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.

Learning to Emulate Chaos: Adversarial Optimal Transport Regularization

Chaos arises in many complex dynamical systems, from weather to power grids, but is difficult to accurately model using data-driven emulators, including neural operator architectures. For chaotic systems, the inherent sensitivity to initial conditions makes exact long-term forecasts theoretically infeasible, meaning that traditional squared-error losses often fail when trained on noisy data. Recent work has focused on training emulators to match the statistical properties of chaotic attractors by introducing regularization based on handcrafted local features and summary statistics, as well as learned statistics extracted from a diverse dataset of trajectories. In this work, we propose a family of adversarial optimal transport objectives that jointly learn high-quality summary statistics and a physically consistent emulator. We theoretically analyze and experimentally validate a Sinkhorn divergence formulation (2-Wasserstein) and a WGAN-style dual formulation (1-Wasserstein). Our experiments across a variety of chaotic systems, including systems with high-dimensional chaotic attractors, show that emulators trained with our approach exhibit significantly improved long-term statistical fidelity.

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.

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.