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Daniel Truhn

Publications and source records attributed to Daniel Truhn.

At least 37 records · Page 2Linked to original sources
arXiv2026

Hallucination Filtering in Radiology Vision-Language Models Using Discrete Semantic Entropy

To determine whether using discrete semantic entropy (DSE) to reject questions likely to generate hallucinations can improve the accuracy of black-box vision-language models (VLMs) in radiologic image based visual question answering (VQA). This retrospective study evaluated DSE using two publicly available, de-identified datasets: the VQA-Med 2019 benchmark (500 images with clinical questions and short-text answers) and a diagnostic radiology dataset (206 cases: 60 computed tomography scans, 60 magnetic resonance images, 60 radiographs, 26 angiograms) with corresponding ground-truth diagnoses. GPT-4o and GPT-4.1 (Generative Pretrained Transformer; OpenAI) answered each question 15 times using a temperature of 1.0. Baseline accuracy was determined using low-temperature answers (temperature 0.1). Meaning-equivalent responses were grouped using bidirectional entailment checks, and DSE was computed from the relative frequencies of the resulting semantic clusters. Accuracy was recalculated after excluding questions with DSE > 0.6 or > 0.3. p-values and 95% confidence intervals were obtained using bootstrap resampling and a Bonferroni-corrected threshold of p < .004 for statistical significance. Across 706 image-question pairs, baseline accuracy was 51.7% for GPT-4o and 54.8% for GPT-4.1. After filtering out high-entropy questions (DSE > 0.3), accuracy on the remaining questions was 76.3% (retained questions: 334/706) for GPT-4o and 63.8% (retained questions: 499/706) for GPT-4.1 (both p < .001). Accuracy gains were observed across both datasets and largely remained statistically significant after Bonferroni correction. DSE enables reliable hallucination detection in black-box VLMs by quantifying semantic inconsistency. This method significantly improves diagnostic answer accuracy and offers a filtering strategy for clinical VLM applications.

cs.CV↗
arXiv2026

MedicalPatchNet: A Patch-Based Self-Explainable AI Architecture for Chest X-ray Classification

Deep neural networks excel in radiological image classification but frequently suffer from poor interpretability, limiting clinical acceptance. We present MedicalPatchNet, an inherently self-explainable architecture for chest X-ray classification that transparently attributes decisions to distinct image regions. MedicalPatchNet splits images into non-overlapping patches, independently classifies each patch, and aggregates predictions, enabling intuitive visualization of each patch's diagnostic contribution without post-hoc techniques. Trained on the CheXpert dataset (223,414 images), MedicalPatchNet matches the classification performance (AUROC 0.907 vs. 0.908) of EfficientNetV2-S, while improving interpretability: MedicalPatchNet demonstrates improved interpretability with higher pathology localization accuracy (mean hit-rate 0.485 vs. 0.376 with Grad-CAM) on the CheXlocalize dataset. By providing explicit, reliable explanations accessible even to non-AI experts, MedicalPatchNet mitigates risks associated with shortcut learning, thus improving clinical trust. Our model is publicly available with reproducible training and inference scripts and contributes to safer, explainable AI-assisted diagnostics across medical imaging domains. We make the code publicly available: https://github.com/TruhnLab/MedicalPatchNet

cs.CV↗
arXiv2025

Multi-step retrieval and reasoning improves radiology question answering with large language models

Clinical decision-making in radiology increasingly benefits from artificial intelligence (AI), particularly through large language models (LLMs). However, traditional retrieval-augmented generation (RAG) systems for radiology question answering (QA) typically rely on single-step retrieval, limiting their ability to handle complex clinical reasoning tasks. Here we propose radiology Retrieval and Reasoning (RaR), a multi-step retrieval and reasoning framework designed to improve diagnostic accuracy, factual consistency, and clinical reliability of LLMs in radiology question answering. We evaluated 25 LLMs spanning diverse architectures, parameter scales (0.5B to >670B), and training paradigms (general-purpose, reasoning-optimized, clinically fine-tuned), using 104 expert-curated radiology questions from previously established RSNA-RadioQA and ExtendedQA datasets. To assess generalizability, we additionally tested on an unseen internal dataset of 65 real-world radiology board examination questions. RaR significantly improved mean diagnostic accuracy over zero-shot prompting and conventional online RAG. The greatest gains occurred in small-scale models, while very large models (>200B parameters) demonstrated minimal changes (<2% improvement). Additionally, RaR retrieval reduced hallucinations (mean 9.4%) and retrieved clinically relevant context in 46% of cases, substantially aiding factual grounding. Even clinically fine-tuned models showed gains from RaR (e.g., MedGemma-27B), indicating that retrieval remains beneficial despite embedded domain knowledge. These results highlight the potential of RaR to enhance factuality and diagnostic accuracy in radiology QA, warranting future studies to validate their clinical utility. All datasets, code, and the full RaR framework are publicly available to support open research and clinical translation.

cs.CL↗
arXiv2025

Evaluating Reasoning Faithfulness in Medical Vision-Language Models using Multimodal Perturbations

Vision-language models (VLMs) often produce chain-of-thought (CoT) explanations that sound plausible yet fail to reflect the underlying decision process, undermining trust in high-stakes clinical use. Existing evaluations rarely catch this misalignment, prioritizing answer accuracy or adherence to formats. We present a clinically grounded framework for chest X-ray visual question answering (VQA) that probes CoT faithfulness via controlled text and image modifications across three axes: clinical fidelity, causal attribution, and confidence calibration. In a reader study (n=4), evaluator-radiologist correlations fall within the observed inter-radiologist range for all axes, with strong alignment for attribution (Kendall's $τ_b=0.670$), moderate alignment for fidelity ($τ_b=0.387$), and weak alignment for confidence tone ($τ_b=0.091$), which we report with caution. Benchmarking six VLMs shows that answer accuracy and explanation quality can be decoupled, acknowledging injected cues does not ensure grounding, and text cues shift explanations more than visual cues. While some open-source models match final answer accuracy, proprietary models score higher on attribution (25.0% vs. 1.4%) and often on fidelity (36.1% vs. 31.7%), highlighting deployment risks and the need to evaluate beyond final answer accuracy.

cs.CL↗
arXiv2025

Differential privacy for medical deep learning: methods, tradeoffs, and deployment implications

Differential privacy (DP) is a key technique for protecting sensitive patient data in medical deep learning (DL). As clinical models grow more data-dependent, balancing privacy with utility and fairness has become a critical challenge. This scoping review synthesizes recent developments in applying DP to medical DL, with a particular focus on DP-SGD and alternative mechanisms across centralized and federated settings. Using a structured search strategy, we identified 74 studies published up to March 2025. Our analysis spans diverse data modalities, training setups, and downstream tasks, and highlights the tradeoffs between privacy guarantees, model accuracy, and subgroup fairness. We find that while DP-especially at strong privacy budgets-can preserve performance in well-structured imaging tasks, severe degradation often occurs under strict privacy, particularly in underrepresented or complex modalities. Furthermore, privacy-induced performance gaps disproportionately affect demographic subgroups, with fairness impacts varying by data type and task. A small subset of studies explicitly addresses these tradeoffs through subgroup analysis or fairness metrics, but most omit them entirely. Beyond DP-SGD, emerging approaches leverage alternative mechanisms, generative models, and hybrid federated designs, though reporting remains inconsistent. We conclude by outlining key gaps in fairness auditing, standardization, and evaluation protocols, offering guidance for future work toward equitable and clinically robust privacy-preserving DL systems in medicine.

cs.LG↗
arXiv2025

Effect of Reporting Mode and Clinical Experience on Radiologists' Gaze and Image Analysis Behavior in Chest Radiography

Structured reporting (SR) and artificial intelligence (AI) may transform how radiologists interact with imaging studies. This prospective study (July to December 2024) evaluated the impact of three reporting modes: free-text (FT), structured reporting (SR), and AI-assisted structured reporting (AI-SR), on image analysis behavior, diagnostic accuracy, efficiency, and user experience. Four novice and four non-novice readers (radiologists and medical students) each analyzed 35 bedside chest radiographs per session using a customized viewer and an eye-tracking system. Outcomes included diagnostic accuracy (compared with expert consensus using Cohen's $κ$), reporting time per radiograph, eye-tracking metrics, and questionnaire-based user experience. Statistical analysis used generalized linear mixed models with Bonferroni post-hoc tests with a significance level of ($P \le .01$). Diagnostic accuracy was similar in FT ($κ= 0.58$) and SR ($κ= 0.60$) but higher in AI-SR ($κ= 0.71$, $P < .001$). Reporting times decreased from $88 \pm 38$ s (FT) to $37 \pm 18$ s (SR) and $25 \pm 9$ s (AI-SR) ($P < .001$). Saccade counts for the radiograph field ($205 \pm 135$ (FT), $123 \pm 88$ (SR), $97 \pm 58$ (AI-SR)) and total fixation duration for the report field ($11 \pm 5$ s (FT), $5 \pm 3$ s (SR), $4 \pm 1$ s (AI-SR)) were lower with SR and AI-SR ($P < .001$ each). Novice readers shifted gaze towards the radiograph in SR, while non-novice readers maintained their focus on the radiograph. AI-SR was the preferred mode. In conclusion, SR improves efficiency by guiding visual attention toward the image, and AI-prefilled SR further enhances diagnostic accuracy and user satisfaction.

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

Large Language Model-Based Uncertainty-Adjusted Label Extraction for Artificial Intelligence Model Development in Upper Extremity Radiography

Objectives: To evaluate GPT-4o's ability to extract diagnostic labels (with uncertainty) from free-text radiology reports and to test how these labels affect multi-label image classification of musculoskeletal radiographs. Methods: This retrospective study included radiography series of the clavicle (n=1,170), elbow (n=3,755), and thumb (n=1,978). After anonymization, GPT-4o filled out structured templates by indicating imaging findings as present ("true"), absent ("false"), or "uncertain." To assess the impact of label uncertainty, "uncertain" labels of the training and validation sets were automatically reassigned to "true" (inclusive) or "false" (exclusive). Label-image-pairs were used for multi-label classification using ResNet50. Label extraction accuracy was manually verified on internal (clavicle: n=233, elbow: n=745, thumb: n=393) and external test sets (n=300 for each). Performance was assessed using macro-averaged receiver operating characteristic (ROC) area under the curve (AUC), precision recall curves, sensitivity, specificity, and accuracy. AUCs were compared with the DeLong test. Results: Automatic extraction was correct in 98.6% (60,618 of 61,488) of labels in the test sets. Across anatomic regions, label-based model training yielded competitive performance measured by macro-averaged AUC values for inclusive (e.g., elbow: AUC=0.80 [range, 0.62-0.87]) and exclusive models (elbow: AUC=0.80 [range, 0.61-0.88]). Models generalized well on external datasets (elbow [inclusive]: AUC=0.79 [range, 0.61-0.87]; elbow [exclusive]: AUC=0.79 [range, 0.63-0.89]). No significant differences were observed across labeling strategies or datasets (p>=0.15). Conclusion: GPT-4o extracted labels from radiologic reports to train competitive multi-label classification models with high accuracy. Detected uncertainty in the radiologic reports did not influence the performance of these models.

cs.AI↗
arXiv2025

T2 Radiomic Features Are More Sensitive Than Mean T2 for Cartilage Load Response: A Stress MRI Study

Objective: To assess response-to-loading in a human cadaveric knee joint model under different loading conditions before and after meniscectomy Design: In this prospective study, stress magnetic resonance imaging was performed using an MR-compatible loading device and quantitative T2 mapping in unloaded (UL), 0$°$ neutrally loaded (LN) and 10$°$ varus loaded (LV) condition before and after meniscectomy. Mean T2 values and four radiomic texture parameters were assessed within the cartilage of medial femur (MF) and medial tibia (MT) for all conditions. Results: Medial joint space width decreased from UL to LN to LV and after meniscectomy (all p<0.05). T2 values did not show any significant dependency on pressure or meniscectomy (all p>0.05). The radiomic parameter variance could assess loading induced textural T2 changes in the MF (UL vs. LN: p=0.042; UL vs. LV: p<0.001; LN vs. LV: p=0.022), and, in part, in the MT (LN vs. LV: p<0.013). Meniscectomy did not significantly alter the T2 mean values or radiomic parameters, respectively. Conclusions: T2-based radiomic features were more sensitive to assess cartilage response to loading than T2-mapping alone.

physics.med-ph↗
arXiv2025

Diagnostic Accuracy of Open-Source Vision-Language Models on Diverse Medical Imaging Tasks

This retrospective study evaluated five VLMs (Qwen2.5, Phi-4, Gemma3, Llama3.2, and Mistral3.1) using the MedFMC dataset. This dataset includes 22,349 images from 7,461 patients encompassing chest radiography (19 disease multi-label classifications), colon pathology (tumor detection), endoscopy (colorectal lesion identification), neonatal jaundice assessment (skin color-based treatment necessity), and retinal fundoscopy (5-point diabetic retinopathy grading). Diagnostic accuracy was compared in three experimental settings: visual input only, multimodal input, and chain-of-thought reasoning. Model accuracy was assessed against ground truth labels, with statistical comparisons using bootstrapped confidence intervals (p<.05). Qwen2.5 achieved the highest accuracy for chest radiographs (90.4%) and endoscopy images (84.2%), significantly outperforming the other models (p<.001). In colon pathology, Qwen2.5 (69.0%) and Phi-4 (69.6%) performed comparably (p=.41), both significantly exceeding other VLMs (p<.001). Similarly, for neonatal jaundice assessment, Qwen2.5 (58.3%) and Phi-4 (58.1%) showed comparable leading accuracies (p=.93) significantly exceeding their counterparts (p<.001). All models struggled with retinal fundoscopy; Qwen2.5 and Gemma3 achieved the highest, albeit modest, accuracies at 18.6% (comparable, p=.99), significantly better than other tested models (p<.001). Unexpectedly, multimodal input reduced accuracy for some models and modalities, and chain-of-thought reasoning prompts also failed to improve accuracy. The open-source VLMs demonstrated promising diagnostic capabilities, particularly in chest radiograph interpretation. However, performance in complex domains such as retinal fundoscopy was limited, underscoring the need for further development and domain-specific adaptation before widespread clinical application.

eess.IV↗
arXiv2025

Three-dimensional end-to-end deep learning for brain MRI analysis

Deep learning (DL) methods are increasingly outperforming classical approaches in brain imaging, yet their generalizability across diverse imaging cohorts remains inadequately assessed. As age and sex are key neurobiological markers in clinical neuroscience, influencing brain structure and disease risk, this study evaluates three of the existing three-dimensional architectures, namely Simple Fully Connected Network (SFCN), DenseNet, and Shifted Window (Swin) Transformers, for age and sex prediction using T1-weighted MRI from four independent cohorts: UK Biobank (UKB, n=47,390), Dallas Lifespan Brain Study (DLBS, n=132), Parkinson's Progression Markers Initiative (PPMI, n=108 healthy controls), and Information eXtraction from Images (IXI, n=319). We found that SFCN consistently outperformed more complex architectures with AUC of 1.00 [1.00-1.00] in UKB (internal test set) and 0.85-0.91 in external test sets for sex classification. For the age prediction task, SFCN demonstrated a mean absolute error (MAE) of 2.66 (r=0.89) in UKB and 4.98-5.81 (r=0.55-0.70) across external datasets. Pairwise DeLong and Wilcoxon signed-rank tests with Bonferroni corrections confirmed SFCN's superiority over Swin Transformer across most cohorts (p<0.017, for three comparisons). Explainability analysis further demonstrates the regional consistency of model attention across cohorts and specific to each task. Our findings reveal that simpler convolutional networks outperform the denser and more complex attention-based DL architectures in brain image analysis by demonstrating better generalizability across different datasets.

cs.CV↗
arXiv2025

RadioRAG: Online Retrieval-augmented Generation for Radiology Question Answering

Large language models (LLMs) often generate outdated or inaccurate information based on static training datasets. Retrieval-augmented generation (RAG) mitigates this by integrating outside data sources. While previous RAG systems used pre-assembled, fixed databases with limited flexibility, we have developed Radiology RAG (RadioRAG), an end-to-end framework that retrieves data from authoritative radiologic online sources in real-time. We evaluate the diagnostic accuracy of various LLMs when answering radiology-specific questions with and without access to additional online information via RAG. Using 80 questions from the RSNA Case Collection across radiologic subspecialties and 24 additional expert-curated questions with reference standard answers, LLMs (GPT-3.5-turbo, GPT-4, Mistral-7B, Mixtral-8x7B, and Llama3 [8B and 70B]) were prompted with and without RadioRAG in a zero-shot inference scenario RadioRAG retrieved context-specific information from Radiopaedia in real-time. Accuracy was investigated. Statistical analyses were performed using bootstrapping. The results were further compared with human performance. RadioRAG improved diagnostic accuracy across most LLMs, with relative accuracy increases ranging up to 54% for different LLMs. It matched or exceeded non-RAG models and the human radiologist in question answering across radiologic subspecialties, particularly in breast imaging and emergency radiology. However, the degree of improvement varied among models; GPT-3.5-turbo and Mixtral-8x7B-instruct-v0.1 saw notable gains, while Mistral-7B-instruct-v0.2 showed no improvement, highlighting variability in RadioRAG's effectiveness. LLMs benefit when provided access to domain-specific data beyond their training data. RadioRAG shows potential to improve LLM accuracy and factuality in radiology question answering by integrating real-time domain-specific data.

cs.CL↗
arXiv2025

Enhancing Privacy: The Utility of Stand-Alone Synthetic CT and MRI for Tumor and Bone Segmentation

AI requires extensive datasets, while medical data is subject to high data protection. Anonymization is essential, but poses a challenge for some regions, such as the head, as identifying structures overlap with regions of clinical interest. Synthetic data offers a potential solution, but studies often lack rigorous evaluation of realism and utility. Therefore, we investigate to what extent synthetic data can replace real data in segmentation tasks. We employed head and neck cancer CT scans and brain glioma MRI scans from two large datasets. Synthetic data were generated using generative adversarial networks and diffusion models. We evaluated the quality of the synthetic data using MAE, MS-SSIM, Radiomics and a Visual Turing Test (VTT) performed by 5 radiologists and their usefulness in segmentation tasks using DSC. Radiomics indicates high fidelity of synthetic MRIs, but fall short in producing highly realistic CT tissue, with correlation coefficient of 0.8784 and 0.5461 for MRI and CT tumors, respectively. DSC results indicate limited utility of synthetic data: tumor segmentation achieved DSC=0.064 on CT and 0.834 on MRI, while bone segmentation a mean DSC=0.841. Relation between DSC and correlation is observed, but is limited by the complexity of the task. VTT results show synthetic CTs' utility, but with limited educational applications. Synthetic data can be used independently for the segmentation task, although limited by the complexity of the structures to segment. Advancing generative models to better tolerate heterogeneous inputs and learn subtle details is essential for enhancing their realism and expanding their application potential.

eess.IV↗
arXiv2025

LLM Agents Making Agent Tools

Tool use has turned large language models (LLMs) into powerful agents that can perform complex multi-step tasks by dynamically utilising external software components. However, these tools must be implemented in advance by human developers, hindering the applicability of LLM agents in domains demanding large numbers of highly specialised tools, like in life sciences and medicine. Motivated by the growing trend of scientific studies accompanied by public code repositories, we propose ToolMaker, an agentic framework that autonomously transforms papers with code into LLM-compatible tools. Given a GitHub URL and short task description, ToolMaker autonomously installs dependencies and generates code to perform the task, using a closed-loop self-correction mechanism for debugging. To evaluate our approach, we introduce a benchmark comprising 15 complex computational tasks spanning various domains with over 100 unit tests to assess correctness and robustness. Our method correctly implements 80% of the tasks, substantially outperforming current state-of-the-art software engineering agents. ToolMaker therefore is a step towards fully autonomous agent-based scientific workflows. Our code and benchmark are publicly available at https://github.com/KatherLab/ToolMaker.

cs.CL↗
arXiv2025

MedAlpaca -- An Open-Source Collection of Medical Conversational AI Models and Training Data

As large language models (LLMs) like OpenAI's GPT series continue to make strides, we witness the emergence of artificial intelligence applications in an ever-expanding range of fields. In medicine, these LLMs hold considerable promise for improving medical workflows, diagnostics, patient care, and education. Yet, there is an urgent need for open-source models that can be deployed on-premises to safeguard patient privacy. In our work, we present an innovative dataset consisting of over 160,000 entries, specifically crafted to fine-tune LLMs for effective medical applications. We investigate the impact of fine-tuning these datasets on publicly accessible pre-trained LLMs, and subsequently, we juxtapose the performance of pre-trained-only models against the fine-tuned models concerning the examinations that future medical doctors must pass to achieve certification.

cs.CL↗
arXiv2025

Unconditional Latent Diffusion Models Memorize Patient Imaging Data: Implications for Openly Sharing Synthetic Data

AI models present a wide range of applications in the field of medicine. However, achieving optimal performance requires access to extensive healthcare data, which is often not readily available. Furthermore, the imperative to preserve patient privacy restricts patient data sharing with third parties and even within institutes. Recently, generative AI models have been gaining traction for facilitating open-data sharing by proposing synthetic data as surrogates of real patient data. Despite the promise, some of these models are susceptible to patient data memorization, where models generate patient data copies instead of novel synthetic samples. Considering the importance of the problem, surprisingly it has received relatively little attention in the medical imaging community. To this end, we assess memorization in unconditional latent diffusion models. We train latent diffusion models on CT, MR, and X-ray datasets for synthetic data generation. We then detect the amount of training data memorized utilizing our novel self-supervised copy detection approach and further investigate various factors that can influence memorization. Our findings show a surprisingly high degree of patient data memorization across all datasets. Comparison with non-diffusion generative models, such as autoencoders and generative adversarial networks, indicates that while latent diffusion models are more susceptible to memorization, overall they outperform non-diffusion models in synthesis quality. Further analyses reveal that using augmentation strategies, small architecture, and increasing dataset can reduce memorization while over-training the models can enhance it. Collectively, our results emphasize the importance of carefully training generative models on private medical imaging datasets, and examining the synthetic data to ensure patient privacy before sharing it for medical research and applications.

eess.IV↗
arXiv2024

Benchmarking foundation models as feature extractors for weakly-supervised computational pathology

Advancements in artificial intelligence have driven the development of numerous pathology foundation models capable of extracting clinically relevant information. However, there is currently limited literature independently evaluating these foundation models on truly external cohorts and clinically-relevant tasks to uncover adjustments for future improvements. In this study, we benchmarked 19 histopathology foundation models on 13 patient cohorts with 6,818 patients and 9,528 slides from lung, colorectal, gastric, and breast cancers. The models were evaluated on weakly-supervised tasks related to biomarkers, morphological properties, and prognostic outcomes. We show that a vision-language foundation model, CONCH, yielded the highest performance when compared to vision-only foundation models, with Virchow2 as close second. The experiments reveal that foundation models trained on distinct cohorts learn complementary features to predict the same label, and can be fused to outperform the current state of the art. An ensemble combining CONCH and Virchow2 predictions outperformed individual models in 55% of tasks, leveraging their complementary strengths in classification scenarios. Moreover, our findings suggest that data diversity outweighs data volume for foundation models. Our work highlights actionable adjustments to improve pathology foundation models.

eess.IV↗