application of CHPs to the level of individual CHPs through automation, achieving a wider and precise organ localization, paving the way for clinical monitoring, and personalized optimization, and large-scale research.

physics.med-ph↗

arXiv2020

Automatic phantom test pattern classification through transfer learning with deep neural networks

Imaging phantoms are test patterns used to measure image quality in computer tomography (CT) systems. A new phantom platform (Mercury Phantom, Gammex) provides test patterns for estimating the task transfer function (TTF) or noise power spectrum (NPF) and simulates different patient sizes. Determining which image slices are suitable for analysis currently requires manual annotation of these patterns by an expert, as subtle defects may make an image unsuitable for measurement. We propose a method of automatically classifying these test patterns in a series of phantom images using deep learning techniques. By adapting a convolutional neural network based on the VGG19 architecture with weights trained on ImageNet, we use transfer learning to produce a classifier for this domain. The classifier is trained and evaluated with over 3,500 phantom images acquired at a university medical center. Input channels for color images are successfully adapted to convey contextual information for phantom images. A series of ablation studies are employed to verify design aspects of the classifier and evaluate its performance under varying training conditions. Our solution makes extensive use of image augmentation to produce a classifier that accurately classifies typical phantom images with 98% accuracy, while maintaining as much as 86% accuracy when the phantom is improperly imaged.

cs.CV↗