arXiv subjects

Florence d'Alché-Buc

Publications and source records attributed to Florence d'Alché-Buc.

At least 19 recordsLinked to original sources

arXiv2026

Finetuning-Free Diffusion Model with Adaptive Constraint Guidance for Inorganic Crystal Structure Generation

Generative diffusion models have emerged as powerful tools for the discovery of inorganic crystal structures, yet steering their sampling process toward user-defined physical and chemical objectives remains challenging. We present a computational framework that integrates adaptive constraint guidance into a pre-trained crystal diffusion model, enabling the generation of candidate structures that satisfy targeted structural and chemical requirements without model retraining. The approach incorporates differentiable constraint functions directly during sampling, providing an interpretable mechanism for expert-driven exploration of the crystal structure space. To assess the reliability of generated candidates, we introduce a multi-stage validation workflow combining descriptor-based analysis, duplicate removal, comparison with reference crystal databases, graph neural network energy prediction, and thermodynamic stability evaluation through convex-hull analysis. The framework is applied to several classes of inorganic compounds and to constraints involving atomic volume, local coordination environments, and near-neighbor structural motifs. Results demonstrate that adaptive guidance effectively redirects the sampling distribution toward structures exhibiting the desired characteristics while preserving chemical plausibility. Subsequent validation reveals which generated candidates remain viable after energetic and thermodynamic screening. The proposed methodology provides a practical and transparent strategy for incorporating expert knowledge into crystal generative models and establishes a general computational framework for constrained materials discovery.

cond-mat.mtrl-sci↗

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

Conformal Graph Prediction with Z-Gromov-Wasserstein Distances

Supervised graph prediction addresses regression problems where the outputs are structured graphs. Although several approaches exist for graph-valued prediction, principled uncertainty quantification remains limited. We propose a conformal prediction framework for graph-valued outputs, providing distribution-free coverage guarantees in structured output spaces. Our method defines nonconformity via the Z-Gromov-Wasserstein distance, instantiated in practice through Fused Gromov-Wasserstein (FGW), enabling permutation invariant comparison between predicted and candidate graphs. To obtain adaptive prediction sets, we introduce Score Conformalized Quantile Regression (SCQR), an extension of Conformalized Quantile Regression (CQR) to handle complex output spaces such as graph-valued outputs. We evaluate the proposed approach on a synthetic task and a real problem of molecule identification.

stat.ML↗

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

Abnormal component analysis

At the crossway of machine learning and data analysis, anomaly detection aims at identifying observations that exhibit abnormal behaviour. Be it measurement errors, disease development, severe weather, production quality default(s) (items) or failed equipment, financial frauds or crisis events, their on-time identification and isolation constitute an important task in almost any area of industry and science. While a substantial body of literature is devoted to detection of anomalies, little attention is payed to their explanation. This is the case mostly due to intrinsically non-supervised nature of the task and non-robustness of the exploratory methods like principal component analysis (PCA). We introduce a new statistical tool dedicated for exploratory analysis of abnormal observations using data depth as a score. Abnormal component analysis (shortly ACA) is a method that searches a low-dimensional data representation that best visualises and explains anomalies. This low-dimensional representation not only allows to distinguish groups of anomalies better than the methods of the state of the art, but as well provides a -- linear in variables and thus easily interpretable -- explanation for anomalies. In a comparative simulation and real-data study, ACA also proves advantageous for anomaly analysis with respect to methods present in the literature.

stat.ME↗

arXiv2025

Tailoring Mixup to Data for Calibration

Among all data augmentation techniques proposed so far, linear interpolation of training samples, also called Mixup, has found to be effective for a large panel of applications. Along with improved predictive performance, Mixup is also a good technique for improving calibration. However, mixing data carelessly can lead to manifold mismatch, i.e., synthetic data lying outside original class manifolds, which can deteriorate calibration. In this work, we show that the likelihood of assigning a wrong label with mixup increases with the distance between data to mix. To this end, we propose to dynamically change the underlying distributions of interpolation coefficients depending on the similarity between samples to mix, and define a flexible framework to do so without losing in diversity. We provide extensive experiments for classification and regression tasks, showing that our proposed method improves predictive performance and calibration of models, while being much more efficient.

cs.LG↗

arXiv2025

Restyling Unsupervised Concept Based Interpretable Networks with Generative Models

Developing inherently interpretable models for prediction has gained prominence in recent years. A subclass of these models, wherein the interpretable network relies on learning high-level concepts, are valued because of closeness of concept representations to human communication. However, the visualization and understanding of the learnt unsupervised dictionary of concepts encounters major limitations, especially for large-scale images. We propose here a novel method that relies on mapping the concept features to the latent space of a pretrained generative model. The use of a generative model enables high quality visualization, and lays out an intuitive and interactive procedure for better interpretation of the learnt concepts by imputing concept activations and visualizing generated modifications. Furthermore, leveraging pretrained generative models has the additional advantage of making the training of the system more efficient. We quantitatively ascertain the efficacy of our method in terms of accuracy of the interpretable prediction network, fidelity of reconstruction, as well as faithfulness and consistency of learnt concepts. The experiments are conducted on multiple image recognition benchmarks for large-scale images. Project page available at https://jayneelparekh.github.io/VisCoIN_project_page/

cs.CV↗

arXiv2024

Learning Differentiable Surrogate Losses for Structured Prediction

Structured prediction involves learning to predict complex structures rather than simple scalar values. The main challenge arises from the non-Euclidean nature of the output space, which generally requires relaxing the problem formulation. Surrogate methods build on kernel-induced losses or more generally, loss functions admitting an Implicit Loss Embedding, and convert the original problem into a regression task followed by a decoding step. However, designing effective losses for objects with complex structures presents significant challenges and often requires domain-specific expertise. In this work, we introduce a novel framework in which a structured loss function, parameterized by neural networks, is learned directly from output training data through Contrastive Learning, prior to addressing the supervised surrogate regression problem. As a result, the differentiable loss not only enables the learning of neural networks due to the finite dimension of the surrogate space but also allows for the prediction of new structures of the output data via a decoding strategy based on gradient descent. Numerical experiments on supervised graph prediction problems show that our approach achieves similar or even better performance than methods based on a pre-defined kernel.

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

Deep Sketched Output Kernel Regression for Structured Prediction

By leveraging the kernel trick in the output space, kernel-induced losses provide a principled way to define structured output prediction tasks for a wide variety of output modalities. In particular, they have been successfully used in the context of surrogate non-parametric regression, where the kernel trick is typically exploited in the input space as well. However, when inputs are images or texts, more expressive models such as deep neural networks seem more suited than non-parametric methods. In this work, we tackle the question of how to train neural networks to solve structured output prediction tasks, while still benefiting from the versatility and relevance of kernel-induced losses. We design a novel family of deep neural architectures, whose last layer predicts in a data-dependent finite-dimensional subspace of the infinite-dimensional output feature space deriving from the kernel-induced loss. This subspace is chosen as the span of the eigenfunctions of a randomly-approximated version of the empirical kernel covariance operator. Interestingly, this approach unlocks the use of gradient descent algorithms (and consequently of any neural architecture) for structured prediction. Experiments on synthetic tasks as well as real-world supervised graph prediction problems show the relevance of our method.

stat.ML↗

arXiv2024

Sketch In, Sketch Out: Accelerating both Learning and Inference for Structured Prediction with Kernels

Leveraging the kernel trick in both the input and output spaces, surrogate kernel methods are a flexible and theoretically grounded solution to structured output prediction. If they provide state-of-the-art performance on complex data sets of moderate size (e.g., in chemoinformatics), these approaches however fail to scale. We propose to equip surrogate kernel methods with sketching-based approximations, applied to both the input and output feature maps. We prove excess risk bounds on the original structured prediction problem, showing how to attain close-to-optimal rates with a reduced sketch size that depends on the eigendecay of the input/output covariance operators. From a computational perspective, we show that the two approximations have distinct but complementary impacts: sketching the input kernel mostly reduces training time, while sketching the output kernel decreases the inference time. Empirically, our approach is shown to scale, achieving state-of-the-art performance on benchmark data sets where non-sketched methods are intractable.

stat.ML↗

arXiv2023

Fast kernel half-space depth for data with non-convex supports

Data depth is a statistical function that generalizes order and quantiles to the multivariate setting and beyond, with applications spanning over descriptive and visual statistics, anomaly detection, testing, etc. The celebrated halfspace depth exploits data geometry via an optimization program to deliver properties of invariances, robustness, and non-parametricity. Nevertheless, it implicitly assumes convex data supports and requires exponential computational cost. To tackle distribution's multimodality, we extend the halfspace depth in a Reproducing Kernel Hilbert Space (RKHS). We show that the obtained depth is intuitive and establish its consistency with provable concentration bounds that allow for homogeneity testing. The proposed depth can be computed using manifold gradient making faster than halfspace depth by several orders of magnitude. The performance of our depth is demonstrated through numerical simulations as well as applications such as anomaly detection on real data and homogeneity testing.

stat.ML↗

arXiv2023

Fast Kernel Methods for Generic Lipschitz Losses via $p$-Sparsified Sketches

Kernel methods are learning algorithms that enjoy solid theoretical foundations while suffering from important computational limitations. Sketching, which consists in looking for solutions among a subspace of reduced dimension, is a well studied approach to alleviate these computational burdens. However, statistically-accurate sketches, such as the Gaussian one, usually contain few null entries, such that their application to kernel methods and their non-sparse Gram matrices remains slow in practice. In this paper, we show that sparsified Gaussian (and Rademacher) sketches still produce theoretically-valid approximations while allowing for important time and space savings thanks to an efficient \emph{decomposition trick}. To support our method, we derive excess risk bounds for both single and multiple output kernel problems, with generic Lipschitz losses, hereby providing new guarantees for a wide range of applications, from robust regression to multiple quantile regression. Our theoretical results are complemented with experiments showing the empirical superiority of our approach over SOTA sketching methods.

stat.ML↗

arXiv2023

Exploiting Edge Features in Graphs with Fused Network Gromov-Wasserstein Distance

Pairwise comparison of graphs is key to many applications in Machine learning ranging from clustering, kernel-based classification/regression and more recently supervised graph prediction. Distances between graphs usually rely on informative representations of these structured objects such as bag of substructures or other graph embeddings. A recently popular solution consists in representing graphs as metric measure spaces, allowing to successfully leverage Optimal Transport, which provides meaningful distances allowing to compare them: the Gromov-Wasserstein distances. However, this family of distances overlooks edge attributes, which are essential for many structured objects. In this work, we introduce an extension of Gromov-Wasserstein distance for comparing graphs whose both nodes and edges have features. We propose novel algorithms for distance and barycenter computation. We empirically show the effectiveness of the novel distance in learning tasks where graphs occur in either input space or output space, such as classification and graph prediction.

stat.ML↗

arXiv2023

Tackling Interpretability in Audio Classification Networks with Non-negative Matrix Factorization

This paper tackles two major problem settings for interpretability of audio processing networks, post-hoc and by-design interpretation. For post-hoc interpretation, we aim to interpret decisions of a network in terms of high-level audio objects that are also listenable for the end-user. This is extended to present an inherently interpretable model with high performance. To this end, we propose a novel interpreter design that incorporates non-negative matrix factorization (NMF). In particular, an interpreter is trained to generate a regularized intermediate embedding from hidden layers of a target network, learnt as time-activations of a pre-learnt NMF dictionary. Our methodology allows us to generate intuitive audio-based interpretations that explicitly enhance parts of the input signal most relevant for a network's decision. We demonstrate our method's applicability on a variety of classification tasks, including multi-label data for real-world audio and music.

cs.SD↗

arXiv2022

Wind power predictions from nowcasts to 4-hour forecasts: a learning approach with variable selection

We study short-term prediction of wind speed and wind power (every 10 minutes up to 4 hours ahead). Accurate forecasts for these quantities are crucial to mitigate the negative effects of wind farms' intermittent production on energy systems and markets. We use machine learning to combine outputs from numerical weather prediction models with local observations. The former provide valuable information on higher scales dynamics while the latter gives the model fresher and location-specific data. So as to make the results usable for practitioners, we focus on well-known methods which can handle a high volume of data. We study first variable selection using both a linear technique and a nonlinear one. Then we exploit these results to forecast wind speed and wind power still with an emphasis on linear models versus nonlinear ones. For the wind power prediction, we also compare the indirect approach (wind speed predictions passed through a power curve) and the indirect one (directly predict wind power).

cs.LG↗

arXiv2022

Vector-Valued Least-Squares Regression under Output Regularity Assumptions

We propose and analyse a reduced-rank method for solving least-squares regression problems with infinite dimensional output. We derive learning bounds for our method, and study under which setting statistical performance is improved in comparison to full-rank method. Our analysis extends the interest of reduced-rank regression beyond the standard low-rank setting to more general output regularity assumptions. We illustrate our theoretical insights on synthetic least-squares problems. Then, we propose a surrogate structured prediction method derived from this reduced-rank method. We assess its benefits on three different problems: image reconstruction, multi-label classification, and metabolite identification.

stat.ML↗