LEAVS: An LLM-based Labeler for Abdominal CT Supervision

Extracting structured labels from radiology reports has been employed to create vision models to simultaneously detect several types of abnormalities. However, existing works focus mainly on the chest region. Few works have been investigated on abdominal radiology reports due to more complex anatomy and a wider range of pathologies in the abdomen. We propose LEAVS (Large language model Extractor for Abdominal Vision Supervision). This labeler can annotate the certainty of presence and the urgency of seven types of abnormalities for nine abdominal organs on CT radiology reports. To ensure broad coverage, we chose abnormalities that encompass most of the finding types from CT reports. Our approach employs a specialized chain-of-thought prompting strategy for a locally-run LLM using sentence extraction and multiple-choice questions in a tree-based decision system. We demonstrate that the LLM can extract several abnormality types across abdominal organs with an average F1 score of 0.89, significantly outperforming competing labelers and humans. Additionally, we show that extraction of urgency labels achieved performance comparable to human annotations. Finally, we demonstrate that the abnormality labels contain valuable information for training a single vision model that classifies several organs as normal or abnormal. We release our code and structured annotations for a public CT dataset containing over 1,000 CT volumes.

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.

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.

Efficient 2D CT Foundation Model for Contrast Phase Classification

Purpose: The purpose of this study is to harness the efficiency of a 2D foundation model to develop a robust phase classifier that is resilient to domain shifts. Materials and Methods: This retrospective study utilized three public datasets from separate institutions. A 2D foundation model was trained on the DeepLesion dataset (mean age: 51.2, s.d.: 17.6; 2398 males) to generate embeddings from 2D CT slices for downstream contrast phase classification. The classifier was trained on the VinDr Multiphase dataset and externally validated on the WAW-TACE dataset. The 2D model was also compared to three 3D supervised models. Results: On the VinDr dataset (146 male, 63 female, 56 unidentified), the model achieved near-perfect AUROC scores and F1 scores of 99.2%, 94.2%, and 93.1% for non-contrast, arterial, and venous phases, respectively. The `Other' category scored lower (F1: 73.4%) due to combining multiple contrast phases into one class. On the WAW-TACE dataset (mean age: 66.1, s.d.: 10.0; 185 males), the model showed strong performance with AUROCs of 91.0% and 85.6%, and F1 scores of 87.3% and 74.1% for non-contrast and arterial phases. Venous phase performance was lower, with AUROC and F1 scores of 81.7% and 70.2% respectively, due to label mismatches. Compared to 3D supervised models, the approach trained faster, performed as well or better, and showed greater robustness to domain shifts. Conclusion: The robustness of the 2D Foundation model may be potentially useful for automation of hanging protocols and data orchestration for clinical deployment of AI algorithms.

Demystifying Large Language Models for Medicine: A Primer

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.

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.

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.

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.

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.