arXiv subjects

Paul Krzakala

Publications and source records attributed to Paul Krzakala.

5 recordsLinked to original sources

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

SOTAlign: Semi-Supervised Alignment of Unimodal Vision and Language Models via Optimal Transport

The Platonic Representation Hypothesis posits that neural networks trained on different modalities converge toward a shared statistical model of the world. Recent work exploits this convergence by aligning frozen pretrained vision and language models with lightweight alignment layers, but typically relies on contrastive losses and millions of paired samples. In this work, we ask whether meaningful alignment can be achieved with substantially less supervision. We introduce a semi-supervised setting in which pretrained unimodal encoders are aligned using a small number of image-text pairs together with large amounts of unpaired data. To address this challenge, we propose SOTAlign, a two-stage framework that first recovers a coarse shared geometry from limited paired data using a linear teacher, and then refines the alignment on unpaired samples via an optimal-transport-based divergence that transfers relational structure without overconstraining the target space. SOTAlign effectively leverages unpaired images and text, learning robust joint embeddings across datasets and encoder pairs, and significantly outperforming supervised and semi-supervised baselines. Code is available at https://github.com/ExplainableML/SOTAlign.

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↗

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↗