Doing well with less! On Sampling Techniques for Empirical Pairwise Loss Estimation/Minimization

Many machine learning problems, including similarity learning, ranking, and clustering, rely on empirical pairwise loss functions whose quadratic computational cost quickly becomes prohibitive at scale. We demonstrate how a frugal approach that retains only a fraction of the available information on pairs can achieve estimation or optimization performance comparable to that obtained by using all pairs, by leveraging survey sampling techniques. A central finding, supported by both theory and experiments, is that such sampling plans must target pairs directly rather than individual observations. In particular, for pairwise losses between high-dimensional vectors such as embeddings in vision or graph learning, assigning higher inclusion probabilities to informative pairs using suitable auxiliary information yields performance close to full pairwise evaluation, providing a principled and theoretically grounded trade-off between accuracy and computational cost.

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.

k-hop Fairness: Addressing Disparities in Graph Link Prediction Beyond First-Order Neighborhoods

Link prediction (LP) plays a central role in graph-based applications, particularly in social recommendation. However, real-world graphs often reflect structural biases, most notably homophily, the tendency of nodes with similar attributes to connect. While this property can improve predictive performance, it also risks reinforcing existing social disparities. In response, fairness-aware LP methods have emerged, often seeking to mitigate these effects by promoting inter-group connections, that is, links between nodes with differing sensitive attributes (e.g., gender), following the principle of dyadic fairness. However, dyadic fairness overlooks potential disparities within the sensitive groups themselves. To overcome this issue, we propose $k$-hop fairness, a structural notion of fairness for LP, that assesses disparities conditioned on the distance between nodes in the graph. We formalize this notion through predictive fairness and structural bias metrics, and propose pre- and post-processing mitigation strategies. Experiments across standard LP benchmarks reveal: (1) a strong tendency of models to reproduce structural biases at different $k$-hops; (2) interdependence between structural biases at different hops when rewiring graphs; and (3) that our post-processing method achieves favorable $k$-hop performance-fairness trade-offs compared to existing fair LP baselines.

How Predicted Links Influence Network Evolution: Disentangling Choice and Algorithmic Feedback in Dynamic Graphs

Link prediction models are increasingly used to recommend interactions in evolving networks, yet their impact on network structure is typically assessed from static snapshots. In particular, observed homophily conflates intrinsic interaction tendencies with amplification effects induced by network dynamics and algorithmic feedback. We propose a temporal framework based on multivariate Hawkes processes that disentangles these two sources and introduce an instantaneous bias measure derived from interaction intensities, capturing current reinforcement dynamics beyond cumulative metrics. We provide a theoretical characterization of the stability and convergence of the induced dynamics, and experiments show that the proposed measure reliably reflects algorithmic feedback effects across different link prediction strategies.

TopoFair: Linking Topological Bias to Fairness in Link Prediction Benchmarks

Graph link prediction (LP) plays a critical role in socially impactful applications, such as job recommendation and friendship formation. Ensuring fairness in this task is thus essential. While many fairness-aware methods manipulate graph structures to mitigate prediction disparities, the topological biases inherent to social graph structures remain poorly understood and are often reduced to homophily alone. This undermines the generalization potential of fairness interventions and limits their applicability across diverse network topologies. In this work, we propose a novel benchmarking framework for fair LP, centered on the structural biases of the underlying graphs. We begin by reviewing and formalizing a broad taxonomy of topological bias measures relevant to fairness in graphs. In parallel, we introduce a flexible graph generation method that simultaneously ensures fidelity to real-world graph patterns and enables controlled variation across a wide spectrum of structural biases. We apply this framework to evaluate both classical and fairness-aware LP models across multiple use cases. Our results provide a fine-grained empirical analysis of the interactions between predictive fairness and structural biases. This new perspective reveals the sensitivity of fairness interventions to beyond-homophily biases and underscores the need for structurally grounded fairness evaluations in graph learning.

Drop the mask! GAMM-A Taxonomy for Graph Attributes Missing Mechanisms

Exploring missing data in attributed graphs introduces unique challenges beyond those found in tabular datasets. In this work, we extend the taxonomy for missing data mechanisms to attributed graphs by proposing GAMM (Graph Attributes Missing Mechanisms), a framework that systematically links missingness probability to both node attributes and the underlying graph structure. Our taxonomy enriches the conventional definitions of masking mechanisms by introducing graph-specific dependencies. We empirically demonstrate that state-of-the-art imputation methods, while effective on traditional masks, significantly struggle when confronted with these more realistic graph-aware missingness scenarios.

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.

Modeling Musical Genre Trajectories through Pathlet Learning

The increasing availability of user data on music streaming platforms opens up new possibilities for analyzing music consumption. However, understanding the evolution of user preferences remains a complex challenge, particularly as their musical tastes change over time. This paper uses the dictionary learning paradigm to model user trajectories across different musical genres. We define a new framework that captures recurring patterns in genre trajectories, called pathlets, enabling the creation of comprehensible trajectory embeddings. We show that pathlet learning reveals relevant listening patterns that can be analyzed both qualitatively and quantitatively. This work improves our understanding of users' interactions with music and opens up avenues of research into user behavior and fostering diversity in recommender systems. A dataset of 2000 user histories tagged by genre over 17 months, supplied by Deezer (a leading music streaming company), is also released with the code.

Fair Text Classification via Transferable Representations

Group fairness is a central research topic in text classification, where reaching fair treatment between sensitive groups (e.g., women and men) remains an open challenge. We propose an approach that extends the use of the Wasserstein Dependency Measure for learning unbiased neural text classifiers. Given the challenge of distinguishing fair from unfair information in a text encoder, we draw inspiration from adversarial training by inducing independence between representations learned for the target label and those for a sensitive attribute. We further show that Domain Adaptation can be efficiently leveraged to remove the need for access to the sensitive attributes in the dataset we cure. We provide both theoretical and empirical evidence that our approach is well-founded.

Histoires Morales: A French Dataset for Assessing Moral Alignment

Aligning language models with human values is crucial, especially as they become more integrated into everyday life. While models are often adapted to user preferences, it is equally important to ensure they align with moral norms and behaviours in real-world social situations. Despite significant progress in languages like English and Chinese, French has seen little attention in this area, leaving a gap in understanding how LLMs handle moral reasoning in this language. To address this gap, we introduce Histoires Morales, a French dataset derived from Moral Stories, created through translation and subsequently refined with the assistance of native speakers to guarantee grammatical accuracy and adaptation to the French cultural context. We also rely on annotations of the moral values within the dataset to ensure their alignment with French norms. Histoires Morales covers a wide range of social situations, including differences in tipping practices, expressions of honesty in relationships, and responsibilities toward animals. To foster future research, we also conduct preliminary experiments on the alignment of multilingual models on French and English data and the robustness of the alignment. We find that while LLMs are generally aligned with human moral norms by default, they can be easily influenced with user-preference optimization for both moral and immoral data.