arXiv subjects

Akshay Chaudhari

Publications and source records attributed to Akshay Chaudhari.

At least 19 recordsLinked to original sources

arXiv2026

Symbal: Detecting Systematic Misalignments in Model-Generated Captions

Multimodal large language models (MLLMs) often introduce errors when generating image captions, resulting in misaligned image-text pairs. Our work focuses on a class of captioning errors that we refer to as systematic misalignments, where a recurring error in MLLM-generated captions is closely associated with the presence of a specific visual feature in the paired image. Given a vision-language dataset with MLLM-generated captions, our aim in this work is to detect such errors, a task we refer to as systematic misalignment detection. As our first key contribution, we present Symbal, which utilizes a structured, dual-stage setup with off-the-shelf foundation models to identify systematic misalignments and summarize results in natural language. As our second key contribution, we introduce SymbalBench, a benchmark designed to evaluate automated methods on our proposed task. SymbalBench consists of 1.7 million image-text pairs from two domains (natural and medical images), organized into 420 vision-language datasets with annotated systematic misalignments. Symbal exhibits strong performance on this benchmark, correctly identifying systematic misalignments in 63.8% of datasets, a nearly 4x improvement over the closest baseline. We supplement our evaluations on SymbalBench with real-world evaluations, showing that (1) Symbal can accurately surface systematic misalignments in captions generated by four MLLMs and (2) Symbal is a powerful tool for auditing off-the-shelf image-caption datasets. Ultimately, our novel task, method, and benchmark can aid users with auditing MLLM-generated captions and identifying critical errors, without requiring access to the underlying MLLM. Code is available at https://github.com/Stanford-AIMI/Symbal.

cs.CV↗

arXiv2026

CheXmix: Unified Generative Pretraining for Vision Language Models in Medical Imaging

Recent medical multimodal foundation models are built as multimodal LLMs (MLLMs) by connecting a CLIP-pretrained vision encoder to an LLM using LLaVA-style finetuning. This two-stage, decoupled approach introduces a projection layer that can distort visual features. This is especially concerning in medical imaging where subtle cues are essential for accurate diagnoses. In contrast, early-fusion generative approaches such as Chameleon eliminate the projection bottleneck by processing image and text tokens within a single unified sequence, enabling joint representation learning that leverages the inductive priors of language models. We present CheXmix, a unified early-fusion generative model trained on a large corpus of chest X-rays paired with radiology reports. We expand on Chameleon's autoregressive framework by introducing a two-stage multimodal generative pretraining strategy that combines the representational strengths of masked autoencoders with MLLMs. The resulting models are highly flexible, supporting both discriminative and generative tasks at both coarse and fine-grained scales. Our approach outperforms well-established generative models across all masking ratios by 6.0% and surpasses CheXagent by 8.6% on AUROC at high image masking ratios on the CheXpert classification task. We further inpaint images over 51.0% better than text-only generative models and outperform CheXagent by 45% on the GREEN metric for radiology report generation. These results demonstrate that CheXmix captures fine-grained information across a broad spectrum of chest X-ray tasks. Our code is at: https://github.com/StanfordMIMI/CheXmix.

cs.CV↗

arXiv2026

A Generative Foundation Model for Multimodal Histopathology

Accurate diagnosis and treatment of complex diseases require integrating histological, molecular, and clinical data, yet in practice these modalities are often incomplete owing to tissue scarcity, assay cost, and workflow constraints. Existing computational approaches attempt to impute missing modalities from available data but rely on task-specific models trained on narrow, single source-target pairs, limiting their generalizability. Here we introduce MuPD (Multimodal Pathology Diffusion), a generative foundation model that embeds hematoxylin and eosin (H&E)-stained histology, molecular RNA profiles, and clinical text into a shared latent space through a diffusion transformer with decoupled cross-modal attention. Pretrained on 100 million histology image patches, 1.6 million text-histology pairs, and 10.8 million RNA-histology pairs spanning 34 human organs, MuPD supports diverse cross-modal synthesis tasks with minimal or no task-specific fine-tuning. For text-conditioned and image-to-image generation, MuPD synthesizes histologically faithful tissue architectures, reducing Fr\'echet inception distance (FID) scores by 50% relative to domain-specific models and improving few-shot classification accuracy by up to 47% through synthetic data augmentation. For RNA-conditioned histology generation, MuPD reduces FID by 23% compared with the next-best method while preserving cell-type distributions across five cancer types. As a virtual stainer, MuPD translates H&E images to immunohistochemistry and multiplex immunofluorescence, improving average marker correlation by 37% over existing approaches. These results demonstrate that a single, unified generative model pretrained across heterogeneous pathology modalities can substantially outperform specialized alternatives, providing a scalable computational framework for multimodal histopathology.

cs.CV↗

arXiv2026

Diffusion MRI Transformer with a Diffusion Space Rotary Positional Embedding (D-RoPE)

Diffusion Magnetic Resonance Imaging (dMRI) plays a critical role in studying microstructural changes in the brain. It is, therefore, widely used in clinical practice; yet progress in learning general-purpose representations from dMRI has been limited. A key challenge is that existing deep learning approaches are not well-suited to capture the unique properties of diffusion signals. Brain dMRI is normally composed of several brain volumes, each with different attenuation characteristics dependent on the direction and strength of the diffusion-sensitized gradients. Thus, there is a need to jointly model spatial, diffusion-weighting, and directional dependencies in dMRI. Furthermore, varying acquisition protocols (e.g., differing numbers of directions) further limit traditional models. To address these gaps, we introduce a diffusion space rotatory positional embedding (D-RoPE) plugged into our dMRI transformer to capture both the spatial structure and directional characteristics of diffusion data, enabling robust and transferable representations across diverse acquisition settings and an arbitrary number of diffusion directions. After self-supervised masked autoencoding pretraining, tests on several downstream tasks show that the learned representations and the pretrained model can provide competitive or superior performance compared to several baselines in these downstream tasks (even compared to a fully trained baseline); the finetuned features from our pretrained encoder resulted in a 6% higher accuracy in classifying mild cognitive impairment and a 0.05 increase in the correlation coefficient when predicting cognitive scores. Code is available at: github.com/gustavochau/D-RoPE.

cs.CV↗

arXiv2026

MARCUS: An agentic, multimodal vision-language model for cardiac diagnosis and management

Cardiovascular disease remains the leading cause of global mortality, with progress hindered by human interpretation of complex cardiac tests. Current AI vision-language models are limited to single-modality inputs and are non-interactive. We present MARCUS (Multimodal Autonomous Reasoning and Chat for Ultrasound and Signals), an agentic vision-language system for end-to-end interpretation of electrocardiograms (ECGs), echocardiograms, and cardiac magnetic resonance imaging (CMR) independently and as multimodal input. MARCUS employs a hierarchical agentic architecture comprising modality-specific vision-language expert models, each integrating domain-trained visual encoders with multi-stage language model optimization, coordinated by a multimodal orchestrator. Trained on 13.5 million images (0.25M ECGs, 1.3M echocardiogram images, 12M CMR images) and our novel expert-curated dataset spanning 1.6 million questions, MARCUS achieves state-of-the-art performance surpassing frontier models (GPT-5 Thinking, Gemini 2.5 Pro Deep Think). Across internal (Stanford) and external (UCSF) test cohorts, MARCUS achieves accuracies of 87-91% for ECG, 67-86% for echocardiography, and 85-88% for CMR, outperforming frontier models by 34-45% (P<0.001). On multimodal cases, MARCUS achieved 70% accuracy, nearly triple that of frontier models (22-28%), with 1.7-3.0x higher free-text quality scores. Our agentic architecture also confers resistance to mirage reasoning, whereby vision-language models derive reasoning from unintended textual signals or hallucinated visual content. MARCUS demonstrates that domain-specific visual encoders with an agentic orchestrator enable multimodal cardiac interpretation. We release our models, code, and benchmark open-source.

cs.AI↗

arXiv2026

Learning Generalizable 3D Medical Image Representations from Mask-Guided Self-Supervision

Foundation models have transformed vision and language by learning general-purpose representations from large-scale unlabeled data, yet 3D medical imaging lacks analogous approaches. Existing self-supervised methods rely on low-level reconstruction or contrastive objectives that fail to capture the anatomical semantics critical for medical image analysis, limiting transfer to downstream tasks. We present MASS (MAsk-guided Self-Supervised learning), which treats in-context segmentation as the pretext task for learning general-purpose medical imaging representations. MASS's key insight is that automatically generated class-agnostic masks provide sufficient structural supervision for learning semantically rich representations. By training on thousands of diverse mask proposals spanning anatomical structures and pathological findings, MASS learns what semantically defines medical structures: the holistic combination of appearance, shape, spatial context, and anatomical relationships. We demonstrate effectiveness across data regimes: from small-scale pretraining on individual datasets (20-200 scans) to large-scale multi-modal pretraining on 5K CT, MRI, and PET volumes, all without annotations. MASS demonstrates: (i) few-shot segmentation on novel structures, (ii) matching full supervision with only 20-40\% labeled data while outperforming self-supervised baselines by over 20 in Dice score in low-data regimes, and (iii) frozen-encoder classification on unseen pathologies that matches full supervised training with thousands of samples. Mask-guided self-supervised pretraining captures broadly generalizable knowledge, opening a path toward 3D medical imaging foundation models without expert annotations. Code is available: https://github.com/Stanford-AIMI/MASS.

cs.CV↗

arXiv2026

Attention Head Entropy of LLMs Predicts Answer Correctness

Large language models (LLMs) often generate plausible yet incorrect answers, posing risks in safety-critical settings such as medicine. Human evaluation is expensive, and LLM-as-judge approaches risk introducing hidden errors. Recent white-box methods detect contextual hallucinations using model internals, focusing on the localization of the attention mass, but two questions remain open: do these approaches extend to predicting answer correctness, and do they generalize out-of-domains? We introduce Head Entropy, a method that predicts answer correctness from attention entropy patterns, specifically measuring the spread of the attention mass. Using sparse logistic regression on per-head 2-Renyi entropies, Head Entropy matches or exceeds baselines in-distribution and generalizes substantially better on out-of-domains, it outperforms the closest baseline on average by +8.5% AUROC. We further show that attention patterns over the question/context alone, before answer generation, already carry predictive signal using Head Entropy with on average +17.7% AUROC over the closest baseline. We evaluate across 5 instruction-tuned LLMs and 3 QA datasets spanning general knowledge, multi-hop reasoning, and medicine.

cs.LG↗

arXiv2025

TRoVe: Discovering Error-Inducing Static Feature Biases in Temporal Vision-Language Models

Vision-language models (VLMs) have made great strides in addressing temporal understanding tasks, which involve characterizing visual changes across a sequence of images. However, recent works have suggested that when making predictions, VLMs may rely on static feature biases, such as background or object features, rather than dynamic visual changes. Static feature biases are a type of shortcut and can contribute to systematic prediction errors on downstream tasks; as a result, identifying and characterizing error-inducing static feature biases is critical prior to real-world model deployment. In this work, we introduce TRoVe, an automated approach for discovering error-inducing static feature biases learned by temporal VLMs. Given a trained VLM and an annotated validation dataset associated with a downstream classification task, TRoVe extracts candidate static features from the dataset and scores each feature by (i) the effect of the feature on classification errors as well as (ii) the extent to which the VLM relies on the feature when making predictions. In order to quantitatively evaluate TRoVe, we introduce an evaluation framework consisting of 101 trained temporal VLMs paired with ground-truth annotations for learned static feature biases. We use this framework to demonstrate that TRoVe can accurately identify error-inducing static feature biases in VLMs, achieving a 28.6% improvement over the closest baseline. Finally, we apply TRoVe to 7 off-the-shelf VLMs and 2 temporal understanding tasks, surfacing previously-unknown static feature biases and demonstrating that knowledge of learned biases can aid in improving model performance at test time. Our code is available at https://github.com/Stanford-AIMI/TRoVe.

cs.CV↗

arXiv2025

Prompt Triage: Structured Optimization Enhances Vision-Language Model Performance on Medical Imaging Benchmarks

Vision-language foundation models (VLMs) show promise for diverse imaging tasks but often underperform on medical benchmarks. Prior efforts to improve performance include model finetuning, which requires large domain-specific datasets and significant compute, or manual prompt engineering, which is hard to generalize and often inaccessible to medical institutions seeking to deploy these tools. These challenges motivate interest in approaches that draw on a model's embedded knowledge while abstracting away dependence on human-designed prompts to enable scalable, weight-agnostic performance improvements. To explore this, we adapt the Declarative Self-improving Python (DSPy) framework for structured automated prompt optimization in medical vision-language systems through a comprehensive, formal evaluation. We implement prompting pipelines for five medical imaging tasks across radiology, gastroenterology, and dermatology, evaluating 10 open-source VLMs with four prompt optimization techniques. Optimized pipelines achieved a median relative improvement of 53% over zero-shot prompting baselines, with the largest gains ranging from 300% to 3,400% on tasks where zero-shot performance is low. These results highlight the substantial potential of applying automated prompt optimization to medical AI systems, demonstrating significant gains for vision-based applications requiring accurate clinical image interpretation. By reducing dependence on prompt design to elicit intended outputs, these techniques allow clinicians to focus on patient care and clinical decision-making. Furthermore, our experiments offer scalability and preserve data privacy, demonstrating performance improvement on open-source VLMs. We publicly release our evaluation pipelines to support reproducible research on specialized medical tasks, available at https://github.com/DaneshjouLab/prompt-triage-lab.

cs.CV↗

arXiv2025

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

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.

cs.AI↗

arXiv2025

MedHELM: Holistic Evaluation of Large Language Models for Medical Tasks

While large language models (LLMs) achieve near-perfect scores on medical licensing exams, these evaluations inadequately reflect the complexity and diversity of real-world clinical practice. We introduce MedHELM, an extensible evaluation framework for assessing LLM performance for medical tasks with three key contributions. First, a clinician-validated taxonomy spanning 5 categories, 22 subcategories, and 121 tasks developed with 29 clinicians. Second, a comprehensive benchmark suite comprising 35 benchmarks (17 existing, 18 newly formulated) providing complete coverage of all categories and subcategories in the taxonomy. Third, a systematic comparison of LLMs with improved evaluation methods (using an LLM-jury) and a cost-performance analysis. Evaluation of 9 frontier LLMs, using the 35 benchmarks, revealed significant performance variation. Advanced reasoning models (DeepSeek R1: 66% win-rate; o3-mini: 64% win-rate) demonstrated superior performance, though Claude 3.5 Sonnet achieved comparable results at 40% lower estimated computational cost. On a normalized accuracy scale (0-1), most models performed strongly in Clinical Note Generation (0.73-0.85) and Patient Communication & Education (0.78-0.83), moderately in Medical Research Assistance (0.65-0.75), and generally lower in Clinical Decision Support (0.56-0.72) and Administration & Workflow (0.53-0.63). Our LLM-jury evaluation method achieved good agreement with clinician ratings (ICC = 0.47), surpassing both average clinician-clinician agreement (ICC = 0.43) and automated baselines including ROUGE-L (0.36) and BERTScore-F1 (0.44). Claude 3.5 Sonnet achieved comparable performance to top models at lower estimated cost. These findings highlight the importance of real-world, task-specific evaluation for medical use of LLMs and provides an open source framework to enable this.

cs.CL↗

arXiv2025

Aligning Large Language Models with Healthcare Stakeholders: A Pathway to Trustworthy AI Integration

The wide exploration of large language models (LLMs) raises the awareness of alignment between healthcare stakeholder preferences and model outputs. This alignment becomes a crucial foundation to empower the healthcare workflow effectively, safely, and responsibly. Yet the varying behaviors of LLMs may not always match with healthcare stakeholders' knowledge, demands, and values. To enable a human-AI alignment, healthcare stakeholders will need to perform essential roles in guiding and enhancing the performance of LLMs. Human professionals must participate in the entire life cycle of adopting LLM in healthcare, including training data curation, model training, and inference. In this review, we discuss the approaches, tools, and applications of alignments between healthcare stakeholders and LLMs. We demonstrate that LLMs can better follow human values by properly enhancing healthcare knowledge integration, task understanding, and human guidance. We provide outlooks on enhancing the alignment between humans and LLMs to build trustworthy real-world healthcare applications.

cs.CY↗

arXiv2025

Eyes Tell the Truth: GazeVal Highlights Shortcomings of Generative AI in Medical Imaging

The demand for high-quality synthetic data for model training and augmentation has never been greater in medical imaging. However, current evaluations predominantly rely on computational metrics that fail to align with human expert recognition. This leads to synthetic images that may appear realistic numerically but lack clinical authenticity, posing significant challenges in ensuring the reliability and effectiveness of AI-driven medical tools. To address this gap, we introduce GazeVal, a practical framework that synergizes expert eye-tracking data with direct radiological evaluations to assess the quality of synthetic medical images. GazeVal leverages gaze patterns of radiologists as they provide a deeper understanding of how experts perceive and interact with synthetic data in different tasks (i.e., diagnostic or Turing tests). Experiments with sixteen radiologists revealed that 96.6% of the generated images (by the most recent state-of-the-art AI algorithm) were identified as fake, demonstrating the limitations of generative AI in producing clinically accurate images.

cs.CV↗

arXiv2025

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

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.

eess.IV↗

arXiv2025

Explaining 3D Computed Tomography Classifiers with Counterfactuals

Counterfactual explanations enhance the interpretability of deep learning models in medical imaging, yet adapting them to 3D CT scans poses challenges due to volumetric complexity and resource demands. We extend the Latent Shift counterfactual generation method from 2D applications to explain 3D computed tomography (CT) scans classifiers. We address the challenges associated with 3D classifiers, such as limited training samples and high memory demands, by implementing a slice-based autoencoder and gradient blocking except for specific chunks of slices. This method leverages a 2D encoder trained on CT slices, which are subsequently combined to maintain 3D context. We demonstrate this technique on two models for clinical phenotype prediction and lung segmentation. Our approach is both memory-efficient and effective for generating interpretable counterfactuals in high-resolution 3D medical imaging.

cs.CV↗

arXiv2025

Embedding-Driven Diversity Sampling to Improve Few-Shot Synthetic Data Generation

Accurate classification of clinical text often requires fine-tuning pre-trained language models, a process that is costly and time-consuming due to the need for high-quality data and expert annotators. Synthetic data generation offers an alternative, though pre-trained models may not capture the syntactic diversity of clinical notes. We propose an embedding-driven approach that uses diversity sampling from a small set of real clinical notes to guide large language models in few-shot prompting, generating synthetic text that better reflects clinical syntax. We evaluated this method using the CheXpert dataset on a classification task, comparing it to random few-shot and zero-shot approaches. Using cosine similarity and a Turing test, our approach produced synthetic notes that more closely align with real clinical text. Our pipeline reduced the data needed to reach the 0.85 AUC cutoff by 40% for AUROC and 30% for AUPRC, while augmenting models with synthetic data improved AUROC by 57% and AUPRC by 68%. Additionally, our synthetic data was 0.9 times as effective as real data, a 60% improvement in value.

cs.CL↗

arXiv2024

Regulating radiology AI medical devices that evolve in their lifecycle

Over time, the distribution of medical image data drifts due to factors such as shifts in patient demographics, acquisition devices, and disease manifestations. While human radiologists can adjust their expertise to accommodate such variations, deep learning models cannot. In fact, such models are highly susceptible to even slight variations in image characteristics. Consequently, manufacturers must conduct regular updates to ensure that they remain safe and effective. Performing such updates in the United States and European Union required, until recently, obtaining re-approval. Given the time and financial burdens associated with these processes, updates were infrequent, and obsolete systems remained in operation for too long. During 2024, several regulatory developments promised to streamline the safe rollout of model updates: The European Artificial Intelligence Act came into effect last August, and the Food and Drug Administration (FDA) issued final marketing submission recommendations for a Predetermined Change Control Plan (PCCP) in December. We provide an overview of these developments and outline the key building blocks necessary for successfully deploying dynamic systems. At the heart of these regulations - and as prerequisites for manufacturers to conduct model updates without re-approval - are clear descriptions of data collection and re-training processes, coupled with robust real-world quality monitoring mechanisms.

cs.CY↗

arXiv2024

Best Practices for Large Language Models in Radiology

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.

cs.AI↗