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.

Biomedical Large Languages Models Seem not to be Superior to Generalist Models on Unseen Medical Data

Large language models (LLMs) have shown potential in biomedical applications, leading to efforts to fine-tune them on domain-specific data. However, the effectiveness of this approach remains unclear. This study evaluates the performance of biomedically fine-tuned LLMs against their general-purpose counterparts on a variety of clinical tasks. We evaluated their performance on clinical case challenges from the New England Journal of Medicine (NEJM) and the Journal of the American Medical Association (JAMA) and on several clinical tasks (e.g., information extraction, document summarization, and clinical coding). Using benchmarks specifically chosen to be likely outside the fine-tuning datasets of biomedical models, we found that biomedical LLMs mostly perform inferior to their general-purpose counterparts, especially on tasks not focused on medical knowledge. While larger models showed similar performance on case tasks (e.g., OpenBioLLM-70B: 66.4% vs. Llama-3-70B-Instruct: 65% on JAMA cases), smaller biomedical models showed more pronounced underperformance (e.g., OpenBioLLM-8B: 30% vs. Llama-3-8B-Instruct: 64.3% on NEJM cases). Similar trends were observed across the CLUE (Clinical Language Understanding Evaluation) benchmark tasks, with general-purpose models often performing better on text generation, question answering, and coding tasks. Our results suggest that fine-tuning LLMs to biomedical data may not provide the expected benefits and may potentially lead to reduced performance, challenging prevailing assumptions about domain-specific adaptation of LLMs and highlighting the need for more rigorous evaluation frameworks in healthcare AI. Alternative approaches, such as retrieval-augmented generation, may be more effective in enhancing the biomedical capabilities of LLMs without compromising their general knowledge.

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.

LongHealth: A Question Answering Benchmark with Long Clinical Documents

Background: Recent advancements in large language models (LLMs) offer potential benefits in healthcare, particularly in processing extensive patient records. However, existing benchmarks do not fully assess LLMs' capability in handling real-world, lengthy clinical data. Methods: We present the LongHealth benchmark, comprising 20 detailed fictional patient cases across various diseases, with each case containing 5,090 to 6,754 words. The benchmark challenges LLMs with 400 multiple-choice questions in three categories: information extraction, negation, and sorting, challenging LLMs to extract and interpret information from large clinical documents. Results: We evaluated nine open-source LLMs with a minimum of 16,000 tokens and also included OpenAI's proprietary and cost-efficient GPT-3.5 Turbo for comparison. The highest accuracy was observed for Mixtral-8x7B-Instruct-v0.1, particularly in tasks focused on information retrieval from single and multiple patient documents. However, all models struggled significantly in tasks requiring the identification of missing information, highlighting a critical area for improvement in clinical data interpretation. Conclusion: While LLMs show considerable potential for processing long clinical documents, their current accuracy levels are insufficient for reliable clinical use, especially in scenarios requiring the identification of missing information. The LongHealth benchmark provides a more realistic assessment of LLMs in a healthcare setting and highlights the need for further model refinement for safe and effective clinical application. We make the benchmark and evaluation code publicly available.

From Text to Image: Exploring GPT-4Vision's Potential in Advanced Radiological Analysis across Subspecialties

The study evaluates and compares GPT-4 and GPT-4Vision for radiological tasks, suggesting GPT-4Vision may recognize radiological features from images, thereby enhancing its diagnostic potential over text-based descriptions.

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.

Transformers for CT Reconstruction From Monoplanar and Biplanar Radiographs

Computed Tomography (CT) scans provide detailed and accurate information of internal structures in the body. They are constructed by sending x-rays through the body from different directions and combining this information into a three-dimensional volume. Such volumes can then be used to diagnose a wide range of conditions and allow for volumetric measurements of organs. In this work, we tackle the problem of reconstructing CT images from biplanar x-rays only. X-rays are widely available and even if the CT reconstructed from these radiographs is not a replacement of a complete CT in the diagnostic setting, it might serve to spare the patients from radiation where a CT is only acquired for rough measurements such as determining organ size. We propose a novel method based on the transformer architecture, by framing the underlying task as a language translation problem. Radiographs and CT images are first embedded into latent quantized codebook vectors using two different autoencoder networks. We then train a GPT model, to reconstruct the codebook vectors of the CT image, conditioned on the codebook vectors of the x-rays and show that this approach leads to realistic looking images. To encourage further research in this direction, we make our code publicly available on GitHub: XXX.