arXiv subjects

Ronald M. Summers

Publications and source records attributed to Ronald M. Summers.

At least 37 records · Page 2Linked to original sources

arXiv2025

A Continual Learning-driven Model for Accurate and Generalizable Segmentation of Clinically Comprehensive and Fine-grained Whole-body Anatomies in CT

Precision medicine in the quantitative management of chronic diseases and oncology would be greatly improved if the Computed Tomography (CT) scan of any patient could be segmented, parsed and analyzed in a precise and detailed way. However, there is no such fully annotated CT dataset with all anatomies delineated for training because of the exceptionally high manual cost, the need for specialized clinical expertise, and the time required to finish the task. To this end, we proposed a novel continual learning-driven CT model that can segment complete anatomies presented using dozens of previously partially labeled datasets, dynamically expanding its capacity to segment new ones without compromising previously learned organ knowledge. Existing multi-dataset approaches are not able to dynamically segment new anatomies without catastrophic forgetting and would encounter optimization difficulty or infeasibility when segmenting hundreds of anatomies across the whole range of body regions. Our single unified CT segmentation model, CL-Net, can highly accurately segment a clinically comprehensive set of 235 fine-grained whole-body anatomies. Composed of a universal encoder, multiple optimized and pruned decoders, CL-Net is developed using 13,952 CT scans from 20 public and 16 private high-quality partially labeled CT datasets of various vendors, different contrast phases, and pathologies. Extensive evaluation demonstrates that CL-Net consistently outperforms the upper limit of an ensemble of 36 specialist nnUNets trained per dataset with the complexity of 5% model size and significantly surpasses the segmentation accuracy of recent leading Segment Anything-style medical image foundation models by large margins. Our continual learning-driven CL-Net model would lay a solid foundation to facilitate many downstream tasks of oncology and chronic diseases using the most widely adopted CT imaging.

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arXiv2025

Leveraging Multiphase CT for Quality Enhancement of Portal Venous CT: Utility for Pancreas Segmentation

Multiphase CT studies are routinely obtained in clinical practice for diagnosis and management of various diseases, such as cancer. However, the CT studies can be acquired with low radiation doses, different scanners, and are frequently affected by motion and metal artifacts. Prior approaches have targeted the quality improvement of one specific CT phase (e.g., non-contrast CT). In this work, we hypothesized that leveraging multiple CT phases for the quality enhancement of one phase may prove advantageous for downstream tasks, such as segmentation. A 3D progressive fusion and non-local (PFNL) network was developed. It was trained with three degraded (low-quality) phases (non-contrast, arterial, and portal venous) to enhance the quality of the portal venous phase. Then, the effect of scan quality enhancement was evaluated using a proxy task of pancreas segmentation, which is useful for tracking pancreatic cancer. The proposed approach improved the pancreas segmentation by 3% over the corresponding low-quality CT scan. To the best of our knowledge, we are the first to harness multiphase CT for scan quality enhancement and improved pancreas segmentation.

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arXiv2024

Hidden flaws behind expert-level accuracy of multimodal GPT-4 vision in medicine

Recent studies indicate that Generative Pre-trained Transformer 4 with Vision (GPT-4V) outperforms human physicians in medical challenge tasks. However, these evaluations primarily focused on the accuracy of multi-choice questions alone. Our study extends the current scope by conducting a comprehensive analysis of GPT-4V's rationales of image comprehension, recall of medical knowledge, and step-by-step multimodal reasoning when solving New England Journal of Medicine (NEJM) Image Challenges - an imaging quiz designed to test the knowledge and diagnostic capabilities of medical professionals. Evaluation results confirmed that GPT-4V performs comparatively to human physicians regarding multi-choice accuracy (81.6% vs. 77.8%). GPT-4V also performs well in cases where physicians incorrectly answer, with over 78% accuracy. However, we discovered that GPT-4V frequently presents flawed rationales in cases where it makes the correct final choices (35.5%), most prominent in image comprehension (27.2%). Regardless of GPT-4V's high accuracy in multi-choice questions, our findings emphasize the necessity for further in-depth evaluations of its rationales before integrating such multimodal AI models into clinical workflows.

cs.CV↗

arXiv2024

Expert Knowledge-Aware Image Difference Graph Representation Learning for Difference-Aware Medical Visual Question Answering

To contribute to automating the medical vision-language model, we propose a novel Chest-Xray Difference Visual Question Answering (VQA) task. Given a pair of main and reference images, this task attempts to answer several questions on both diseases and, more importantly, the differences between them. This is consistent with the radiologist's diagnosis practice that compares the current image with the reference before concluding the report. We collect a new dataset, namely MIMIC-Diff-VQA, including 700,703 QA pairs from 164,324 pairs of main and reference images. Compared to existing medical VQA datasets, our questions are tailored to the Assessment-Diagnosis-Intervention-Evaluation treatment procedure used by clinical professionals. Meanwhile, we also propose a novel expert knowledge-aware graph representation learning model to address this task. The proposed baseline model leverages expert knowledge such as anatomical structure prior, semantic, and spatial knowledge to construct a multi-relationship graph, representing the image differences between two images for the image difference VQA task. The dataset and code can be found at https://github.com/Holipori/MIMIC-Diff-VQA. We believe this work would further push forward the medical vision language model.

cs.CV↗

arXiv2024

MRISegmentator-Abdomen: A Fully Automated Multi-Organ and Structure Segmentation Tool for T1-weighted Abdominal MRI

Background: Segmentation of organs and structures in abdominal MRI is useful for many clinical applications, such as disease diagnosis and radiotherapy. Current approaches have focused on delineating a limited set of abdominal structures (13 types). To date, there is no publicly available abdominal MRI dataset with voxel-level annotations of multiple organs and structures. Consequently, a segmentation tool for multi-structure segmentation is also unavailable. Methods: We curated a T1-weighted abdominal MRI dataset consisting of 195 patients who underwent imaging at National Institutes of Health (NIH) Clinical Center. The dataset comprises of axial pre-contrast T1, arterial, venous, and delayed phases for each patient, thereby amounting to a total of 780 series (69,248 2D slices). Each series contains voxel-level annotations of 62 abdominal organs and structures. A 3D nnUNet model, dubbed as MRISegmentator-Abdomen (MRISegmentator in short), was trained on this dataset, and evaluation was conducted on an internal test set and two large external datasets: AMOS22 and Duke Liver. The predicted segmentations were compared against the ground-truth using the Dice Similarity Coefficient (DSC) and Normalized Surface Distance (NSD). Findings: MRISegmentator achieved an average DSC of 0.861$\pm$0.170 and a NSD of 0.924$\pm$0.163 in the internal test set. On the AMOS22 dataset, MRISegmentator attained an average DSC of 0.829$\pm$0.133 and a NSD of 0.908$\pm$0.067. For the Duke Liver dataset, an average DSC of 0.933$\pm$0.015 and a NSD of 0.929$\pm$0.021 was obtained. Interpretation: The proposed MRISegmentator provides automatic, accurate, and robust segmentations of 62 organs and structures in T1-weighted abdominal MRI sequences. The tool has the potential to accelerate research on various clinical topics, such as abnormality detection, radiotherapy, disease classification among others.

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arXiv2024

Deep Learning Segmentation of Ascites on Abdominal CT Scans for Automatic Volume Quantification

Purpose: To evaluate the performance of an automated deep learning method in detecting ascites and subsequently quantifying its volume in patients with liver cirrhosis and ovarian cancer. Materials and Methods: This retrospective study included contrast-enhanced and non-contrast abdominal-pelvic CT scans of patients with cirrhotic ascites and patients with ovarian cancer from two institutions, National Institutes of Health (NIH) and University of Wisconsin (UofW). The model, trained on The Cancer Genome Atlas Ovarian Cancer dataset (mean age, 60 years +/- 11 [s.d.]; 143 female), was tested on two internal (NIH-LC and NIH-OV) and one external dataset (UofW-LC). Its performance was measured by the Dice coefficient, standard deviations, and 95% confidence intervals, focusing on ascites volume in the peritoneal cavity. Results: On NIH-LC (25 patients; mean age, 59 years +/- 14 [s.d.]; 14 male) and NIH-OV (166 patients; mean age, 65 years +/- 9 [s.d.]; all female), the model achieved Dice scores of 0.855 +/- 0.061 (CI: 0.831-0.878) and 0.826 +/- 0.153 (CI: 0.764-0.887), with median volume estimation errors of 19.6% (IQR: 13.2-29.0) and 5.3% (IQR: 2.4-9.7) respectively. On UofW-LC (124 patients; mean age, 46 years +/- 12 [s.d.]; 73 female), the model had a Dice score of 0.830 +/- 0.107 (CI: 0.798-0.863) and median volume estimation error of 9.7% (IQR: 4.5-15.1). The model showed strong agreement with expert assessments, with r^2 values of 0.79, 0.98, and 0.97 across the test sets. Conclusion: The proposed deep learning method performed well in segmenting and quantifying the volume of ascites in concordance with expert radiologist assessments.

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arXiv2024

How Well Do Multi-modal LLMs Interpret CT Scans? An Auto-Evaluation Framework for Analyses

Automatically interpreting CT scans can ease the workload of radiologists. However, this is challenging mainly due to the scarcity of adequate datasets and reference standards for evaluation. This study aims to bridge this gap by introducing a novel evaluation framework, named ``GPTRadScore''. This framework assesses the capabilities of multi-modal LLMs, such as GPT-4 with Vision (GPT-4V), Gemini Pro Vision, LLaVA-Med, and RadFM, in generating descriptions for prospectively-identified findings. By employing a decomposition technique based on GPT-4, GPTRadScore compares these generated descriptions with gold-standard report sentences, analyzing their accuracy in terms of body part, location, and type of finding. Evaluations demonstrated a high correlation with clinician assessments and highlighted its potential over traditional metrics, such as BLEU, METEOR, and ROUGE. Furthermore, to contribute to future studies, we plan to release a benchmark dataset annotated by clinicians. Using GPTRadScore, we found that while GPT-4V and Gemini Pro Vision fare better, their performance revealed significant areas for improvement, primarily due to limitations in the dataset used for training these models. To demonstrate this potential, RadFM was fine-tuned and it resulted in significant accuracy improvements: location accuracy rose from 3.41\% to 12.8\%, body part accuracy from 29.12\% to 53\%, and type accuracy from 9.24\% to 30\%, thereby validating our hypothesis.

cs.AI↗

arXiv2024

Shadow and Light: Digitally Reconstructed Radiographs for Disease Classification

In this paper, we introduce DRR-RATE, a large-scale synthetic chest X-ray dataset derived from the recently released CT-RATE dataset. DRR-RATE comprises of 50,188 frontal Digitally Reconstructed Radiographs (DRRs) from 21,304 unique patients. Each image is paired with a corresponding radiology text report and binary labels for 18 pathology classes. Given the controllable nature of DRR generation, it facilitates the inclusion of lateral view images and images from any desired viewing position. This opens up avenues for research into new and novel multimodal applications involving paired CT, X-ray images from various views, text, and binary labels. We demonstrate the applicability of DRR-RATE alongside existing large-scale chest X-ray resources, notably the CheXpert dataset and CheXnet model. Experiments demonstrate that CheXnet, when trained and tested on the DRR-RATE dataset, achieves sufficient to high AUC scores for the six common pathologies cited in common literature: Atelectasis, Cardiomegaly, Consolidation, Lung Lesion, Lung Opacity, and Pleural Effusion. Additionally, CheXnet trained on the CheXpert dataset can accurately identify several pathologies, even when operating out of distribution. This confirms that the generated DRR images effectively capture the essential pathology features from CT images. The dataset and labels are publicly accessible at https://huggingface.co/datasets/farrell236/DRR-RATE.

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arXiv2024

Automated classification of multi-parametric body MRI series

Multi-parametric MRI (mpMRI) studies are widely available in clinical practice for the diagnosis of various diseases. As the volume of mpMRI exams increases yearly, there are concomitant inaccuracies that exist within the DICOM header fields of these exams. This precludes the use of the header information for the arrangement of the different series as part of the radiologist's hanging protocol, and clinician oversight is needed for correction. In this pilot work, we propose an automated framework to classify the type of 8 different series in mpMRI studies. We used 1,363 studies acquired by three Siemens scanners to train a DenseNet-121 model with 5-fold cross-validation. Then, we evaluated the performance of the DenseNet-121 ensemble on a held-out test set of 313 mpMRI studies. Our method achieved an average precision of 96.6%, sensitivity of 96.6%, specificity of 99.6%, and F1 score of 96.6% for the MRI series classification task. To the best of our knowledge, we are the first to develop a method to classify the series type in mpMRI studies acquired at the level of the chest, abdomen, and pelvis. Our method has the capability for robust automation of hanging protocols in modern radiology practice.

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arXiv2024

Enhanced Muscle and Fat Segmentation for CT-Based Body Composition Analysis: A Comparative Study

Purpose: Body composition measurements from routine abdominal CT can yield personalized risk assessments for asymptomatic and diseased patients. In particular, attenuation and volume measures of muscle and fat are associated with important clinical outcomes, such as cardiovascular events, fractures, and death. This study evaluates the reliability of an Internal tool for the segmentation of muscle and fat (subcutaneous and visceral) as compared to the well-established public TotalSegmentator tool. Methods: We assessed the tools across 900 CT series from the publicly available SAROS dataset, focusing on muscle, subcutaneous fat, and visceral fat. The Dice score was employed to assess accuracy in subcutaneous fat and muscle segmentation. Due to the lack of ground truth segmentations for visceral fat, Cohen's Kappa was utilized to assess segmentation agreement between the tools. Results: Our Internal tool achieved a 3% higher Dice (83.8 vs. 80.8) for subcutaneous fat and a 5% improvement (87.6 vs. 83.2) for muscle segmentation respectively. A Wilcoxon signed-rank test revealed that our results were statistically different with p<0.01. For visceral fat, the Cohen's kappa score of 0.856 indicated near-perfect agreement between the two tools. Our internal tool also showed very strong correlations for muscle volume (R^2=0.99), muscle attenuation (R^2=0.93), and subcutaneous fat volume (R^2=0.99) with a moderate correlation for subcutaneous fat attenuation (R^2=0.45). Conclusion: Our findings indicated that our Internal tool outperformed TotalSegmentator in measuring subcutaneous fat and muscle. The high Cohen's Kappa score for visceral fat suggests a reliable level of agreement between the two tools. These results demonstrate the potential of our tool in advancing the accuracy of body composition analysis.

cs.CV↗

arXiv2024

Towards long-tailed, multi-label disease classification from chest X-ray: Overview of the CXR-LT challenge

Many real-world image recognition problems, such as diagnostic medical imaging exams, are "long-tailed" $\unicode{x2013}$ there are a few common findings followed by many more relatively rare conditions. In chest radiography, diagnosis is both a long-tailed and multi-label problem, as patients often present with multiple findings simultaneously. While researchers have begun to study the problem of long-tailed learning in medical image recognition, few have studied the interaction of label imbalance and label co-occurrence posed by long-tailed, multi-label disease classification. To engage with the research community on this emerging topic, we conducted an open challenge, CXR-LT, on long-tailed, multi-label thorax disease classification from chest X-rays (CXRs). We publicly release a large-scale benchmark dataset of over 350,000 CXRs, each labeled with at least one of 26 clinical findings following a long-tailed distribution. We synthesize common themes of top-performing solutions, providing practical recommendations for long-tailed, multi-label medical image classification. Finally, we use these insights to propose a path forward involving vision-language foundation models for few- and zero-shot disease classification.

cs.CV↗

arXiv2024

Self and Mixed Supervision to Improve Training Labels for Multi-Class Medical Image Segmentation

Accurate training labels are a key component for multi-class medical image segmentation. Their annotation is costly and time-consuming because it requires domain expertise. This work aims to develop a dual-branch network and automatically improve training labels for multi-class image segmentation. Transfer learning is used to train the network and improve inaccurate weak labels sequentially. The dual-branch network is first trained by weak labels alone to initialize model parameters. After the network is stabilized, the shared encoder is frozen, and strong and weak decoders are fine-tuned by strong and weak labels together. The accuracy of weak labels is iteratively improved in the fine-tuning process. The proposed method was applied to a three-class segmentation of muscle, subcutaneous and visceral adipose tissue on abdominal CT scans. Validation results on 11 patients showed that the accuracy of training labels was statistically significantly improved, with the Dice similarity coefficient of muscle, subcutaneous and visceral adipose tissue increased from 74.2% to 91.5%, 91.2% to 95.6%, and 77.6% to 88.5%, respectively (p<0.05). In comparison with our earlier method, the label accuracy was also significantly improved (p<0.05). These experimental results suggested that the combination of the dual-branch network and transfer learning is an efficient means to improve training labels for multi-class segmentation.

cs.CV↗

arXiv2024

Understanding metric-related pitfalls in image analysis validation

Validation metrics are key for the reliable tracking of scientific progress and for bridging the current chasm between artificial intelligence (AI) research and its translation into practice. However, increasing evidence shows that particularly in image analysis, metrics are often chosen inadequately in relation to the underlying research problem. This could be attributed to a lack of accessibility of metric-related knowledge: While taking into account the individual strengths, weaknesses, and limitations of validation metrics is a critical prerequisite to making educated choices, the relevant knowledge is currently scattered and poorly accessible to individual researchers. Based on a multi-stage Delphi process conducted by a multidisciplinary expert consortium as well as extensive community feedback, the present work provides the first reliable and comprehensive common point of access to information on pitfalls related to validation metrics in image analysis. Focusing on biomedical image analysis but with the potential of transfer to other fields, the addressed pitfalls generalize across application domains and are categorized according to a newly created, domain-agnostic taxonomy. To facilitate comprehension, illustrations and specific examples accompany each pitfall. As a structured body of information accessible to researchers of all levels of expertise, this work enhances global comprehension of a key topic in image analysis validation.

cs.CV↗

arXiv2024

Metrics reloaded: Recommendations for image analysis validation

Increasing evidence shows that flaws in machine learning (ML) algorithm validation are an underestimated global problem. Particularly in automatic biomedical image analysis, chosen performance metrics often do not reflect the domain interest, thus failing to adequately measure scientific progress and hindering translation of ML techniques into practice. To overcome this, our large international expert consortium created Metrics Reloaded, a comprehensive framework guiding researchers in the problem-aware selection of metrics. Following the convergence of ML methodology across application domains, Metrics Reloaded fosters the convergence of validation methodology. The framework was developed in a multi-stage Delphi process and is based on the novel concept of a problem fingerprint - a structured representation of the given problem that captures all aspects that are relevant for metric selection, from the domain interest to the properties of the target structure(s), data set and algorithm output. Based on the problem fingerprint, users are guided through the process of choosing and applying appropriate validation metrics while being made aware of potential pitfalls. Metrics Reloaded targets image analysis problems that can be interpreted as a classification task at image, object or pixel level, namely image-level classification, object detection, semantic segmentation, and instance segmentation tasks. To improve the user experience, we implemented the framework in the Metrics Reloaded online tool, which also provides a point of access to explore weaknesses, strengths and specific recommendations for the most common validation metrics. The broad applicability of our framework across domains is demonstrated by an instantiation for various biological and medical image analysis use cases.

cs.CV↗

arXiv2024

Automated Plaque Detection and Agatston Score Estimation on Non-Contrast CT Scans: A Multicenter Study

Coronary artery calcification (CAC) is a strong and independent predictor of cardiovascular disease (CVD). However, manual assessment of CAC often requires radiological expertise, time, and invasive imaging techniques. The purpose of this multicenter study is to validate an automated cardiac plaque detection model using a 3D multiclass nnU-Net for gated and non-gated non-contrast chest CT volumes. CT scans were performed at three tertiary care hospitals and collected as three datasets, respectively. Heart, aorta, and lung segmentations were determined using TotalSegmentator, while plaques in the coronary arteries and heart valves were manually labeled for 801 volumes. In this work we demonstrate how the nnU-Net semantic segmentation pipeline may be adapted to detect plaques in the coronary arteries and valves. With a linear correction, nnU-Net deep learning methods may also accurately estimate Agatston scores on chest non-contrast CT scans. Compared to manual Agatson scoring, automated Agatston scoring indicated a slope of the linear regression of 0.841 with an intercept of +16 HU (R2 = 0.97). These results are an improvement over previous work assessing automated Agatston score computation in non-gated CT scans.

cs.CV↗

arXiv2024

Automated Classification of Body MRI Sequence Type Using Convolutional Neural Networks

Multi-parametric MRI of the body is routinely acquired for the identification of abnormalities and diagnosis of diseases. However, a standard naming convention for the MRI protocols and associated sequences does not exist due to wide variations in imaging practice at institutions and myriad MRI scanners from various manufacturers being used for imaging. The intensity distributions of MRI sequences differ widely as a result, and there also exists information conflicts related to the sequence type in the DICOM headers. At present, clinician oversight is necessary to ensure that the correct sequence is being read and used for diagnosis. This poses a challenge when specific series need to be considered for building a cohort for a large clinical study or for developing AI algorithms. In order to reduce clinician oversight and ensure the validity of the DICOM headers, we propose an automated method to classify the 3D MRI sequence acquired at the levels of the chest, abdomen, and pelvis. In our pilot work, our 3D DenseNet-121 model achieved an F1 score of 99.5% at differentiating 5 common MRI sequences obtained by three Siemens scanners (Aera, Verio, Biograph mMR). To the best of our knowledge, we are the first to develop an automated method for the 3D classification of MRI sequences in the chest, abdomen, and pelvis, and our work has outperformed the previous state-of-the-art MRI series classifiers.

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arXiv2024

Weakly Supervised Detection of Pheochromocytomas and Paragangliomas in CT

Pheochromocytomas and Paragangliomas (PPGLs) are rare adrenal and extra-adrenal tumors which have the potential to metastasize. For the management of patients with PPGLs, CT is the preferred modality of choice for precise localization and estimation of their progression. However, due to the myriad variations in size, morphology, and appearance of the tumors in different anatomical regions, radiologists are posed with the challenge of accurate detection of PPGLs. Since clinicians also need to routinely measure their size and track their changes over time across patient visits, manual demarcation of PPGLs is quite a time-consuming and cumbersome process. To ameliorate the manual effort spent for this task, we propose an automated method to detect PPGLs in CT studies via a proxy segmentation task. As only weak annotations for PPGLs in the form of prospectively marked 2D bounding boxes on an axial slice were available, we extended these 2D boxes into weak 3D annotations and trained a 3D full-resolution nnUNet model to directly segment PPGLs. We evaluated our approach on a dataset consisting of chest-abdomen-pelvis CTs of 255 patients with confirmed PPGLs. We obtained a precision of 70% and sensitivity of 64.1% with our proposed approach when tested on 53 CT studies. Our findings highlight the promising nature of detecting PPGLs via segmentation, and furthers the state-of-the-art in this exciting yet challenging area of rare cancer management.

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arXiv2024

Weakly-Supervised Detection of Bone Lesions in CT

The skeletal region is one of the common sites of metastatic spread of cancer in the breast and prostate. CT is routinely used to measure the size of lesions in the bones. However, they can be difficult to spot due to the wide variations in their sizes, shapes, and appearances. Precise localization of such lesions would enable reliable tracking of interval changes (growth, shrinkage, or unchanged status). To that end, an automated technique to detect bone lesions is highly desirable. In this pilot work, we developed a pipeline to detect bone lesions (lytic, blastic, and mixed) in CT volumes via a proxy segmentation task. First, we used the bone lesions that were prospectively marked by radiologists in a few 2D slices of CT volumes and converted them into weak 3D segmentation masks. Then, we trained a 3D full-resolution nnUNet model using these weak 3D annotations to segment the lesions and thereby detected them. Our automated method detected bone lesions in CT with a precision of 96.7% and recall of 47.3% despite the use of incomplete and partial training data. To the best of our knowledge, we are the first to attempt the direct detection of bone lesions in CT via a proxy segmentation task.

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