arXiv subjects

Benjamin Hou

Publications and source records attributed to Benjamin Hou.

At least 19 recordsLinked to original sources

arXiv2026

Automatic Cephalometric Landmark Localization on CBCT-Derived Digitally Reconstructed Radiographs for Skeletal Malocclusion Classification

Manual cephalometric landmark annotation is important for craniofacial assessment but is labor-intensive and difficult to scale. We introduce CephViT, a Vision Transformer-based model for automated 2D lateral cephalometric landmark localization, and evaluate its use in downstream skeletal malocclusion classification. CephViT was trained and benchmarked on a public lateral cephalogram dataset, achieving a mean radial error of 1.28 +/- 1.42 mm and a successful detection rate of 92.0% at 3.0 mm. Because the private evaluation cohort consisted of 3D CBCT scans, lateral cephalogram-like digitally reconstructed radiographs (DRRs) were generated from each volume and used as 2D inputs to the landmark localization model. Landmark coordinates were normalized into a common coordinate frame, and skeletal malocclusion classification was performed using landmarks shared between the reference and DRR-based pipelines. Classification performance using DRR-localized landmarks was comparable to that obtained using manually annotated reference landmarks, with accuracies of 70.0% and 68.3%, respectively. These results support the feasibility of automated cephalometric analysis on CBCT-derived DRRs for skeletal malocclusion assessment.

cs.CV↗

arXiv2026

A Unified 2D Framework for DeepLesion Detection, Segmentation and Short Report Generation

In previous work, we integrated large language models (LLMs) into the lesion segmentation model based on the ULS23 DeepLesion dataset, using short-form findings from the reports. In this study, we developed a unified 2D lesion analysis framework that integrates LLM-based reasoning, lesion bounding box detection, segmentation, and radiology report generation from the original DeepLesion dataset. In the testing phase, we achieved relatively high lesion bounding box detection accuracy with mAP50 of 70.1%, mAP50-95 of 46.4%; Lesion segmentation performance with a Dice score of 62.6%; short report generation accuracy with BLEU_1 score of 64.3%, BLEU_4 score of 49.6%, METEOR of 34.7%, and ROUGE_L of 60.1%. In this work, we address the challenging issue of segmentation in the original DeepLesion dataset and achieve a 28.5% Dice score improvement over the nnUNet lesion segmentation model. We also integrated spatial and anatomical context into the DeepLesion short report generation. We released the implementation, dataset, and models on Github. https://github.com/ruida/2D_DeepLesion_Foundation

cs.CV↗

arXiv2026

Toward Multimodal Conversational AI for Age-Related Macular Degeneration

Despite strong performance of deep learning models in retinal disease detection, most systems produce static predictions without clinical reasoning or interactive explanation. Recent advances in multimodal large language models (MLLMs) integrate diagnostic predictions with clinically meaningful dialogue to support clinical decision-making and patient counseling. In this study, OcularChat, an MLLM, was fine-tuned from Qwen2.5-VL using simulated patient-physician dialogues to diagnose age-related macular degeneration (AMD) through visual question answering on color fundus photographs (CFPs). A total of 705,850 simulated dialogues paired with 46,167 CFPs were generated to train OcularChat to identify key AMD features and produce reasoned predictions. OcularChat demonstrated strong classification performance in AREDS, achieving accuracies of 0.954, 0.849, and 0.678 for the three diagnostic tasks: advanced AMD, pigmentary abnormalities, and drusen size, significantly outperforming existing MLLMs. On AREDS2, OcularChat remained the top-performing method on all tasks. Across three independent ophthalmologist graders, OcularChat achieved higher mean scores than a strong baseline model for advanced AMD (3.503 vs. 2.833), pigmentary abnormalities (3.272 vs. 2.828), drusen size (3.064 vs. 2.433), and overall impression (2.978 vs. 2.464) on a 5-point clinical grading rubric. Beyond strong objective performance in AMD severity classification, OcularChat demonstrated the ability to provide diagnostic reasoning, clinically relevant explanations, and interactive dialogue, with high performance in subjective ophthalmologist evaluation. These findings suggest that MLLMs may enable accurate, interpretable, and clinically useful image-based diagnosis and classification of AMD.

cs.CV↗

arXiv2026

CT-Bench: A Benchmark for Multimodal Lesion Understanding in Computed Tomography

Artificial intelligence (AI) can automatically delineate lesions on computed tomography (CT) and generate radiology report content, yet progress is limited by the scarcity of publicly available CT datasets with lesion-level annotations. To bridge this gap, we introduce CT-Bench, a first-of-its-kind benchmark dataset comprising two components: a Lesion Image and Metadata Set containing 20,335 lesions from 7,795 CT studies with bounding boxes, descriptions, and size information, and a multitask visual question answering benchmark with 2,850 QA pairs covering lesion localization, description, size estimation, and attribute categorization. Hard negative examples are included to reflect real-world diagnostic challenges. We evaluate multiple state-of-the-art multimodal models, including vision-language and medical CLIP variants, by comparing their performance to radiologist assessments, demonstrating the value of CT-Bench as a comprehensive benchmark for lesion analysis. Moreover, fine-tuning models on the Lesion Image and Metadata Set yields significant performance gains across both components, underscoring the clinical utility of CT-Bench.

cs.CV↗

arXiv2025

Text Embedded Swin-UMamba for DeepLesion Segmentation

Segmentation of lesions on CT enables automatic measurement for clinical assessment of chronic diseases (e.g., lymphoma). Integrating large language models (LLMs) into the lesion segmentation workflow has the potential to combine imaging features with descriptions of lesion characteristics from the radiology reports. In this study, we investigate the feasibility of integrating text into the Swin-UMamba architecture for the task of lesion segmentation. The publicly available ULS23 DeepLesion dataset was used along with short-form descriptions of the findings from the reports. On the test dataset, our method achieved a high Dice score of 82.64, and a low Hausdorff distance of 6.34 pixels was obtained for lesion segmentation. The proposed Text-Swin-U/Mamba model outperformed prior approaches: 37.79% improvement over the LLM-driven LanGuideMedSeg model (p < 0.001), and surpassed the purely image-based XLSTM-UNet and nnUNet models by 2.58% and 1.01%, respectively. The dataset and code can be accessed at https://github.com/ruida/LLM-Swin-UMamba

cs.CV↗

arXiv2025

Longitudinal Assessment of Lung Lesion Burden in CT

In the U.S., lung cancer is the second major cause of death. Early detection of suspicious lung nodules is crucial for patient treatment planning, management, and improving outcomes. Many approaches for lung nodule segmentation and volumetric analysis have been proposed, but few have looked at longitudinal changes in total lung tumor burden. In this work, we trained two 3D models (nnUNet) with and without anatomical priors to automatically segment lung lesions and quantified total lesion burden for each patient. The 3D model without priors significantly outperformed ($p < .001$) the model trained with anatomy priors. For detecting clinically significant lesions $>$ 1cm, a precision of 71.3\%, sensitivity of 68.4\%, and F1-score of 69.8\% was achieved. For segmentation, a Dice score of 77.1 $\pm$ 20.3 and Hausdorff distance error of 11.7 $\pm$ 24.1 mm was obtained. The median lesion burden was 6.4 cc (IQR: 2.1, 18.1) and the median volume difference between manual and automated measurements was 0.02 cc (IQR: -2.8, 1.2). Agreements were also evaluated with linear regression and Bland-Altman plots. The proposed approach can produce a personalized evaluation of the total tumor burden for a patient and facilitate interval change tracking over time.

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arXiv2025

Segment-and-Classify: ROI-Guided Generalizable Contrast Phase Classification in CT Using XGBoost

Purpose: To automate contrast phase classification in CT using organ-specific features extracted from a widely used segmentation tool with a lightweight decision tree classifier. Materials and Methods: This retrospective study utilized three public CT datasets from separate institutions. The phase prediction model was trained on the WAW-TACE (median age: 66 [60,73]; 185 males) dataset, and externally validated on the VinDr-Multiphase (146 males; 63 females; 56 unk) and C4KC-KiTS (median age: 61 [50.68; 123 males) datasets. Contrast phase classification was performed using organ-specific features extracted by TotalSegmentator, followed by prediction using a gradient-boosted decision tree classifier. Results: On the VinDr-Multiphase dataset, the phase prediction model achieved the highest or comparable AUCs across all phases (>0.937), with superior F1-scores in the non-contrast (0.994), arterial (0.937), and delayed (0.718) phases. Statistical testing indicated significant performance differences only in the arterial and delayed phases (p<0.05). On the C4KC-KiTS dataset, the phase prediction model achieved the highest AUCs across all phases (>0.991), with superior F1-scores in arterial/venous (0.968) and delayed (0.935) phases. Statistical testing confirmed significant improvements over all baseline models in these two phases (p<0.05). Performance in the non-contrast class, however, was comparable across all models, with no statistically significant differences observed (p>0.05). Conclusion: The lightweight model demonstrated strong performance relative to all baseline models, and exhibited robust generalizability across datasets from different institutions.

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arXiv2024

Beyond Multiple-Choice Accuracy: Real-World Challenges of Implementing Large Language Models in Healthcare

Large Language Models (LLMs) have gained significant attention in the medical domain for their human-level capabilities, leading to increased efforts to explore their potential in various healthcare applications. However, despite such a promising future, there are multiple challenges and obstacles that remain for their real-world uses in practical settings. This work discusses key challenges for LLMs in medical applications from four unique aspects: operational vulnerabilities, ethical and social considerations, performance and assessment difficulties, and legal and regulatory compliance. Addressing these challenges is crucial for leveraging LLMs to their full potential and ensuring their responsible integration into healthcare.

cs.AI↗

arXiv2024

Entry-level guide to the use of large language models for medical research

Frontier large language models (LLMs), such as GPT-5, Claude 4.5, Gemini 3, Llama 4, and DeepSeek-R1, represent a transformative class of AI tools capable of revolutionizing various aspects of healthcare by generating human-like responses across diverse contexts and adapting to novel tasks following human instructions. Their potential application spans a broad range of medical tasks, such as clinical documentation, matching patients to clinical trials, and answering medical questions. In this paper, we propose an actionable guideline to help healthcare professionals more effectively and efficiently utilize LLMs in their work, along with a set of best practices. The overall workflow consists of several main phases, including formulating the task, choosing LLMs, prompt engineering, fine-tuning, and model deployment. We start with the discussion of critical considerations in identifying medical tasks that align with the core capabilities of LLMs and selecting models based on the selected task and data, performance requirements, and model interface. We then review the strategies, such as prompt engineering and fine-tuning, to adapt standard LLMs to specialized medical tasks. Deployment considerations, including regulatory compliance, ethical guidelines, and continuous monitoring for fairness and bias, are also discussed. By providing a structured step-by-step methodology, this entry-level tutorial aims to equip healthcare professionals with the tools necessary to effectively integrate LLMs into clinical practice, ensuring that these powerful technologies are applied in a safe, reliable, and impactful manner.

cs.AI↗

arXiv2024

AI Workflow, External Validation, and Development in Eye Disease Diagnosis

Timely disease diagnosis is challenging due to increasing disease burdens and limited clinician availability. AI shows promise in diagnosis accuracy but faces real-world application issues due to insufficient validation in clinical workflows and diverse populations. This study addresses gaps in medical AI downstream accountability through a case study on age-related macular degeneration (AMD) diagnosis and severity classification. We designed and implemented an AI-assisted diagnostic workflow for AMD, comparing diagnostic performance with and without AI assistance among 24 clinicians from 12 institutions with real patient data sampled from the Age-Related Eye Disease Study (AREDS). Additionally, we demonstrated continual enhancement of an existing AI model by incorporating approximately 40,000 additional medical images (named AREDS2 dataset). The improved model was then systematically evaluated using both AREDS and AREDS2 test sets, as well as an external test set from Singapore. AI assistance markedly enhanced diagnostic accuracy and classification for 23 out of 24 clinicians, with the average F1-score increasing by 20% from 37.71 (Manual) to 45.52 (Manual + AI) (P-value < 0.0001), achieving an improvement of over 50% in some cases. In terms of efficiency, AI assistance reduced diagnostic times for 17 out of the 19 clinicians tracked, with time savings of up to 40%. Furthermore, a model equipped with continual learning showed robust performance across three independent datasets, recording a 29% increase in accuracy, and elevating the F1-score from 42 to 54 in the Singapore population.

eess.IV↗

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.

eess.IV↗

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

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.

eess.IV↗

arXiv2024

Generalist Foundation Models from a Multimodal Dataset for 3D Computed Tomography

Advancements in medical imaging AI, particularly in 3D imaging, have been limited due to the scarcity of comprehensive datasets. We introduce CT-RATE, a public dataset that pairs 3D medical images with corresponding textual reports. CT-RATE comprises 25,692 non-contrast 3D chest CT scans from 21,304 unique patients. Each scan is accompanied by its corresponding radiology report. Leveraging CT-RATE, we develop CT-CLIP, a CT-focused contrastive language-image pretraining framework designed for broad applications without the need for task-specific training. We demonstrate how CT-CLIP can be used in multi-abnormality detection and case retrieval, and outperforms state-of-the-art fully supervised models across all key metrics. By combining CT-CLIP's vision encoder with a pretrained large language model, we create CT-CHAT, a vision-language foundational chat model for 3D chest CT volumes. Finetuned on over 2.7 million question-answer pairs derived from the CT-RATE dataset, CT-CHAT underscores the necessity for specialized methods in 3D medical imaging. Collectively, the open-source release of CT-RATE, CT-CLIP, and CT-CHAT not only addresses critical challenges in 3D medical imaging but also lays the groundwork for future innovations in medical AI and improved patient care.

cs.CV↗

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

Leveraging Professional Radiologists' Expertise to Enhance LLMs' Evaluation for Radiology Reports

In radiology, Artificial Intelligence (AI) has significantly advanced report generation, but automatic evaluation of these AI-produced reports remains challenging. Current metrics, such as Conventional Natural Language Generation (NLG) and Clinical Efficacy (CE), often fall short in capturing the semantic intricacies of clinical contexts or overemphasize clinical details, undermining report clarity. To overcome these issues, our proposed method synergizes the expertise of professional radiologists with Large Language Models (LLMs), like GPT-3.5 and GPT-4 1. Utilizing In-Context Instruction Learning (ICIL) and Chain of Thought (CoT) reasoning, our approach aligns LLM evaluations with radiologist standards, enabling detailed comparisons between human and AI generated reports. This is further enhanced by a Regression model that aggregates sentence evaluation scores. Experimental results show that our "Detailed GPT-4 (5-shot)" model achieves a 0.48 score, outperforming the METEOR metric by 0.19, while our "Regressed GPT-4" model shows even greater alignment with expert evaluations, exceeding the best existing metric by a 0.35 margin. Moreover, the robustness of our explanations has been validated through a thorough iterative strategy. We plan to publicly release annotations from radiology experts, setting a new standard for accuracy in future assessments. This underscores the potential of our approach in enhancing the quality assessment of AI-driven medical reports.

cs.CL↗

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↗

arXiv2023

Semantic Image Synthesis for Abdominal CT

As a new emerging and promising type of generative models, diffusion models have proven to outperform Generative Adversarial Networks (GANs) in multiple tasks, including image synthesis. In this work, we explore semantic image synthesis for abdominal CT using conditional diffusion models, which can be used for downstream applications such as data augmentation. We systematically evaluated the performance of three diffusion models, as well as to other state-of-the-art GAN-based approaches, and studied the different conditioning scenarios for the semantic mask. Experimental results demonstrated that diffusion models were able to synthesize abdominal CT images with better quality. Additionally, encoding the mask and the input separately is more effective than na\"ive concatenating.

cs.CV↗