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Rémi Flamary

Rémi Flamary contributes to research discovery and scholarly infrastructure.

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Published work

10 published item(s)

preprint2026arXiv

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.

preprint2026arXiv

MSAlign: Aligning Molecule and Mass Spectra Foundation Models 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. While the recent release of benchmark datasets such as MassSpecGym and Spectraverse has considerably accelerated the development of novel machine learning approaches, the complexity of data preprocessing pipelines and the lack of unified implementations make methods and results difficult to reproduce and compare. We make three contributions. First, we propose a unified framework encompassing recent approaches based on representation alignment and contrastive learning. Second, we introduce MSAlign, inspired by multimodal alignment in vision-language models, which learns a shared representation space by aligning two frozen foundation models (DreaMS for mass spectra and ChemBERTa for molecules) through lightweight MLP projections trained with a candidate-based contrastive objective. MSAlign is simple to implement, fast to train and consistently outperforms existing approaches across all benchmarks. 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.

preprint2022arXiv

Learning to Predict Graphs with Fused Gromov-Wasserstein Barycenters

This paper introduces a novel and generic framework to solve the flagship task of supervised labeled graph prediction by leveraging Optimal Transport tools. We formulate the problem as regression with the Fused Gromov-Wasserstein (FGW) loss and propose a predictive model relying on a FGW barycenter whose weights depend on inputs. First we introduce a non-parametric estimator based on kernel ridge regression for which theoretical results such as consistency and excess risk bound are proved. Next we propose an interpretable parametric model where the barycenter weights are modeled with a neural network and the graphs on which the FGW barycenter is calculated are additionally learned. Numerical experiments show the strength of the method and its ability to interpolate in the labeled graph space on simulated data and on a difficult metabolic identification problem where it can reach very good performance with very little engineering.

preprint2022arXiv

Multi-source Domain Adaptation via Weighted Joint Distributions Optimal Transport

The problem of domain adaptation on an unlabeled target dataset using knowledge from multiple labelled source datasets is becoming increasingly important. A key challenge is to design an approach that overcomes the covariate and target shift both among the sources, and between the source and target domains. In this paper, we address this problem from a new perspective: instead of looking for a latent representation invariant between source and target domains, we exploit the diversity of source distributions by tuning their weights to the target task at hand. Our method, named Weighted Joint Distribution Optimal Transport (WJDOT), aims at finding simultaneously an Optimal Transport-based alignment between the source and target distributions and a re-weighting of the sources distributions. We discuss the theoretical aspects of the method and propose a conceptually simple algorithm. Numerical experiments indicate that the proposed method achieves state-of-the-art performance on simulated and real-life datasets.

preprint2022arXiv

Semi-relaxed Gromov-Wasserstein divergence with applications on graphs

Comparing structured objects such as graphs is a fundamental operation involved in many learning tasks. To this end, the Gromov-Wasserstein (GW) distance, based on Optimal Transport (OT), has proven to be successful in handling the specific nature of the associated objects. More specifically, through the nodes connectivity relations, GW operates on graphs, seen as probability measures over specific spaces. At the core of OT is the idea of conservation of mass, which imposes a coupling between all the nodes from the two considered graphs. We argue in this paper that this property can be detrimental for tasks such as graph dictionary or partition learning, and we relax it by proposing a new semi-relaxed Gromov-Wasserstein divergence. Aside from immediate computational benefits, we discuss its properties, and show that it can lead to an efficient graph dictionary learning algorithm. We empirically demonstrate its relevance for complex tasks on graphs such as partitioning, clustering and completion.

preprint2022arXiv

Sliding window strategy for convolutional spike sorting with Lasso : Algorithm, theoretical guarantees and complexity

Spike sorting is a class of algorithms used in neuroscience to attribute the time occurences of particular electric signals, called action potential or spike, to neurons. We rephrase this problem as a particular optimization problem : Lasso for convolutional models in high dimension. Lasso (i.e. least absolute shrinkage and selection operator) is a very generic tool in machine learning that help us to look for sparse solutions (here the time occurrences). However, for the size of the problem at hand in this neuroscience context, the classical Lasso solvers are failing. We present here a new and much faster algorithm. Making use of biological properties related to neurons, we explain how the particular structure of the problem allows several optimizations, leading to an algorithm with a temporal complexity which grows linearly with respect to the size of the recorded signal and can be performed online. Moreover the spatial separability of the initial problem allows to break it into subproblems, further reducing the complexity and making possible its application on the latest recording devices which comprise a large number of sensors. We provide several mathematical results: the size and numerical complexity of the subproblems can be estimated mathematically by using percolation theory. We also show under reasonable assumptions that the Lasso estimator retrieves the true time occurrences of the spikes {with large probability}. Finally the theoretical time complexity of the algorithm is given. Numerical simulations are also provided in order to illustrate the efficiency of our approach.

preprint2022arXiv

Template based Graph Neural Network with Optimal Transport Distances

Current Graph Neural Networks (GNN) architectures generally rely on two important components: node features embedding through message passing, and aggregation with a specialized form of pooling. The structural (or topological) information is implicitly taken into account in these two steps. We propose in this work a novel point of view, which places distances to some learnable graph templates at the core of the graph representation. This distance embedding is constructed thanks to an optimal transport distance: the Fused Gromov-Wasserstein (FGW) distance, which encodes simultaneously feature and structure dissimilarities by solving a soft graph-matching problem. We postulate that the vector of FGW distances to a set of template graphs has a strong discriminative power, which is then fed to a non-linear classifier for final predictions. Distance embedding can be seen as a new layer, and can leverage on existing message passing techniques to promote sensible feature representations. Interestingly enough, in our work the optimal set of template graphs is also learnt in an end-to-end fashion by differentiating through this layer. After describing the corresponding learning procedure, we empirically validate our claim on several synthetic and real life graph classification datasets, where our method is competitive or surpasses kernel and GNN state-of-the-art approaches. We complete our experiments by an ablation study and a sensitivity analysis to parameters.

preprint2021arXiv

Minibatch optimal transport distances; analysis and applications

Optimal transport distances have become a classic tool to compare probability distributions and have found many applications in machine learning. Yet, despite recent algorithmic developments, their complexity prevents their direct use on large scale datasets. To overcome this challenge, a common workaround is to compute these distances on minibatches i.e. to average the outcome of several smaller optimal transport problems. We propose in this paper an extended analysis of this practice, which effects were previously studied in restricted cases. We first consider a large variety of Optimal Transport kernels. We notably argue that the minibatch strategy comes with appealing properties such as unbiased estimators, gradients and a concentration bound around the expectation, but also with limits: the minibatch OT is not a distance. To recover some of the lost distance axioms, we introduce a debiased minibatch OT function and study its statistical and optimisation properties. Along with this theoretical analysis, we also conduct empirical experiments on gradient flows, generative adversarial networks (GANs) or color transfer that highlight the practical interest of this strategy.

preprint2021arXiv

Representation Transfer by Optimal Transport

Learning generic representations with deep networks requires massive training samples and significant computer resources. To learn a new specific task, an important issue is to transfer the generic teacher's representation to a student network. In this paper, we propose to use a metric between representations that is based on a functional view of neurons. We use optimal transport to quantify the match between two representations, yielding a distance that embeds some invariances inherent to the representation of deep networks. This distance defines a regularizer promoting the similarity of the student's representation with that of the teacher. Our approach can be used in any learning context where representation transfer is applicable. We experiment here on two standard settings: inductive transfer learning, where the teacher's representation is transferred to a student network of same architecture for a new related task, and knowledge distillation, where the teacher's representation is transferred to a student of simpler architecture for the same task (model compression). Our approach also lends itself to solving new learning problems; we demonstrate this by showing how to directly transfer the teacher's representation to a simpler architecture student for a new related task.

preprint2021arXiv

Unbalanced minibatch Optimal Transport; applications to Domain Adaptation

Optimal transport distances have found many applications in machine learning for their capacity to compare non-parametric probability distributions. Yet their algorithmic complexity generally prevents their direct use on large scale datasets. Among the possible strategies to alleviate this issue, practitioners can rely on computing estimates of these distances over subsets of data, {\em i.e.} minibatches. While computationally appealing, we highlight in this paper some limits of this strategy, arguing it can lead to undesirable smoothing effects. As an alternative, we suggest that the same minibatch strategy coupled with unbalanced optimal transport can yield more robust behavior. We discuss the associated theoretical properties, such as unbiased estimators, existence of gradients and concentration bounds. Our experimental study shows that in challenging problems associated to domain adaptation, the use of unbalanced optimal transport leads to significantly better results, competing with or surpassing recent baselines.