Thomas Bonald

Roman Plaud, Alexandre Perez-Lebel, Antoine Saillenfest et al.

Probabilistic models are typically trained using task-agnostic objectives like log-loss, which can lead to significant errors in downstream estimation. This disconnect is especially critical in Inverse Probability Weighting (IPW) for causal inference, where propensity score errors near $0$ and $1$ often lead to high bias and variance. We propose a principled framework for deriving task-specific strictly proper scoring rules by matching the local curvature of the downstream error metric. We apply this to the Average Treatment Effect (ATE) estimation, deriving a closed-form loss and its corresponding canonical probability mapping that can be readily integrated with any model like a neural network or a gradient boosting algorithm. Extensive evaluations on causal inference benchmarks demonstrate that our tailored objective consistently outperforms standard likelihood-based and covariate-balancing approaches.

Fabian Suchanek, Mehwish Alam, Thomas Bonald et al.

Knowledge Bases (KBs) find applications in many knowledge-intensive tasks and, most notably, in information retrieval. Wikidata is one of the largest public general-purpose KBs. Yet, its collaborative nature has led to a convoluted schema and taxonomy. The YAGO 4 KB cleaned up the taxonomy by incorporating the ontology of Schema.org, resulting in a cleaner structure amenable to automated reasoning. However, it also cut away large parts of the Wikidata taxonomy, which is essential for information retrieval. In this paper, we extend YAGO 4 with a large part of the Wikidata taxonomy - while respecting logical constraints and the distinction between classes and instances. This yields YAGO 4.5, a new, logically consistent version of YAGO that adds a rich layer of informative classes. An intrinsic and an extrinsic evaluation show the value of the new resource.

Rajaa El Hamdani, Thomas Bonald, Fragkiskos Malliaros et al.

This paper investigates the factuality of large language models (LLMs) as knowledge bases in the legal domain, in a realistic usage scenario: we allow for acceptable variations in the answer, and let the model abstain from answering when uncertain. First, we design a dataset of diverse factual questions about case law and legislation. We then use the dataset to evaluate several LLMs under different evaluation methods, including exact, alias, and fuzzy matching. Our results show that the performance improves significantly under the alias and fuzzy matching methods. Further, we explore the impact of abstaining and in-context examples, finding that both strategies enhance precision. Finally, we demonstrate that additional pre-training on legal documents, as seen with SaulLM, further improves factual precision from 63% to 81%.

Armand Boschin, Thomas Bonald, Marc Jeanmougin

We present the self-encoder, a neural network trained to guess the identity of each data sample. Despite its simplicity, it learns a very useful representation of data, in a self-supervised way. Specifically, the self-encoder learns to distribute the data samples in the embedding space so that they are linearly separable from one another. This induces a geometry where two samples are close in the embedding space when they are not easy to differentiate. The self-encoder can then be combined with a nearest-neighbor classifier or regressor for any subsequent supervised task. Unlike regular nearest neighbors, the predictions resulting from this encoding of data are invariant to any scaling of features, making any preprocessing like min-max scaling not necessary. The experiments show the efficiency of the approach, especially on heterogeneous data mixing numerical features and categorical features.

Léo Laugier, Raghuram Vadapalli, Thomas Bonald et al.

This paper explores a novel application of textual semantic similarity to user-preference representation for rating prediction. The approach represents a user's preferences as a graph of textual snippets from review text, where the edges are defined by semantic similarity. This textual, memory-based approach to rating prediction enables review-based explanations for recommendations. The method is evaluated quantitatively, highlighting that leveraging text in this way outperforms both strong memory-based and model-based collaborative filtering baselines.

Yiwen Peng, Thomas Bonald, Mehwish Alam

Due to its collaborative nature, Wikidata is known to have a complex taxonomy, with recurrent issues like the ambiguity between instances and classes, the inaccuracy of some taxonomic paths, the presence of cycles, and the high level of redundancy across classes. Manual efforts to clean up this taxonomy are time-consuming and prone to errors or subjective decisions. We present WiKC, a new version of Wikidata taxonomy cleaned automatically using a combination of Large Language Models (LLMs) and graph mining techniques. Operations on the taxonomy, such as cutting links or merging classes, are performed with the help of zero-shot prompting on an open-source LLM. The quality of the refined taxonomy is evaluated from both intrinsic and extrinsic perspectives, on a task of entity typing for the latter, showing the practical interest of WiKC.

Thomas Bonald, Nathan de Lara

The task of semi-supervised classification aims at assigning labels to all nodes of a graph based on the labels known for a few nodes, called the seeds. One of the most popular algorithms relies on the principle of heat diffusion, where the labels of the seeds are spread by thermoconductance and the temperature of each node at equilibrium is used as a score function for each label. In this paper, we prove that this algorithm is not consistent unless the temperatures of the nodes at equilibrium are centered before scoring. This crucial step does not only make the algorithm provably consistent on a block model but brings significant performance gains on real graphs.

Clement Wang, Antoine Vialle, Robin Vaysse et al.

Mini-batch training of Graph Neural Networks (GNNs) is fundamentally different from training on i.i.d. data: sampling a subgraph alters the topology and introduces boundary effects, leading prior work to develop structure-aware samplers that preserve local connectivity and reduce embedding variance. Surprisingly, we demonstrate that the simplest possible scheme, Random Node Sampling (RNS), training on the induced subgraph of uniformly sampled nodes, matches or outperforms full-graph training on 8 of 10 datasets at a fraction of the wall-clock time and memory. To explain this, we apply backward error analysis to graph mini-batch Stochastic Gradient Descent (SGD) and show that it implicitly minimizes the sampled loss plus a regularizer proportional to the mini-batch gradient variance, a quantity directly shaped by the sampler. Although RNS discards local structure, it produces mini-batches whose expected loss is closer to the full-graph loss, and whose per-batch gradients have lower variance, yielding a better implicit objective. Our analysis reframes the choice of graph sampler as a form of implicit regularization, and identifies RNS as a strong, theoretically grounded method for scalable GNN training.

Rajaa El Hamdani, Samy Haffoudhi, Nils Holzenberger et al.

Language models (LMs) encode substantial factual knowledge, but often produce answers judged as incorrect. We hypothesize that many of these answers are actually correct, but are expressed in alternative surface forms that are dismissed due to an overly strict evaluation, leading to an underestimation of models' parametric knowledge. We propose Retrieval-Constrained Decoding (RCD), a decoding strategy that restricts model outputs to unique surface forms. We introduce YAGO-QA, a dataset of 19,137 general knowledge questions. Evaluating open-source LMs from 135M to 70B parameters, we show that standard decoding undervalues their knowledge. For instance, Llama-3.1-70B scores only 32.3% F1 with vanilla decoding but 46.0% with RCD. Similarly, Llama-3.1-8B reaches 33.0% with RCD, outperforming the larger model under vanilla decoding. We publicly share the code and dataset at https://github.com/Rajjaa/disambiguated-LLM.

Roman Plaud, Alexandre Perez-Lebel, Matthieu Labeau et al.

Hierarchical classification offers an approach to incorporate the concept of mistake severity by leveraging a structured, labeled hierarchy. However, decoding in such settings frequently relies on heuristic decision rules, which may not align with task-specific evaluation metrics. In this work, we propose a framework for the optimal decoding of an output probability distribution with respect to a target metric. We derive optimal decision rules for increasingly complex prediction settings, providing universal algorithms when candidates are limited to the set of nodes. In the most general case of predicting a subset of nodes, we focus on rules dedicated to the hierarchical $hF_β$ scores, tailored to hierarchical settings. To demonstrate the practical utility of our approach, we conduct extensive empirical evaluations, showcasing the superiority of our proposed optimal strategies, particularly in underdetermined scenarios. These results highlight the potential of our methods to enhance the performance and reliability of hierarchical classifiers in real-world applications. The code is available at https://github.com/RomanPlaud/hierarchical_decision_rules

Armand Boschin, Thomas Bonald

Developing new ideas and algorithms in the fields of graph processing and relational learning requires public datasets. While Wikidata is the largest open source knowledge graph, involving more than fifty million entities, it is larger than needed in many cases and even too large to be processed easily. Still, it is a goldmine of relevant facts and relations. Using this knowledge graph is time consuming and prone to task specific tuning which can affect reproducibility of results. Providing a unified framework to extract topic-specific subgraphs solves this problem and allows researchers to evaluate algorithms on common datasets. This paper presents various topic-specific subgraphs of Wikidata along with the generic Python code used to extract them. These datasets can help develop new methods of knowledge graph processing and relational learning.

Simon Delarue, Thomas Bonald, Tiphaine Viard

Graph Neural Networks (GNNs) and their message passing framework that leverages both structural and feature information, have become a standard method for solving graph-based machine learning problems. However, these approaches still struggle to generalise well beyond datasets that exhibit strong homophily, where nodes of the same class tend to connect. This limitation has led to the development of complex neural architectures that pose challenges in terms of efficiency and scalability. In response to these limitations, we focus on simpler and more scalable approaches and introduce Graph-aware Logistic Regression (GLR), a non-neural model designed for node classification tasks. Unlike traditional graph algorithms that use only a fraction of the information accessible to GNNs, our proposed model simultaneously leverages both node features and the relationships between entities. However instead of relying on message passing, our approach encodes each node's relationships as an additional feature vector, which is then combined with the node's self attributes. Extensive experimental results, conducted within a rigorous evaluation framework, show that our proposed GLR approach outperforms both foundational and sophisticated state-of-the-art GNN models in node classification tasks. Going beyond the traditional limited benchmarks, our experiments indicate that GLR increases generalisation ability while reaching performance gains in computation time up to two orders of magnitude compared to it best neural competitor.

Yiwen Peng, Thomas Bonald, Fabian M. Suchanek

Knowledge graph alignment is the task of matching equivalent entities (that is, instances and classes) and relations across two knowledge graphs. Most existing methods focus on pure entity-level alignment, computing the similarity of entities in some embedding space. They lack interpretable reasoning and need training data to work. In this paper, we propose FLORA, a simple yet effective method that (1) is unsupervised, i.e., does not require training data, (2) provides a holistic alignment for entities and relations iteratively, (3) is based on fuzzy logic and thus delivers interpretable results, (4) provably converges, (5) allows dangling entities, i.e., entities without a counterpart in the other KG, and (6) achieves state-of-the-art results on major benchmarks.

Denys Lazarenko, Thomas Bonald

A well-known metric for quantifying the similarity between two clusterings is the adjusted mutual information. Compared to mutual information, a corrective term based on random permutations of the labels is introduced, preventing two clusterings being similar by chance. Unfortunately, this adjustment makes the metric computationally expensive. In this paper, we propose a novel adjustment based on {pairwise} label permutations instead of full label permutations. Specifically, we consider permutations where only two samples, selected uniformly at random, exchange their labels. We show that the corresponding adjusted metric, which can be expressed explicitly, behaves similarly to the standard adjusted mutual information for assessing the quality of a clustering, while having a much lower time complexity. Both metrics are compared in terms of quality and performance on experiments based on synthetic and real data.

Nathan de Lara, Thomas Bonald

Semi-supervised classification on graphs aims at assigning labels to all nodes of a graph based on the labels known for a few nodes, called the seeds. The most popular algorithm relies on the principle of heat diffusion, where the labels of the seeds are spread by thermo-conductance and the temperature of each node is used as a score function for each label. Using a simple block model, we prove that this algorithm is not consistent unless the temperatures of the nodes are centered before classification. We show that this simple modification of the algorithm is enough to get significant performance gains on real data.

Edouard Pineau, Sébastien Razakarivony, Thomas Bonald

In this paper, we show that slow feature analysis (SFA), a common time series decomposition method, naturally fits into the flow-based models (FBM) framework, a type of invertible neural latent variable models. Building upon recent advances on blind source separation, we show that such a fit makes the time series decomposition identifiable.

Nathan de Lara, Thomas Bonald

Spectral embedding is a popular technique for the representation of graph data. Several regularization techniques have been proposed to improve the quality of the embedding with respect to downstream tasks like clustering. In this paper, we explain on a simple block model the impact of the complete graph regularization, whereby a constant is added to all entries of the adjacency matrix. Specifically, we show that the regularization forces the spectral embedding to focus on the largest blocks, making the representation less sensitive to noise or outliers. We illustrate these results on both on both synthetic and real data, showing how regularization improves standard clustering scores.

Thomas Bonald, Alexandre Hollocou, Marc Lelarge

We present a novel spectral embedding of graphs that incorporates weights assigned to the nodes, quantifying their relative importance. This spectral embedding is based on the first eigenvectors of some properly normalized version of the Laplacian. We prove that these eigenvectors correspond to the configurations of lowest energy of an equivalent physical system, either mechanical or electrical, in which the weight of each node can be interpreted as its mass or its capacitance, respectively. Experiments on a real dataset illustrate the impact of weighting on the embedding.

Thomas Bonald, Bertrand Charpentier

Hierarchical graph clustering is a common technique to reveal the multi-scale structure of complex networks. We propose a novel metric for assessing the quality of a hierarchical clustering. This metric reflects the ability to reconstruct the graph from the dendrogram, which encodes the hierarchy. The optimal representation of the graph defines a class of reducible linkages leading to regular dendrograms by greedy agglomerative clustering.

Thomas Bonald, Bertrand Charpentier, Alexis Galland et al.

We present a novel hierarchical graph clustering algorithm inspired by modularity-based clustering techniques. The algorithm is agglomerative and based on a simple distance between clusters induced by the probability of sampling node pairs. We prove that this distance is reducible, which enables the use of the nearest-neighbor chain to speed up the agglomeration. The output of the algorithm is a regular dendrogram, which reveals the multi-scale structure of the graph. The results are illustrated on both synthetic and real datasets.

Alexandre Hollocou, Julien Maudet, Thomas Bonald et al.

We introduce a novel algorithm to perform graph clustering in the edge streaming setting. In this model, the graph is presented as a sequence of edges that can be processed strictly once. Our streaming algorithm has an extremely low memory footprint as it stores only three integers per node and does not keep any edge in memory. We provide a theoretical justification of the design of the algorithm based on the modularity function, which is a usual metric to evaluate the quality of a graph partition. We perform experiments on massive real-life graphs ranging from one million to more than one billion edges and we show that this new algorithm runs more than ten times faster than existing algorithms and leads to similar or better detection scores on the largest graphs.

Thomas Bonald, Richard Combes

We consider the problem of accurately estimating the reliability of workers based on noisy labels they provide, which is a fundamental question in crowdsourcing. We propose a novel lower bound on the minimax estimation error which applies to any estimation procedure. We further propose Triangular Estimation (TE), an algorithm for estimating the reliability of workers. TE has low complexity, may be implemented in a streaming setting when labels are provided by workers in real time, and does not rely on an iterative procedure. We further prove that TE is minimax optimal and matches our lower bound. We conclude by assessing the performance of TE and other state-of-the-art algorithms on both synthetic and real-world data sets.

Thomas Bonald, Richard Combes

We propose a streaming algorithm for the binary classification of data based on crowdsourcing. The algorithm learns the competence of each labeller by comparing her labels to those of other labellers on the same tasks and uses this information to minimize the prediction error rate on each task. We provide performance guarantees of our algorithm for a fixed population of independent labellers. In particular, we show that our algorithm is optimal in the sense that the cumulative regret compared to the optimal decision with known labeller error probabilities is finite, independently of the number of tasks to label. The complexity of the algorithm is linear in the number of labellers and the number of tasks, up to some logarithmic factors. Numerical experiments illustrate the performance of our algorithm compared to existing algorithms, including simple majority voting and expectation-maximization algorithms, on both synthetic and real datasets.

Emilie Kaufmann, Thomas Bonald, Marc Lelarge

This paper presents a novel spectral algorithm with additive clustering designed to identify overlapping communities in networks. The algorithm is based on geometric properties of the spectrum of the expected adjacency matrix in a random graph model that we call stochastic blockmodel with overlap (SBMO). An adaptive version of the algorithm, that does not require the knowledge of the number of hidden communities, is proved to be consistent under the SBMO when the degrees in the graph are (slightly more than) logarithmic. The algorithm is shown to perform well on simulated data and on real-world graphs with known overlapping communities.