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.

Decomposing Vision-based LLM Predictions for Auto-Evaluation with GPT-4

The volume of CT exams being done in the world has been rising every year, which has led to radiologist burn-out. Large Language Models (LLMs) have the potential to reduce their burden, but their adoption in the clinic depends on radiologist trust, and easy evaluation of generated content. Presently, many automated methods are available to evaluate the reports generated for chest radiographs, but such an approach is not available for CT presently. In this paper, we propose a novel evaluation framework to judge the capabilities of vision-language LLMs in generating accurate summaries of CT-based abnormalities. CT slices containing an abnormality (e.g., lesion) were input to a vision-based LLM (GPT-4V, LLaVA-Med, and RadFM), and it generated a free-text summary of the predicted characteristics of the abnormality. Next, a GPT-4 model decomposed the summary into specific aspects (body part, location, type, and attributes), automatically evaluated the characteristics against the ground-truth, and generated a score for each aspect based on its clinical relevance and factual accuracy. These scores were then contrasted against those obtained from a clinician, and a high correlation ( 85%, p < .001) was observed. Although GPT-4V outperformed other models in our evaluation, it still requires overall improvement. Our evaluation method offers valuable insights into the specific areas that need the most enhancement, guiding future development in this field.

Enhancing chest X-ray datasets with privacy-preserving large language models and multi-type annotations: a data-driven approach for improved classification

In chest X-ray (CXR) image analysis, rule-based systems are usually employed to extract labels from reports, but concerns exist about label quality. These datasets typically offer only presence labels, sometimes with binary uncertainty indicators, which limits their usefulness. 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 5 percentage points (pp) in F1 score for categorical presence annotations and more than 30 pp increase in F1 score for the location annotations over competing labelers. Additionally, using these improved annotations in classification supervision, we demonstrate substantial advancements in model quality, with an increase of 1.7 pp in AUROC over models trained with annotations from the state-of-the-art approach. We share code and annotations.

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.

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.

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.

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.

Utilizing Longitudinal Chest X-Rays and Reports to Pre-Fill Radiology Reports

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 by >=3% on F1 score, and >=2% for BLEU-4, METEOR and ROUGE-L respectively. The dataset and code will be made publicly available.

Disparities in Dermatology AI Performance on a Diverse, Curated Clinical Image Set

Access to dermatological care is a major issue, with an estimated 3 billion people lacking access to care globally. Artificial intelligence (AI) may aid in triaging skin diseases. However, most AI models have not been rigorously assessed on images of diverse skin tones or uncommon diseases. To ascertain potential biases in algorithm performance in this context, we curated the Diverse Dermatology Images (DDI) dataset-the first publicly available, expertly curated, and pathologically confirmed image dataset with diverse skin tones. Using this dataset of 656 images, we show that state-of-the-art dermatology AI models perform substantially worse on DDI, with receiver operator curve area under the curve (ROC-AUC) dropping by 27-36 percent compared to the models' original test results. All the models performed worse on dark skin tones and uncommon diseases, which are represented in the DDI dataset. Additionally, we find that dermatologists, who typically provide visual labels for AI training and test datasets, also perform worse on images of dark skin tones and uncommon diseases compared to ground truth biopsy annotations. Finally, fine-tuning AI models on the well-characterized and diverse DDI images closed the performance gap between light and dark skin tones. Moreover, algorithms fine-tuned on diverse skin tones outperformed dermatologists on identifying malignancy on images of dark skin tones. Our findings identify important weaknesses and biases in dermatology AI that need to be addressed to ensure reliable application to diverse patients and diseases.

Disparities in Dermatology AI: Assessments Using Diverse Clinical Images

More than 3 billion people lack access to care for skin disease. AI diagnostic tools may aid in early skin cancer detection; however most models have not been assessed on images of diverse skin tones or uncommon diseases. To address this, we curated the Diverse Dermatology Images (DDI) dataset - the first publicly available, pathologically confirmed images featuring diverse skin tones. We show that state-of-the-art dermatology AI models perform substantially worse on DDI, with ROC-AUC dropping 29-40 percent compared to the models' original results. We find that dark skin tones and uncommon diseases, which are well represented in the DDI dataset, lead to performance drop-offs. Additionally, we show that state-of-the-art robust training methods cannot correct for these biases without diverse training data. Our findings identify important weaknesses and biases in dermatology AI that need to be addressed to ensure reliable application to diverse patients and across all disease.