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Large language models (LLMs) 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 primer paper, we propose an actionable guideline to help healthcare professionals more efficiently utilize LLMs in their work, along with a set of best practices. This approach consists of several main phases, including formulating the task, choosing LLMs, prompt engineering, fine-tuning, and deployment. We start with the discussion of critical considerations in identifying healthcare 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 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., Comment: Under review

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.

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.

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.

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., Comment: We made the segmentation model publicly available

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.

In chest X-ray (CXR) image analysis, rule-based systems are usually employed to extract labels from reports for dataset releases. However, there is still room for improvement in label quality. These labelers typically output only presence labels, sometimes with binary uncertainty indicators, which limits their usefulness. Supervised deep learning models have also been developed for report labeling but lack adaptability, similar to rule-based systems. In this work, we present MAPLEZ (Medical report Annotations with Privacy-preserving Large language model using Expeditious Zero shot answers), a novel approach leveraging a locally executable Large Language Model (LLM) to extract and enhance findings labels on CXR reports. MAPLEZ extracts not only binary labels indicating the presence or absence of a finding but also the location, severity, and radiologists' uncertainty about the finding. Over eight abnormalities from five test sets, we show that our method can extract these annotations with an increase of 3.6 percentage points (pp) in macro F1 score for categorical presence annotations and more than 20 pp increase in F1 score for the location annotations over competing labelers. Additionally, using the combination of improved annotations and multi-type annotations in classification supervision, we demonstrate substantial advancements in model quality, with an increase of 1.1 pp in AUROC over models trained with annotations from the best alternative approach. We share code and annotations., Comment: Code and data: https://github.com/rsummers11/CADLab/tree/master/MAPLEZ_LLM_report_labeler/

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., Comment: 7 Pages, 3 figures, SPIE Medical Imaging 2024, Computer-aided diagnosis

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., Comment: Accepted at SPIE Medical Imaging 2024

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., Comment: Accepted at SPIE 2024. arXiv admin note: text overlap with arXiv:2402.00175

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., Comment: Accepted at SPIE 2024

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., Comment: Accepted at SPIE 2024

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.

Purpose: Lymph nodes (LNs) in the chest have a tendency to enlarge due to various pathologies, such as lung cancer or pneumonia. Clinicians routinely measure nodal size to monitor disease progression, confirm metastatic cancer, and assess treatment response. However, variations in their shapes and appearances make it cumbersome to identify LNs, which reside outside of most organs. Methods: We propose to segment LNs in the mediastinum by leveraging the anatomical priors of 28 different structures (e.g., lung, trachea etc.) generated by the public TotalSegmentator tool. The CT volumes from 89 patients available in the public NIH CT Lymph Node dataset were used to train three 3D nnUNet models to segment LNs. The public St. Olavs dataset containing 15 patients (out-of-training-distribution) was used to evaluate the segmentation performance. Results: For the 15 test patients, the 3D cascade nnUNet model obtained the highest Dice score of 72.2 +- 22.3 for mediastinal LNs with short axis diameter $\geq$ 8mm and 54.8 +- 23.8 for all LNs respectively. These results represent an improvement of 10 points over a current approach that was evaluated on the same test dataset. Conclusion: To our knowledge, we are the first to harness 28 distinct anatomical priors to segment mediastinal LNs, and our work can be extended to other nodal zones in the body. The proposed method has immense potential for improved patient outcomes through the identification of enlarged nodes in initial staging CT scans., Comment: Submitted to CARS 2024

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.

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., Comment: This paper has been accepted at Deep Generative Models workshop at MICCAI 2023

The integration of AI into radiology introduces opportunities for improved clinical care provision and efficiency but it demands a meticulous approach to mitigate potential risks as with any other new technology. Beginning with rigorous pre-deployment evaluation and validation, the focus should be on ensuring models meet the highest standards of safety, effectiveness and efficacy for their intended applications. Input and output guardrails implemented during production usage act as an additional layer of protection, identifying and addressing individual failures as they occur. Continuous post-deployment monitoring allows for tracking population-level performance (data drift), fairness, and value delivery over time. Scheduling reviews of post-deployment model performance and educating radiologists about new algorithmic-driven findings is critical for AI to be effective in clinical practice. Recognizing that no single AI solution can provide absolute assurance even when limited to its intended use, the synergistic application of quality assurance at multiple levels - regulatory, clinical, technical, and ethical - is emphasized. Collaborative efforts between stakeholders spanning healthcare systems, industry, academia, and government are imperative to address the multifaceted challenges involved. Trust in AI is an earned privilege, contingent on a broad set of goals, among them transparently demonstrating that the AI adheres to the same rigorous safety, effectiveness and efficacy standards as other established medical technologies. By doing so, developers can instil confidence among providers and patients alike, enabling the responsible scaling of AI and the realization of its potential benefits. The roadmap presented herein aims to expedite the achievement of deployable, reliable, and safe AI in radiology., Comment: 14 pages, 3 figures

Pericoronary adipose tissue (PCAT) is the deposition of fat in the vicinity of the coronary arteries. It is an indicator of coronary inflammation and associated with coronary artery disease. Non-invasive coronary CT angiography (CCTA) is presently used to obtain measures of the thickness, volume, and attenuation of fat deposition. However, prior works solely focus on measuring PCAT using semi-automated approaches at the right coronary artery (RCA) over the left coronary artery (LCA). In this pilot work, we developed a fully automated approach for the measurement of PCAT mean attenuation and volume in the region around both coronary arteries. First, we used a large subset of patients from the public ImageCAS dataset (n = 735) to train a 3D full resolution nnUNet to segment LCA and RCA. Then, we automatically measured PCAT in the surrounding arterial regions. We evaluated our method on a held-out test set of patients (n = 183) from the same dataset. A mean Dice score of 83% and PCAT attenuation of -73.81 $\pm$ 12.69 HU was calculated for the RCA, while a mean Dice score of 81% and PCAT attenuation of -77.51 $\pm$ 7.94 HU was computed for the LCA. To the best of our knowledge, we are the first to develop a fully automated method to measure PCAT attenuation and volume at both the RCA and LCA. Our work underscores how automated PCAT measurement holds promise as a biomarker for identification of inflammation and cardiac disease., Comment: 5 pages, 4 figures, IEE ISBI2024 conference

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., Comment: Update after major revision

Patients undergoing chest X-rays (CXR) often endure multiple lung diseases. When evaluating a patient's condition, due to the complex pathologies, subtle texture changes of different lung lesions in images, and patient condition differences, radiologists may make uncertain even when they have experienced long-term clinical training and professional guidance, which makes much noise in extracting disease labels based on CXR reports. In this paper, we re-extract disease labels from CXR reports to make them more realistic by considering disease severity and uncertainty in classification. Our contributions are as follows: 1. We re-extracted the disease labels with severity and uncertainty by a rule-based approach with keywords discussed with clinical experts. 2. To further improve the explainability of chest X-ray diagnosis, we designed a multi-relationship graph learning method with an expert uncertainty-aware loss function. 3. Our multi-relationship graph learning method can also interpret the disease classification results. Our experimental results show that models considering disease severity and uncertainty outperform previous state-of-the-art methods.

Pruning has emerged as a powerful technique for compressing deep neural networks, reducing memory usage and inference time without significantly affecting overall performance. However, the nuanced ways in which pruning impacts model behavior are not well understood, particularly for long-tailed, multi-label datasets commonly found in clinical settings. This knowledge gap could have dangerous implications when deploying a pruned model for diagnosis, where unexpected model behavior could impact patient well-being. To fill this gap, we perform the first analysis of pruning's effect on neural networks trained to diagnose thorax diseases from chest X-rays (CXRs). On two large CXR datasets, we examine which diseases are most affected by pruning and characterize class "forgettability" based on disease frequency and co-occurrence behavior. Further, we identify individual CXRs where uncompressed and heavily pruned models disagree, known as pruning-identified exemplars (PIEs), and conduct a human reader study to evaluate their unifying qualities. We find that radiologists perceive PIEs as having more label noise, lower image quality, and higher diagnosis difficulty. This work represents a first step toward understanding the impact of pruning on model behavior in deep long-tailed, multi-label medical image classification. All code, model weights, and data access instructions can be found at https://github.com/VITA-Group/PruneCXR., Comment: Early accepted to MICCAI 2023

Blood vessel segmentation in medical imaging is one of the essential steps for vascular disease diagnosis and interventional planning in a broad spectrum of clinical scenarios in image-based medicine and interventional medicine. Unfortunately, manual annotation of the vessel masks is challenging and resource-intensive due to subtle branches and complex structures. To overcome this issue, this paper presents a self-supervised vessel segmentation method, dubbed the contrastive diffusion adversarial representation learning (C-DARL) model. Our model is composed of a diffusion module and a generation module that learns the distribution of multi-domain blood vessel data by generating synthetic vessel images from diffusion latent. Moreover, we employ contrastive learning through a mask-based contrastive loss so that the model can learn more realistic vessel representations. To validate the efficacy, C-DARL is trained using various vessel datasets, including coronary angiograms, abdominal digital subtraction angiograms, and retinal imaging. Experimental results confirm that our model achieves performance improvement over baseline methods with noise robustness, suggesting the effectiveness of C-DARL for vessel segmentation.

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.

We propose a method to incorporate the intensity information of a target lesion on CT scans in training segmentation and detection networks. We first build an intensity-based lesion probability (ILP) function from an intensity histogram of the target lesion. It is used to compute the probability of being the lesion for each voxel based on its intensity. Finally, the computed ILP map of each input CT scan is provided as additional supervision for network training, which aims to inform the network about possible lesion locations in terms of intensity values at no additional labeling cost. The method was applied to improve the segmentation of three different lesion types, namely, small bowel carcinoid tumor, kidney tumor, and lung nodule. The effectiveness of the proposed method on a detection task was also investigated. We observed improvements of 41.3% -> 47.8%, 74.2% -> 76.0%, and 26.4% -> 32.7% in segmenting small bowel carcinoid tumor, kidney tumor, and lung nodule, respectively, in terms of per case Dice scores. An improvement of 64.6% -> 75.5% was achieved in detecting kidney tumors in terms of average precision. The results of different usages of the ILP map and the effect of varied amount of training data are also presented., Comment: Computerized Medical Imaging and Graphics 2023

Despite the reduction in turn-around times in radiology reports with the use of speech recognition software, persistent communication errors can significantly impact the interpretation of the radiology report. Pre-filling a radiology report holds promise in mitigating reporting errors, and despite efforts in the literature to generate medical reports, there exists a lack of approaches that exploit the longitudinal nature of patient visit records in the MIMIC-CXR dataset. To address this gap, we propose to use longitudinal multi-modal data, i.e., previous patient visit CXR, current visit CXR, and previous visit report, to pre-fill the 'findings' section of a current patient visit report. We first gathered the longitudinal visit information for 26,625 patients from the MIMIC-CXR dataset and created a new dataset called Longitudinal-MIMIC. With this new dataset, a transformer-based model was trained to capture the information from longitudinal patient visit records containing multi-modal data (CXR images + reports) via a cross-attention-based multi-modal fusion module and a hierarchical memory-driven decoder. In contrast to previous work that only uses current visit data as input to train a model, our work exploits the longitudinal information available to pre-fill the 'findings' section of radiology reports. Experiments show that our approach outperforms several recent approaches. Code will be published at https://github.com/CelestialShine/Longitudinal-Chest-X-Ray.

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., Comment: Shared first authors: Annika Reinke and Minu D. Tizabi; shared senior authors: Lena Maier-Hein and Paul F. J\"ager. Published in Nature Methods. arXiv admin note: text overlap with arXiv:2206.01653

Imaging exams, such as chest radiography, will yield a small set of common findings and a much larger set of uncommon findings. While a trained radiologist can learn the visual presentation of rare conditions by studying a few representative examples, teaching a machine to learn from such a "long-tailed" distribution is much more difficult, as standard methods would be easily biased toward the most frequent classes. In this paper, we present a comprehensive benchmark study of the long-tailed learning problem in the specific domain of thorax diseases on chest X-rays. We focus on learning from naturally distributed chest X-ray data, optimizing classification accuracy over not only the common "head" classes, but also the rare yet critical "tail" classes. To accomplish this, we introduce a challenging new long-tailed chest X-ray benchmark to facilitate research on developing long-tailed learning methods for medical image classification. The benchmark consists of two chest X-ray datasets for 19- and 20-way thorax disease classification, containing classes with as many as 53,000 and as few as 7 labeled training images. We evaluate both standard and state-of-the-art long-tailed learning methods on this new benchmark, analyzing which aspects of these methods are most beneficial for long-tailed medical image classification and summarizing insights for future algorithm design. The datasets, trained models, and code are available at https://github.com/VITA-Group/LongTailCXR., Comment: DALI 2022 (MICCAI workshop)

Finding small lesions is very challenging due to lack of noticeable features, severe class imbalance, as well as the size itself. One approach to improve small lesion segmentation is to reduce the region of interest and inspect it at a higher sensitivity rather than performing it for the entire region. It is usually implemented as sequential or joint segmentation of organ and lesion, which requires additional supervision on organ segmentation. Instead, we propose to utilize an intensity distribution of a target lesion at no additional labeling cost to effectively separate regions where the lesions are possibly located from the background. It is incorporated into network training as an auxiliary task. We applied the proposed method to segmentation of small bowel carcinoid tumors in CT scans. We observed improvements for all metrics (33.5% $\rightarrow$ 38.2%, 41.3% $\rightarrow$ 47.8%, 30.0% $\rightarrow$ 35.9% for the global, per case, and per tumor Dice scores, respectively.) compared to the baseline method, which proves the validity of our idea. Our method can be one option for explicitly incorporating intensity distribution information of a target in network training.

We present a new graph-based method for small bowel path tracking based on cylindrical constraints. A distinctive characteristic of the small bowel compared to other organs is the contact between parts of itself along its course, which makes the path tracking difficult together with the indistinct appearance of the wall. It causes the tracked path to easily cross over the walls when relying on low-level features like the wall detection. To circumvent this, a series of cylinders that are fitted along the course of the small bowel are used to guide the tracking to more reliable directions. It is implemented as soft constraints using a new cost function. The proposed method is evaluated against ground-truth paths that are all connected from start to end of the small bowel for 10 abdominal CT scans. The proposed method showed clear improvements compared to the baseline method in tracking the path without making an error. Improvements of 6.6% and 17.0%, in terms of the tracked length, were observed for two different settings related to the small bowel segmentation., Comment: Published in: 2022 IEEE 19th International Symposium on Biomedical Imaging (ISBI)

Small bowel path tracking is a challenging problem considering its many folds and contact along its course. For the same reason, it is very costly to achieve the ground-truth (GT) path of the small bowel in 3D. In this work, we propose to train a deep reinforcement learning tracker using datasets with different types of annotations. Specifically, we utilize CT scans that have only GT small bowel segmentation as well as ones with the GT path. It is enabled by designing a unique environment that is compatible for both, including a reward definable even without the GT path. The performed experiments proved the validity of the proposed method. The proposed method holds a high degree of usability in this problem by being able to utilize the scans with weak annotations, and thus by possibly reducing the required annotation cost., Comment: Accepted to MICCAI 2022

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., Comment: Shared first authors: Lena Maier-Hein, Annika Reinke. arXiv admin note: substantial text overlap with arXiv:2104.05642 Published in Nature Methods