Sonia Laguna

Simon Böhi, Irene Cannistraci, Sergio Muñoz Gonzalez et al.

Echocardiography is a widely used modality for cardiac assessment due to its non-invasive and cost-effective nature, but the sparse and heterogeneous spatiotemporal views of the heart pose distinct challenges. Existing masked autoencoder (MAE) approaches typically process images or short clips independently, failing to capture the inherent multi-view structure required for coherent cardiac representation. We introduce Latent Attention Masked Autoencoder (LAMAE), a foundation model architecture tailored to the multi-view nature of medical imaging. LAMAE augments the standard MAE with a latent attention module that enables information exchange across frames and views directly in latent space. This allows the model to aggregate variable-length sequences and distinct views, reconstructing a holistic representation of cardiac function from partial observations. We pretrain LAMAE on MIMIC-IV-ECHO, a large-scale, uncurated dataset reflecting real-world clinical variability. To the best of our knowledge, we present the first results for predicting ICD-10 codes from MIMIC-IV-ECHO videos. Furthermore, we empirically demonstrate that representations learned from adult data transfer effectively to pediatric cohorts despite substantial anatomical differences. These results provide evidence that incorporating structural priors, such as multi-view attention, yields significantly more robust and transferable representations.

Moritz Vandenhirtz, Samuel Ruipérez-Campillo, Simon Böhi et al.

Electrocardiograms (ECGs) are among the most widely available clinical signals and play a central role in cardiovascular diagnosis. While recent foundation models (FMs) have shown promise for learning transferable ECG representations, most existing pretraining approaches treat leads as independent channels and fail to explicitly leverage their strong structural redundancy. We introduce the latent attention masked autoencoder (LAMAE) FM that directly exploits this structure by learning cross-lead connection mechanisms during self-supervised pretraining. Our approach models higher-order interactions across leads through latent attention, enabling permutation-invariant aggregation and adaptive weighting of lead-specific representations. We provide empirical evidence on the Mimic-IV-ECG database that leveraging the cross-lead connection constitutes an effective form of structural supervision, improving representation quality and transferability. Our method shows strong performance in predicting ICD-10 codes, outperforming independent-lead masked modeling and alignment-based baselines.

Jonas Mirlach, Sonia Laguna, Julia E. Vogt

Machine unlearning aims to remove the influence of specific data from trained models while preserving general utility. Existing approximate unlearning methods often rely on performance-degradation heuristics, such as loss maximization or random labeling. However, these signals can be poorly conditioned, leading to unstable optimization and harming the model's generalization. We argue that unlearning should instead prioritize distributional indistinguishability, aligning the model's behavior on forget data with its behavior on truly unseen data. Motivated by this, we propose Reference-Guided Unlearning (ReGUn), a framework that leverages a disjoint held-out dataset to provide a principled, class-conditioned reference for distillation. We demonstrate across various model architectures, natural image datasets, and varying forget fractions that ReGUn consistently outperforms standard approximate baselines, achieving a superior forgetting-utility trade-off.

Eleonora Gualdoni, Sonia Laguna, Louis Bethune et al.

Multi-domain fine-tuning of large language models requires improving performance on target domains while preserving performance on constrained domains, such as general knowledge, instruction following, or safety evaluations. Existing data mixing strategies rely on fixed heuristics or adaptive rules that cannot explicitly enforce preservation of such capabilities. We propose DynaMiCS, a dynamic mixture optimizer that casts multi-domain fine-tuning as a constrained optimization problem. At each update, DynaMiCS performs short domain-specific probing runs to estimate a slope matrix of local cross-domain effects, capturing how training on each fine-tuning dataset affects each evaluation domain. These estimates are then used to compute mixture weights through optimization over the probability simplex, with the objective of improving target-domain performance while keeping constrained-domain losses below reference levels. Across multi-domain fine-tuning scenarios with varying numbers of target and constrained domains, DynaMiCS achieves stronger target-domain improvements and higher constraint satisfaction than fixed-mixture baselines, at lower computational cost and without reference models, per-example scoring, or manually tuned mixture weights.

Sonia Laguna, Jorge da Silva Goncalves, Moritz Vandenhirtz et al.

Machine unlearning is rapidly becoming a practical requirement, driven by privacy regulations, data errors, and the need to remove harmful or corrupted training samples. Despite this, most existing methods tackle the problem purely from a post-hoc perspective. They attempt to erase the influence of targeted training samples through parameter updates that typically require access to the full training data. This creates a mismatch with real deployment scenarios where unlearning requests can be anticipated, revealing a fundamental limitation of post-hoc approaches. We propose \textit{unlearning by design}, a novel paradigm in which models are directly trained to support forgetting as an inherent capability. We instantiate this idea with Machine UNlearning via KEY deletion (MUNKEY), a memory augmented transformer that decouples instance-specific memorization from model weights. Here, unlearning corresponds to removing the instance-identifying key, enabling direct zero-shot forgetting without weight updates or access to the original samples or labels. Across natural image benchmarks, fine-grained recognition, and medical datasets, MUNKEY outperforms all post-hoc baselines. Our results establish that unlearning by design enables fast, deployment-oriented unlearning while preserving predictive performance.

Nicolas Dickenmann, Yanis Merzouki, Sonia Laguna et al.

EasyRead pictograms are simple, visually clear images that represent specific concepts and support comprehension for people with intellectual disabilities, low literacy, or language barriers. The large-scale production of EasyRead content has traditionally been constrained by the cost and expertise required to manually design pictograms. In contrast, automatic generation of such images could significantly reduce production time and cost, enabling broader accessibility across digital and printed materials. However, modern diffusion-based image generation models tend to produce outputs that exhibit excessive visual detail and lack stylistic stability across random seeds, limiting their suitability for clear and consistent pictogram generation. This challenge highlights the need for methods specifically tailored to accessibility-oriented visual content. In this work, we present a unified pipeline for generating EasyRead pictograms by fine-tuning a Stable Diffusion model using LoRA adapters on a curated corpus that combines augmented samples from multiple pictogram datasets. Since EasyRead pictograms lack a unified formal definition, we introduce an EasyRead score to benchmark pictogram quality and consistency. Our results demonstrate that diffusion models can be effectively steered toward producing coherent EasyRead-style images, indicating that generative models can serve as practical tools for scalable and accessible pictogram production.

Mikael Makonnen, Moritz Vandenhirtz, Sonia Laguna et al.

Concept Bottleneck Models (CBMs) aim to enhance interpretability by structuring predictions around human-understandable concepts. However, unintended information leakage, where predictive signals bypass the concept bottleneck, compromises their transparency. This paper introduces an information-theoretic measure to quantify leakage in CBMs, capturing the extent to which concept embeddings encode additional, unintended information beyond the specified concepts. We validate the measure through controlled synthetic experiments, demonstrating its effectiveness in detecting leakage trends across various configurations. Our findings highlight that feature and concept dimensionality significantly influence leakage, and that classifier choice impacts measurement stability, with XGBoost emerging as the most reliable estimator. Additionally, preliminary investigations indicate that the measure exhibits the anticipated behavior when applied to soft joint CBMs, suggesting its reliability in leakage quantification beyond fully synthetic settings. While this study rigorously evaluates the measure in controlled synthetic experiments, future work can extend its application to real-world datasets.

Nicolas Deperrois, Hidetoshi Matsuo, Samuel Ruipérez-Campillo et al.

The widespread use of chest X-rays (CXRs), coupled with a shortage of radiologists, has driven growing interest in automated CXR analysis and AI-assisted reporting. While existing vision-language models (VLMs) show promise in specific tasks such as report generation or abnormality detection, they often lack support for interactive diagnostic capabilities. In this work we present RadVLM, a compact, multitask conversational foundation model designed for CXR interpretation. To this end, we curate a large-scale instruction dataset comprising over 1 million image-instruction pairs containing both single-turn tasks -- such as report generation, abnormality classification, and visual grounding -- and multi-turn, multi-task conversational interactions. After fine-tuning RadVLM on this instruction dataset, we evaluate it across different tasks along with re-implemented baseline VLMs. Our results show that RadVLM achieves state-of-the-art performance in conversational capabilities and visual grounding while remaining competitive in other radiology tasks. Ablation studies further highlight the benefit of joint training across multiple tasks, particularly for scenarios with limited annotated data. Together, these findings highlight the potential of RadVLM as a clinically relevant AI assistant, providing structured CXR interpretation and conversational capabilities to support more effective and accessible diagnostic workflows.

Sonia Laguna, Lin Zhang, Can Deniz Bezek et al.

Speed-of-sound (SoS) is a biomechanical characteristic of tissue, and its imaging can provide a promising biomarker for diagnosis. Reconstructing SoS images from ultrasound acquisitions can be cast as a limited-angle computed-tomography problem, with Variational Networks being a promising model-based deep learning solution. Some acquired data frames may, however, get corrupted by noise due to, e.g., motion, lack of contact, and acoustic shadows, which in turn negatively affects the resulting SoS reconstructions. We propose to use the uncertainty in SoS reconstructions to attribute trust to each individual acquired frame. Given multiple acquisitions, we then use an uncertainty based automatic selection among these retrospectively, to improve diagnostic decisions. We investigate uncertainty estimation based on Monte Carlo Dropout and Bayesian Variational Inference. We assess our automatic frame selection method for differential diagnosis of breast cancer, distinguishing between benign fibroadenoma and malignant carcinoma. We evaluate 21 lesions classified as BI-RADS~4, which represents suspicious cases for probable malignancy. The most trustworthy frame among four acquisitions of each lesion was identified using uncertainty based criteria. Selecting a frame informed by uncertainty achieved an area under curve of 76% and 80% for Monte Carlo Dropout and Bayesian Variational Inference, respectively, superior to any uncertainty-uninformed baselines with the best one achieving 64%. A novel use of uncertainty estimation is proposed for selecting one of multiple data acquisitions for further processing and decision making.

Andrea Agostini, Sonia Laguna, Alain Ryser et al.

Building generalizable medical AI systems requires pretraining strategies that are data-efficient and domain-aware. Unlike internet-scale corpora, clinical datasets such as MIMIC-CXR offer limited image counts and scarce annotations, but exhibit rich internal structure through multi-view imaging. We propose a self-supervised framework that leverages the inherent structure of medical datasets. Specifically, we treat paired chest X-rays (i.e., frontal and lateral views) as natural positive pairs, learning to reconstruct each view from sparse patches while aligning their latent embeddings. Our method requires no textual supervision and produces informative representations. Evaluated on MIMIC-CXR, we show strong performance compared to supervised objectives and baselines being trained without leveraging structure. This work provides a lightweight, modality-agnostic blueprint for domain-specific pretraining where data is structured but scarce

Alba Carballo-Castro, Sonia Laguna, Moritz Vandenhirtz et al.

Concept-based machine learning methods have increasingly gained importance due to the growing interest in making neural networks interpretable. However, concept annotations are generally challenging to obtain, making it crucial to leverage all their prior knowledge. By creating concept-enriched models that incorporate concept information into existing architectures, we exploit their interpretable capabilities to the fullest extent. In particular, we propose Concept-Guided Conditional Diffusion, which can generate visual representations of concepts, and Concept-Guided Prototype Networks, which can create a concept prototype dataset and leverage it to perform interpretable concept prediction. These results open up new lines of research by exploiting pre-existing information in the quest for rendering machine learning more human-understandable.

Sonia Laguna, Andrea Agostini, Alain Ryser et al.

Building robust medical machine learning systems requires pretraining strategies that exploit the intrinsic structure present in clinical data. We introduce Multiview Masked Autoencoder (MVMAE), a self-supervised framework that leverages the natural multi-view organization of radiology studies to learn view-invariant and disease-relevant representations. MVMAE combines masked image reconstruction with cross-view alignment, transforming clinical redundancy across projections into a powerful self-supervisory signal. We further extend this approach with MVMAE-V2T, which incorporates radiology reports as an auxiliary text-based learning signal to enhance semantic grounding while preserving fully vision-based inference. Evaluated on a downstream disease classification task on three large-scale public datasets, MIMIC-CXR, CheXpert, and PadChest, MVMAE consistently outperforms supervised and vision-language baselines. Furthermore, MVMAE-V2T provides additional gains, particularly in low-label regimes where structured textual supervision is most beneficial. Together, these results establish the importance of structural and textual supervision as complementary paths toward scalable, clinically grounded medical foundation models.

Wiktor Jan Hoffmann, Sonia Laguna, Moritz Vandenhirtz et al.

Concept Bottleneck Models (CBMs) are interpretable models that predict the target variable through high-level human-understandable concepts, allowing users to intervene on mispredicted concepts to adjust the final output. While recent work has shown that modeling dependencies between concepts can improve CBM performance, especially under interventions, such approaches typically require retraining the entire model, which may be infeasible when access to the original data or compute is limited. In this paper, we introduce Post-hoc Stochastic Concept Bottleneck Models (PSCBMs), a lightweight method that augments any pre-trained CBM with a multivariate normal distribution over concepts by adding only a small covariance-prediction module, without retraining the backbone model. We propose two training strategies and show on real-world data that PSCBMs consistently match or improve both concept and target accuracy over standard CBMs at test time. Furthermore, we show that due to the modeling of concept dependencies, PSCBMs perform much better than CBMs under interventions, while remaining far more efficient than retraining a similar stochastic model from scratch.

Sonia Laguna, Katarzyna Kobalczyk, Julia E. Vogt et al.

We introduce Concept Bottleneck Reward Models (CB-RM), a reward modeling framework that enables interpretable preference learning through selective concept annotation. Unlike standard RLHF methods that rely on opaque reward functions, CB-RM decomposes reward prediction into human-interpretable concepts. To make this framework efficient in low-supervision settings, we formalize an active learning strategy that dynamically acquires the most informative concept labels. We propose an acquisition function based on Expected Information Gain and show that it significantly accelerates concept learning without compromising preference accuracy. Evaluated on the UltraFeedback dataset, our method outperforms baselines in interpretability and sample efficiency, marking a step towards more transparent, auditable, and human-aligned reward models.

Marco Voegeli, Sonia Laguna, Heike Leutheuser et al.

The dead-in-bed syndrome describes the sudden and unexplained death of young individuals with Type 1 Diabetes (T1D) without prior long-term complications. One leading hypothesis attributes this phenomenon to nocturnal hypoglycemia (NH), a dangerous drop in blood glucose during sleep. This study aims to improve NH prediction in children with T1D by leveraging physiological data and machine learning (ML) techniques. We analyze an in-house dataset collected from 16 children with T1D, integrating physiological metrics from wearable sensors. We explore predictive performance through feature engineering, model selection, architectures, and oversampling. To address data limitations, we apply transfer learning from a publicly available adult dataset. Our results achieve an AUROC of 0.75 +- 0.21 on the in-house dataset, further improving to 0.78 +- 0.05 with transfer learning. This research moves beyond glucose-only predictions by incorporating physiological parameters, showcasing the potential of ML to enhance NH detection and improve clinical decision-making for pediatric diabetes management.

Sonia Laguna, Alberto Garcia-Garcia, Marie-Julie Rakotosaona et al.

Modern machine learning models for scene understanding, such as depth estimation and object tracking, rely on large, high-quality datasets that mimic real-world deployment scenarios. To address data scarcity, we propose an end-to-end system for synthetic data generation for scalable, high-quality, and customizable 3D indoor scenes. By integrating and adapting text-to-image and multi-view diffusion models with Neural Radiance Field-based meshing, this system generates highfidelity 3D object assets from text prompts and incorporates them into pre-defined floor plans using a rendering tool. By introducing novel loss functions and training strategies into existing methods, the system supports on-demand scene generation, aiming to alleviate the scarcity of current available data, generally manually crafted by artists. This system advances the role of synthetic data in addressing machine learning training limitations, enabling more robust and generalizable models for real-world applications.

Daphné Chopard, Sonia Laguna, Kieran Chin-Cheong et al.

General movements (GMs) are spontaneous, coordinated body movements in infants that offer valuable insights into the developing nervous system. Assessed through the Prechtl GM Assessment (GMA), GMs are reliable predictors for neurodevelopmental disorders. However, GMA requires specifically trained clinicians, who are limited in number. To scale up newborn screening, there is a need for an algorithm that can automatically classify GMs from infant video recordings. This data poses challenges, including variability in recording length, device type, and setting, with each video coarsely annotated for overall movement quality. In this work, we introduce a tool for extracting features from these recordings and explore various machine learning techniques for automated GM classification.

Moritz Vandenhirtz, Sonia Laguna, Ričards Marcinkevičs et al.

Concept Bottleneck Models (CBMs) have emerged as a promising interpretable method whose final prediction is based on intermediate, human-understandable concepts rather than the raw input. Through time-consuming manual interventions, a user can correct wrongly predicted concept values to enhance the model's downstream performance. We propose Stochastic Concept Bottleneck Models (SCBMs), a novel approach that models concept dependencies. In SCBMs, a single-concept intervention affects all correlated concepts, thereby improving intervention effectiveness. Unlike previous approaches that model the concept relations via an autoregressive structure, we introduce an explicit, distributional parameterization that allows SCBMs to retain the CBMs' efficient training and inference procedure. Additionally, we leverage the parameterization to derive an effective intervention strategy based on the confidence region. We show empirically on synthetic tabular and natural image datasets that our approach improves intervention effectiveness significantly. Notably, we showcase the versatility and usability of SCBMs by examining a setting with CLIP-inferred concepts, alleviating the need for manual concept annotations.

Sonia Laguna, Ričards Marcinkevičs, Moritz Vandenhirtz et al.

Recently, interpretable machine learning has re-explored concept bottleneck models (CBM). An advantage of this model class is the user's ability to intervene on predicted concept values, affecting the downstream output. In this work, we introduce a method to perform such concept-based interventions on pretrained neural networks, which are not interpretable by design, only given a small validation set with concept labels. Furthermore, we formalise the notion of intervenability as a measure of the effectiveness of concept-based interventions and leverage this definition to fine-tune black boxes. Empirically, we explore the intervenability of black-box classifiers on synthetic tabular and natural image benchmarks. We focus on backbone architectures of varying complexity, from simple, fully connected neural nets to Stable Diffusion. We demonstrate that the proposed fine-tuning improves intervention effectiveness and often yields better-calibrated predictions. To showcase the practical utility of our techniques, we apply them to deep chest X-ray classifiers and show that fine-tuned black boxes are more intervenable than CBMs. Lastly, we establish that our methods are still effective under vision-language-model-based concept annotations, alleviating the need for a human-annotated validation set.

Juan Eugenio Iglesias, Riana Schleicher, Sonia Laguna et al.

The recent introduction of portable, low-field MRI (LF-MRI) into the clinical setting has the potential to transform neuroimaging. However, LF-MRI is limited by lower resolution and signal-to-noise ratio, leading to incomplete characterization of brain regions. To address this challenge, recent advances in machine learning facilitate the synthesis of higher resolution images derived from one or multiple lower resolution scans. Here, we report the extension of a machine learning super-resolution (SR) algorithm to synthesize 1 mm isotropic MPRAGE-like scans from LF-MRI T1-weighted and T2-weighted sequences. Our initial results on a paired dataset of LF and high-field (HF, 1.5T-3T) clinical scans show that: (i) application of available automated segmentation tools directly to LF-MRI images falters; but (ii) segmentation tools succeed when applied to SR images with high correlation to gold standard measurements from HF-MRI (e.g., r = 0.85 for hippocampal volume, r = 0.84 for the thalamus, r = 0.92 for the whole cerebrum). This work demonstrates proof-of-principle post-processing image enhancement from lower resolution LF-MRI sequences. These results lay the foundation for future work to enhance the detection of normal and abnormal image findings at LF and ultimately improve the diagnostic performance of LF-MRI. Our tools are publicly available on FreeSurfer (surfer.nmr.mgh.harvard.edu/).