Showing 1–31 of 31 results for author: Bluethgen, C

Sparse Concept Channels in Frozen 3D CT Vision Encoders

Authors: Farhad Nooralahzadeh, Lea Bogensperger, Christian Bluethgen, Michael Krauthammer

Abstract: Large vision-language models are becoming increasingly dominant in 3D medical image interpretation, but we rarely know <i>which</i> internal units encode clinical findings or <i>where</i> that information lives in the representation. We first study this on a 3D chest vision-language model (Pillar-0) by probing its frozen vision embeddings. We show that (i) each radiological finding is encoded by a… ▽ More Large vision-language models are becoming increasingly dominant in 3D medical image interpretation, but we rarely know <i>which</i> internal units encode clinical findings or <i>where</i> that information lives in the representation. We first study this on a 3D chest vision-language model (Pillar-0) by probing its frozen vision embeddings. We show that (i) each radiological finding is encoded by a <i>sparse</i> set of ~10 vision-encoder channels that match full-feature classification performance and far exceed a zero-shot text prompting; (ii) turning off the channels tied to one finding, that finding's score collapses while unrelated labels stay stable; and (iii) the same sparse probe <i>replicates</i> on an architecturally unrelated 3D abdominal VLM (Merlin) suggesting a general property of frozen medical encoders. Our training-free concept channel probe (CCP) method, paired with a corpus-derived report template, outperforms published CT-CHAT on clinical efficacy and NLG metrics (F1 0.549 vs. 0.184; BLEU 0.483 vs. 0.373) at 22x lower latency. Our results provide a clear, reproducible characterization of how frozen medical encoders represent findings, demonstrating direct applicability across models. △ Less

Submitted 23 July, 2026; originally announced July 2026.

CheXanatomy: Anatomy-Aware Vision-Language Modeling for Chest Radiographs

Authors: Sergios Gatidis, Curtis Langlotz, Christian Bluethgen

Abstract: Vision-language models (VLMs) pretrained on large-scale image-text pairs demonstrate strong image-level understanding, but are primarily optimized for global alignment and do not explicitly encode fine-grained anatomical structure, limiting their suitability for spatially precise tasks such as segmentation. We introduce CheXanatomy, a framework that integrates explicit anatomical knowledge into a… ▽ More Vision-language models (VLMs) pretrained on large-scale image-text pairs demonstrate strong image-level understanding, but are primarily optimized for global alignment and do not explicitly encode fine-grained anatomical structure, limiting their suitability for spatially precise tasks such as segmentation. We introduce CheXanatomy, a framework that integrates explicit anatomical knowledge into a pretrained VLM through autoregressive token-space supervision. Instead of adding task-specific decoder heads, the model is trained to generate anatomical segmentation masks via next-token prediction. To enable scalable supervision, we synthesize realistic chest radiographs from CT volumes and forward-project CT segmentation labels to obtain anatomically consistent 2D masks. We evaluate the approach on synthetic and real chest radiographs against a U-Net baseline, including ablations on model scale, input resolution, and vision encoder fine-tuning. Autoregressive anatomical supervision achieves performance comparable to specialized convolutional models in-distribution and demonstrates improved geometric robustness under domain shift to real CXR data. In addition, anatomy-pretrained models exhibit improved sample efficiency when adapting to novel localization tasks under limited supervision. Larger models and higher input image resolution improve performance, while vision encoder fine-tuning has limited effect. These results show that embedding anatomical structure directly into the generative objective promotes spatially grounded representations and supports anatomy-aware medical vision-language modeling. △ Less

Submitted 24 June, 2026; v1 submitted 6 June, 2026; originally announced June 2026.

Universal Boosts, Specific Suppressors: Sparse Autoencoder Steering of Medical Vision-Language Models

Authors: Farhad Nooralahzadeh, Benjamin Gundersen, Nicolas Deperrois, Hidetoshi Matsuom, Mizuho Nishio, Thomas Frauenfelder, Ahmed Allam, Christian Blüthgen, Michael Moor, Michael Krauthammer

Abstract: Medical vision-language models (VLMs) often hallucinate findings when generating chest X-ray reports: they fabricate findings that are not present in the image, miss important ones, or locate them incorrectly. We mitigate this without weight updates by decoding-time residual steering on a per-token sparse autoencoder (SAE) basis: Top-$K$ SAEs on late layers, causal steering against clinical errors… ▽ More Medical vision-language models (VLMs) often hallucinate findings when generating chest X-ray reports: they fabricate findings that are not present in the image, miss important ones, or locate them incorrectly. We mitigate this without weight updates by decoding-time residual steering on a per-token sparse autoencoder (SAE) basis: Top-$K$ SAEs on late layers, causal steering against clinical errors, then combined suppress/boost intervention at inference time. On the MIMIC-CXR test split, our inference-only method improves the quality of generated reports for three radiology VLMs (RadVLM, LLaVA-Rad, and CheXOne), with relative improvements of +5.4%, +7.2%, and +17.0% in the clinical composite metric, and statistically significant GREEN gains on all backbones. A cross-model feature alignment shows that the quality-promoting (boost) directions overlap strongly across architectures, whereas hallucination-linked (suppress) directions are model-specific. Therefore, transferable steering must treat suppression per-backbone, rather than sharing a universal suppress list. The same recipe transfers zero-shot to IU-Xray (Green $+7.7\%$ rel.) without retraining, confirming that the identified features are properties of the model, not of the training corpus. We release causal feature sets and an interactive feature dashboard: https://cxr-sparse-feature-dashboard.netlify.app/. △ Less

Submitted 24 May, 2026; originally announced May 2026.

CheXthought: A global multimodal dataset of clinical chain-of-thought reasoning and visual attention for chest X-ray interpretation

Authors: Sonali Sharma, Jin Long, George Shih, Sarah Eid, Christian Bluethgen, Francine L. Jacobson, Emily B. Tsai, Global Radiology Consortium, Ahmed M. Alaa, Curtis P. Langlotz

Abstract: Chest X-ray interpretation is one of the most frequently performed diagnostic tasks in medicine and a primary target for AI development, yet current vision-language models are primarily trained on datasets of paired images and reports, not the cognitive processes and visual attention that underlie clinical reasoning. Here, we present CheXthought, a global, multimodal resource containing 103,592 ch… ▽ More Chest X-ray interpretation is one of the most frequently performed diagnostic tasks in medicine and a primary target for AI development, yet current vision-language models are primarily trained on datasets of paired images and reports, not the cognitive processes and visual attention that underlie clinical reasoning. Here, we present CheXthought, a global, multimodal resource containing 103,592 chain-of-thought reasoning traces and 6,609,082 synchronized visual attention annotations across 50,312 multi-read chest X-rays from 501 radiologists in 71 countries. Our analysis reveals clinical reasoning patterns in how experts deploy distinct visual search strategies, integrate clinical context, and communicate uncertainty. We demonstrate the clinical utility of CheXthought across four dimensions. First, CheXthought reasoning significantly outperforms state-of-the-art vision-language model chain-of-thought in factual accuracy and spatial grounding. Second, visual attention data used as an inference-time hint recovers missed findings and significantly reduces hallucinations. Third, vision-language models trained on CheXthought data achieve significantly stronger pathology classification, visual faithfulness, temporal reasoning and uncertainty communication. Fourth, leveraging CheXthought's multi-reader annotations, we predict both human-human and human-AI disagreement directly from an image, enabling transparent communication of case difficulty, uncertainty and model reliability. These findings establish CheXthought as a resource for advancing multimodal clinical reasoning and the development of more transparent, interpretable vision-language models. △ Less

Submitted 30 April, 2026; v1 submitted 29 April, 2026; originally announced April 2026.

Comments: 51 pages, 7 figures, 10 tables

RadAgent: A tool-using AI agent for stepwise interpretation of chest computed tomography

Authors: Mélanie Roschewitz, Kenneth Styppa, Yitian Tao, Jiwoong Sohn, Jean-Benoit Delbrouck, Benjamin Gundersen, Nicolas Deperrois, Christian Bluethgen, Julia E. Vogt, Bjoern Menze, Farhad Nooralahzadeh, Michael Krauthammer, Michael Moor

Abstract: Vision-language models (VLM) have markedly advanced AI-driven interpretation and reporting of complex medical imaging, such as computed tomography (CT). Yet, existing methods largely relegate clinicians to passive observers of final outputs, offering no interpretable reasoning trace for them to inspect, validate, or refine. To address this, we introduce RadAgent, a tool-using AI agent that generat… ▽ More Vision-language models (VLM) have markedly advanced AI-driven interpretation and reporting of complex medical imaging, such as computed tomography (CT). Yet, existing methods largely relegate clinicians to passive observers of final outputs, offering no interpretable reasoning trace for them to inspect, validate, or refine. To address this, we introduce RadAgent, a tool-using AI agent that generates CT reports through a stepwise and interpretable process. Each resulting report is accompanied by a fully inspectable trace of intermediate decisions and tool interactions, allowing clinicians to examine how the reported findings are derived. In our experiments, we observe that RadAgent improves chest CT report generation over its 3D VLM counterpart, CT-Chat, across three dimensions. Clinical accuracy improves by 5.8 points (35.4% relative) in macro-F1 and 5.1 points (18.6% relative) in micro-F1. Robustness under adversarial conditions improves by 24.7 points (41.9% relative). Furthermore, RadAgent achieves 37.0% in faithfulness, a new capability entirely absent in its 3D VLM counterpart. By structuring the interpretation of chest CT as an explicit, tool-augmented and iterative reasoning trace, RadAgent brings us closer toward transparent and reliable AI for radiology. △ Less

Submitted 1 June, 2026; v1 submitted 16 April, 2026; originally announced April 2026.

A Reasoning-Enabled Vision-Language Foundation Model for Chest X-ray Interpretation

Authors: Yabin Zhang, Chong Wang, Yunhe Gao, Jiaming Liu, Maya Varma, Justin Xu, Sophie Ostmeier, Jin Long, Sergios Gatidis, Seena Dehkharghani, Arne Michalson, Eun Kyoung Hong, Christian Bluethgen, Haiwei Henry Guo, Alexander Victor Ortiz, Stephan Altmayer, Sandhya Bodapati, Joseph David Janizek, Ken Chang, Jean-Benoit Delbrouck, Akshay S. Chaudhari, Curtis P. Langlotz

Abstract: Chest X-rays (CXRs) are among the most frequently performed imaging examinations worldwide, yet rising imaging volumes increase radiologist workload and the risk of diagnostic errors. Although artificial intelligence (AI) systems have shown promise for CXR interpretation, most generate only final predictions, without making explicit how visual evidence is translated into radiographic findings and… ▽ More Chest X-rays (CXRs) are among the most frequently performed imaging examinations worldwide, yet rising imaging volumes increase radiologist workload and the risk of diagnostic errors. Although artificial intelligence (AI) systems have shown promise for CXR interpretation, most generate only final predictions, without making explicit how visual evidence is translated into radiographic findings and diagnostic predictions. We present CheXOne, a reasoning-enabled vision-language model for CXR interpretation. CheXOne jointly generates diagnostic predictions and explicit, clinically grounded reasoning traces that connect visual evidence, radiographic findings, and these predictions. The model is trained on 14.7 million instruction and reasoning samples curated from 30 public datasets spanning 36 CXR interpretation tasks, using a two-stage framework that combines instruction tuning with reinforcement learning to improve reasoning quality. We evaluate CheXOne in zero-shot settings across visual question answering, report generation, visual grounding and reasoning assessment, covering 17 evaluation settings. CheXOne outperforms existing medical and general-domain foundation models and achieves strong performance on independent public benchmarks. A clinical reader study demonstrates that CheXOne-drafted reports are comparable to or better than resident-written reports in 55% of cases, while effectively addressing clinical indications and enhancing both report writing and CXR interpretation efficiency. Further analyses involving radiologists reveal that the generated reasoning traces show high clinical factuality and provide causal support for the final predictions, offering a plausible explanation for the performance gains. These results suggest that explicit reasoning can improve model performance, interpretability and clinical utility in AI-assisted CXR interpretation. △ Less

Submitted 1 April, 2026; originally announced April 2026.

Comments: Codes: https://github.com/YBZh/CheXOne Models: https://huggingface.co/StanfordAIMI/CheXOne

Agentic Systems in Radiology: Design, Applications, Evaluation, and Challenges

Authors: Christian Bluethgen, Dave Van Veen, Daniel Truhn, Jakob Nikolas Kather, Michael Moor, Malgorzata Polacin, Akshay Chaudhari, Thomas Frauenfelder, Curtis P. Langlotz, Michael Krauthammer, Farhad Nooralahzadeh

Abstract: Building agents, systems that perceive and act upon their environment with a degree of autonomy, has long been a focus of AI research. This pursuit has recently become vastly more practical with the emergence of large language models (LLMs) capable of using natural language to integrate information, follow instructions, and perform forms of "reasoning" and planning across a wide range of tasks. Wi… ▽ More Building agents, systems that perceive and act upon their environment with a degree of autonomy, has long been a focus of AI research. This pursuit has recently become vastly more practical with the emergence of large language models (LLMs) capable of using natural language to integrate information, follow instructions, and perform forms of "reasoning" and planning across a wide range of tasks. With its multimodal data streams and orchestrated workflows spanning multiple systems, radiology is uniquely suited to benefit from agents that can adapt to context and automate repetitive yet complex tasks. In radiology, LLMs and their multimodal variants have already demonstrated promising performance for individual tasks such as information extraction and report summarization. However, using LLMs in isolation underutilizes their potential to support complex, multi-step workflows where decisions depend on evolving context from multiple information sources. Equipping LLMs with external tools and feedback mechanisms enables them to drive systems that exhibit a spectrum of autonomy, ranging from semi-automated workflows to more adaptive agents capable of managing complex processes. This review examines the design of such LLM-driven agentic systems, highlights key applications, discusses evaluation methods for planning and tool use, and outlines challenges such as error cascades, tool-use efficiency, and health IT integration. △ Less

Submitted 13 October, 2025; v1 submitted 10 October, 2025; originally announced October 2025.

Improving Performance, Robustness, and Fairness of Radiographic AI Models with Finely-Controllable Synthetic Data

Authors: Stefania L. Moroianu, Christian Bluethgen, Pierre Chambon, Mehdi Cherti, Jean-Benoit Delbrouck, Magdalini Paschali, Brandon Price, Judy Gichoya, Jenia Jitsev, Curtis P. Langlotz, Akshay S. Chaudhari

Abstract: Achieving robust performance and fairness across diverse patient populations remains a challenge in developing clinically deployable deep learning models for diagnostic imaging. Synthetic data generation has emerged as a promising strategy to address limitations in dataset scale and diversity. We introduce RoentGen-v2, a text-to-image diffusion model for chest radiographs that enables fine-grained… ▽ More Achieving robust performance and fairness across diverse patient populations remains a challenge in developing clinically deployable deep learning models for diagnostic imaging. Synthetic data generation has emerged as a promising strategy to address limitations in dataset scale and diversity. We introduce RoentGen-v2, a text-to-image diffusion model for chest radiographs that enables fine-grained control over both radiographic findings and patient demographic attributes, including sex, age, and race/ethnicity. RoentGen-v2 is the first model to generate clinically plausible images with demographic conditioning, facilitating the creation of a large, demographically balanced synthetic dataset comprising over 565,000 images. We use this large synthetic dataset to evaluate optimal training pipelines for downstream disease classification models. In contrast to prior work that combines real and synthetic data naively, we propose an improved training strategy that leverages synthetic data for supervised pretraining, followed by fine-tuning on real data. Through extensive evaluation on over 137,000 chest radiographs from five institutions, we demonstrate that synthetic pretraining consistently improves model performance, generalization to out-of-distribution settings, and fairness across demographic subgroups. Across datasets, synthetic pretraining led to a 6.5% accuracy increase in the performance of downstream classification models, compared to a modest 2.7% increase when naively combining real and synthetic data. We observe this performance improvement simultaneously with the reduction of the underdiagnosis fairness gap by 19.3%. These results highlight the potential of synthetic imaging to advance equitable and generalizable medical deep learning under real-world data constraints. We open source our code, trained models, and synthetic dataset at https://github.com/StanfordMIMI/RoentGen-v2 . △ Less

Submitted 22 August, 2025; originally announced August 2025.

MedVAL: Toward Expert-Level Medical Text Validation with Language Models

Authors: Asad Aali, Vasiliki Bikia, Maya Varma, Nicole Chiou, Sophie Ostmeier, Arnav Singhvi, Magdalini Paschali, Ashwin Kumar, Andrew Johnston, Karimar Amador-Martinez, Eduardo Juan Perez Guerrero, Paola Naovi Cruz Rivera, Sergios Gatidis, Christian Bluethgen, Eduardo Pontes Reis, Eddy D. Zandee van Rilland, Poonam Laxmappa Hosamani, Kevin R Keet, Minjoung Go, Evelyn Ling, David B. Larson, Curtis Langlotz, Roxana Daneshjou, Jason Hom, Sanmi Koyejo , et al. (2 additional authors not shown)

Abstract: With the growing use of language models (LMs) in clinical environments, there is an immediate need to evaluate the accuracy and safety of LM-generated medical text. Currently, such evaluation relies solely on manual physician review. However, detecting errors in LM-generated text is challenging because 1) manual review is costly and 2) expert-composed reference outputs are often unavailable in rea… ▽ More With the growing use of language models (LMs) in clinical environments, there is an immediate need to evaluate the accuracy and safety of LM-generated medical text. Currently, such evaluation relies solely on manual physician review. However, detecting errors in LM-generated text is challenging because 1) manual review is costly and 2) expert-composed reference outputs are often unavailable in real-world settings. While the "LLM-as-a-judge" paradigm offers scalable evaluation, even frontier LMs can miss subtle but clinically significant errors. We propose MedVAL, a novel, self-supervised, data-efficient distillation method that leverages synthetic data to train evaluator LMs to assess whether LM-generated medical outputs are factually consistent with inputs, without requiring physician labels or reference outputs. To evaluate LM performance, we introduce MedVAL-Bench, a dataset of 840 physician-annotated outputs across 6 diverse medical tasks capturing real-world challenges. Across 10 state-of-the-art LMs spanning open-source and proprietary models, MedVAL distillation significantly improves (p < 0.001) alignment with physicians across seen and unseen tasks, increasing average F1 scores from 66% to 83%. Despite strong baseline performance, MedVAL improves the best-performing proprietary LM (GPT-4o) by 8% without training on physician-labeled data, demonstrating a performance statistically non-inferior to a single human expert on a subset annotated by multiple physicians (p < 0.001). To support a scalable, risk-aware pathway towards clinical integration, we open-source: 1) Codebase (https://github.com/StanfordMIMI/MedVAL), 2) MedVAL-Bench (https://huggingface.co/datasets/stanfordmimi/MedVAL-Bench), 3) MedVAL-4B (https://huggingface.co/stanfordmimi/MedVAL-4B). Our benchmark provides evidence of LMs approaching expert-level ability in validating AI-generated medical text. △ Less

Submitted 6 February, 2026; v1 submitted 3 July, 2025; originally announced July 2025.

SMMILE: An Expert-Driven Benchmark for Multimodal Medical In-Context Learning

Authors: Melanie Rieff, Maya Varma, Ossian Rabow, Subathra Adithan, Julie Kim, Ken Chang, Hannah Lee, Nidhi Rohatgi, Christian Bluethgen, Mohamed S. Muneer, Jean-Benoit Delbrouck, Michael Moor

Abstract: Multimodal in-context learning (ICL) remains underexplored despite significant potential for domains such as medicine. Clinicians routinely encounter diverse, specialized tasks requiring adaptation from limited examples, such as drawing insights from a few relevant prior cases or considering a constrained set of differential diagnoses. While multimodal large language models (MLLMs) have shown adva… ▽ More Multimodal in-context learning (ICL) remains underexplored despite significant potential for domains such as medicine. Clinicians routinely encounter diverse, specialized tasks requiring adaptation from limited examples, such as drawing insights from a few relevant prior cases or considering a constrained set of differential diagnoses. While multimodal large language models (MLLMs) have shown advances in medical visual question answering (VQA), their ability to learn multimodal tasks from context is largely unknown. We introduce SMMILE, the first expert-driven multimodal ICL benchmark for medical tasks. Eleven medical experts curated problems, each including a multimodal query and multimodal in-context examples as task demonstrations. SMMILE encompasses 111 problems (517 question-image-answer triplets) covering 6 medical specialties and 13 imaging modalities. We further introduce SMMILE++, an augmented variant with 1038 permuted problems. A comprehensive evaluation of 15 MLLMs demonstrates that most models exhibit moderate to poor multimodal ICL ability in medical tasks. In open-ended evaluations, ICL contributes only an 8% average improvement over zero-shot on SMMILE and 9.4% on SMMILE++. We observe a susceptibility for irrelevant in-context examples: even a single noisy or irrelevant example can degrade performance by up to 9.5%. Moreover, we observe that MLLMs are affected by a recency bias, where placing the most relevant example last can lead to substantial performance improvements of up to 71%. Our findings highlight critical limitations and biases in current MLLMs when learning multimodal medical tasks from context. SMMILE is available at https://smmile-benchmark.github.io. △ Less

Submitted 5 February, 2026; v1 submitted 26 June, 2025; originally announced June 2025.

Comments: NeurIPS 2025 (Datasets & Benchmarks Track)

Automated Structured Radiology Report Generation

Authors: Jean-Benoit Delbrouck, Justin Xu, Johannes Moll, Alois Thomas, Zhihong Chen, Sophie Ostmeier, Asfandyar Azhar, Kelvin Zhenghao Li, Andrew Johnston, Christian Bluethgen, Eduardo Reis, Mohamed Muneer, Maya Varma, Curtis Langlotz

Abstract: Automated radiology report generation from chest X-ray (CXR) images has the potential to improve clinical efficiency and reduce radiologists' workload. However, most datasets, including the publicly available MIMIC-CXR and CheXpert Plus, consist entirely of free-form reports, which are inherently variable and unstructured. This variability poses challenges for both generation and evaluation: exist… ▽ More Automated radiology report generation from chest X-ray (CXR) images has the potential to improve clinical efficiency and reduce radiologists' workload. However, most datasets, including the publicly available MIMIC-CXR and CheXpert Plus, consist entirely of free-form reports, which are inherently variable and unstructured. This variability poses challenges for both generation and evaluation: existing models struggle to produce consistent, clinically meaningful reports, and standard evaluation metrics fail to capture the nuances of radiological interpretation. To address this, we introduce Structured Radiology Report Generation (SRRG), a new task that reformulates free-text radiology reports into a standardized format, ensuring clarity, consistency, and structured clinical reporting. We create a novel dataset by restructuring reports using large language models (LLMs) following strict structured reporting desiderata. Additionally, we introduce SRR-BERT, a fine-grained disease classification model trained on 55 labels, enabling more precise and clinically informed evaluation of structured reports. To assess report quality, we propose F1-SRR-BERT, a metric that leverages SRR-BERT's hierarchical disease taxonomy to bridge the gap between free-text variability and structured clinical reporting. We validate our dataset through a reader study conducted by five board-certified radiologists and extensive benchmarking experiments. △ Less

Submitted 2 June, 2025; v1 submitted 30 May, 2025; originally announced May 2025.

Comments: Accepted to ACL Main 2025

MedVAE: Efficient Automated Interpretation of Medical Images with Large-Scale Generalizable Autoencoders

Authors: Maya Varma, Ashwin Kumar, Rogier van der Sluijs, Sophie Ostmeier, Louis Blankemeier, Pierre Chambon, Christian Bluethgen, Jip Prince, Curtis Langlotz, Akshay Chaudhari

Abstract: Medical images are acquired at high resolutions with large fields of view in order to capture fine-grained features necessary for clinical decision-making. Consequently, training deep learning models on medical images can incur large computational costs. In this work, we address the challenge of downsizing medical images in order to improve downstream computational efficiency while preserving clin… ▽ More Medical images are acquired at high resolutions with large fields of view in order to capture fine-grained features necessary for clinical decision-making. Consequently, training deep learning models on medical images can incur large computational costs. In this work, we address the challenge of downsizing medical images in order to improve downstream computational efficiency while preserving clinically-relevant features. We introduce MedVAE, a family of six large-scale 2D and 3D autoencoders capable of encoding medical images as downsized latent representations and decoding latent representations back to high-resolution images. We train MedVAE autoencoders using a novel two-stage training approach with 1,052,730 medical images. Across diverse tasks obtained from 20 medical image datasets, we demonstrate that (1) utilizing MedVAE latent representations in place of high-resolution images when training downstream models can lead to efficiency benefits (up to 70x improvement in throughput) while simultaneously preserving clinically-relevant features and (2) MedVAE can decode latent representations back to high-resolution images with high fidelity. Our work demonstrates that large-scale, generalizable autoencoders can help address critical efficiency challenges in the medical domain. Our code is available at https://github.com/StanfordMIMI/MedVAE. △ Less

Submitted 2 June, 2025; v1 submitted 20 February, 2025; originally announced February 2025.

Comments: MIDL 2025 (Oral)

RadVLM: A Multitask Conversational Vision-Language Model for Radiology

Authors: Nicolas Deperrois, Hidetoshi Matsuo, Samuel Ruipérez-Campillo, Moritz Vandenhirtz, Sonia Laguna, Alain Ryser, Koji Fujimoto, Mizuho Nishio, Thomas M. Sutter, Julia E. Vogt, Jonas Kluckert, Thomas Frauenfelder, Christian Blüthgen, Farhad Nooralahzadeh, Michael Krauthammer

Abstract: The widespread use of chest X-rays (CXRs), coupled with a shortage of radiologists, has driven growing interest in automated CXR analysis and AI-assisted reporting. While existing vision-language models (VLMs) show promise in specific tasks such as report generation or abnormality detection, they often lack support for interactive diagnostic capabilities. In this work we present RadVLM, a compact,… ▽ More The widespread use of chest X-rays (CXRs), coupled with a shortage of radiologists, has driven growing interest in automated CXR analysis and AI-assisted reporting. While existing vision-language models (VLMs) show promise in specific tasks such as report generation or abnormality detection, they often lack support for interactive diagnostic capabilities. In this work we present RadVLM, a compact, multitask conversational foundation model designed for CXR interpretation. To this end, we curate a large-scale instruction dataset comprising over 1 million image-instruction pairs containing both single-turn tasks -- such as report generation, abnormality classification, and visual grounding -- and multi-turn, multi-task conversational interactions. After fine-tuning RadVLM on this instruction dataset, we evaluate it across different tasks along with re-implemented baseline VLMs. Our results show that RadVLM achieves state-of-the-art performance in conversational capabilities and visual grounding while remaining competitive in other radiology tasks. Ablation studies further highlight the benefit of joint training across multiple tasks, particularly for scenarios with limited annotated data. Together, these findings highlight the potential of RadVLM as a clinically relevant AI assistant, providing structured CXR interpretation and conversational capabilities to support more effective and accessible diagnostic workflows. △ Less

Submitted 10 October, 2025; v1 submitted 5 February, 2025; originally announced February 2025.

Comments: 21 pages, 15 figures

Best Practices for Large Language Models in Radiology

Authors: Christian Bluethgen, Dave Van Veen, Cyril Zakka, Katherine Link, Aaron Fanous, Roxana Daneshjou, Thomas Frauenfelder, Curtis Langlotz, Sergios Gatidis, Akshay Chaudhari

Abstract: At the heart of radiological practice is the challenge of integrating complex imaging data with clinical information to produce actionable insights. Nuanced application of language is key for various activities, including managing requests, describing and interpreting imaging findings in the context of clinical data, and concisely documenting and communicating the outcomes. The emergence of large… ▽ More At the heart of radiological practice is the challenge of integrating complex imaging data with clinical information to produce actionable insights. Nuanced application of language is key for various activities, including managing requests, describing and interpreting imaging findings in the context of clinical data, and concisely documenting and communicating the outcomes. The emergence of large language models (LLMs) offers an opportunity to improve the management and interpretation of the vast data in radiology. Despite being primarily general-purpose, these advanced computational models demonstrate impressive capabilities in specialized language-related tasks, even without specific training. Unlocking the potential of LLMs for radiology requires basic understanding of their foundations and a strategic approach to navigate their idiosyncrasies. This review, drawing from practical radiology and machine learning expertise and recent literature, provides readers insight into the potential of LLMs in radiology. It examines best practices that have so far stood the test of time in the rapidly evolving landscape of LLMs. This includes practical advice for optimizing LLM characteristics for radiology practices along with limitations, effective prompting, and fine-tuning strategies. △ Less

Submitted 2 December, 2024; originally announced December 2024.

Comments: A redacted version of this preprint has been accepted for publication in Radiology

Journal ref: Radiology 2025

Foundation Models in Radiology: What, How, When, Why and Why Not

Authors: Magdalini Paschali, Zhihong Chen, Louis Blankemeier, Maya Varma, Alaa Youssef, Christian Bluethgen, Curtis Langlotz, Sergios Gatidis, Akshay Chaudhari

Abstract: Recent advances in artificial intelligence have witnessed the emergence of large-scale deep learning models capable of interpreting and generating both textual and imaging data. Such models, typically referred to as foundation models, are trained on extensive corpora of unlabeled data and demonstrate high performance across various tasks. Foundation models have recently received extensive attentio… ▽ More Recent advances in artificial intelligence have witnessed the emergence of large-scale deep learning models capable of interpreting and generating both textual and imaging data. Such models, typically referred to as foundation models, are trained on extensive corpora of unlabeled data and demonstrate high performance across various tasks. Foundation models have recently received extensive attention from academic, industry, and regulatory bodies. Given the potentially transformative impact that foundation models can have on the field of radiology, this review aims to establish a standardized terminology concerning foundation models, with a specific focus on the requirements of training data, model training paradigms, model capabilities, and evaluation strategies. We further outline potential pathways to facilitate the training of radiology-specific foundation models, with a critical emphasis on elucidating both the benefits and challenges associated with such models. Overall, we envision that this review can unify technical advances and clinical needs in the training of foundation models for radiology in a safe and responsible manner, for ultimately benefiting patients, providers, and radiologists. △ Less

Submitted 6 February, 2025; v1 submitted 27 November, 2024; originally announced November 2024.

Comments: This pre-print has been accepted for publication in Radiology. (DOI for the peer-reviewed article: 10.1148/radiol.240597)

Evaluating and Improving the Effectiveness of Synthetic Chest X-Rays for Medical Image Analysis

Authors: Eva Prakash, Jeya Maria Jose Valanarasu, Zhihong Chen, Eduardo Pontes Reis, Andrew Johnston, Anuj Pareek, Christian Bluethgen, Sergios Gatidis, Cameron Olsen, Akshay Chaudhari, Andrew Ng, Curtis Langlotz

Abstract: Purpose: To explore best-practice approaches for generating synthetic chest X-ray images and augmenting medical imaging datasets to optimize the performance of deep learning models in downstream tasks like classification and segmentation. Materials and Methods: We utilized a latent diffusion model to condition the generation of synthetic chest X-rays on text prompts and/or segmentation masks. We e… ▽ More Purpose: To explore best-practice approaches for generating synthetic chest X-ray images and augmenting medical imaging datasets to optimize the performance of deep learning models in downstream tasks like classification and segmentation. Materials and Methods: We utilized a latent diffusion model to condition the generation of synthetic chest X-rays on text prompts and/or segmentation masks. We explored methods like using a proxy model and using radiologist feedback to improve the quality of synthetic data. These synthetic images were then generated from relevant disease information or geometrically transformed segmentation masks and added to ground truth training set images from the CheXpert, CANDID-PTX, SIIM, and RSNA Pneumonia datasets to measure improvements in classification and segmentation model performance on the test sets. F1 and Dice scores were used to evaluate classification and segmentation respectively. One-tailed t-tests with Bonferroni correction assessed the statistical significance of performance improvements with synthetic data. Results: Across all experiments, the synthetic data we generated resulted in a maximum mean classification F1 score improvement of 0.150453 (CI: 0.099108-0.201798; P=0.0031) compared to using only real data. For segmentation, the maximum Dice score improvement was 0.14575 (CI: 0.108267-0.183233; P=0.0064). Conclusion: Best practices for generating synthetic chest X-ray images for downstream tasks include conditioning on single-disease labels or geometrically transformed segmentation masks, as well as potentially using proxy modeling for fine-tuning such generations. △ Less

Submitted 5 November, 2025; v1 submitted 27 November, 2024; originally announced November 2024.

Journal ref: Proceedings of the IEEE/CVF International Conference on Computer Vision (ICCV) Workshops, October 2025, pages 4413-4421

CheXalign: Preference fine-tuning in chest X-ray interpretation models without human feedback

Authors: Dennis Hein, Zhihong Chen, Sophie Ostmeier, Justin Xu, Maya Varma, Eduardo Pontes Reis, Arne Edward Michalson, Christian Bluethgen, Hyun Joo Shin, Curtis Langlotz, Akshay S Chaudhari

Abstract: Radiologists play a crucial role in translating medical images into actionable reports. However, the field faces staffing shortages and increasing workloads. While automated approaches using vision-language models (VLMs) show promise as assistants, they require exceptionally high accuracy. Most current VLMs in radiology rely solely on supervised fine-tuning. Meanwhile, additional preference fine-t… ▽ More Radiologists play a crucial role in translating medical images into actionable reports. However, the field faces staffing shortages and increasing workloads. While automated approaches using vision-language models (VLMs) show promise as assistants, they require exceptionally high accuracy. Most current VLMs in radiology rely solely on supervised fine-tuning. Meanwhile, additional preference fine-tuning in the post-training pipeline has become standard practice in the general domain. The challenge in radiology lies in the prohibitive cost of obtaining radiologist feedback at scale. To address this challenge, we propose an automated pipeline for preference feedback, focusing on chest X-ray radiology report generation (RRG). Specifically, our method leverages publicly available datasets containing pairs of images and radiologist-written reference reports with reference-based metrics, or Judges, eliminating the need for additional radiologist feedback. We investigate reward overoptimization via length exploitation in this setting and introduce a length-controlled version of the GREEN score. Our best-performing setup achieves state-of-the-art CheXbert scores on the MIMIC-CXR dataset for the RRG task while on average maintaining robust performance across six additional image perception and reasoning tasks. △ Less

Submitted 3 August, 2025; v1 submitted 9 October, 2024; originally announced October 2024.

Comments: ACL 2025

Merlin: A Computed Tomography Vision-Language Foundation Model and Dataset

Authors: Louis Blankemeier, Ashwin Kumar, Joseph Paul Cohen, Jiaming Liu, Longchao Liu, Dave Van Veen, Syed Jamal Safdar Gardezi, Hongkun Yu, Magdalini Paschali, Zhihong Chen, Jean-Benoit Delbrouck, Eduardo Reis, Robbie Holland, Cesar Truyts, Christian Bluethgen, Yufu Wu, Long Lian, Malte Engmann Kjeldskov Jensen, Sophie Ostmeier, Maya Varma, Jeya Maria Jose Valanarasu, Zhongnan Fang, Zepeng Huo, Zaid Nabulsi, Diego Ardila , et al. (15 additional authors not shown)

Abstract: The large volume of abdominal computed tomography (CT) scans coupled with the shortage of radiologists have intensified the need for automated medical image analysis tools. Previous state-of-the-art approaches for automated analysis leverage vision-language models (VLMs) that jointly model images and radiology reports. However, current medical VLMs are generally limited to 2D images and short repo… ▽ More The large volume of abdominal computed tomography (CT) scans coupled with the shortage of radiologists have intensified the need for automated medical image analysis tools. Previous state-of-the-art approaches for automated analysis leverage vision-language models (VLMs) that jointly model images and radiology reports. However, current medical VLMs are generally limited to 2D images and short reports. Here to overcome these shortcomings for abdominal CT interpretation, we introduce Merlin, a 3D VLM that learns from volumetric CT scans, electronic health record data and radiology reports. This approach is enabled by a multistage pretraining framework that does not require additional manual annotations. We trained Merlin using a high-quality clinical dataset of paired CT scans (>6 million images from 15,331 CT scans), diagnosis codes (>1.8 million codes) and radiology reports (>6 million tokens). We comprehensively evaluated Merlin on 6 task types and 752 individual tasks that covered diagnostic, prognostic and quality-related tasks. The non-adapted (off-the-shelf) tasks included zero-shot classification of findings (30 findings), phenotype classification (692 phenotypes) and zero-shot cross-modal retrieval (image-to-findings and image-to-impression). The model-adapted tasks included 5-year chronic disease prediction (6 diseases), radiology report generation and 3D semantic segmentation (20 organs). We validated Merlin at scale, with internal testing on 5,137 CT scans and external testing on 44,098 CT scans from 3 independent sites and 2 public datasets. The results demonstrated high generalization across institutions and anatomies. Merlin outperformed 2D VLMs, CT foundation models and off-the-shelf radiology models. We also release our trained models, code, and dataset, available at: https://github.com/StanfordMIMI/Merlin. △ Less

Submitted 4 March, 2026; v1 submitted 10 June, 2024; originally announced June 2024.

Comments: Nature (2026)

GREEN: Generative Radiology Report Evaluation and Error Notation

Authors: Sophie Ostmeier, Justin Xu, Zhihong Chen, Maya Varma, Louis Blankemeier, Christian Bluethgen, Arne Edward Michalson, Michael Moseley, Curtis Langlotz, Akshay S Chaudhari, Jean-Benoit Delbrouck

Abstract: Evaluating radiology reports is a challenging problem as factual correctness is extremely important due to the need for accurate medical communication about medical images. Existing automatic evaluation metrics either suffer from failing to consider factual correctness (e.g., BLEU and ROUGE) or are limited in their interpretability (e.g., F1CheXpert and F1RadGraph). In this paper, we introduce GRE… ▽ More Evaluating radiology reports is a challenging problem as factual correctness is extremely important due to the need for accurate medical communication about medical images. Existing automatic evaluation metrics either suffer from failing to consider factual correctness (e.g., BLEU and ROUGE) or are limited in their interpretability (e.g., F1CheXpert and F1RadGraph). In this paper, we introduce GREEN (Generative Radiology Report Evaluation and Error Notation), a radiology report generation metric that leverages the natural language understanding of language models to identify and explain clinically significant errors in candidate reports, both quantitatively and qualitatively. Compared to current metrics, GREEN offers: 1) a score aligned with expert preferences, 2) human interpretable explanations of clinically significant errors, enabling feedback loops with end-users, and 3) a lightweight open-source method that reaches the performance of commercial counterparts. We validate our GREEN metric by comparing it to GPT-4, as well as to error counts of 6 experts and preferences of 2 experts. Our method demonstrates not only higher correlation with expert error counts, but simultaneously higher alignment with expert preferences when compared to previous approaches. △ Less

Submitted 22 January, 2025; v1 submitted 6 May, 2024; originally announced May 2024.

Journal ref: https://aclanthology.org/2024.findings-emnlp.21/

Generalist Foundation Models from a Multimodal Dataset for 3D Computed Tomography

Authors: Ibrahim Ethem Hamamci, Sezgin Er, Chenyu Wang, Furkan Almas, Ayse Gulnihan Simsek, Sevval Nil Esirgun, Irem Dogan, Omer Faruk Durugol, Benjamin Hou, Suprosanna Shit, Weicheng Dai, Murong Xu, Hadrien Reynaud, Muhammed Furkan Dasdelen, Bastian Wittmann, Tamaz Amiranashvili, Enis Simsar, Mehmet Simsar, Emine Bensu Erdemir, Abdullah Alanbay, Anjany Sekuboyina, Berkan Lafci, Ahmet Kaplan, Zhiyong Lu, Malgorzata Polacin , et al. (5 additional authors not shown)

Abstract: Advancements in medical imaging AI, particularly in 3D imaging, have been limited due to the scarcity of comprehensive datasets. We introduce CT-RATE, a public dataset that pairs 3D medical images with corresponding textual reports. CT-RATE comprises 25,692 non-contrast 3D chest CT scans from 21,304 unique patients. Each scan is accompanied by its corresponding radiology report. Leveraging CT-RATE… ▽ More Advancements in medical imaging AI, particularly in 3D imaging, have been limited due to the scarcity of comprehensive datasets. We introduce CT-RATE, a public dataset that pairs 3D medical images with corresponding textual reports. CT-RATE comprises 25,692 non-contrast 3D chest CT scans from 21,304 unique patients. Each scan is accompanied by its corresponding radiology report. Leveraging CT-RATE, we develop CT-CLIP, a CT-focused contrastive language-image pretraining framework designed for broad applications without the need for task-specific training. We demonstrate how CT-CLIP can be used in multi-abnormality detection and case retrieval, and outperforms state-of-the-art fully supervised models across all key metrics. By combining CT-CLIP's vision encoder with a pretrained large language model, we create CT-CHAT, a vision-language foundational chat model for 3D chest CT volumes. Finetuned on over 2.7 million question-answer pairs derived from the CT-RATE dataset, CT-CHAT underscores the necessity for specialized methods in 3D medical imaging. Collectively, the open-source release of CT-RATE, CT-CLIP, and CT-CHAT not only addresses critical challenges in 3D medical imaging but also lays the groundwork for future innovations in medical AI and improved patient care. △ Less

Submitted 8 February, 2026; v1 submitted 26 March, 2024; originally announced March 2024.

A dataset and benchmark for hospital course summarization with adapted large language models

Authors: Asad Aali, Dave Van Veen, Yamin Ishraq Arefeen, Jason Hom, Christian Bluethgen, Eduardo Pontes Reis, Sergios Gatidis, Namuun Clifford, Joseph Daws, Arash S. Tehrani, Jangwon Kim, Akshay S. Chaudhari

Abstract: Brief hospital course (BHC) summaries are clinical documents that summarize a patient's hospital stay. While large language models (LLMs) depict remarkable capabilities in automating real-world tasks, their capabilities for healthcare applications such as synthesizing BHCs from clinical notes have not been shown. We introduce a novel pre-processed dataset, the MIMIC-IV-BHC, encapsulating clinical… ▽ More Brief hospital course (BHC) summaries are clinical documents that summarize a patient's hospital stay. While large language models (LLMs) depict remarkable capabilities in automating real-world tasks, their capabilities for healthcare applications such as synthesizing BHCs from clinical notes have not been shown. We introduce a novel pre-processed dataset, the MIMIC-IV-BHC, encapsulating clinical note and brief hospital course (BHC) pairs to adapt LLMs for BHC synthesis. Furthermore, we introduce a benchmark of the summarization performance of two general-purpose LLMs and three healthcare-adapted LLMs. Using clinical notes as input, we apply prompting-based (using in-context learning) and fine-tuning-based adaptation strategies to three open-source LLMs (Clinical-T5-Large, Llama2-13B, FLAN-UL2) and two proprietary LLMs (GPT-3.5, GPT-4). We evaluate these LLMs across multiple context-length inputs using natural language similarity metrics. We further conduct a clinical study with five clinicians, comparing clinician-written and LLM-generated BHCs across 30 samples, focusing on their potential to enhance clinical decision-making through improved summary quality. We observe that the Llama2-13B fine-tuned LLM outperforms other domain-adapted models given quantitative evaluation metrics of BLEU and BERT-Score. GPT-4 with in-context learning shows more robustness to increasing context lengths of clinical note inputs than fine-tuned Llama2-13B. Despite comparable quantitative metrics, the reader study depicts a significant preference for summaries generated by GPT-4 with in-context learning compared to both Llama2-13B fine-tuned summaries and the original summaries, highlighting the need for qualitative clinical evaluation. △ Less

Submitted 22 April, 2025; v1 submitted 8 March, 2024; originally announced March 2024.

Journal ref: JAMIA, 2024

A Vision-Language Foundation Model to Enhance Efficiency of Chest X-ray Interpretation

Authors: Zhihong Chen, Maya Varma, Justin Xu, Magdalini Paschali, Dave Van Veen, Andrew Johnston, Alaa Youssef, Louis Blankemeier, Christian Bluethgen, Stephan Altmayer, Jeya Maria Jose Valanarasu, Mohamed Siddig Eltayeb Muneer, Eduardo Pontes Reis, Joseph Paul Cohen, Cameron Olsen, Tanishq Mathew Abraham, Emily B. Tsai, Christopher F. Beaulieu, Jenia Jitsev, Sergios Gatidis, Jean-Benoit Delbrouck, Akshay S. Chaudhari, Curtis P. Langlotz

Abstract: Over 1.4 billion chest X-rays (CXRs) are performed annually due to their cost-effectiveness as an initial diagnostic test. This scale of radiological studies provides a significant opportunity to streamline CXR interpretation and documentation. While foundation models are a promising solution, the lack of publicly available large-scale datasets and benchmarks inhibits their iterative development a… ▽ More Over 1.4 billion chest X-rays (CXRs) are performed annually due to their cost-effectiveness as an initial diagnostic test. This scale of radiological studies provides a significant opportunity to streamline CXR interpretation and documentation. While foundation models are a promising solution, the lack of publicly available large-scale datasets and benchmarks inhibits their iterative development and real-world evaluation. To overcome these challenges, we constructed a large-scale dataset (CheXinstruct), which we utilized to train a vision-language foundation model (CheXagent). We systematically demonstrated competitive performance across eight distinct task types on our novel evaluation benchmark (CheXbench). Beyond technical validation, we assessed the real-world utility of CheXagent in directly drafting radiology reports. Our clinical assessment with eight radiologists revealed a 36% time saving for residents using CheXagent-drafted reports, while attending radiologists showed no significant time difference editing resident-drafted or CheXagent-drafted reports. The CheXagent-drafted reports improved the writing efficiency of both radiology residents and attending radiologists in 81% and 61% of cases, respectively, without loss of quality. Overall, we demonstrate that CheXagent can effectively perform a variety of CXR interpretation tasks and holds potential to assist radiologists in routine clinical workflows. △ Less

Submitted 18 December, 2024; v1 submitted 22 January, 2024; originally announced January 2024.

Comments: 26 pages, 8 figures

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

Authors: Tianyu Han, Laura Žigutytė, Luisa Huck, Marc Huppertz, Robert Siepmann, Yossi Gandelsman, Christian Blüthgen, Firas Khader, Christiane Kuhl, Sven Nebelung, Jakob Kather, Daniel Truhn

Abstract: 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 dat… ▽ More 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. △ Less

Submitted 29 September, 2023; originally announced September 2023.

Adapted Large Language Models Can Outperform Medical Experts in Clinical Text Summarization

Authors: Dave Van Veen, Cara Van Uden, Louis Blankemeier, Jean-Benoit Delbrouck, Asad Aali, Christian Bluethgen, Anuj Pareek, Malgorzata Polacin, Eduardo Pontes Reis, Anna Seehofnerova, Nidhi Rohatgi, Poonam Hosamani, William Collins, Neera Ahuja, Curtis P. Langlotz, Jason Hom, Sergios Gatidis, John Pauly, Akshay S. Chaudhari

Abstract: Analyzing vast textual data and summarizing key information from electronic health records imposes a substantial burden on how clinicians allocate their time. Although large language models (LLMs) have shown promise in natural language processing (NLP), their effectiveness on a diverse range of clinical summarization tasks remains unproven. In this study, we apply adaptation methods to eight LLMs,… ▽ More Analyzing vast textual data and summarizing key information from electronic health records imposes a substantial burden on how clinicians allocate their time. Although large language models (LLMs) have shown promise in natural language processing (NLP), their effectiveness on a diverse range of clinical summarization tasks remains unproven. In this study, we apply adaptation methods to eight LLMs, spanning four distinct clinical summarization tasks: radiology reports, patient questions, progress notes, and doctor-patient dialogue. Quantitative assessments with syntactic, semantic, and conceptual NLP metrics reveal trade-offs between models and adaptation methods. A clinical reader study with ten physicians evaluates summary completeness, correctness, and conciseness; in a majority of cases, summaries from our best adapted LLMs are either equivalent (45%) or superior (36%) compared to summaries from medical experts. The ensuing safety analysis highlights challenges faced by both LLMs and medical experts, as we connect errors to potential medical harm and categorize types of fabricated information. Our research provides evidence of LLMs outperforming medical experts in clinical text summarization across multiple tasks. This suggests that integrating LLMs into clinical workflows could alleviate documentation burden, allowing clinicians to focus more on patient care. △ Less

Submitted 11 April, 2024; v1 submitted 14 September, 2023; originally announced September 2023.

Comments: 27 pages, 19 figures

Journal ref: Nature Medicine, 2024

Exploring the Versatility of Zero-Shot CLIP for Interstitial Lung Disease Classification

Authors: Cara Van Uden, Christian Bluethgen, Maayane Attias, Malgorzata Polacin, Haiwei Henry Guo, Neha Simha, Rishi Raj, Curtis Langlotz

Abstract: Interstitial lung diseases (ILD) present diagnostic challenges due to their varied manifestations and overlapping imaging features. To address this, we propose a machine learning approach that utilizes CLIP, a multimodal (image and text) self-supervised model, for ILD classification. We extensively integrate zero-shot CLIP throughout our workflow, starting from the initial extraction of image patc… ▽ More Interstitial lung diseases (ILD) present diagnostic challenges due to their varied manifestations and overlapping imaging features. To address this, we propose a machine learning approach that utilizes CLIP, a multimodal (image and text) self-supervised model, for ILD classification. We extensively integrate zero-shot CLIP throughout our workflow, starting from the initial extraction of image patches from volumetric CT scans and proceeding to ILD classification using "patch montages". Furthermore, we investigate how domain adaptive pretraining (DAPT) CLIP with task-specific images (CT "patch montages" extracted with ILD-specific prompts for CLIP) and/or text (lung-specific sections of radiology reports) affects downstream ILD classification performance. By leveraging CLIP-extracted "patch montages" and DAPT, we achieve strong zero-shot ILD classification results, including an AUROC of 0.893, without the need for any labeled training data. This work highlights the versatility and potential of multimodal models like CLIP for medical image classification tasks where labeled data is scarce. △ Less

Submitted 12 September, 2023; v1 submitted 1 June, 2023; originally announced June 2023.

Comments: 11 pages, 11 figures

GenerateCT: Text-Conditional Generation of 3D Chest CT Volumes

Authors: Ibrahim Ethem Hamamci, Sezgin Er, Anjany Sekuboyina, Enis Simsar, Alperen Tezcan, Ayse Gulnihan Simsek, Sevval Nil Esirgun, Furkan Almas, Irem Dogan, Muhammed Furkan Dasdelen, Chinmay Prabhakar, Hadrien Reynaud, Sarthak Pati, Christian Bluethgen, Mehmet Kemal Ozdemir, Bjoern Menze

Abstract: GenerateCT, the first approach to generating 3D medical imaging conditioned on free-form medical text prompts, incorporates a text encoder and three key components: a novel causal vision transformer for encoding 3D CT volumes, a text-image transformer for aligning CT and text tokens, and a text-conditional super-resolution diffusion model. Without directly comparable methods in 3D medical imaging,… ▽ More GenerateCT, the first approach to generating 3D medical imaging conditioned on free-form medical text prompts, incorporates a text encoder and three key components: a novel causal vision transformer for encoding 3D CT volumes, a text-image transformer for aligning CT and text tokens, and a text-conditional super-resolution diffusion model. Without directly comparable methods in 3D medical imaging, we benchmarked GenerateCT against cutting-edge methods, demonstrating its superiority across all key metrics. Importantly, we evaluated GenerateCT's clinical applications in a multi-abnormality classification task. First, we established a baseline by training a multi-abnormality classifier on our real dataset. To further assess the model's generalization to external data and performance with unseen prompts in a zero-shot scenario, we employed an external set to train the classifier, setting an additional benchmark. We conducted two experiments in which we doubled the training datasets by synthesizing an equal number of volumes for each set using GenerateCT. The first experiment demonstrated an 11% improvement in the AP score when training the classifier jointly on real and generated volumes. The second experiment showed a 7% improvement when training on both real and generated volumes based on unseen prompts. Moreover, GenerateCT enables the scaling of synthetic training datasets to arbitrary sizes. As an example, we generated 100,000 3D CTs, fivefold the number in our real set, and trained the classifier exclusively on these synthetic CTs. Impressively, this classifier surpassed the performance of the one trained on all available real data by a margin of 8%. Last, domain experts evaluated the generated volumes, confirming a high degree of alignment with the text prompt. Access our code, model weights, training data, and generated data at https://github.com/ibrahimethemhamamci/GenerateCT △ Less

Submitted 12 July, 2024; v1 submitted 25 May, 2023; originally announced May 2023.

RadAdapt: Radiology Report Summarization via Lightweight Domain Adaptation of Large Language Models

Authors: Dave Van Veen, Cara Van Uden, Maayane Attias, Anuj Pareek, Christian Bluethgen, Malgorzata Polacin, Wah Chiu, Jean-Benoit Delbrouck, Juan Manuel Zambrano Chaves, Curtis P. Langlotz, Akshay S. Chaudhari, John Pauly

Abstract: We systematically investigate lightweight strategies to adapt large language models (LLMs) for the task of radiology report summarization (RRS). Specifically, we focus on domain adaptation via pretraining (on natural language, biomedical text, or clinical text) and via discrete prompting or parameter-efficient fine-tuning. Our results consistently achieve best performance by maximally adapting to… ▽ More We systematically investigate lightweight strategies to adapt large language models (LLMs) for the task of radiology report summarization (RRS). Specifically, we focus on domain adaptation via pretraining (on natural language, biomedical text, or clinical text) and via discrete prompting or parameter-efficient fine-tuning. Our results consistently achieve best performance by maximally adapting to the task via pretraining on clinical text and fine-tuning on RRS examples. Importantly, this method fine-tunes a mere 0.32% of parameters throughout the model, in contrast to end-to-end fine-tuning (100% of parameters). Additionally, we study the effect of in-context examples and out-of-distribution (OOD) training before concluding with a radiologist reader study and qualitative analysis. Our findings highlight the importance of domain adaptation in RRS and provide valuable insights toward developing effective natural language processing solutions for clinical tasks. △ Less

Submitted 20 July, 2023; v1 submitted 1 May, 2023; originally announced May 2023.

Comments: 12 pages, 10 figures. Published in ACL BioNLP. Compared to v1, v2 includes minor edits and one additional figure in the appendix. Compared to v2, v3 includes a link to the project's GitHub repository

RoentGen: Vision-Language Foundation Model for Chest X-ray Generation

Authors: Pierre Chambon, Christian Bluethgen, Jean-Benoit Delbrouck, Rogier Van der Sluijs, Małgorzata Połacin, Juan Manuel Zambrano Chaves, Tanishq Mathew Abraham, Shivanshu Purohit, Curtis P. Langlotz, Akshay Chaudhari

Abstract: Multimodal models trained on large natural image-text pair datasets have exhibited astounding abilities in generating high-quality images. Medical imaging data is fundamentally different to natural images, and the language used to succinctly capture relevant details in medical data uses a different, narrow but semantically rich, domain-specific vocabulary. Not surprisingly, multi-modal models trai… ▽ More Multimodal models trained on large natural image-text pair datasets have exhibited astounding abilities in generating high-quality images. Medical imaging data is fundamentally different to natural images, and the language used to succinctly capture relevant details in medical data uses a different, narrow but semantically rich, domain-specific vocabulary. Not surprisingly, multi-modal models trained on natural image-text pairs do not tend to generalize well to the medical domain. Developing generative imaging models faithfully representing medical concepts while providing compositional diversity could mitigate the existing paucity of high-quality, annotated medical imaging datasets. In this work, we develop a strategy to overcome the large natural-medical distributional shift by adapting a pre-trained latent diffusion model on a corpus of publicly available chest x-rays (CXR) and their corresponding radiology (text) reports. We investigate the model's ability to generate high-fidelity, diverse synthetic CXR conditioned on text prompts. We assess the model outputs quantitatively using image quality metrics, and evaluate image quality and text-image alignment by human domain experts. We present evidence that the resulting model (RoentGen) is able to create visually convincing, diverse synthetic CXR images, and that the output can be controlled to a new extent by using free-form text prompts including radiology-specific language. Fine-tuning this model on a fixed training set and using it as a data augmentation method, we measure a 5% improvement of a classifier trained jointly on synthetic and real images, and a 3% improvement when trained on a larger but purely synthetic training set. Finally, we observe that this fine-tuning distills in-domain knowledge in the text-encoder and can improve its representation capabilities of certain diseases like pneumothorax by 25%. △ Less

Submitted 23 November, 2022; originally announced November 2022.

Comments: 19 pages

Improving the Factual Correctness of Radiology Report Generation with Semantic Rewards

Authors: Jean-Benoit Delbrouck, Pierre Chambon, Christian Bluethgen, Emily Tsai, Omar Almusa, Curtis P. Langlotz

Abstract: Neural image-to-text radiology report generation systems offer the potential to improve radiology reporting by reducing the repetitive process of report drafting and identifying possible medical errors. These systems have achieved promising performance as measured by widely used NLG metrics such as BLEU and CIDEr. However, the current systems face important limitations. First, they present an incr… ▽ More Neural image-to-text radiology report generation systems offer the potential to improve radiology reporting by reducing the repetitive process of report drafting and identifying possible medical errors. These systems have achieved promising performance as measured by widely used NLG metrics such as BLEU and CIDEr. However, the current systems face important limitations. First, they present an increased complexity in architecture that offers only marginal improvements on NLG metrics. Secondly, these systems that achieve high performance on these metrics are not always factually complete or consistent due to both inadequate training and evaluation. Recent studies have shown the systems can be substantially improved by using new methods encouraging 1) the generation of domain entities consistent with the reference and 2) describing these entities in inferentially consistent ways. So far, these methods rely on weakly-supervised approaches (rule-based) and named entity recognition systems that are not specific to the chest X-ray domain. To overcome this limitation, we propose a new method, the RadGraph reward, to further improve the factual completeness and correctness of generated radiology reports. More precisely, we leverage the RadGraph dataset containing annotated chest X-ray reports with entities and relations between entities. On two open radiology report datasets, our system substantially improves the scores up to 14.2% and 25.3% on metrics evaluating the factual correctness and completeness of reports. △ Less

Submitted 21 October, 2022; originally announced October 2022.

Comments: Findings of EMNLP 2022

Scale-Agnostic Super-Resolution in MRI using Feature-Based Coordinate Networks

Authors: Dave Van Veen, Rogier van der Sluijs, Batu Ozturkler, Arjun Desai, Christian Bluethgen, Robert D. Boutin, Marc H. Willis, Gordon Wetzstein, David Lindell, Shreyas Vasanawala, John Pauly, Akshay S. Chaudhari

Abstract: We propose using a coordinate network decoder for the task of super-resolution in MRI. The continuous signal representation of coordinate networks enables this approach to be scale-agnostic, i.e. one can train over a continuous range of scales and subsequently query at arbitrary resolutions. Due to the difficulty of performing super-resolution on inherently noisy data, we analyze network behavior… ▽ More We propose using a coordinate network decoder for the task of super-resolution in MRI. The continuous signal representation of coordinate networks enables this approach to be scale-agnostic, i.e. one can train over a continuous range of scales and subsequently query at arbitrary resolutions. Due to the difficulty of performing super-resolution on inherently noisy data, we analyze network behavior under multiple denoising strategies. Lastly we compare this method to a standard convolutional decoder using both quantitative metrics and a radiologist study implemented in Voxel, our newly developed tool for web-based evaluation of medical images. △ Less

Submitted 17 October, 2022; v1 submitted 16 October, 2022; originally announced October 2022.

Journal ref: Medical Imaging with Deep Learning. 2022

Adapting Pretrained Vision-Language Foundational Models to Medical Imaging Domains

Authors: Pierre Chambon, Christian Bluethgen, Curtis P. Langlotz, Akshay Chaudhari

Abstract: Multi-modal foundation models are typically trained on millions of pairs of natural images and text captions, frequently obtained through web-crawling approaches. Although such models depict excellent generative capabilities, they do not typically generalize well to specific domains such as medical images that have fundamentally shifted distributions compared to natural images. Building generative… ▽ More Multi-modal foundation models are typically trained on millions of pairs of natural images and text captions, frequently obtained through web-crawling approaches. Although such models depict excellent generative capabilities, they do not typically generalize well to specific domains such as medical images that have fundamentally shifted distributions compared to natural images. Building generative models for medical images that faithfully depict clinical context may help alleviate the paucity of healthcare datasets. Thus, in this study, we seek to research and expand the representational capabilities of large pretrained foundation models to medical concepts, specifically for leveraging the Stable Diffusion model to generate domain specific images found in medical imaging. We explore the sub-components of the Stable Diffusion pipeline (the variational autoencoder, the U-Net and the text-encoder) to fine-tune the model to generate medical images. We benchmark the efficacy of these efforts using quantitative image quality metrics and qualitative radiologist-driven evaluations that accurately represent the clinical content of conditional text prompts. Our best-performing model improves upon the stable diffusion baseline and can be conditioned to insert a realistic-looking abnormality on a synthetic radiology image, while maintaining a 95% accuracy on a classifier trained to detect the abnormality. △ Less

Submitted 8 October, 2022; originally announced October 2022.

Comments: 17 pages, 8 figures

Journal ref: Foundation Models for Decision Making Workshop at Neural Information Processing Systems, 2022