Medical Slice Transformer: Improved Diagnosis and Explainability on 3D Medical Images with DINOv2

MRI and CT are essential clinical cross-sectional imaging techniques for diagnosing complex conditions. However, large 3D datasets with annotations for deep learning are scarce. While methods like DINOv2 are encouraging for 2D image analysis, these methods have not been applied to 3D medical images. Furthermore, deep learning models often lack explainability due to their "black-box" nature. This study aims to extend 2D self-supervised models, specifically DINOv2, to 3D medical imaging while evaluating their potential for explainable outcomes. We introduce the Medical Slice Transformer (MST) framework to adapt 2D self-supervised models for 3D medical image analysis. MST combines a Transformer architecture with a 2D feature extractor, i.e., DINOv2. We evaluate its diagnostic performance against a 3D convolutional neural network (3D ResNet) across three clinical datasets: breast MRI (651 patients), chest CT (722 patients), and knee MRI (1199 patients). Both methods were tested for diagnosing breast cancer, predicting lung nodule dignity, and detecting meniscus tears. Diagnostic performance was assessed by calculating the Area Under the Receiver Operating Characteristic Curve (AUC). Explainability was evaluated through a radiologist's qualitative comparison of saliency maps based on slice and lesion correctness. P-values were calculated using Delong's test. MST achieved higher AUC values compared to ResNet across all three datasets: breast (0.94$\pm$0.01 vs. 0.91$\pm$0.02, P=0.02), chest (0.95$\pm$0.01 vs. 0.92$\pm$0.02, P=0.13), and knee (0.85$\pm$0.04 vs. 0.69$\pm$0.05, P=0.001). Saliency maps were consistently more precise and anatomically correct for MST than for ResNet. Self-supervised 2D models like DINOv2 can be effectively adapted for 3D medical imaging using MST, offering enhanced diagnostic accuracy and explainability compared to convolutional neural networks.

RadioRAG: Factual Large Language Models for Enhanced Diagnostics in Radiology Using Dynamic Retrieval Augmented Generation

Large language models (LLMs) have advanced the field of artificial intelligence (AI) in medicine. However LLMs often generate outdated or inaccurate information based on static training datasets. Retrieval augmented generation (RAG) mitigates this by integrating outside data sources. While previous RAG systems used pre-assembled, fixed databases with limited flexibility, we have developed Radiology RAG (RadioRAG) as an end-to-end framework that retrieves data from authoritative radiologic online sources in real-time. RadioRAG is evaluated using a dedicated radiologic question-and-answer dataset (RadioQA). We evaluate the diagnostic accuracy of various LLMs when answering radiology-specific questions with and without access to additional online information via RAG. Using 80 questions from RSNA Case Collection across radiologic subspecialties and 24 additional expert-curated questions, for which the correct gold-standard answers were available, LLMs (GPT-3.5-turbo, GPT-4, Mistral-7B, Mixtral-8x7B, and Llama3 [8B and 70B]) were prompted with and without RadioRAG. RadioRAG retrieved context-specific information from www.radiopaedia.org in real-time and incorporated them into its reply. RadioRAG consistently improved diagnostic accuracy across all LLMs, with relative improvements ranging from 2% to 54%. It matched or exceeded question answering without RAG across radiologic subspecialties, particularly in breast imaging and emergency radiology. However, degree of improvement varied among models; GPT-3.5-turbo and Mixtral-8x7B-instruct-v0.1 saw notable gains, while Mistral-7B-instruct-v0.2 showed no improvement, highlighting variability in its effectiveness. LLMs benefit when provided access to domain-specific data beyond their training data. For radiology, RadioRAG establishes a robust framework that substantially improves diagnostic accuracy and factuality in radiological question answering.

On Instabilities of Unsupervised Denoising Diffusion Models in Magnetic Resonance Imaging Reconstruction

Denoising diffusion models offer a promising approach to accelerating magnetic resonance imaging (MRI) and producing diagnostic-level images in an unsupervised manner. However, our study demonstrates that even tiny worst-case potential perturbations transferred from a surrogate model can cause these models to generate fake tissue structures that may mislead clinicians. The transferability of such worst-case perturbations indicates that the robustness of image reconstruction may be compromised due to MR system imperfections or other sources of noise. Moreover, at larger perturbation strengths, diffusion models exhibit Gaussian noise-like artifacts that are distinct from those observed in supervised models and are more challenging to detect. Our results highlight the vulnerability of current state-of-the-art diffusion-based reconstruction models to possible worst-case perturbations and underscore the need for further research to improve their robustness and reliability in clinical settings.

Compute-Efficient Medical Image Classification with Softmax-Free Transformers and Sequence Normalization

The Transformer model has been pivotal in advancing fields such as natural language processing, speech recognition, and computer vision. However, a critical limitation of this model is its quadratic computational and memory complexity relative to the sequence length, which constrains its application to longer sequences. This is especially crucial in medical imaging where high-resolution images can reach gigapixel scale. Efforts to address this issue have predominantely focused on complex techniques, such as decomposing the softmax operation integral to the Transformer's architecture. This paper addresses this quadratic computational complexity of Transformer models and introduces a remarkably simple and effective method that circumvents this issue by eliminating the softmax function from the attention mechanism and adopting a sequence normalization technique for the key, query, and value tokens. Coupled with a reordering of matrix multiplications this approach reduces the memory- and compute complexity to a linear scale. We evaluate this approach across various medical imaging datasets comprising fundoscopic, dermascopic, radiologic and histologic imaging data. Our findings highlight that these models exhibit a comparable performance to traditional transformer models, while efficiently handling longer sequences.

An Ordinal Regression Framework for a Deep Learning Based Severity Assessment for Chest Radiographs

This study investigates the application of ordinal regression methods for categorizing disease severity in chest radiographs. We propose a framework that divides the ordinal regression problem into three parts: a model, a target function, and a classification function. Different encoding methods, including one-hot, Gaussian, progress-bar, and our soft-progress-bar, are applied using ResNet50 and ViT-B-16 deep learning models. We show that the choice of encoding has a strong impact on performance and that the best encoding depends on the chosen weighting of Cohen's kappa and also on the model architecture used. We make our code publicly available on GitHub.

Time-efficient combined morphologic and quantitative joint MRI based on clinical image contrasts -- An exploratory in-situ study of standardized cartilage defects

OBJECTIVES: Quantitative MRI techniques such as T2 and T1$\rho$ mapping are beneficial in evaluating cartilage and meniscus. We aimed to evaluate the MIXTURE (Multi-Interleaved X-prepared Turbo-Spin Echo with IntUitive RElaxometry) sequences that provide morphologic images with clinical turbo spin-echo (TSE) contrasts and additional parameter maps versus reference TSE sequences in an in-situ model of human cartilage defects. MATERIALS AND METHODS: Prospectively, standardized cartilage defects of 8mm, 5mm, and 3mm diameter were created in the lateral femora of 10 human cadaveric knee specimens (81$\pm$10 years, nine male/one female). Using a clinical 3T MRI scanner and knee coil, MIXTURE sequences combining (i) proton-density weighted fat-saturated (PD-w FS) images and T2 maps and (ii) T1-weighted images and T1$\rho$ maps were acquired before and after defect creation, alongside the corresponding 2D TSE and 3D TSE reference sequences. Defect delineability, bone texture, and cartilage relaxation times were quantified. Inter-sequence comparisons were made using appropriate parametric and non-parametric tests. RESULTS: Overall, defect delineability and texture features were not significantly different between the MIXTURE and reference sequences. After defect creation, relaxation times increased significantly in the central femur (for T2) and all regions combined (for T1$\rho$). CONCLUSION: MIXTURE sequences permit time-efficient simultaneous morphologic and quantitative joint assessment based on clinical image contrasts. While providing T2 or T1$\rho$ maps in clinically feasible scan time, morphologic image features, i.e., cartilage defect delineability and bone texture, were comparable between MIXTURE and corresponding reference sequences.

Mind the Gap: Federated Learning Broadens Domain Generalization in Diagnostic AI Models

Developing robust artificial intelligence (AI) models that generalize well to unseen datasets is challenging and usually requires large and variable datasets, preferably from multiple institutions. In federated learning (FL), a model is trained collaboratively at numerous sites that hold local datasets without exchanging them. So far, the impact of training strategy, i.e., local versus collaborative, on the diagnostic on-domain and off-domain performance of AI models interpreting chest radiographs has not been assessed. Consequently, using 610,000 chest radiographs from five institutions across the globe, we assessed diagnostic performance as a function of training strategy (i.e., local vs. collaborative), network architecture (i.e., convolutional vs. transformer-based), generalization performance (i.e., on-domain vs. off-domain), imaging finding (i.e., cardiomegaly, pleural effusion, pneumonia, atelectasis, consolidation, pneumothorax, and no abnormality), dataset size (i.e., from n=18,000 to 213,921 radiographs), and dataset diversity. Large datasets not only showed minimal performance gains with FL but, in some instances, even exhibited decreases. In contrast, smaller datasets revealed marked improvements. Thus, on-domain performance was mainly driven by training data size. However, off-domain performance leaned more on training diversity. When trained collaboratively across diverse external institutions, AI models consistently surpassed models trained locally for off-domain tasks, emphasizing FL's potential in leveraging data diversity. In conclusion, FL can bolster diagnostic privacy, reproducibility, and off-domain reliability of AI models and, potentially, optimize healthcare outcomes.

Reconstruction of Patient-Specific Confounders in AI-based Radiologic Image Interpretation using Generative Pretraining

Detecting misleading patterns in automated diagnostic assistance systems, such as those powered by Artificial Intelligence, is critical to ensuring their reliability, particularly in healthcare. Current techniques for evaluating deep learning models cannot visualize confounding factors at a diagnostic level. Here, we propose a self-conditioned diffusion model termed DiffChest and train it on a dataset of 515,704 chest radiographs from 194,956 patients from multiple healthcare centers in the United States and Europe. DiffChest explains classifications on a patient-specific level and visualizes the confounding factors that may mislead the model. We found high inter-reader agreement when evaluating DiffChest's capability to identify treatment-related confounders, with Fleiss' Kappa values of 0.8 or higher across most imaging findings. Confounders were accurately captured with 11.1% to 100% prevalence rates. Furthermore, our pretraining process optimized the model to capture the most relevant information from the input radiographs. DiffChest achieved excellent diagnostic accuracy when diagnosing 11 chest conditions, such as pleural effusion and cardiac insufficiency, and at least sufficient diagnostic accuracy for the remaining conditions. Our findings highlight the potential of pretraining based on diffusion models in medical image classification, specifically in providing insights into confounding factors and model robustness.

Medical Foundation Models are Susceptible to Targeted Misinformation Attacks

Large language models (LLMs) have broad medical knowledge and can reason about medical information across many domains, holding promising potential for diverse medical applications in the near future. In this study, we demonstrate a concerning vulnerability of LLMs in medicine. Through targeted manipulation of just 1.1% of the model's weights, we can deliberately inject an incorrect biomedical fact. The erroneous information is then propagated in the model's output, whilst its performance on other biomedical tasks remains intact. We validate our findings in a set of 1,038 incorrect biomedical facts. This peculiar susceptibility raises serious security and trustworthiness concerns for the application of LLMs in healthcare settings. It accentuates the need for robust protective measures, thorough verification mechanisms, and stringent management of access to these models, ensuring their reliable and safe use in medical practice.

Empowering Clinicians and Democratizing Data Science: Large Language Models Automate Machine Learning for Clinical Studies

A knowledge gap persists between Machine Learning (ML) developers (e.g., data scientists) and practitioners (e.g., clinicians), hampering the full utilization of ML for clinical data analysis. We investigated the potential of the chatGPT Advanced Data Analysis (ADA), an extension of GPT-4, to bridge this gap and perform ML analyses efficiently. Real-world clinical datasets and study details from large trials across various medical specialties were presented to chatGPT ADA without specific guidance. ChatGPT ADA autonomously developed state-of-the-art ML models based on the original study's training data to predict clinical outcomes such as cancer development, cancer progression, disease complications, or biomarkers such as pathogenic gene sequences. Strikingly, these ML models matched or outperformed their published counterparts. We conclude that chatGPT ADA offers a promising avenue to democratize ML in medicine, making advanced analytics accessible to non-ML experts and promoting broader applications in medical research and practice.