arXiv subjects

Daniel Truhn

Publications and source records attributed to Daniel Truhn.

At least 19 recordsLinked to original sources

arXiv2026

Auditable CT Phenotyping Through Report-derived Radiological Observations

Medical image foundation models can predict clinical phenotypes from computed tomography (CT), but strong performance leaves open whether they read disease-specific findings or shortcuts that correlate with the diagnosis. We tested this in 221 electronic-health-record (EHR) phenotypes using Auditable CT phenotyping (ACT), built on report-derived radiological observations. We trained ACT on 38,317 patients, mined 376,194 observations and evaluated it in 25,183 held-out patients. ACT exceeded five vision-language baselines on zero-shot annotation, and CT-CLIP across 221 phenotypes from unseen CT pulmonary angiography, both under zero-shot scoring (0.651 versus 0.572) and under linear probing (0.709 versus 0.662). Reading each probe exposes what accuracy conceals: only 97 observations occupy the 221 rank-1 positions, and one phrase describing aortic and coronary calcification ranks first for 20 phenotypes, including osteoporosis, urinary tract infection and major depressive disorder. Restricting the bank to clinician-specified evidence redirects those probes onto phenotype-related observations in 86 phenotypes at no accuracy cost (0.751 versus 0.741). Accurate CT-based EHR phenotyping can therefore rest on observations that are not valid evidence for the coded phenotype and that ACT can identify and intervene on.

cs.CV↗

arXiv2026

FRAME: separating sampling variation from representational cause in medical imaging fairness

Subgroup performance differences are the standard evidence for fairness bias in medical imaging, and the usual response removes the demographic information that a model encodes. Here we introduce Fair-model Reference And Mechanism Evaluation (FRAME), a two-step framework for auditing such a claim. The first step derives a fair-model reference, the distribution of the difference under exact fairness at the observed subgroup sizes. In the second step, we test the remainder with two operators in representation space. One operator cannot change a within-group ranking by construction. Across 702,206 images and 36 encoders, the reference accounts for a median 41% of the reported race difference and 22% of the age difference. Injecting demographic decodability leaves the remainder unchanged, while entangling the group with the disease direction raises the race difference from 0.077 to 0.118. No intervention we tested changes the remainder more than a change of random seed does. Those interventions reduce a difference at the operating point and leave the within-group ranking difference at a median of 0.000. Applied to 89 differences in 9 published studies across 6 medical imaging modalities, the reference accounts for a median 25% of a rate difference and 70% of a difference in the area under the receiver operating characteristic curve. Image-text pretraining instead raises worst-group performance by about 0.05. Applying FRAME before choosing an intervention could distinguish differences that need a mechanistic explanation from differences compatible with sampling variation at the current cohort sizes.

cs.CV↗

arXiv2026

Self-supervision drives representational convergence in medical foundation models more than clinical supervision

Medical image encoders from different groups are increasingly treated as interchangeable, on the assumption that scale and clinical supervision concentrate their representations onto a shared structure. Whether this convergence is real, what produces it, and whether it is clinically usable are untested, and the similarity measures behind such claims are fragile. We present a controlled dissection across 18 image and 7 text encoders, all open-weight and run locally, spanning 7M to 27B parameters and five imaging modalities, including 650,982 chest radiographs from six datasets. To isolate cause, we train encoders that vary only the objective under fixed data, architecture, and scale, and reproduce the effect in a synthetic model. Convergence is modest but above a random floor, driven by the self-supervised objective, not clinical supervision: matched self-supervised encoders aligned most (40.4% on chest radiography), with label-supervised (21.1%) and image-text (3.3%) far lower, and did not grow with size (Spearman 0.302, p=0.223) or capability. It is within-modality, does not reach clinical language, and does not reproduce how radiologists judge case similarity. Yet a linear classifier transfers across encoders and to five held-out hospitals, retaining about 85% of within-encoder performance. Convergence in medical imaging is therefore set by the pretraining objective, not inherited from scale or clinical supervision. Interoperability is accordingly something to design for through that objective, and to validate where the shared geometry is weakest, across patient subgroups and against clinical judgment.

cs.CV↗

arXiv2026

Bayesian uncertainty estimation improves clinical decision making in medical AI agents

Machine learning models for medical image analysis typically lack a reliable measure of confidence, limiting their use in ambiguous or atypical cases. Here we show that Monte Carlo dropout, applied to a multi-task chest-radiograph classifier (eight thoracic findings, 137,593 training images), provides an epistemic uncertainty signal that tracks generalisation across training-set scales and flags confident yet error-prone predictions. Adding this signal to the point prediction raised error-detection AUROC from 0.74 to 0.77 ($\Delta$AUROC +0.023, 95% CI [+0.014, +0.033]). In a controlled 2x2 factorial experiment, a clinical-decision-support agent exploited this uncertainty only when it was delivered as a binary error-risk flag rather than as raw scores, cutting confident misdiagnoses on unreliable findings from 8.5% to 2.7%. Epistemic uncertainty estimation thus carries decision-relevant information beyond point predictions, but its value for downstream agents depends on how it is communicated.

cs.LG↗

arXiv2026

Foundation-model-guided radiogenomic discovery linking cancer genomes to cancer scans

The function of many genes is still unknown, and conventional driver-discovery methods, which rely on how frequently a gene is mutated, cannot assess genes that are only rarely affected. Here we pair Evo~2-based genome analysis with routine clinical imaging to identify gene--phenotype associations at genome-wide scale. For every somatic mutation across three TCGA cohorts (cRCC=clear cell renal cell carcinoma, HCC=hepatocellular carcinoma, and BC=breast cancer; $n = 340$ total), Evo~2 predicts a severity score, with no task-specific training. Per-gene severity summaries are then correlated with radiomic features extracted from paired tumor segmentations, controlling for total mutation burden. In TCGA-cRCC ($n = 162$), this sweep recovers established renal-cancer drivers and identifies 46 additional genes reaching false discovery rate (FDR) significance absent from curated cancer-gene panels, several of which are Mendelian ciliopathy and cytoskeletal-disease genes. These results demonstrate that pairing a genomic language model with widely available clinical imaging can serve as a hypothesis-free discovery tool for gene--imaging associations invisible to conventional approaches.

q-bio.GN↗

arXiv2026

CANDOR: Chance-Calibrated Discordance in Frozen Foundation Encoders

Frozen encoders are chosen by how well a lightweight head reads a finding from their features, not whether the geometry separates it. Nearest-neighbor discordance does, but with unequal banks the opposite-label neighbor wins on density, not geometry, so prevalence alone makes an uninformed encoder look blind. We introduce CANDOR, a discordance measure whose equal-size banks are symmetric under a label swap, fixing its chance level at exactly one half. Across 22 encoders, 20 datasets from 7 domains, and 605,443 images, this correction reverses the conclusion. Collapse falls below chance almost everywhere, so no encoder is blind, yet all are weak: the best chest model reads pneumothorax at 84.5 AUROC and still places 18.4% of those positives nearer an opposite-label film than its own kind in the same hospital. The same encoder that resolves bird species at 4.5 leaves chest findings at 42.8 and glaucoma at 49.8, at chance and worse than random weights. Such a case caps the normalized margin of any Lipschitz head, yet some head among eleven is correct on all but 2.8% of cases where one head misses 35.9%: the deficit is selection, not information. Erasure retention is associated with collapse; we detect no association with the objective, scale, recency, or size of the finding. Because the chance level is fixed, CANDOR can be read before any head is trained, flagging which findings a frozen encoder supports poorly.

cs.LG↗

arXiv2026

Vision-language models for chest radiography do not always need the image

Medical vision-language models report strong chest radiograph accuracy, and this is increasingly read as evidence that they use the image. That inference is unsafe: a model exploiting finding-name priors scores like one that reads the scan, and no standard benchmark separates them. We introduce a causal audit that intervenes on the image, occluding the relevant region, occluding an irrelevant one, and swapping in another patient's same-label scan, and combines three behavioral metrics to test whether a correct answer depends on the image. Across nine systems, a text-only model with no image access reaches within 5.7 accuracy points of the best multimodal one, and a 119-billion-parameter multimodal model is statistically indistinguishable from a 7-billion text-only baseline. The audit splits the cohort into three models that ignore the image, one that is unstable, and five that use it selectively, for a subset of findings; the categories hold across a second dataset, resolution, and prompt phrasing. Against board-certified radiologists, a text-only model is statistically indistinguishable from a radiologist's accuracy while grounding at zero, whereas the image-using models ground at radiologist-comparable rates. Reported confidence flags ungrounded answers only when a model uses the image. Grounding audits, not accuracy, should gate clinical deployment.

cs.CV↗

arXiv2026

Cross-modal linkage risk in clinical vision-language models

Vision-language models (VLMs) trained on paired chest radiographs and radiology reports learn a shared embedding space that can preserve instance-level image-report correspondence. This poses a privacy risk in settings where radiographs and reports are deliberately kept separate after acquisition, such as image-only data sharing or access-controlled reports, because a de-identified image may be re-linked to its original narrative report through cosine similarity alone. We formalized this as image-to-report retrieval and used public paired cohorts, in which the true pairing is known by design, as ground-truth benchmarks to audit the risk rather than as the privacy scenario. Evaluating VLMs of increasing clinical specialization on 406,241 paired examples from 126,804 patients across MIMIC-CXR (43,793 held-out pairs) and external CheXpert Plus (29,296 pairs), we found that re-linkage rose systematically with specialization: the strongest VLM retrieved the correct report at 15 times chance at a candidate pool of N = 100, 50 times chance at N = 10,000, and well above chance at full-database scale. The signal persisted under pathology-matched hard negatives that removed disease-label shortcuts, indicating correspondence beyond broad diagnostic categories. To reduce it without retraining, we froze both encoders and applied differentially private optimization only to the projection heads defining the alignment layer (epsilon = 0.34, delta = 6x10-6). This reduced Recall@1 by 61.8% at N = 10,000 on MIMIC-CXR and transferred to CheXpert Plus without retraining, while image-side utility was largely preserved: macro AUROC for linear-probe classification across 14 labels shifted only from 79.63% to 79.43%. Targeted DP finetuning of the shared alignment layer can substantially reduce cross-modal re-linkage without materially degrading the image representations that make these models clinically useful.

cs.CV↗

arXiv2026

Safety and accuracy follow different scaling laws in clinical large language models

Clinical LLMs are often scaled by increasing model size, context length, retrieval complexity, or inference-time compute, with the implicit expectation that higher accuracy implies safer behavior. This assumption is incomplete in medicine, where a few confident, high-risk, or evidence-contradicting errors can matter more than average benchmark performance. We introduce SaFE-Scale, a framework for measuring how clinical LLM safety changes across model scale, evidence quality, retrieval strategy, context exposure, and inference-time compute. To instantiate this framework, we introduce RadSaFE-200, a Radiology Safety-Focused Evaluation benchmark of 200 multiple-choice questions with clinician-defined clean evidence, conflict evidence, and option-level labels for high-risk error, unsafe answer, and evidence contradiction. We evaluated 34 locally deployed LLMs across six deployment conditions: closed-book prompting (zero-shot), clean evidence, conflict evidence, standard RAG, agentic RAG, and max-context prompting. Clean evidence produced the strongest improvement, increasing mean accuracy from 73.5% to 94.1%, while reducing high-risk error from 12.0% to 2.6%, contradiction from 12.7% to 2.3%, and dangerous overconfidence from 8.0% to 1.6%. Standard RAG and agentic RAG did not reproduce this safety profile: agentic RAG improved accuracy over standard RAG and reduced contradiction, but high-risk error and dangerous overconfidence remained elevated. Max-context prompting increased latency without closing the safety gap, and additional inference-time compute produced only limited gains. Worst-case analysis showed that clinically consequential errors concentrated in a small subset of questions. Clinical LLM safety is therefore not a passive consequence of scaling, but a deployment property shaped by evidence quality, retrieval design, context construction, and collective failure behavior.

cs.CL↗

arXiv2026

From Clinical Intent to Clinical Model: Autonomous Coding-Agents for Clinician-driven AI Development

Developing AI models that are useful in clinical practice, requires efficient collaboration between clinicians and AI developers. This poses a practical challenge: clinicians must repeatedly communicate and refine their requirements with AI developers before those requirements can be translated into executable model development. This iterative process is time-consuming, and even after repeated discussion, misalignment may still exist because the two sides do not fully share each other's expertise. Coding agents may help close this gap. They can write and refine code on their own, and they carry working knowledge of both medicine and AI to understand commands formulated by both medical experts and developers. We present a prototype that lets clinicians drive AI development directly. A clinician describes the task in plain language, and the system turns the description into a working pipeline, refines it through repeated experiments together with the clinician, and returns a model that meets the stated clinical objective. Across five clinical tasks, the system reliably produces models that matched the clinician's request and reached competitive performance. Most notably, on chest radiographs the system sharply reduced the model's reliance on chest drains, a well-known shortcut for pneumothorax classification, from 60% to 31% on one dataset and from 50% to 18% on another. Our results suggest that coding agents can shift clinical AI development toward a more clinician-driven mode, allowing domain experts to shape models directly instead of relaying requirements through specialized AI teams.

cs.CV↗

arXiv2026

Case-Grounded Evidence Verification: A Framework for Constructing Evidence-Sensitive Supervision

Evidence-grounded reasoning requires more than attaching retrieved text to a prediction: a model should make decisions that depend on whether the provided evidence supports the target claim. In practice, this often fails because supervision is weak, evidence is only loosely tied to the claim, and evaluation does not test evidence dependence directly. We introduce case-grounded evidence verification, a general framework in which a model receives a local case context, external evidence, and a structured claim, and must decide whether the evidence supports the claim for that case. Our key contribution is a supervision construction procedure that generates explicit support examples together with semantically controlled non-support examples, including counterfactual wrong-state and topic-related negatives, without manual evidence annotation. We instantiate the framework in radiology and train a standard verifier on the resulting support task. The learned verifier substantially outperforms both case-only and evidence-only baselines, remains strong under correct evidence, and collapses when evidence is removed or swapped, indicating genuine evidence dependence. This behavior transfers across unseen evidence articles and an external case distribution, though performance degrades under evidence-source shift and remains sensitive to backbone choice. Overall, the results suggest that a major bottleneck in evidence grounding is not only model capacity, but the lack of supervision that encodes the causal role of evidence.

cs.CL↗

arXiv2026

Agentic retrieval-augmented reasoning reshapes collective reliability under model variability in radiology question answering

Agentic retrieval-augmented reasoning pipelines are increasingly used to structure how large language models (LLMs) incorporate external evidence in clinical decision support. These systems iteratively retrieve curated domain knowledge and synthesize it into structured reports before answer selection. Although such pipelines can improve performance, their impact on reliability under model variability remains unclear. In real-world deployment, heterogeneous models may align, diverge, or synchronize errors in ways not captured by accuracy. We evaluated 34 LLMs on 169 expert-curated publicly available radiology questions, comparing zero-shot inference with a radiology-specific multi-step agentic retrieval condition in which all models received identical structured evidence reports derived from curated radiology knowledge. Agentic inference reduced inter-model decision dispersion (median entropy 0.48 vs. 0.13) and increased robustness of correctness across models (mean 0.74 vs. 0.81). Majority consensus also increased overall (P<0.001). Consensus strength and robust correctness remained correlated under both strategies (\r{ho}=0.88 for zero-shot; \r{ho}=0.87 for agentic), although high agreement did not guarantee correctness. Response verbosity showed no meaningful association with correctness. Among 572 incorrect outputs, 72% were associated with moderate or high clinically assessed severity, although inter-rater agreement was low (\k{appa}=0.02). Agentic retrieval therefore was associated with more concentrated decision distributions, stronger consensus, and higher cross-model robustness of correctness. These findings suggest that evaluating agentic systems through accuracy or agreement alone may not always be sufficient, and that complementary analyses of stability, cross-model robustness, and potential clinical impact are needed to characterize reliability under model variability.

cs.LG↗

arXiv2026

Differential privacy representation geometry for medical image analysis

Differential privacy (DP)'s effect in medical imaging is typically evaluated only through end-to-end performance, leaving the mechanism of privacy-induced utility loss unclear. We introduce Differential Privacy Representation Geometry for Medical Imaging (DP-RGMI), a framework that interprets DP as a structured transformation of representation space and decomposes performance degradation into encoder geometry and task-head utilization. Geometry is quantified by representation displacement from initialization and spectral effective dimension, while utilization is measured as the gap between linear-probe and end-to-end utility. Across over 594,000 images from four chest X-ray datasets and multiple pretrained initializations, we show that DP is consistently associated with a utilization gap even when linear separability is largely preserved. At the same time, displacement and spectral dimension exhibit non-monotonic, initialization- and dataset-dependent reshaping, indicating that DP alters representation anisotropy rather than uniformly collapsing features. Correlation analysis reveals that the association between end-to-end performance and utilization is robust across datasets but can vary by initialization, while geometric quantities capture additional prior- and dataset-conditioned variation. These findings position DP-RGMI as a reproducible framework for diagnosing privacy-induced failure modes and informing privacy model selection.

cs.CV↗

arXiv2026

Can Agents Distinguish Visually Hard-to-Separate Diseases in a Zero-Shot Setting? A Pilot Study

The rapid progress of multimodal large language models (MLLMs) has led to increasing interest in agent-based systems. While most prior work in medical imaging concentrates on automating routine clinical workflows, we study an underexplored yet clinically significant setting: distinguishing visually hard-to-separate diseases in a zero-shot setting. We benchmark representative agents on two imaging-only proxy diagnostic tasks, (1) melanoma vs. atypical nevus and (2) pulmonary edema vs. pneumonia, where visual features are highly confounded despite substantial differences in clinical management. We introduce a multi-agent framework based on contrastive adjudication. Experimental results show improved diagnostic performance (an 11-percentage-point gain in accuracy on dermoscopy data) and reduced unsupported claims on qualitative samples, although overall performance remains insufficient for clinical deployment. We acknowledge the inherent uncertainty in human annotations and the absence of clinical context, which further limit the translation to real-world settings. Within this controlled setting, this pilot study provides preliminary insights into zero-shot agent performance in visually confounded scenarios.

cs.CV↗

arXiv2026

The pretraining domain outweighs the training objective in setting the privacy-utility trade-off of differentially private medical image analysis

Differential privacy protects the patients whose images train medical imaging models, but it lowers diagnostic accuracy, and the initialization is the strongest known remedy. Practice increasingly favors large generic self-supervised encoders. Yet the pretraining objective and the pretraining domain are confounded in existing comparisons, so which one preserves utility under privacy is unknown, and the pretraining corpus is treated as public even when it holds patient images. We trained ConvNeXt classifiers with differentially private stochastic gradient descent from five initializations that vary the objective and the domain independently, at four privacy budgets and without privacy, and evaluated them locally on more than 590,000 chest radiographs from five external datasets in four countries. Supervised pretraining on chest radiographs ranked first in 24 of 25 dataset and budget combinations. Its lead over ImageNet grew from 2.5 to 14.6 points of macro-averaged area under the receiver operating characteristic curve as the budget tightened, and the domain effect exceeded the objective effect by a factor of 2.2 to 3.4. Pretraining that corpus privately cost about 5 points and, under privacy, still beat every public initialization. Low-rank adaptation removed about half the residual gap, and in-domain pretraining raised the worst-performing demographic subgroup. Under privacy, what a model was pretrained on outweighs how it was pretrained.

cs.CV↗

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 $\kappa$), 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 ($\kappa = 0.58$) and SR ($\kappa = 0.60$) but higher in AI-SR ($\kappa = 0.71$, $P < .001$). 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

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 $\tau_b=0.670$), moderate alignment for fidelity ($\tau_b=0.387$), and weak alignment for confidence tone ($\tau_b=0.091$), 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

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↗