arXiv subjects

Mauricio Reyes

Publications and source records attributed to Mauricio Reyes.

At least 19 recordsLinked to original sources

arXiv2026

HarMoE: Multi-Source Chest Radiograph Pretraining with Dataset-Disentangled Experts

Recent vision-language models for chest X-ray understanding are largely built on image-report alignment and therefore rely heavily on MIMIC-CXR as the dominant pretraining source. While effective at scale, this paradigm underexplores an important alternative source of supervision: a range of existing multi-label classification datasets, which provide cleaner and more explicit disease signals than free-text reports, and can offer broader pathology coverage when combined across sources. However, learning from such heterogeneous datasets is nontrivial, as differences in label ontologies, annotation protocols, acquisition pipelines, and report styles can cause models to entangle clinical semantics with dataset identity, leading to poor transfer despite increased scale. In this work, we revisit radiology VLM construction from the perspective of harmonized multi-source learning. We propose HarMoE, a dataset-aware mixture-of-experts framework that learns shared cross-dataset medical semantics while confining source-specific variation to lightweight residual experts in deeper decoder layers. To further exploit clean supervision from labeled datasets, we train in a unified disease vocabulary with masked multi-dataset supervision, enabling the model to leverage complementary annotations without introducing false negatives. Experiments on large-scale chest X-ray benchmarks show that HarMoE consistently improves zero-shot classification, out-of-distribution transfer, and grounding over strong baselines. Our results suggest that building robust radiology VLMs requires moving beyond single-source image-report alignment toward structured knowledge construction from heterogeneous datasets with cleaner supervision and broader coverage. Code and the 873k harmonized dataset will be released at https://github.com/Roypic/harmoe.

cs.CV↗

arXiv2026

EnTrust: Modeling Inter-Modal Conflict for Trustworthy Multimodal Medical Image Analysis

Multimodal medical imaging fuses complementary anatomical and functional information, yet modalities frequently disagree in pathologically heterogeneous regions. Current segmentation models handle this in one of two inadequate ways: deterministic fusion that averages away disagreement, or post-hoc uncertainty estimation decoupled from the fusion process that produces it. Both obscure the clinically critical question: why is this prediction unreliable? We present EnTrust, a framework that treats inter-modal conflict as the primary source of predictive uncertainty. Our EnFuse module decomposes multimodal features into three disentangled components: shared anatomical consensus (F_c), modality-specific cues (F_{u,m}), and spatially localized conflict signals (F_{cf}), with independence enforced via a cross-covariance objective. This structured decomposition conditions SegDiff, a diffusion-based generative segmentation model whose sampled hypotheses diverge specifically in regions of modal disagreement. TrustMap then translates this hypothesis divergence into calibrated, pixel-wise uncertainty using ensemble entropy, conflict-guided perturbation probing, and a learned calibration head, enabling clinicians to understand not only where predictions are uncertain, but why. Across four benchmarks spanning brain, cardiac, lesion, and oncology domains, EnTrust achieves state-of-the-art segmentation accuracy while reducing calibration error by 40% compared to the strongest baseline. Notably, it outperforms 5x deep ensembles using a single model at roughly half the memory footprint. Code and checkpoints are available at https://github.com/GenMI-Lab/EnTrust.git.

cs.CV↗

arXiv2026

KEPIL: Knowledge-Enhanced Prompt-Image Learning for Prompt-Robust Disease Detection

Vision--language models (VLMs) show promise for clinical decision support in radiology because they enable joint reasoning over radiological images and clinical text, thereby leveraging complementary clinical information. However, radiological findings are long-tailed in practice, leaving some conditions underrepresented and making zero-shot inference essential. Yet current CLIP-style medical VLMs are sensitive to prompt variations and often lack trustworthy external knowledge at inference time, which hinders reliable clinical deployment. We present \textit{KEPIL}, a prompt-robust framework that integrates curated medical knowledge to stabilize zero-shot generalization. KEPIL comprises: (i) \emph{dynamic prompt enrichment} using ontologies with LLM assistance, (ii) a \emph{semantic-aware contrastive loss} aligning embeddings of equivalent prompt variants via a dual-embedding objective, and (iii) \emph{entity-centric report standardization} to yield ontology-aligned representations. Across seven benchmarks, KEPIL achieves state-of-the-art zero-shot inference performance; under prompt-variation tests, it improves AUC by $6.37\%$ on \textit{CheXpert} and by $4.11\%$ on average. These results suggest that structured knowledge and robust prompt design are key to clinically reliable radiology-facing VLMs. Code will be released at https://github.com/Roypic/KEPIL.

cs.CV↗

arXiv2026

Harmonized Feature Conditioning and Frequency-Prompt Personalization for Multi-Rater Medical Segmentation

Multi-rater medical image segmentation captures the inherent ambiguity of clinical interpretation, where diagnostic boundaries vary across experts and imaging devices. Existing approaches often reduce this diversity to consensus labels or treat rater differences as noise, resulting in overconfident and poorly calibrated models. We propose a harmonized probabilistic framework that disentangles acquisition artifacts from genuine annotator variability through adaptive feature conditioning and frequency-domain personalization. A lightweight Harmonizer Network implicitly models scanner-specific artifacts and performs dynamic feature modulation to standardize latent representations, ensuring that uncertainty reflects anatomy rather than noise. To represent rater-specific styles, we introduce a novel High-Frequency Prompt Modules that operate in the spectral domain to encode annotator-dependent boundary precision and textural sensitivity. These prompts adaptively modulate harmonized features to produce personalized yet anatomically consistent segmentations. Furthermore, a Generalized Energy Distance based regularization aligns the generative distribution with empirical annotation variability, promoting diversity where experts disagree and consensus where they converge. Experiments on LIDC-IDRI and NPC-170 show SOTA aggregated and individualized segmentation, with notable GED reductions and improved Dice scores, especially on noisy cases. Beyond accuracy, the model exhibits clinically meaningful uncertainty. Confidence rises in agreement regions and declines in ambiguous areas, supporting its use as a reliable and interpretable tool for multi-expert clinical workflows.

cs.CV↗

arXiv2026

MG-NECOLA: A Field-Level Emulator for $f(R)$ Gravity and Massive Neutrino Cosmologies

Accurate modeling of non-linear gravitational dynamics is essential for constraining extensions to the standard cosmological model using large-scale structure observations. While high-resolution $N$-body simulations provide the required fidelity, they are computationally prohibitive for the large ensembles needed to analyze Modified Gravity (MG) scenarios. We present MG-NECOLA, a field-level emulator based on a convolutional neural network that upgrades fast, approximate MG-PICOLA simulations to near--$N$-body accuracy at a fraction of the computational cost. Trained on a suite of QUIJOTE_MG simulations for $f(R)$ gravity, MG-NECOLA achieves nearly sub-percent accuracy ($\lesssim 1\%$) in both the matter power spectrum and bispectrum up to $k \simeq 1~h\,\mathrm{Mpc}^{-1}$. Crucially, although being trained on a fixed cosmology, the network generalizes robustly to cosmologies outside its training manifold keeping the error below $5\%$. It successfully recovers the General Relativity limit ($Λ$CDM) without introducing spurious MG signals and accurately captures the power suppression induced by massive neutrinos ($M_ν\leq 0.4$ eV), despite being trained on cosmologies with massless neutrinos. The pipeline delivers a speed-up factor of $\sim 1500\times$ relative to full $N$-body runs, generating a high-fidelity realization in O$(10^3)$ CPU seconds compared to O$(10^6)$ for the baseline. This accuracy-efficiency trade-off establishes MG-NECOLA as a powerful tool for generating the massive mock catalogs required for next-generation galaxy surveys.

astro-ph.CO↗

arXiv2026

Grounding Clinical AI Competency in Human Cognition Through the Clinical World Model and Skill-Mix Framework

The competency of any intelligent agent is bounded by its formal account of the world in which it operates. Clinical AI lacks such an account. Existing frameworks address evaluation, regulation, or system design in isolation, without a shared model of the clinical world to connect them. We introduce the Clinical World Model, a framework that formalizes care as a tripartite interaction among Patient, Provider, and Ecosystem. To formalize how any agent, whether human or artificial, transforms information into clinical action, we develop parallel decision-making architectures for providers, patients, and AI agents, grounded in validated principles of clinical cognition. The Clinical AI Skill-Mix operationalizes competency through eight dimensions. Five define the clinical competency space (condition, phase, care setting, provider role, and task) and three specify how AI engages human reasoning (assigned authority, agent facing, and anchoring layer). The combinatorial product of these dimensions yields a space of billions of distinct competency coordinates. A central structural implication is that validation within one coordinate provides minimal evidence for performance in another, rendering the competency space irreducible. The framework supplies a common grammar through which clinical AI can be specified, evaluated, and bounded across stakeholders. By making this structure explicit, the Clinical World Model reframes the field's central question from whether AI works to in which competency coordinates reliability has been demonstrated, and for whom.

cs.AI↗

arXiv2025

MG-NECOLA: Fast Neural Emulators for Modified Gravity Cosmologies

Observations of the large-scale structure (LSS) provide a powerful test of gravity on cosmological scales, but high-resolution N-body simulations of modified gravity (MG) are prohibitively expensive. We present MG-NECOLA, a convolutional neural network that enhances fast MG-PICOLA simulations to near-N-body fidelity at a fraction of the cost. MG-NECOLA reproduces QUIJOTE-MG N-body results in the power spectrum and bispectrum with better than 1% accuracy down to non-linear scales ($k \simeq 1~h~\mathrm{Mpc}^{-1}$), while reducing computational time by several orders of magnitude. Importantly, although trained only on $f(R)$ models with massless neutrinos, the network generalizes robustly to scenarios with massive neutrinos, preserving accuracy to within 5% at non-linear scales. This combination of precision and robustness establishes MG-NECOLA as a practical emulator for producing large ensembles of high-fidelity simulations, enabling efficient exploration of modified gravity and beyond-$Λ$CDM cosmologies in upcoming surveys.

astro-ph.CO↗

arXiv2025

XBench: A Comprehensive Benchmark for Visual-Language Explanations in Chest Radiography

Vision-language models (VLMs) have recently shown remarkable zero-shot performance in medical image understanding, yet their grounding ability, the extent to which textual concepts align with visual evidence, remains underexplored. In the medical domain, however, reliable grounding is essential for interpretability and clinical adoption. In this work, we present the first systematic benchmark for evaluating cross-modal interpretability in chest X-rays across seven CLIP-style VLM variants. We generate visual explanations using cross-attention and similarity-based localization maps, and quantitatively assess their alignment with radiologist-annotated regions across multiple pathologies. Our analysis reveals that: (1) while all VLM variants demonstrate reasonable localization for large and well-defined pathologies, their performance substantially degrades for small or diffuse lesions; (2) models that are pretrained on chest X-ray-specific datasets exhibit improved alignment compared to those trained on general-domain data. (3) The overall recognition ability and grounding ability of the model are strongly correlated. These findings underscore that current VLMs, despite their strong recognition ability, still fall short in clinically reliable grounding, highlighting the need for targeted interpretability benchmarks before deployment in medical practice. XBench code is available at https://github.com/Roypic/Benchmarkingattention

cs.CV↗

arXiv2025

Hybrid Explanation-Guided Learning for Transformer-Based Chest X-Ray Diagnosis

Transformer-based deep learning models have demonstrated exceptional performance in medical imaging by leveraging attention mechanisms for feature representation and interpretability. However, these models are prone to learning spurious correlations, leading to biases and limited generalization. While human-AI attention alignment can mitigate these issues, it often depends on costly manual supervision. In this work, we propose a Hybrid Explanation-Guided Learning (H-EGL) framework that combines self-supervised and human-guided constraints to enhance attention alignment and improve generalization. The self-supervised component of H-EGL leverages class-distinctive attention without relying on restrictive priors, promoting robustness and flexibility. We validate our approach on chest X-ray classification using the Vision Transformer (ViT), where H-EGL outperforms two state-of-the-art Explanation-Guided Learning (EGL) methods, demonstrating superior classification accuracy and generalization capability. Additionally, it produces attention maps that are better aligned with human expertise.

cs.CV↗

arXiv2025

ISLES'24: Final Infarct Prediction with Multimodal Imaging and Clinical Data. Where Do We Stand?

Accurate estimation of brain infarction (i.e., irreversibly damaged tissue) is critical for guiding treatment decisions in acute ischemic stroke. Reliable infarct prediction informs key clinical interventions, including the need for patient transfer to comprehensive stroke centers, the potential benefit of additional reperfusion attempts during mechanical thrombectomy, decisions regarding secondary neuroprotective treatments, and ultimately, prognosis of clinical outcomes. This work introduces the Ischemic Stroke Lesion Segmentation (ISLES) 2024 challenge, which focuses on the prediction of final infarct volumes from pre-interventional acute stroke imaging and clinical data. ISLES24 provides a comprehensive, multimodal setting where participants can leverage all clinically and practically available data, including full acute CT imaging, sub-acute follow-up MRI, and structured clinical information, across a train set of 150 cases. On the hidden test set of 98 cases, the top-performing model, a multimodal nnU-Net-based architecture, achieved a Dice score of 0.285 (+/- 0.213) and an absolute volume difference of 21.2 (+/- 37.2) mL, underlining the significant challenges posed by this task and the need for further advances in multimodal learning. This work makes two primary contributions: first, we establish a standardized, clinically realistic benchmark for post-treatment infarct prediction, enabling systematic evaluation of multimodal algorithmic strategies on a longitudinal stroke dataset; second, we analyze current methodological limitations and outline key research directions to guide the development of next-generation infarct prediction models.

eess.IV↗

arXiv2025

ISLES'24 -- A Real-World Longitudinal Multimodal Stroke Dataset

Stroke remains a leading cause of global morbidity and mortality, imposing a heavy socioeconomic burden. Advances in endovascular reperfusion therapy and CT and MR imaging for treatment guidance have significantly improved patient outcomes. Developing machine learning algorithms that can create accurate models of brain function from stroke images for tasks like lesion identification and tissue survival prediction requires large, diverse, and well annotated public datasets. While several high-quality image datasets in stroke exist, they include only single time point data. Data over different time points are essential to accurately identify lesions and predict prognosis. Here, we provide comprehensive longitudinal stroke data, including (sub-)acute CT imaging with angiography and perfusion, follow-up MRI after 2-9 days, and acute and longitudinal clinical data up to a three-month outcome. The dataset also includes vessel occlusion masks from acute CT angiography and delineated infarction masks in follow-up MRI. This multicenter dataset consists of 245 cases and is a solid basis for developing powerful machine-learning algorithms to facilitate clinical decision-making.

cs.CV↗

arXiv2025

In the Picture: Medical Imaging Datasets, Artifacts, and their Living Review

Datasets play a critical role in medical imaging research, yet issues such as label quality, shortcuts, and metadata are often overlooked. This lack of attention may harm the generalizability of algorithms and, consequently, negatively impact patient outcomes. While existing medical imaging literature reviews mostly focus on machine learning (ML) methods, with only a few focusing on datasets for specific applications, these reviews remain static -- they are published once and not updated thereafter. This fails to account for emerging evidence, such as biases, shortcuts, and additional annotations that other researchers may contribute after the dataset is published. We refer to these newly discovered findings of datasets as research artifacts. To address this gap, we propose a living review that continuously tracks public datasets and their associated research artifacts across multiple medical imaging applications. Our approach includes a framework for the living review to monitor data documentation artifacts, and an SQL database to visualize the citation relationships between research artifact and dataset. Lastly, we discuss key considerations for creating medical imaging datasets, review best practices for data annotation, discuss the significance of shortcuts and demographic diversity, and emphasize the importance of managing datasets throughout their entire lifecycle. Our demo is publicly available at http://inthepicture.itu.dk/.

cs.CV↗

arXiv2025

On the Interplay of Human-AI Alignment,Fairness, and Performance Trade-offs in Medical Imaging

Deep neural networks excel in medical imaging but remain prone to biases, leading to fairness gaps across demographic groups. We provide the first systematic exploration of Human-AI alignment and fairness in this domain. Our results show that incorporating human insights consistently reduces fairness gaps and enhances out-of-domain generalization, though excessive alignment can introduce performance trade-offs, emphasizing the need for calibrated strategies. These findings highlight Human-AI alignment as a promising approach for developing fair, robust, and generalizable medical AI systems, striking a balance between expert guidance and automated efficiency. Our code is available at https://github.com/Roypic/Aligner.

cs.CV↗

arXiv2025

nuGAN: Generative Adversarial Emulator for Cosmic Web with Neutrinos

Understanding the impact of neutrino masses on the evolution of Universe is a crucial aspect of modern cosmology. Due to their large free streaming lengths, neutrinos significantly influence the formation of cosmic structures at non-linear scales. To maximize the information yield from current and future galaxy surveys, it is essential to generate precise theoretical predictions of structure formation. One approach to achieve this is by running large sets of cosmological numerical simulations, which is a computationally intensive process. In this study, we propose a deep learning-based generative adversarial network (GAN) model to emulate the Universe for a variety of neutrino masses. Our model called $ν$GAN (for neutrino GAN) is able to generate 2D cosmic webs of the Universe for a number of neutrino masses ranging from 0.0 eV to 0.4 eV. The generated maps exhibit statistical independence, lack correlations with training data, and very closely resemble the distribution of matter in true maps. We assess the accuracy of our results both visually and through key statistics used in cosmology and computer vision analyses. Our results indicate that samples generated by $ν$GAN are accurate within a 5% error on power spectrum between k=0.01 to k=0.5 h/Mpc. Although this accuracy covers the mildly non-linear scales, consistent with other works and observations, achieving higher accuracy at fully non-linear scales requires more sophisticated models, such as diffusion models. Nevertheless, our work opens up new avenues for building emulators to generate fast and massive neutrino simulations, potentially revolutionizing cosmological predictions and analyses. This work serves as a proof-of-concept, paving the way for future extensions with higher-resolution 3D data and advanced generative models.

astro-ph.CO↗

arXiv2025

From Claims to Evidence: A Unified Framework and Critical Analysis of CNN vs. Transformer vs. Mamba in Medical Image Segmentation

While numerous architectures for medical image segmentation have been proposed, achieving competitive performance with state-of-the-art models networks such as nnUNet, still leave room for further innovation. In this work, we introduce nnUZoo, an open source benchmarking framework built upon nnUNet, which incorporates various deep learning architectures, including CNNs, Transformers, and Mamba-based models. Using this framework, we provide a fair comparison to demystify performance claims across different medical image segmentation tasks. Additionally, in an effort to enrich the benchmarking, we explored five new architectures based on Mamba and Transformers, collectively named X2Net, and integrated them into nnUZoo for further evaluation. The proposed models combine the features of conventional U2Net, nnUNet, CNN, Transformer, and Mamba layers and architectures, called X2Net (UNETR2Net (UNETR), SwT2Net (SwinTransformer), SS2D2Net (SwinUMamba), Alt1DM2Net (LightUMamba), and MambaND2Net (MambaND)). We extensively evaluate the performance of different models on six diverse medical image segmentation datasets, including microscopy, ultrasound, CT, MRI, and PET, covering various body parts, organs, and labels. We compare their performance, in terms of dice score and computational efficiency, against their baseline models, U2Net, and nnUNet. CNN models like nnUNet and U2Net demonstrated both speed and accuracy, making them effective choices for medical image segmentation tasks. Transformer-based models, while promising for certain imaging modalities, exhibited high computational costs. Proposed Mamba-based X2Net architecture (SS2D2Net) achieved competitive accuracy with no significantly difference from nnUNet and U2Net, while using fewer parameters. However, they required significantly longer training time, highlighting a trade-off between model efficiency and computational cost.

eess.IV↗

arXiv2024

DWARF: Disease-weighted network for attention map refinement

The interpretability of deep learning is crucial for evaluating the reliability of medical imaging models and reducing the risks of inaccurate patient recommendations. This study addresses the "human out of the loop" and "trustworthiness" issues in medical image analysis by integrating medical professionals into the interpretability process. We propose a disease-weighted attention map refinement network (DWARF) that leverages expert feedback to enhance model relevance and accuracy. Our method employs cyclic training to iteratively improve diagnostic performance, generating precise and interpretable feature maps. Experimental results demonstrate significant improvements in interpretability and diagnostic accuracy across multiple medical imaging datasets. This approach fosters effective collaboration between AI systems and healthcare professionals, ultimately aiming to improve patient outcomes

cs.CV↗

arXiv2024

A Robust Ensemble Algorithm for Ischemic Stroke Lesion Segmentation: Generalizability and Clinical Utility Beyond the ISLES Challenge

Diffusion-weighted MRI (DWI) is essential for stroke diagnosis, treatment decisions, and prognosis. However, image and disease variability hinder the development of generalizable AI algorithms with clinical value. We address this gap by presenting a novel ensemble algorithm derived from the 2022 Ischemic Stroke Lesion Segmentation (ISLES) challenge. ISLES'22 provided 400 patient scans with ischemic stroke from various medical centers, facilitating the development of a wide range of cutting-edge segmentation algorithms by the research community. Through collaboration with leading teams, we combined top-performing algorithms into an ensemble model that overcomes the limitations of individual solutions. Our ensemble model achieved superior ischemic lesion detection and segmentation accuracy on our internal test set compared to individual algorithms. This accuracy generalized well across diverse image and disease variables. Furthermore, the model excelled in extracting clinical biomarkers. Notably, in a Turing-like test, neuroradiologists consistently preferred the algorithm's segmentations over manual expert efforts, highlighting increased comprehensiveness and precision. Validation using a real-world external dataset (N=1686) confirmed the model's generalizability. The algorithm's outputs also demonstrated strong correlations with clinical scores (admission NIHSS and 90-day mRS) on par with or exceeding expert-derived results, underlining its clinical relevance. This study offers two key findings. First, we present an ensemble algorithm (https://github.com/Tabrisrei/ISLES22_Ensemble) that detects and segments ischemic stroke lesions on DWI across diverse scenarios on par with expert (neuro)radiologists. Second, we show the potential for biomedical challenge outputs to extend beyond the challenge's initial objectives, demonstrating their real-world clinical applicability.

eess.IV↗

arXiv2024

Understanding metric-related pitfalls in image analysis validation

Validation metrics are key for the reliable tracking of scientific progress and for bridging the current chasm between artificial intelligence (AI) research and its translation into practice. However, increasing evidence shows that particularly in image analysis, metrics are often chosen inadequately in relation to the underlying research problem. This could be attributed to a lack of accessibility of metric-related knowledge: While taking into account the individual strengths, weaknesses, and limitations of validation metrics is a critical prerequisite to making educated choices, the relevant knowledge is currently scattered and poorly accessible to individual researchers. Based on a multi-stage Delphi process conducted by a multidisciplinary expert consortium as well as extensive community feedback, the present work provides the first reliable and comprehensive common point of access to information on pitfalls related to validation metrics in image analysis. Focusing on biomedical image analysis but with the potential of transfer to other fields, the addressed pitfalls generalize across application domains and are categorized according to a newly created, domain-agnostic taxonomy. To facilitate comprehension, illustrations and specific examples accompany each pitfall. As a structured body of information accessible to researchers of all levels of expertise, this work enhances global comprehension of a key topic in image analysis validation.

cs.CV↗