Alain Ryser

Laura Manduchi, Moritz Vandenhirtz, Alain Ryser et al.

We propose Tree Variational Autoencoder (TreeVAE), a new generative hierarchical clustering model that learns a flexible tree-based posterior distribution over latent variables. TreeVAE hierarchically divides samples according to their intrinsic characteristics, shedding light on hidden structures in the data. It adapts its architecture to discover the optimal tree for encoding dependencies between latent variables. The proposed tree-based generative architecture enables lightweight conditional inference and improves generative performance by utilizing specialized leaf decoders. We show that TreeVAE uncovers underlying clusters in the data and finds meaningful hierarchical relations between the different groups on a variety of datasets, including real-world imaging data. We present empirically that TreeVAE provides a more competitive log-likelihood lower bound than the sequential counterparts. Finally, due to its generative nature, TreeVAE is able to generate new samples from the discovered clusters via conditional sampling.

Alain Ryser, Laura Manduchi, Fabian Laumer et al.

We propose a novel anomaly detection method for echocardiogram videos. The introduced method takes advantage of the periodic nature of the heart cycle to learn three variants of a variational latent trajectory model (TVAE). While the first two variants (TVAE-C and TVAE-R) model strict periodic movements of the heart, the third (TVAE-S) is more general and allows shifts in the spatial representation throughout the video. All models are trained on the healthy samples of a novel in-house dataset of infant echocardiogram videos consisting of multiple chamber views to learn a normative prior of the healthy population. During inference, maximum a posteriori (MAP) based anomaly detection is performed to detect out-of-distribution samples in our dataset. The proposed method reliably identifies severe congenital heart defects, such as Ebstein's Anomaly or Shone-complex. Moreover, it achieves superior performance over MAP-based anomaly detection with standard variational autoencoders when detecting pulmonary hypertension and right ventricular dilation. Finally, we demonstrate that the proposed method enables interpretable explanations of its output through heatmaps highlighting the regions corresponding to anomalous heart structures.

Thomas M. Sutter, Laura Manduchi, Alain Ryser et al.

Partitioning a set of elements into subsets of a priori unknown sizes is essential in many applications. These subset sizes are rarely explicitly learned - be it the cluster sizes in clustering applications or the number of shared versus independent generative latent factors in weakly-supervised learning. Probability distributions over correct combinations of subset sizes are non-differentiable due to hard constraints, which prohibit gradient-based optimization. In this work, we propose the differentiable hypergeometric distribution. The hypergeometric distribution models the probability of different group sizes based on their relative importance. We introduce reparameterizable gradients to learn the importance between groups and highlight the advantage of explicitly learning the size of subsets in two typical applications: weakly-supervised learning and clustering. In both applications, we outperform previous approaches, which rely on suboptimal heuristics to model the unknown size of groups.

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 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.

Samuel Ruipérez-Campillo, Alain Ryser, Thomas M. Sutter et al.

In the field of cardiac electrophysiology (EP), effectively reducing noise in intra-cardiac signals is crucial for the accurate diagnosis and treatment of arrhythmias and cardiomyopathies. However, traditional noise reduction techniques fall short in addressing the diverse noise patterns from various sources, often non-linear and non-stationary, present in these signals. This work introduces a Variational Autoencoder (VAE) model, aimed at improving the quality of intra-ventricular monophasic action potential (MAP) signal recordings. By constructing representations of clean signals from a dataset of 5706 time series from 42 patients diagnosed with ischemic cardiomyopathy, our approach demonstrates superior denoising performance when compared to conventional filtering methods commonly employed in clinical settings. We assess the effectiveness of our VAE model using various metrics, indicating its superior capability to denoise signals across different noise types, including time-varying non-linear noise frequently found in clinical settings. These results reveal that VAEs can eliminate diverse sources of noise in single beats, outperforming state-of-the-art denoising techniques and potentially improving treatment efficacy in cardiac EP.

Alice Bizeul, Thomas Sutter, Alain Ryser et al. · eth-zurich

Predicting masked from visible parts of an image is a powerful self-supervised approach for visual representation learning. However, the common practice of masking random patches of pixels exhibits certain failure modes, which can prevent learning meaningful high-level features, as required for downstream tasks. We propose an alternative masking strategy that operates on a suitable transformation of the data rather than on the raw pixels. Specifically, we perform principal component analysis and then randomly mask a subset of components, which accounts for a fixed ratio of the data variance. The learning task then amounts to reconstructing the masked components from the visible ones. Compared to local patches of pixels, the principal components of images carry more global information. We thus posit that predicting masked from visible components involves more high-level features, allowing our masking strategy to extract more useful representations. This is corroborated by our empirical findings which demonstrate improved image classification performance for component over pixel masking. Our method thus constitutes a simple and robust data-driven alternative to traditional masked image modeling approaches.

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

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.

Thomas M. Sutter, Alain Ryser, Joram Liebeskind et al.

Partitioning a set of elements into an unknown number of mutually exclusive subsets is essential in many machine learning problems. However, assigning elements, such as samples in a dataset or neurons in a network layer, to an unknown and discrete number of subsets is inherently non-differentiable, prohibiting end-to-end gradient-based optimization of parameters. We overcome this limitation by proposing a novel two-step method for inferring partitions, which allows its usage in variational inference tasks. This new approach enables reparameterized gradients with respect to the parameters of the new random partition model. Our method works by inferring the number of elements per subset and, second, by filling these subsets in a learned order. We highlight the versatility of our general-purpose approach on three different challenging experiments: variational clustering, inference of shared and independent generative factors under weak supervision, and multitask learning.