arXiv subjects

Rémi Flamary

Publications and source records attributed to Rémi Flamary.

At least 19 recordsLinked to original sources

arXiv2026

Multi-Task Learning of Conditional Mean Operators: applications to dynamical systems and uncertainty quantification

Estimating conditional statistics and learning representations of a population of conditional distributions are central problems in many data-driven applications, including uncertainty quantification and dynamical systems analysis. Conditional mean operators (CMOs), a class of linear operators between function spaces, resolve these objectives by providing access to a broad class of conditional statistics. However, existing methods typically estimate each CMO independently or constrain it to prespecified function spaces, thereby preventing the exploitation of shared structure across related distributions. In this work, we posit that related CMOs share finite-dimensional input and output function spaces, and are specialized for each task with a linear operator mapping these spaces. Based on this hypothesis, we introduce MTL-CMO, a multi-task framework that jointly learns shared function spaces and task-specific operators across multiple datasets. We further introduce T-CMO, a transfer learning method that reuses the shared spaces to estimate, in closed form, the operator of a new conditional distribution. We establish statistical guarantees quantifying the benefits of jointly learning the shared function spaces. Our experiments demonstrate that learning shared function spaces improves uncertainty quantification across a broad range of conditional distributions and, when applied to Langevin and plasma dynamics, yields compact representations of complex dynamics that retain physically meaningful information and enable parameter identification.

stat.ML↗

arXiv2026

MSAlign: Aligning Molecule and Mass Spectra representations for Metabolite Identification

Accurately identifying metabolites i.e. small molecules from mass spectrometry data remains a core challenge in metabolomics, with broad applications in drug discovery, environmental analysis, and clinical research. We address the Molecule Retrieval task, which consists in recovering the chemical structure of a metabolite from its MS/MS spectrum given a set of candidate molecules. We make three contributions. First, we propose a unified framework encompassing recent approaches based on representation alignment and contrastive learning. Second, we introduce MSAlign, a lightweight model that achieves state-of-the art performances by aligning two frozen foundation models (DreaMS for mass spectra and MolDeBERTa for molecules) and demonstrate that a score fusion strategy further improves the performance for a very small computational cost. Third, we investigate a long-standing evaluation problem: data splitting strategies in molecule retrieval implicitly trade off data leakage against domain shift. We formalize this tension by introducing a quantitative measure of distribution shift, and use it to evaluate splitting strategies in existing benchmarks. All datasets, splits, candidate sets, and a unified implementation of MSAlign and baselines are publicly released to support reproducible research.

cs.LG↗

arXiv2026

Graph Matching Relaxations and Amortization for Supervised Graph Prediction

End-to-end Supervised Graph Prediction (SGP) requires a permutation-invariant loss to compare predicted and target graphs with arbitrary node orderings. Such losses typically involve a costly graph-matching problem. We first study three Optimal Transport relaxations of this problem and show, theoretically and empirically, that the Gromov-Wasserstein (GW) objective is the most suitable for SGP. Then, to avoid solving the resulting inner optimization for every training example, we propose to amortize the graph matching (node alignment) problem. For each training sample, the loss function leverages a transport plan provided by a parametric matcher based on the differentiable Sinkhorn algorithm applied on empirical node distributions. The graph prediction module and the matcher are jointly learned. We showcase the efficiency of this approach on toy and real world SGP problems of increasing complexity including a novel Mass-spectra to Scaffold task that we introduce.

stat.ML↗

arXiv2026

Geometric Dictionary Learning of Dynamical Systems with Optimal Transport

Learning dynamical systems through operator-theoretic representations provides a powerful framework for analyzing complex dynamics, as spectral quantities such as eigenvalues and invariant structures encode characteristic time scales and long-term behavior. However, dynamical operators are typically estimated independently for each system, preventing the discovery of shared structure across related dynamics. To address this limitation, we posit that related dynamical systems lie near a low-dimensional manifold in spectral operator space. Based on this hypothesis, we introduce DOODL (Dynamical OperatOr Dictionary Learning), a framework that learns a dictionary of characteristic spectral dynamics whose combinations approximate this manifold and yield compact, interpretable embeddings of individual systems. Beyond representation learning, DOODL enables fast and interpretable operator estimation from short and partially observed trajectories by constraining the estimation to the learned operator manifold. Experiments on metastable Langevin dynamics and turbulent plasma simulations demonstrate that DOODL scales to highly complex multiscale regimes while capturing characteristic spectral structure governing the dynamics rather than merely fitting trajectories, achieving errors one to two orders of magnitude lower than independent operator estimation methods in challenging low-data regimes.

stat.ML↗

arXiv2026

A barycenter-based approach for the multi-model ensembling of subseasonal forecasts

Ensemble forecasts and their combination are examined from the perspective of probability spaces. Manipulating ensemble forecasts as discrete probability distributions, multi-model ensemble (MME) forecasts are reformulated as barycenters of these distributions. We consider two barycenters, each defined with respect to a different distance metric: the L2 barycenter, which correspond to the traditional pooling method, and the Wasserstein barycenter, which better preserves certain geometric properties of the input ensemble distributions. As a proof of concept, we apply the L2 and Wasserstein barycenters to the combination of four models from the Subseasonal to Seasonal (S2S) prediction project database. Their performance is evaluated for the prediction of weekly 2m temperature, 10m wind speed, and 500hPa geopotential height over European winters. By construction, both barycenter-based MMEs have the same ensemble mean, but differ in their representation of the forecast uncertainty. Notably, the L2 barycenter has a larger ensemble spread, making it more prone to under-confidence. While both methods perform similarly on average in terms of the Continuous Ranked Probability Score (CRPS), the Wasserstein barycenter performs better more frequently.

stat.AP↗

arXiv2026

Learning fMRI activations dictionaries across individual geometries via optimal transport

Dictionary learning is a powerful tool for creating interpretable representations. When applied to functional magnetic resonance imaging (fMRI) data, the resulting patterns of brain activity can be used for various downstream tasks, such as brain state classification or population-level analysis. However, a major challenge is the variability in brain geometry across individuals. This is usually addressed by projecting each individual brain geometry onto a common template, which removes subject-specific information. In this work, we introduce a novel approach to dictionary learning on fMRI data that explicitly accounts for this variability. We use the optimal transport-based Fused Gromov-Wasserstein (FGW) distance to compare graphs with different geometries and features. To address the challenge of computing multiple FGW distances for large graphs such as those arising from fMRI data, we rely on amortized optimization to learn a neural network that predicts an approximation of the optimal transport plans, which substantially reduces the computational cost. Additionally, we learn dictionary atoms that depend on the FGW trade-off parameter, which controls the balance between feature alignment and structural consistency. Numerical experiments on the HCP dataset demonstrate that the proposed approach captures different levels of geometric variability in the data and provides representations that preserve essential information.

cs.LG↗

arXiv2026

PSDNorm: Test-Time Temporal Normalization for Deep Learning in Sleep Staging

Distribution shift poses a significant challenge in machine learning, particularly in biomedical applications using data collected across different subjects, institutions, and recording devices, such as sleep data. While existing normalization layers, BatchNorm, LayerNorm and InstanceNorm, help mitigate distribution shifts, when applied over the time dimension they ignore the dependencies and auto-correlation inherent to the vector coefficients they normalize. In this paper, we propose PSDNorm that leverages Monge mapping and temporal context to normalize feature maps in deep learning models for signals. Evaluations with architectures based on U-Net or transformer backbones trained on 10K subjects across 10 datasets, show that PSDNorm achieves state-of-the-art performance on unseen left-out datasets while being more robust to data scarcity.

cs.LG↗

arXiv2025

The quest for the GRAph Level autoEncoder (GRALE)

Although graph-based learning has attracted a lot of attention, graph representation learning is still a challenging task whose resolution may impact key application fields such as chemistry or biology. To this end, we introduce GRALE, a novel graph autoencoder that encodes and decodes graphs of varying sizes into a shared embedding space. GRALE is trained using an Optimal Transport-inspired loss that compares the original and reconstructed graphs and leverages a differentiable node matching module, which is trained jointly with the encoder and decoder. The proposed attention-based architecture relies on Evoformer, the core component of AlphaFold, which we extend to support both graph encoding and decoding. We show, in numerical experiments on simulated and molecular data, that GRALE enables a highly general form of pre-training, applicable to a wide range of downstream tasks, from classification and regression to more complex tasks such as graph interpolation, editing, matching, and prediction.

cs.LG↗

arXiv2025

SKADA-Bench: Benchmarking Unsupervised Domain Adaptation Methods with Realistic Validation On Diverse Modalities

Unsupervised Domain Adaptation (DA) consists of adapting a model trained on a labeled source domain to perform well on an unlabeled target domain with some data distribution shift. While many methods have been proposed in the literature, fair and realistic evaluation remains an open question, particularly due to methodological difficulties in selecting hyperparameters in the unsupervised setting. With SKADA-bench, we propose a framework to evaluate DA methods on diverse modalities, beyond computer vision task that have been largely explored in the literature. We present a complete and fair evaluation of existing shallow algorithms, including reweighting, mapping, and subspace alignment. Realistic hyperparameter selection is performed with nested cross-validation and various unsupervised model selection scores, on both simulated datasets with controlled shifts and real-world datasets across diverse modalities, such as images, text, biomedical, and tabular data. Our benchmark highlights the importance of realistic validation and provides practical guidance for real-life applications, with key insights into the choice and impact of model selection approaches. SKADA-bench is open-source, reproducible, and can be easily extended with novel DA methods, datasets, and model selection criteria without requiring re-evaluating competitors. SKADA-bench is available on Github at https://github.com/scikit-adaptation/skada-bench.

cs.LG↗

arXiv2025

Differentiable Expectation-Maximisation and Applications to Gaussian Mixture Model Optimal Transport

The Expectation-Maximisation (EM) algorithm is a central tool in statistics and machine learning, widely used for latent-variable models such as Gaussian Mixture Models (GMMs). Despite its ubiquity, EM is typically treated as a non-differentiable black box, preventing its integration into modern learning pipelines where end-to-end gradient propagation is essential. In this work, we present and compare several differentiation strategies for EM, from full automatic differentiation to approximate methods, assessing their accuracy and computational efficiency. As a key application, we leverage this differentiable EM in the computation of the Mixture Wasserstein distance $\mathrm{MW}_2$ between GMMs, allowing $\mathrm{MW}_2$ to be used as a differentiable loss in imaging and machine learning tasks. To complement our practical use of $\mathrm{MW}_2$, we contribute a novel stability result which provides theoretical justification for the use of $\mathrm{MW}_2$ with EM, and also introduce a novel unbalanced variant of $\mathrm{MW}_2$. Numerical experiments on barycentre computation, colour and style transfer, image generation, and texture synthesis illustrate the versatility of the proposed approach in different settings.

cs.LG↗

arXiv2025

A Spectral-Grassmann Wasserstein metric for operator representations of dynamical systems

The geometry of dynamical systems estimated from trajectory data is a major challenge for machine learning applications. Koopman and transfer operators provide a linear representation of nonlinear dynamics through their spectral decomposition, offering a natural framework for comparison. We propose a novel approach representing each system as a distribution of its joint operator eigenvalues and spectral projectors and defining a metric between systems leveraging optimal transport. The proposed metric is invariant to the sampling frequency of trajectories. It is also computationally efficient, supported by finite-sample convergence guarantees, and enables the computation of Fréchet means, providing interpolation between dynamical systems. Experiments on simulated and real-world datasets show that our approach consistently outperforms standard operator-based distances in machine learning applications, including dimensionality reduction and classification, and provides meaningful interpolation between dynamical systems.

stat.ML↗

arXiv2025

Unsupervised Learning for Optimal Transport plan prediction between unbalanced graphs

Optimal transport between graphs, based on Gromov-Wasserstein and other extensions, is a powerful tool for comparing and aligning graph structures. However, solving the associated non-convex optimization problems is computationally expensive, which limits the scalability of these methods to large graphs. In this work, we present Unbalanced Learning of Optimal Transport (ULOT), a deep learning method that predicts optimal transport plans between two graphs. Our method is trained by minimizing the fused unbalanced Gromov-Wasserstein (FUGW) loss. We propose a novel neural architecture with cross-attention that is conditioned on the FUGW tradeoff hyperparameters. We evaluate ULOT on synthetic stochastic block model (SBM) graphs and on real cortical surface data obtained from fMRI. ULOT predicts transport plans with competitive loss up to two orders of magnitude faster than classical solvers. Furthermore, the predicted plan can be used as a warm start for classical solvers to accelerate their convergence. Finally, the predicted transport plan is fully differentiable with respect to the graph inputs and FUGW hyperparameters, enabling the optimization of functionals of the ULOT plan.

cs.LG↗

arXiv2025

Distributional Reduction: Unifying Dimensionality Reduction and Clustering with Gromov-Wasserstein

Unsupervised learning aims to capture the underlying structure of potentially large and high-dimensional datasets. Traditionally, this involves using dimensionality reduction (DR) methods to project data onto lower-dimensional spaces or organizing points into meaningful clusters (clustering). In this work, we revisit these approaches under the lens of optimal transport and exhibit relationships with the Gromov-Wasserstein problem. This unveils a new general framework, called distributional reduction, that recovers DR and clustering as special cases and allows addressing them jointly within a single optimization problem. We empirically demonstrate its relevance to the identification of low-dimensional prototypes representing data at different scales, across multiple image and genomic datasets.

cs.LG↗

arXiv2025

Properties of Discrete Sliced Wasserstein Losses

The Sliced Wasserstein (SW) distance has become a popular alternative to the Wasserstein distance for comparing probability measures. Widespread applications include image processing, domain adaptation and generative modelling, where it is common to optimise some parameters in order to minimise SW, which serves as a loss function between discrete probability measures (since measures admitting densities are numerically unattainable). All these optimisation problems bear the same sub-problem, which is minimising the Sliced Wasserstein energy. In this paper we study the properties of $\mathcal{E}: Y \longmapsto \mathrm{SW}_2^2(γ_Y, γ_Z)$, i.e. the SW distance between two uniform discrete measures with the same amount of points as a function of the support $Y \in \mathbb{R}^{n \times d}$ of one of the measures. We investigate the regularity and optimisation properties of this energy, as well as its Monte-Carlo approximation $\mathcal{E}_p$ (estimating the expectation in SW using only $p$ samples) and show convergence results on the critical points of $\mathcal{E}_p$ to those of $\mathcal{E}$, as well as an almost-sure uniform convergence and a uniform Central Limit result on the process $\mathcal{E}_p(Y)$. Finally, we show that in a certain sense, Stochastic Gradient Descent methods minimising $\mathcal{E}$ and $\mathcal{E}_p$ converge towards (Clarke) critical points of these energies.

stat.ML↗

arXiv2024

Any2Graph: Deep End-To-End Supervised Graph Prediction With An Optimal Transport Loss

We propose Any2graph, a generic framework for end-to-end Supervised Graph Prediction (SGP) i.e. a deep learning model that predicts an entire graph for any kind of input. The framework is built on a novel Optimal Transport loss, the Partially-Masked Fused Gromov-Wasserstein, that exhibits all necessary properties (permutation invariance, differentiability and scalability) and is designed to handle any-sized graphs. Numerical experiments showcase the versatility of the approach that outperform existing competitors on a novel challenging synthetic dataset and a variety of real-world tasks such as map construction from satellite image (Sat2Graph) or molecule prediction from fingerprint (Fingerprint2Graph).

cs.LG↗

arXiv2024

Multi-Source and Test-Time Domain Adaptation on Multivariate Signals using Spatio-Temporal Monge Alignment

Machine learning applications on signals such as computer vision or biomedical data often face significant challenges due to the variability that exists across hardware devices or session recordings. This variability poses a Domain Adaptation (DA) problem, as training and testing data distributions often differ. In this work, we propose Spatio-Temporal Monge Alignment (STMA) to mitigate these variabilities. This Optimal Transport (OT) based method adapts the cross-power spectrum density (cross-PSD) of multivariate signals by mapping them to the Wasserstein barycenter of source domains (multi-source DA). Predictions for new domains can be done with a filtering without the need for retraining a model with source data (test-time DA). We also study and discuss two special cases of the method, Temporal Monge Alignment (TMA) and Spatial Monge Alignment (SMA). Non-asymptotic concentration bounds are derived for the mappings estimation, which reveals a bias-plus-variance error structure with a variance decay rate of $\mathcal{O}(n_\ell^{-1/2})$ with $n_\ell$ the signal length. This theoretical guarantee demonstrates the efficiency of the proposed computational schema. Numerical experiments on multivariate biosignals and image data show that STMA leads to significant and consistent performance gains between datasets acquired with very different settings. Notably, STMA is a pre-processing step complementary to state-of-the-art deep learning methods.

cs.LG↗

arXiv2024

Reconstructing discrete measures from projections. Consequences on the empirical Sliced Wasserstein Distance

This paper deals with the reconstruction of a discrete measure $γ_Z$ on $\mathbb{R}^d$ from the knowledge of its pushforward measures $P_i\#γ_Z$ by linear applications $P_i: \mathbb{R}^d \rightarrow \mathbb{R}^{d_i}$ (for instance projections onto subspaces). The measure $γ_Z$ being fixed, assuming that the rows of the matrices $P_i$ are independent realizations of laws which do not give mass to hyperplanes, we show that if $\sum_i d_i > d$, this reconstruction problem has almost certainly a unique solution. This holds for any number of points in $γ_Z$. A direct consequence of this result is an almost-sure separability property on the empirical Sliced Wasserstein distance.

math.PR↗

arXiv2024

Weakly supervised covariance matrices alignment through Stiefel matrices estimation for MEG applications

This paper introduces a novel domain adaptation technique for time series data, called Mixing model Stiefel Adaptation (MSA), specifically addressing the challenge of limited labeled signals in the target dataset. Leveraging a domain-dependent mixing model and the optimal transport domain adaptation assumption, we exploit abundant unlabeled data in the target domain to ensure effective prediction by establishing pairwise correspondence with equivalent signal variances between domains. Theoretical foundations are laid for identifying crucial Stiefel matrices, essential for recovering underlying signal variances from a Riemannian representation of observed signal covariances. We propose an integrated cost function that simultaneously learns these matrices, pairwise domain relationships, and a predictor, classifier, or regressor, depending on the task. Applied to neuroscience problems, MSA outperforms recent methods in brain-age regression with task variations using magnetoencephalography (MEG) signals from the Cam-CAN dataset.

eess.SP↗