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Mauricio Reyes

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4 papers

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AAAI Conference 2026 Conference Paper

VALIANT: Prompt Instability for Active Learning in Black-Box Medical Imaging

Dwarikanath Mahapatra
Behzad Bozorgtabar
Sudipta Roy
Imran Razzak
Mauricio Reyes

The deployment of large, black-box foundation models for medical image classification is often hindered by the high cost of acquiring large, task-specific labeled datasets for fine-tuning. While active learning (AL) presents a promising solution, many state-of-the-art AL methods are computationally expensive or require full access to internal model parameters. We present VALIANT (Visual Adaptation and Learning Integration for Active learNing Tasks), a new active learning framework designed to efficiently adapt black-box foundation models by overcoming these limitations. VALIANT introduces a lightweight Visual Prompt Decoder (VIPD), trained via unsupervised Zero-Order Optimization (ZOO), to generate task-specific visual prompts without internal model access. Our core contribution is a perturbation-based ranking strategy that leverages this VIPD to formulate a computationally efficient, gradient-aware informativeness metric. This metric, which we term prompt instability, identifies the most impactful samples for the labeling budget. VALIANT further enhances this process by incorporating anatomical information from unsupervised segmentation maps to generate more discriminative visual prompts. Extensive evaluations on multiple medical datasets demonstrate VALIANT’s superior performance and significant reduction in labeling costs compared to a range of existing active learning techniques, positioning it as a scalable and practical solution for medical image analysis.

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JBHI Journal 2025 Journal Article

ROXSI: Robust Cross-Sequence Semantic Interaction for Brain Tumor Segmentation on Multi-Sequence MR Images

Zhuo Kuang
Zengqiang Yan
Aly Abayazeed
Franca Wagner
Li Yu
Mauricio Reyes

Deep learning-based brain tumor segmentation on multi-sequence magnetic resonance imaging (MRI) has gained widespread attention due to its great potential in supporting brain disease diagnosis. Although, compared to single-sequence images, more information is available from multi-sequence MR images, noise and artifacts on any given MR sequence can result in significant performance degradations. As in clinical routine, it is not always possible to maintain high imaging quality across all MR sequences (e. g. , foreign bodies, ventricular drainage, shunts, involuntary patient motion, etc.), ensuring robustness of brain tumor segmentation from multi-sequence MR images is of great importance in clinical practice, but rarely explored. Accordingly, in this paper, we propose a robust brain tumor segmentation framework to mitigate the performance degradation caused by noise and artifacts on multi-sequence MR images. Specifically, based on semantic affinity, we propose a unique cross-sequence semantic interaction module (CSSI) to exploit inter-sequence correlations and extract noise-resilient features. In addition, we incorporate a batch-level covariance mechanism to suppress the redundant background information and improve the semantic enhancement effect of the CSSI module. In order to further improve segmentation performance, we also incorporate a sequence-level variance regularization mechanism to exploit sequence-specific features. To validate the robustness of ROXSI, brain tumor segmentation performance was evaluated under the existence of four common artifacts, at five different perturbation levels. We further performed a blinded qualitative clinical evaluation with two experienced neuro-radiologists, evaluating results from ROXSI and other popular CNN and Transformer-based segmentation models. Experimental results on two benchmark datasets demonstrate the superior robustness of ROXSI over other state-of-the-art segmentation methods.

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AAAI Conference 2024 Conference Paper

Combining Graph Transformers Based Multi-Label Active Learning and Informative Data Augmentation for Chest Xray Classification

Dwarikanath Mahapatra
Behzad Bozorgtabar
Zongyuan Ge
Mauricio Reyes
Jean-Philippe Thiran

Informative sample selection in active learning (AL) helps a machine learning system attain optimum performance with minimum labeled samples, thus improving human-in-the-loop computer-aided diagnosis systems with limited labeled data. Data augmentation is highly effective for enlarging datasets with less labeled data. Combining informative sample selection and data augmentation should leverage their respective advantages and improve performance of AL systems. We propose a novel approach to combine informative sample selection and data augmentation for multi-label active learning. Conventional informative sample selection approaches have mostly focused on the single-label case which do not perform optimally in the multi-label setting. We improve upon state-of-the-art multi-label active learning techniques by representing disease labels as graph nodes, use graph attention transformers (GAT) to learn more effective inter-label relationships and identify most informative samples. We generate transformations of these informative samples which are also informative. Experiments on public chest xray datasets show improved results over state-of-the-art multi-label AL techniques in terms of classification performance, learning rates, and robustness. We also perform qualitative analysis to determine the realism of generated images.

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YNICL Journal 2020 Journal Article

Automatic detection of lesion load change in Multiple Sclerosis using convolutional neural networks with segmentation confidence

Richard McKinley
Rik Wepfer
Lorenz Grunder
Fabian Aschwanden
Tim Fischer
Christoph Friedli
Raphaela Muri
Christian Rummel

The detection of new or enlarged white-matter lesions is a vital task in the monitoring of patients undergoing disease-modifying treatment for multiple sclerosis. However, the definition of 'new or enlarged' is not fixed, and it is known that lesion-counting is highly subjective, with high degree of inter- and intra-rater variability. Automated methods for lesion quantification, if accurate enough, hold the potential to make the detection of new and enlarged lesions consistent and repeatable. However, the majority of lesion segmentation algorithms are not evaluated for their ability to separate radiologically progressive from radiologically stable patients, despite this being a pressing clinical use-case. In this paper, we explore the ability of a deep learning segmentation classifier to separate stable from progressive patients by lesion volume and lesion count, and find that neither measure provides a good separation. Instead, we propose a method for identifying lesion changes of high certainty, and establish on an internal dataset of longitudinal multiple sclerosis cases that this method is able to separate progressive from stable time-points with a very high level of discrimination (AUC = 0.999), while changes in lesion volume are much less able to perform this separation (AUC = 0.71). Validation of the method on two external datasets confirms that the method is able to generalize beyond the setting in which it was trained, achieving an accuracies of 75 % and 85 % in separating stable and progressive time-points.

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