Pathology foundation models improve transferable representation learning for histopathology, but recent gains often rely on encoders with hundreds of millions of parameters and high inference cost. We propose TAP-Path, a task-adaptive compression framework that directly restructures a pretrained Virchow2 encoder rather than distilling it into a separate student. TAP-Path combines validation-driven transformer-block selection, physical removal of redundant blocks, input-adaptive patch-token pruning, multi-depth feature recovery, and a lightweight gated task head. The final model retains 24 of 32 transformer blocks and 70% of patch tokens after pruning, reducing encoder parameters by 24.96% (631.24M to 473.70M) and analytical encoder compute by 35.20% (340.13G to 220.40G FLOPs). Across three task-head optimization seeds, TAP-Path achieved $87.98 \pm 0.067%$ test accuracy, $81.26 \pm 0.49%$ balanced accuracy, and $82.38 \pm 0.48%$ macro-F1 on a 32-class histopathology benchmark, compared with 86.89% for full Virchow2 and 87.67% for UNI2-h. TAP-Path achieved a Brier score of $0.1800 \pm 0.0005$ and failure-detection AUROC of $0.9047 \pm 0.0060$. A validation-only rare-aware objective improved rare-class balanced accuracy in a secondary operating analysis. Frozen external evaluation on 433 CPTAC samples yielded $91.22 \pm 0.83%$ accuracy and $91.10 \pm 0.81%$ balanced accuracy. These results show that task-adaptive structural and token sparsification can improve the accuracy-efficiency trade-off of large pathology foundation models while preserving reliability under internal and external evaluation.
Early screening of chronic kidney disease (CKD) is critical for timely intervention, yet most machine learning (ML) and deep learning (DL) approaches require labeled data and model training, limiting their use in real-world screening settings. This study evaluates the effectiveness of large language models (LLMs) for CKD screening under zero-shot and few-shot in-context learning settings and compares them with traditional ML and DL methods. We propose a framework that uses clinically selected tabular features and structured prompt templates to enable LLM-based inference without task-specific training. LLM performance is evaluated across multiple prompt styles, feature configurations, and data settings, and compared with standard ML, DL, and tabular foundation model (TFM) baselines, and existing CKD screening tools. The results show that LLMs can achieve competitive performance using only a small number of examples, often matching or outperforming traditional approaches in low-data settings. However, their performance remains model-dependent and less stable as input complexity increases. In contrast, ML, DL, and TFM models show more consistent improvement with larger training data. Overall, the findings highlight a trade-off between data efficiency and stability, suggesting that LLMs may serve as a flexible complementary approach for CKD screening when labeled data are limited.
Emanuele Cardinale, Marco Proietti, Alessandro Cacciatore +3cs.CV cs.AI
Noisy annotations pose a significant challenge for supervised deep learning, as neural networks rely on large-scale, high-quality labeled data whose corruption can severely impair model performance. Although robustness to label noise has been extensively studied for classification tasks, it remains relatively underexplored in Pose Estimation (PE). This limitation becomes critical in clinical contexts, including neonatology, where PE of preterm infants is used to support the assessment of spontaneous motility, a key indicator of neurodevelopmental trajectories. In such settings, infants' images labeling is further hindered by visual challenges (e.g., keypoint self-occlusions, caregiver interference), making the annotation process inherently susceptible to errors. To tackle noisy annotations in PE, we introduce REliable keypoint selection via Memory of traINing Dynamics (REMIND), a clustering-based keypoint-selection strategy that exploits keypoint-wise training dynamics to identify noisy labels without assuming any prior knowledge of the noise distribution, thus enabling noise-free model training. When evaluated on the proprietary NeoPose dataset, comprising 46 videos of 46 preterm infants recorded in real clinical settings, REMIND correctly identifies noisy annotations across multiple corruption scenarios, achieving up to 93\% Area Under the Curve (AUC) with three different PE architectures used in the relevant literature. To our knowledge, this is the first study to explicitly address label noise in preterm infants' PE, paving the way for the design of trustworthy learning-based algorithms for infants'monitoring support when data quality cannot be guaranteed.
Despite strong performance on held-out electroencephalography (EEG) data, seizure detectors may fail under real-world acquisition variability, artifacts, and adversarial inputs. We introduce RobustSeiz, an open-source, model-agnostic framework that provides a standardized, reproducible protocol for stress-testing and comparing seizure detectors under controlled, clinically motivated distribution shifts before deployment. We standardize four public scalp-EEG corpora (CHB-MIT, TUSZ, Siena, and SeizeIT1) into BIDS-EEG trees and evaluate subject-independent detectors on held-out splits. Environment, noise, and adversarial transforms are swept over predefined hyperparameter grids. Each run reports sample- and event-level sensitivity, precision, F1, false positives per 24 h, Lead and Lag onset timing, and Monte Carlo dropout predictive agreement. RobustSeiz includes a Dockerized GPU pipeline, experiment registry, and full-evaluation and research-subset modes. We demonstrate the framework with a contemporary seizure detector on TUSZ across the complete implemented shift grid; an AWGN analysis illustrates how perturbation severity changes detection quality, onset timing, and predictive agreement. RobustSeiz provides a shared benchmarking standard for evaluating seizure-detector robustness under realistic clinical stressors, extending pre-deployment assessment beyond clean-data accuracy.
Brain-MRI inpainting replaces a masked region of a scan with synthesized, anatomically plausible healthy tissue, so that analysis tools built for healthy brains can be applied to images they would otherwise reject. On the BraTS local-synthesis benchmark, which ranks submissions on the structural similarity index (SSIM), the peak signal-to-noise ratio, and the mean squared error (MSE) jointly, the strongest recent models are accurate, but several report blurry synthesized regions and attribute this to the mean-seeking behavior of the $\ell_1$ and MSE terms in their training losses. We address this in post-processing, forming a deep ensemble of the two co-first-place 2025 models and training a lightweight residual refiner on the ensemble's own outputs under an $\ell_1$ loss augmented with a structural-similarity term whose weight $λ$ we vary. At a moderate $λ$ the refiner improves SSIM over the ensemble, from $0.8767$ to $0.8780$ on a held-out reproduction of the official scorer and from $0.8555$ to $0.8572$ on the official validation leaderboard, with essentially no change in MSE. The gain is small but consistent, improving $62.6\%$ of the held-out cases with a signed-rank $p=2.2\times10^{-7}$, whereas over-weighting the structural term reverses it. Two ablations bound the effect. Adding any third model to the two-model ensemble degrades it, and classical unsharp masking fails to improve SSIM at any strength (best $0.8765$ against $0.8767$), so the gain reflects learned rather than indiscriminate sharpening. The result is a cheap, reproducible post-processing stage that improves an already strong ensemble without any large-scale retraining.
Several studies have evaluated the ability of Large Language Models (LLMs) for meal planning, yielding positive outcomes. These models can process natural language inputs and leverage learned knowledge from their pretraining to generate meal plans. In this work, we investigate the ability of LLMs to analyze the suitability of given recipes for diabetes. The primary challenge for LLMs is to retrieve relevant dietary guidelines for diabetes, decompose recipes into ingredients and cooking methods, and apply these guidelines to determine the recipe's suitability. To study these challenges, we employ three kinds of prompts namely, (i) Direct Query Prompt (ii) Context-Guided Prompt, and (iii) Exemplary Context Prompt that incorporate different levels of diabetes dietary guidelines from medical sources. We introduce a benchmark dataset curated for this investigation consisting of 7607 recipes that include 3807 recipes suitable for diabetes and 3800 recipes not suitable for diabetes. Our results demonstrate that most LLMs are cautious in predicting recipes as suitable to prevent detrimental outcomes. Further, the models that can reason using the dietary guidelines performed better in predicting the suitability of recipes for diabetes. Overall, Mistral-7B and Llama 70B showed superior performance to their counterparts.
Tomas Guija-Valiente, Blanca Rodriguez-Gonzalez, Norberto Malpica +1cs.CV cs.AI cs.LG
Medical image inpainting has the potential to improve automated brain MRI analysis by reconstructing healthy tissue within pathological regions. We introduce RARF, a task-agnostic region-aware rectified flow framework for masked data generation. We instantiate the framework for 3D brain MRI inpainting as our submission to the BraTS Inpainting Challenge 2026. RARF restricts the stochastic interpolation process to the inpainting region, while the observed voxels remain fixed and provide patient-specific anatomical context. A three-dimensional neural network receives the partially voided image, with Gaussian noise filling the missing region, together with the inpainting mask and the corresponding timestep. The model is trained using masked flow-matching and reconstruction-consistency objectives, combined with mask-aware preprocessing and data augmentation. During inference, the learned velocity field transports the initial noise toward a plausible reconstruction of the missing tissue, which is then combined with the unchanged observed anatomy. Experiments under the BraTS evaluation protocol show that the proposed approach produces competitive reconstructions while maintaining anatomical consistency. Source code is available at: https://github.com/TomasGuija/rarf.
Understanding the frequency of factual errors in chatbot-generated text and evaluating systems that detect these errors is critical for determining chatbot safety. Yet factual-error detection is often treated as a single-pass, single-annotator labeling problem. In long-form chatbot responses, factual errors can be subtle and embedded within mostly correct text. We develop a multi-perspective annotation study of medically relevant chatbot responses, combining first-pass annotation, LLM-as-a-Judge (LaJ) candidate discovery, and two forms of adjudication: medical-expert and evidence-based fact-checking. First-pass annotators frequently miss factual errors later validated by adjudicators. LaJ improves candidate discovery, but is insufficient on its own: It misses factual errors that annotators catch. We also find disagreement among adjudicators, suggesting that adjudication over multiple candidate sources can improve benchmark completeness, but does not eliminate the need to apply judgment and expertise. Applied to an existing benchmark, this technique reveals a similar pattern of missing annotations. Together, these results suggest that in the settings examined here, single-pass hallucination benchmarks may achieve scale at the cost of undercounting factual errors. Multi-pass adjudication can improve coverage, but inferences drawn from the benchmarks are still sensitive to the judgment, expertise, and evidence used to determine error presence.
Federated Learning (FL) with Differential Privacy (DP) is increasingly adopted to preserve data confidentiality in distributed machine learning. However, DP noise distorts learned representations and degrades explanation fidelity, limiting differentially private FL where trustworthy explanations are required, such as assistive clinical diagnosis. Prior work adapted DP noise with static feature-importance signals, restricting explainability to post hoc analysis and precluding noise calibration to explanation quality during training. We propose XCal-FL, a closed-loop, explainability-driven local training algorithm for image classification in cross-silo FL that dynamically calibrates DP noise from three complementary signals: (1) prediction logit variations, measuring causal influence on model confidence, (2) counterfactual margins, capturing decision-boundary sensitivity, and (3) saliency concentration, quantifying spatial coherence of model attention, while enforcing formal DP guarantees via adaptive privacy accounting. Experiments on three medical imaging datasets across varying FL configurations show that XCal-FL yields more accurate and interpretable global models, improving predictive performance by over 10\% and explanation fidelity by up to 5$\times$ over static-noise FL, and outperforming state-of-the-art adaptive DP methods in fidelity. XCal-FL also achieves higher privacy-budget efficiency, turning each unit of cumulative privacy loss into larger gains in both accuracy and explanation fidelity. Our analysis further reveals that, unlike predictive performance, which scales roughly linearly with privacy loss, explanation fidelity exhibits non-linear dynamics. These findings suggest explainability is a distinct dimension of the privacy trade-off that cannot be inferred from utility alone, with implications for training and privacy-budget allocation in decision-critical applications.
Athlete monitoring data may be recorded minute by minute throughout a match or training session, while injury information may only indicate whether the entire session was injury-associated. This creates a modelling problem: assigning the same session-level label to every minute would imply that injury status is known at each exact time, even though within-session injury onset is unknown. Our novelty is a fixed-landmark, one-representation-per-athlete-session formulation that directly addresses this mismatch. Instead of labelling every minute, we construct one representation per athlete-session at each landmark using information observed up to that point. This keeps the target at the session level and avoids unsupported minute-level injury supervision. A landmark is a fixed time point within the same session, such as 10, 20, or 30 minutes. At each landmark, we assess whether the whole session is injury-associated or non-injury-associated and examine how discrimination changes as more within-session information becomes available. Using 2020 SoccerMon data, we analyse 3,743 athlete-sessions from 48 elite women's football athletes, including 22 injury-associated sessions from five athletes. We evaluate pre-session, cumulative, dynamic, and combined representations with athlete-disjoint validation, athlete-cluster bootstrap uncertainty, common-cohort sensitivity analysis, alternative negative-athlete fold allocations, equal-athlete weighting, and Logistic Regression, Random Forest, and XGBoost benchmarks. Primary CUM+DYN Logistic Regression yields ROC-AUC 0.367-0.607 and PR-AUC 0.0080-0.0150 across landmarks, with wide uncertainty. PRE-containing representations show higher point estimates at several landmarks but remain uncertain.
The joint interpretation of metabolic function and anatomical structure is essential for clinical diagnosis in whole-body PET/CT. Although recent advances in 3D medical vision-language models have demonstrated remarkable progress, current efforts are limited to regional CT imaging, leaving a critical void in comprehensive whole-body PET/CT analysis. In this work, we introduce MetaStructAtlas, a large-scale dataset for grounded whole-body PET/CT interpretation that synthesizes multimodal imaging with integrated anatomical, metabolic, and semantic annotations. MetaStructAtlas provides 490 co-registered 3D PET and CT volumes with 50,470 organ-level segmentation masks and grounded radiology reports. To facilitate interactive reasoning, we further developed MetaStructVQA, a standardized 3D grounded visual question-answering benchmark containing 100,565 QA pairs. This framework explicitly links diagnostic queries to visual evidence across modalities, encompassing anatomical, morphological, and metabolic characteristics. Finally, we evaluate state-of-the-art 3D medical VLMs on MetaStructVQA, establishing a robust foundation for multimodal representation learning and integrated whole-body reasoning in nuclear medicine.
Histopathological subtyping relies on the recognition of characteristic histological patterns. These patterns may be expressed by individual tissue structures or by the spatial distribution and co-occurrence of multiple structures, and they often span irregularly shaped tissue regions, termed semantic units in this work. However, conventional patch-based representations may fragment such units and fail to explicitly preserve their internal spatial organization, while efficiently modeling relationships among numerous spatially separated units remains challenging. To address these limitations, we propose the Semantic-Aware Subgraph State Space Model (SASG-SSM), a flexible and efficient framework for whole slide image (WSI) classification. Semantic-Aware Subgraphs (SASGs) first approximate irregularly shaped semantic units by adaptively grouping spatially connected patches guided by class-agnostic visual-semantic priors. By representing patches as graph nodes with adjacency edges, SASGs preserve their internal spatial organization rather than treating them as an unordered set. A Subgraph State Space Module (SG-SSM) subsequently combines a graph neural network encoder for intra-subgraph topology encoding with a Mamba-based state space encoder for efficient contextualization across large numbers of subgraphs. This module integrates local structural information within semantic units with global contextual information arising from their distribution and co-occurrence across the WSI, while efficiently modeling a large number of spatially distributed regions. Extensive experiments across four WSI subtyping datasets demonstrate consistent advantages over representative state-of-the-art methods. Further evaluations under small-cohort and few-shot settings demonstrate robustness and data efficiency under limited training data. Code will be released at https://github.com/HLSvois/SASG-SSM.
Nuno Vivas Brás, Benjamin Memmi, Maëlle Bouhassane +4cs.CV
Accurate segmentation of corneal layers in optical coherence tomography (OCT) is essential for quantitative assessment of corneal morphology, including layer thickness and structural changes associated with disease or surgery. However, automatic segmentation remains challenging because corneal interfaces are thin, affected by speckle noise, and variable across acquisition devices. In this work, we propose ARCOS, a patch-based zero-shot boundary localization framework for corneal layer segmentation in clinical anterior-segment OCT images. Rather than performing conventional region classification, the method predicts boundary heatmaps for the main corneal interfaces from overlapping native-resolution patches. Patch-level predictions are stitched across the full B-scan and converted into boundary locations to obtain continuous, anatomically ordered layer segmentations. The network combines multi-scale feature fusion with a self-conditioned refinement module that uses intermediate boundary information to improve local heatmap predictions while preserving spatial detail. The method was evaluated on clinical OCT images acquired from multiple devices and compared with representative segmentation baselines using boundary localization and derived thickness metrics. The proposed method achieved an off-by-one boundary localization accuracy of 95.1% and a mean absolute boundary error of 0.514 pixels on the matched-device test set. In zero-shot cross-device evaluation, it maintained an average off-by-one accuracy of 84.3% and a mean absolute boundary error of 0.855 pixels across unseen acquisition devices, outperforming the baseline models. Thickness estimates derived from the predicted boundaries showed low error across corneal regions, supporting the method's use for quantitative corneal OCT analysis.
Mia MacGregor, Aakash Welgamage Don, Mark Bartlettcs.AI
Clinical trials in the UK can cost up to £1.3 million, with approximately 90% drug failure rate. Toxicity is a major contributing factor in drug failure. Testing is time and cost intensive. In recent years, the use of artificial intelligence has been increasingly explored to aid in the prediction of drug toxicity, with extensive use of large language models (LLMs). However, LLMs can show considerable variation when minor changes are made to prompts, which raises concerns about their sensitivity to prompt engineering. Prompt engineering is used to optimise a prompt given to an LLM to generate the desired output. This paper proposes a method to analyse prompt engineering for drug toxicity prediction. The aim of the paper is to investigate the importance of prompt phrasing for drug toxicity prediction. LLMs were prompted to identify chemical properties of significance when predicting drug toxicity. Prompts were constructed to investigate; job role, prompt structuring, and rule interpretation. LLMs were then used to generate datasets, using the identified features from initial prompting, which were then passed to machine learning algorithms. The experiments show that the natural variance which occurs in LLMs outweighs any fine-tuning of prompts. There were, however, substantial improvements in model performance when using chemoinformatic code to extract features instead of using LLM-generated values. The proposed analysis methodology is applicable to a wide range of prompt types across different areas of bioinformatics.
Antonio Scardace, Francesco Guarnera, Sebastiano Battiato +1cs.CV
While deep generative models offer new opportunities for medical image synthesis and data sharing, their ability to memorize and reproduce training samples raises serious concerns about patient confidentiality. Detecting such memorization at scale remains challenging: traditional pixel-based metrics are sensitive to generation artifacts, whereas generic embedding-based metrics often lack the anatomical sensitivity required for medical data. To address this challenge, we introduce DeepSSIM++, a self-supervised similarity metric for scalable memorization auditing in medical generative models. By leveraging multi-scale feature aggregation and anatomy-preserving augmentations, DeepSSIM++ learns an embedding space where cosine similarity approximates the Structural Similarity Index (SSIM), eliminating the need for exact pixel-level registration. Compared with state-of-the-art baselines, DeepSSIM++ achieves an average Macro F1 improvement of 33 percentage points under ideal alignment and 46 percentage points under realistic spatial and intensity perturbations. Furthermore, it accelerates large-scale similarity computation by several orders of magnitude compared with analytical SSIM. By combining anatomical sensitivity and computational efficiency, DeepSSIM++ provides an open-source tool for scalable memorization auditing in medical generative AI. Code and data are publicly available at: https://github.com/brAIn-science/DeepSSIM.
Lesion segmentation in medical images plays a critical role in clinical diagnosis and treatment planning. Despite significant advances, lesion segmentation remains challenging due to two major factors: (1) complex background interference; (2) diverse lesion morphology. Existing encoder-decoder based methods mainly focus on enhancing feature extraction or redesigning decoding strategies. However, they lack early prior guidance and feature reconfiguration during the encoding stage, limiting their effectiveness in handling these challenges. To address these limitations, we propose FreNet, a feature reconfiguration framework with visual priors, which performs pixel-level reconfiguration before encoding and feature-level reconfiguration during encoding for precise medical lesion segmentation. To suppress background responses, we propose an Implicit Prior Neural Network (IPNN), which models a continuous spatial field and leverages visual prior from SAM to reconfigure input image before encoding stage. To better handle diverse lesion morphology, we design a Dual-domain Feature Reconfiguration (DFR) module to progressively reconfigure backbone features during encoding stage. Within DFR, the Frequency Decoupling Module (FDM) decouples backbone features in frequency domain to enhance foreground-background discriminability, while the Spatial Localization Module (SLM) spatially relocates and improving spatial stability after frequency decoupling. Extensive experiments on 9 medical image segmentation benchmarks across three imaging modalities demonstrate that FreNet significantly outperforms state-of-the-art (SOTA) methods. On the challenging ETIS dataset, our method achieves Dice improvements of 5.0% over SOTA method and 7.2% over SAM.
Neonatal respiratory diseases are a major cause of neonatal morbidity and mortality, posing substantial challenges in clinical practice. Despite recent advances, existing Multimodal Large Language Models (MLLMs) face two key limitations in neonatal diagnosis: (1) domain gap arising from predominantly adult training data; (2) insufficient integration of multidimensional clinical context for accurate diagnosis. To address these challenges, we collect two real-world clinical datasets (NeoCXR and NeoCXR-EV) and propose NeoRed, to the best of our knowledge, the first MLLM tailored for neonatal respiratory disease, filling the gap in neonatal diagnostic reports generation. To enhance joint diagnosis from heterogeneous clinical context and chest X-rays, we design a novel Knowledge-Logic-Alignment (KLA) framework which constrains model behavior from three perspectives: 1) Knowledge Prior Injection (KPI) incorporates neonatologist-inspired diagnostic priors into multimodal representations, guiding disease-specific attention across modalities; 2) Diagnostic Logic Constraint (DLC) aligns the semantics of generated reports with multimodal diagnostic logic; and 3) Visual Semantic Alignment (VSA) establishes semantic correspondence between visual features and imaging conclusions. Extensive experiments demonstrate that NeoRed enables accurate neonatal diagnostic reports generation, achieving ROUGE-L of 53.29% and Clinical Efficacy F1 score of 65.19% on NeoCXR, outperforming existing MLLMs. NeoRed also preserves competitive report generation performance on adult benchmarks (MIMIC-CXR and IU-Xray). Datasets will be available upon application.
Tracking depression from multi-session counseling dialogues requires estimating both current symptom severity and how it changes across sessions. Yet progress on this task is constrained by the scarcity of longitudinal counseling data with standardized session-level depression labels. Existing resources typically provide either multi-session conversations without depression labels or labeled interviews in a single session. Building such a benchmark poses three challenges: maintaining longitudinal consistency and diversity, grounding symptom progression in empirical patterns, and expressing controlled depression states naturally without exposing target labels. To address these challenges, we introduce LongCounsel-8, a benchmark suite of three independently generated datasets totaling 7,749 five-session counseling trajectories, grounded in real-world client profiles, depression trajectories, symptom compositions, and counseling patterns. We combine profile-grounded simulation, empirically informed state construction, and indirect behavioral realization to address these challenges. Across the benchmark, simulated self-reports closely recover the controlled states, supporting label fidelity. Experiments on existing depression tracking methods reveal three key findings: (1) lower single-session score error does not guarantee accurate identification of trend, i.e., improvement or worsening; (2) existing methods are consistently less reliable on worsening trajectories; and (3) additional session history may reduce the accuracy of trend prediction. Together, these findings establish LongCounsel-8 as a foundation for advancing depression assessment from static, single-session prediction toward reliable longitudinal tracking of mental-health change.
Proteins are fundamental to biological processes, with their function determined by the complex interplay between the amino acid sequence and the three-dimensional structure. Developing generative models capable of understanding this intrinsically multi-modal relationship is crucial for fields like drug discovery and protein engineering. Existing models often rely on a multi-stage training process where autoencoders that tokenize data into latent representations are trained in a first stage. Secondly, a generative model is trained on the latent representation of the autoencoder(s), i.e., generative modeling in a latent space. We hypothesize that this multi-stage training is not necessary to obtain performant co-design models and thus present SimpleDesign, an effective multi-modal protein design model trained directly in the data space. SimpleDesign leverages a single-stage end-to-end objective that combines discrete cross-entropy for sequences and a regression objective for structures. In order to effectively model the difference in sequence and structure modalities, we develop a Mixture-of-Transformer architecture that allows modality-specific processing while keeping global self-attention over both modalities. We train SimpleDesign on over 2M sequence-structure pairs achieving strong performance across co-design and unconditional sequence/structure generation benchmarks.
Accountability means a decision can be examined, justified, and contested. LLMs make this hard: fluent output may be ungrounded, incomplete, or unfaithful to the decision process. Achieving accountability requires verified rationales (how was the decision reached), assumptions (what was assumed rather than known), policy consistency (the same treatment for the same facts), and pivotal conditions (what would change the outcome). We introduce self-faithfulness as an automatic test of accountability: changing the pivotal conditions should change the decision. We examine accountable AI through clinical trial matching, a high-stakes task central to evidence-based medicine. Although LLM-based matchers match patients to trials reasonably accurately, they apply decision policies inconsistently and produce rationales that are unfaithful to their own decisions. We introduce VERDICT, an LLM-based agent that translates a decision task, its constraints, and its policy into Satisfiability Modulo Theories (SMT), then derives the decision with SMT and MaxSMT solvers -- so policies are applied consistently and decisions are accountable by construction. Across a SIGIR 2016-derived dataset and TREC 2021, VERDICT achieves the strongest decision accuracy among LLM-only and neurosymbolic baselines, applies policies with perfect consistency, and produces clinician-preferred rationales grounded in explicit assumptions and pivotal conditions, with improved counterfactual self-faithfulness.
Remote voice studies often retain a final audio file with limited evidence about how it was captured, transferred, processed, and accepted. This paper presents VocalCap, an institution-controlled, browser-based system for self-guided capture of voice and related acoustic signals by participants without technical training. A versioned protocol drives the workflow. Each accepted recording retains a browser-native object, a client-lossless Float32 WAV derived from the same MediaStream, and a server-canonical mono PCM16 WAV, linked to evidence of capture execution, technical quality, byte-level integrity, recovery, and transformation provenance. IndexedDB preserves accepted browser artifacts until server confirmation, while session completion requires successful verification of every task and artifact. Software tests challenged the acquisition contracts with malformed or altered objects, exact-zero interruptions, channel-topology variants, and interrupted or repeated operations. A post hoc technical audit of 39 consented pilot recordings found 25 sample-identical stereo files and 14 files with signal confined to the left channel. Topology-aware active-channel selection limited the canonical root-mean-square level difference to less than 0.001 dB in all 14 affected files; equal-weight stereo averaging would have introduced approximately 6.02 dB of attenuation. Production end-to-end verification completed two five-task profiles in Chromium and WebKit, yielding 10 accepted recordings and 30 retained artifacts that passed server-side integrity and format checks. The results verify VocalCap's software behavior under the tested browser-engine conditions. Device-level acoustic agreement, target-population usability, clinical validity, and biomarker performance remain subjects for separate studies.
Moo K. Chung, Keith J. Worsley, Steve Robbins +1cs.CV q-bio.NC
We present a unified computational approach to tensor-based morphometry in detecting the brain surface shape differences between two clinical groups based on magnetic resonance images. Our approach is novel in a sense that we combined surface modeling, surface data smoothing and statistical analysis in a coherent unified mathematical framework. The cerebral cortex has the topology of a 2D highly convoluted sheet. Between two different clinical groups, the local surface area and curvature of the cortex may differ. It is highly likely that such surface shape differences are not uniform over the whole cortex. By computing how such surface metrics differ, the regions of the most rapid structural differences can be localized. To increase the signal to noise ratio, diffusion smoothing based on the explicit estimation of Laplace-Beltrami operator has been developed and applied to the surface metrics. As an illustration, we demonstrate how this new tensor-based surface morphometry can be applied in localizing the cortical regions of the gray matter tissue growth and loss in the brain images longitudinally collected in the group of children.
A benchmark score credits final answers, but not the route by which an item can be answered. In medical multimodal multiple-choice questions (MCQs), this distinction matters because a correct answer can be supported by the intended image finding or by benchmark-preserved cues in the wording of answers, non-visual clinical text, visible image text, artificial annotations, or device/context artifacts. We call the resulting score-level overinterpretation reasoning inflation. Here, a route is an observable input path that can support answer selection, not a claim about the model's hidden cognition. Across six medical multimodal MCQ datasets, we separate candidate cues from behavioral evidence through prompt- and image-side audits, modality ablations, and matched repairs that preserve the medical target and answer key. In a 13-configuration open-model panel, full-input accuracy is 62.63%, while text-only and options-only settings achieve 53.96% and 29.71%, respectively. Removing length-gap, absolute/conspicuous, and spatial/prepositional cues lowers accuracy by 6.58, 3.50, and 4.77 percentage points. We also construct MedQA-MM, a 1,000-item shortcut-mitigated subset, where text-only and options-only accuracy fall to 5.21% and 12.33%. This does not imply that models never use images; it shows that medical image-reasoning claims require route-level evidence.
Francesco Mantegna, Gereon Elvers, Dulhan Jayalath +18cs.LG
The ambition of the 2025 PNPL competition (Landau et al., 2025) was to launch a multi-year curriculum for non-invasive speech decoding. Designed to progress from foundational tasks toward the linguistic complexity required for a practical brain-computer interface (BCI), it set the stage with speech detection and phoneme classification tasks. Winning submissions reached F1-macro scores of 95.6% and 73.6% on the respective tasks (Elvers et al., 2026), highly significant advances. This success was built on the LibriBrain dataset (Özdogan et al., 2025), the largest within-subject MEG dataset recorded at the time with ${\sim}50$ hours of data for one subject. However, while within-subject scale drives strong decoding performance, a practical BCI must generalise to new users from minutes of data, not hours. The 2026 PNPL competition responds to this challenge with LibriBrain100 (Mantegna et al., 2026), an extended LibriBrain dataset with 32 additional subjects (${\sim}40$ minutes each) plus even more within-subject data (${\sim}80$ hours). Advancing the curriculum of tasks to focus on word classification, two complementary tracks are presented in this competition: the Deep track targets within-subject word classification at scale, aiming at the best possible performance; the Broad track targets cross-subject generalisation, progressively reducing the amount of subject-specific fine-tuning data from ${\sim}40$ to ${\sim}20$ to ${\sim}10$ minutes, a duration that falls within a clinically feasible range and brings us a step closer to a non-invasive BCI capable of restoring communication to people living with profound paralysis.
Maryam Bagherian, Albert Hung, Ivo Dinov +1math.NA cs.LG
Many biomedical challenges can be posed as tensor completion problems where the observed entries of a multidimensional array (a tensor) are used to impute the missing values. In such settings, incorporating side information about the modes of the tensor, such as gene-gene similarity, can significantly enhance the solutions of the completion problem. Most existing tensor completion methods can only incorporate side information in the form of matrices. In this study, we introduce a novel framework to incorporate side information in the form of tensors. Our new approach, called Coupled Tensor-Tensor Completion (CTTC), leverages the hidden connections among multimodal tensors to improve tensor completion performance. In addition to practical utility, CTTC has theoretical foundations in distance metric learning and group theory. We derive an alternating algorithm to solve the CTTC optimization problem and establish its convergence to a stationary point. Finally, we show that CTTC outperforms state-of-the-art tensor completion methods at predicting drug effects. Results: Compared with other tensor completion methods, including HaLRTC, CTRC, Cell, and NTDDR, CTTC demonstrates superior run-time and RSE tensor completion accuracy on two benchmark datasets, DTD and LINCS.
Phillip Chlap, Mark Lee, Trevor Leong +11physics.med-ph cs.CV
Training deep learning-based medical image segmentation models is challenging with limited curated datasets. For AGITG TOPGEAR, a gastric cancer trial, the Clinical Target Volume (CTV) is complex and defined by multiple anatomical landmarks, making upfront training data preparation difficult for an automated contour QA segmentation model. We investigate anatomical priors, derived from surrounding organ segmentations, to provide spatial context and improve TOPGEAR CTV segmentation accuracy. We also evaluate active learning, iteratively expanding the training dataset by selecting cases expected to improve performance. One hundred TOPGEAR CT scans were retrospectively analyzed. An initial set of 10 expert-contoured cases was used to train an nnU-Net model. TotalSegmentator generated a voxel-wise anatomical prior map from surrounding structures as an additional input channel. Active learning was simulated over four iterations, selecting cases by model uncertainty and segmentation performance. All models used five-fold cross-validation for an ensemble uncertainty measure. Evaluation used a hold-out testing set of 50 cases. The anatomical prior improved CTV segmentation accuracy, increasing mean Dice Similarity Coefficient (DSC) from 0.84 to 0.86. Active learning similarly improved performance to 0.86, with greatest benefit in the final round. Combining the anatomical prior with active learning achieved the highest accuracy, with a DSC of 0.87. Model uncertainty correlated with DSC, supporting its use in identifying suboptimal predictions and guiding active learning. Anatomical priors and active learning each improved CTV segmentation accuracy and generalizability, with their combination achieving the best performance, supporting integration into segmentation model development for automated contour QA in radiotherapy clinical trials.
Smartphone skin photographs are indispensable to teledermatology, yet assessing the diagnostic suitability of submitted cases (gradability) remains a critical bottleneck in mobile care workflows. Dermatologists routinely review multiple photographic views (regional, angled, and close-up) to identify consistent textural detail rather than relying on a single image. We present the Semantic Tri-view Pipeline, an interpretable architecture for automated teledermatology gradability screening that formalizes epidermal micro-relief as a computable biomarker of image quality. Using an expert-annotated subset of the public SCIN dataset, we train a lightweight DeepLabV3+ model to segment micro-relief fidelity. These spatial masks are then aggregated across up to three case views with a logistic regression classifier, leveraging viewpoint redundancy to support robustness under uncontrolled smartphone acquisition. This approach learns context-aware, clinically intelligible heuristics, such as penalizing high-fidelity texture in regional distance views. Evaluated at a predefined 90% sensitivity operating point, the system's apparent errors largely reflect subjective clinical variance on borderline cases where clinicians rely on non-visual metadata. On SCIN, performance improves from an AUC of 0.81 (80.6% PPV) on variance-heavy majority-consensus cases to 0.96 (97.7% PPV) on optically unambiguous unanimous cases. Overall, this work delivers an interpretable, privacy-by-design, edge-ready system that can provide real-time feedback during case submission to filter ungradable photo sets before review.
Young Seok Jeon, Beatrice Brown-Mulry, Rohan Satya Isaac +5cs.CV
There is growing interest in adopting CLIP-style vision--language model (VLM) pretraining for mammography. However, models that directly employ the standard CLIP architecture and training objective exhibit limited zero-shot performance in clinically important tasks such as cancer, finding-type, and BI-RADS predictions. We argue that this underwhelming performance is due to neglecting two characteristics of mammography data: (1) its high-res nature, and (2) homogeneity of radiology reports, largely driven by a predominance of negative/benign findings on examinations. We propose TopKSigLIP, a VLM designed to address these two limitations through a novel architecture and learning objectives. Instead of downscaling high-res mammography images to satisfy GPU memory constraints, TopKSigLIP introduces TopK-Patch module that learns to sample a sparse set of high-res patches likely to contain lesions, sidestepping the resolution--batch size tradeoff of VLM training. The sampled patch locations additionally serve as a built-in localization tool. To address report homogeneity, we replace the contrastive loss, which falsely repels semantically similar pairs, with a Sup-sigmoid loss. Sup-sigmoid loss extends the sigmoid loss from SigLIP with soft labels derived from structured data. TopKSigLIP outperforms existing open-source mammography and general medical VLMs on both internal and external benchmarks on density assessment, BI-RADS classification, finding subtyping, and cancer prediction under zero-shot evaluation. TopKSigLIP remains competitive under linear probing despite using a significantly smaller vision encoder and smaller training batches than baselines. The TopK-Patch module additionally achieves superior lesion localization over post-hoc Grad-CAM. Code and weights are made public:https://github.com/Youngseok0001/TopKSigLIP.
Michal Průšek, Adam Novozámský, Filip Šroubekcs.CV
Segmenting a new biomedical dataset usually means a domain-specific model trained on substantial annotation, or a foundation model steered at inference time. We present Exemplar, a few-shot segmenter that fuses a frozen DINOv3 backbone with a fixed bank of classical native-resolution filter responses in one lightweight head, fitted from the support masks alone. In the few-mask, native-resolution regime, classical priors and frozen self-supervised features are complementary: fused in one head, a single fixed configuration spans eleven biomedical imaging datasets. Under the same head, the classical bank alone reaches 0.693 on the eleven-dataset panel, scored by foreground intersection-over-union or centreline Dice, and the frozen features alone 0.672; the bank leads on seven of the eleven and the features on the rest, and fused they reach 0.782. Against five forward-pass few-shot methods, Exemplar leads in 54 of 55 method-dataset comparisons, 52 of them significant after Holm correction. From a single annotated mask it reaches 0.703 on the same panel, against 0.682 for a from-scratch nnU-Net trained on that same mask. At eight masks nnU-Net overtakes it on the panel mean, chiefly on centreline agreement, but takes 16-77x longer to fit.
Dulhan Jayalath, Benjamin Ballyk, Oiwi Parker Jonescs.LG q-bio.NC
Speech brain-computer interfaces (speech BCIs) translate neural activity into language, offering a path towards restoring speech for people with paralysis and, more broadly, enabling new forms of natural human-computer interaction. Despite this promise, the field lacks a common measure of progress because systems use different datasets, recording methods, types of speech, and vocabularies, so their reported scores are rarely comparable. Underlying this measurement problem are two unresolved questions: (i) what distribution of words should a speech BCI enable a user to communicate, and (ii) how much information from this distribution can a system convey. We address both by deriving open-vocabulary mutual information (OVMI), an information-theoretic quantity that measures the information conveyed by a decoder relative to a reference distribution over the words a user may wish to communicate. This allows capabilities measured under different conditions, such as distinct vocabularies, to be evaluated on a common communication scale. We show that ordinarily reported accuracy, word error rate (WER), and other metrics computed only over the words a system supports can overstate how much of a user's intended speech the system can communicate. We then use OVMI to compare existing systems, expose trade-offs between how much of the user's language a system supports and how accurately it decodes those words, show that these comparisons depend on what the user is expected to communicate, and demonstrate that selecting a vocabulary to maximise OVMI yields up to 16.3% relative improvement in accuracy across three speech domains. OVMI therefore provides the speech BCI community with a principled way to compare heterogeneous systems, improve vocabulary design, and measure progress in the field.