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Fabien Gandon

Publications and source records attributed to Fabien Gandon.

At least 19 recordsLinked to original sources

Oracle, will I ever learn? A study of prediction convergence and complementarity across link prediction models

Knowledge graphs have become an important source of structured knowledge for Web applications, including search, question answering, and recommender systems. In these applications, link prediction can serve either as a prediction task itself or as a means to enrich incomplete knowledge graphs for downstream tasks. Interestingly, different link prediction models, or even different training runs of the same model, can produce substantially different predictions for the same query. This suggests a variability in the capture of the underlying knowledge by models, thus raising a fundamental question: to what extent do different models capture complementary knowledge, and how much of this knowledge could be recovered by combining them? We propose to measure model complementarity through the performance of an oracle that, for each query, selects the best prediction among a considered set of models, hence providing an upper bound on the performance achievable through model combination. Across several architectures and benchmarks, we find a substantial gap between individual models and their oracle, revealing that different models capture complementary knowledge. Yet, this complementarity rapidly saturates as more models are added, leaving a persistent subset of queries unsolved even by a large number of models. These findings reveal both the potential of model complementarity and a fundamental limit to what current link prediction models can collectively recover; thereby highlighting the need for further research to build robust Web applications.

cs.LG

LLM-Assisted Ontology Engineering and Construction of a French Legal Knowledge Graph

Maintenance regulations are complex legal texts that are difficult to exploit when addressing a specific case and challenging to integrate into operational systems. This paper presents a two-stage LLM-assisted workflow for French maintenance regulations: ontology engineering from a SEMLEG-based core ontology, followed by construction of an ontology-grounded French legal knowledge graph. The first stage consists in the open extraction of typed entities and triples from a stratified corpus sample, the normalization of labels through embedding-based fusion, and the induction of candidate object properties with their signature (domain and range). The second stage uses the resulting ontology to guide the closed extraction of triples and RDF graph construction over the full corpus. Experiments with GPT-4.1 and mistral-large-2512 show robust structured outputs, near-complete class alignment, and a substantial reduction of duplicated entities and predicates after fusion. Fewer than 20% of triples introduce unseen properties, while lower exact signature compliance reveals new domain-range combinations for existing predicates. These results point to predicate normalization and the validation of newly observed relation signatures as key refinement steps for industrial maintenance settings.

cs.AI

Are you Talking Logic to Me? Assessing Language Models Syllogistic Reasoning Capabilities

Language models (LMs) struggle with logical tasks like reasoning on syllogisms. It has been shown that Knowledge Representation (KR) plays a crucial role in expressing input information to help models solve tasks. This observation motivates our study of the impact of different formal KR notations on syllogistic reasoning by extending the FOLIO and P-FOLIO datasets. Our experiments on Small Language Models (SLMs) in Supervised Fine-Tuning (SFT) and Zero-Shot (ZS) settings show that the choice of input notation can yield performances competitive with natural language while enabling faster inference. We also propose a syllogistic categorization method (SEF) and use it to enrich ZS prompts with logical definitions, which boost reasoning in small models. We open-source our framework, Common Logic Grammar Construction (CLGC), as the first Python library for automatically generating syllogisms in KR notations and defining their SEF categories.

cs.CL

SEF-CLGC at SemEval-2026 Task 11: Logical Notation Impact on Language Model Performance

This paper revisits our pipeline called Syllogistic Evaluation Framework-Common Logic Grammar Construction (SEF-CLGC). We combine formal logical notations with Small Language Models (SLMs) to evaluate reasoning performance on the SemEval-2026 Task 11 Subtask 1: Disentangling Content and Formal Reasoning in Large Language Models. Our experiments show that by relying solely on SLMs, trained on a combination of natural and symbolic languages, our best model achieves a content score of 27.80% on the task while significantly lowering the content bias in reasoning.

cs.CL

Link Prediction or Perdition: the Seeds of Instability in Knowledge Graph Embeddings

Embedding models (KGEMs) constitute the main link prediction approach to complete knowledge graphs. Standard evaluation protocols emphasize rank-based metrics such as MRR or Hits@$K$, but usually overlook the influence of random seeds on result stability. Moreover, these metrics conceal potential instabilities in individual predictions and in the organization of embedding spaces. In this work, we conduct a systematic stability analysis of multiple KGEMs across several datasets. We find that high-performance models actually produce divergent predictions at the triple level and highly variable embedding spaces. By isolating stochastic factors (i.e., initialization, triple ordering, negative sampling, dropout, hardware), we show that each independently induces instability of comparable magnitude. Furthermore, for a given model, hyperparameter configurations with better MRR are not guaranteed to be more stable. Moreover, voting, albeit a known remediation mechanism, only provides a limited enhancement of stability. These findings highlight critical limitations of current benchmarking protocols, and raise concerns about the reliability of KGEMs for knowledge graph completion.

cs.LG

MetaboKG: An Analysis-centric Knowledge Graph Framework for Untargeted Metabolomics

Untargeted metabolomics generates large volumes of tandem mass spectrometry (MS/MS) data and computational annotations that can reveal molecular mechanisms across organisms and environments. Public reuse has improved through harmonized repository metadata and access infrastructures such as Pan-ReDU, and through metabolomics knowledge graphs such as ENPKG and METRIN-KG. Yet the analytical layer remains fragmented: spectra, features, workflow outputs, annotations, confidence evidence, and contextual metadata are still scattered across repositories and tabular artifacts. We present MetaboKG, an analysis-centric knowledge graph framework for engineering reusable metabolomics knowledge from public repositories, metadata, and GNPS molecular network results. MetaboKG contributes a transformation workflow that preserves links between repository exports, analytical files, spectra, features, and annotation results; a semantic model grounded in PROV-O and SIO and aligned with the Mass Spectrometry ontology (MS), ChEBI, NCBITaxon, ENVO, and NCIT to represent provenance, analytical evidence, metadata attributes, and controlled vocabulary terms; and a Universal Annotation Identifier strategy extending the Universal Spectrum Identifier (USI) with workflow-specific components for late binding, incremental ingestion, and post hoc linkage across analyses. We demonstrate MetaboKG at the public-repository scale on 680 GNPS molecular networking results and evaluate it through competency questions covering biochemical enrichment, environmental specificity, and cross instrument analytical variation. Results show that graph-based integration supports traceable annotation reuse and reproducible SPARQL exploration of biochemical relationships that remain fragmented across repository-native resources.

cs.DB

Which Are the Low-Resource Languages of the Semantic Web?

Emerging digital technologies are exacerbating the existing divide in Open Access Data (OAD) between high-and low-resource languages, excluding many communities from the global digital transformation. Multilingual Linked Open Data Knowledge Graphs (LOD KGs) could contribute to mitigating this divide through cross-lingual transfer; however, no clear quantitative definition of low-resource languages has yet been established in the context of LOD KGs. In this poster, we present a methodology to analyze the distribution of languages across LOD KGs and propose a preliminary multi-level categorization based on DBpedia, BabelNet, and Wikidata. This categorization is leveraged to bring a formal definition of low-, high-, and medium-resource languages that could be later leveraged to select cross-lingual transfer candidates.

cs.AI

T2S-Metrics: Unified Library for Evaluating SPARQL Queries Generated From Natural Language

The evaluation of Question Answering (QA) systems over Knowledge Graphs has historically suffered from fragmentation, inconsistency, and limited reproducibility. While significant progress has been made in semantic parsing and SPARQL query generation, evaluation methodologies remain diverse, ad hoc, and often incomparable across studies. Existing benchmarks typically focus on a small subset of metrics, such as query exact match or answer-level F1, neglecting syntactic validity, semantic faithfulness, execution correctness, results ranking quality, and computational efficiency. In this paper, we present t2s-metrics, an open-source, extensible, and unified evaluation library designed specifically for SPARQL query comparison and execution-based assessment. t2s-metrics provides a broad and extensible set of over 20 evaluation metrics, collected from the literature and practical evaluation needs, spanning lexical, syntactic, semantic, structural, execution-based and ranking-based dimensions. These include query-based metrics such as token-level Precision, Recall, and F1; BLEU, ROUGE, METEOR, and CodeBLEU variants; variable-normalized metrics (SP-BLEU, SP-F1); graph-and URI-based exact match metrics; as well as answer set-based metrics such as F1-QALD and Jaccard similarity; ranking metrics including MRR, NDCG, P@k, and Hit@k; and LLM-as-a-Judge metrics. Taking inspiration from the ir-metrics library for Information Retrieval, t2s-metrics provides a modular abstraction layer that decouples metric specification from implementation, enabling consistent, transparent, and reproducible evaluation of SPARQLbased QA systems. We argue that t2s-metrics constitutes a necessary step toward systematic, standardized evaluation in question answering over knowledge graphs and facilitates deeper diagnostic insights into system behavior beyond answer correctness.

cs.IR

Mimosa Framework: Toward Evolving Multi-Agent Systems for Scientific Research

Current Autonomous Scientific Research (ASR) systems, despite leveraging large language models (LLMs) and agentic architectures, remain constrained by fixed workflows and toolsets that prevent adaptation to evolving tasks and environments. We introduce Mimosa, an evolving multi-agent framework that automatically synthesizes task-specific multi-agent workflows and iteratively refines them through experimental feedback. Mimosa leverages the Model Context Protocol (MCP) for dynamic tool discovery, generates workflow topologies via a meta-orchestrator, executes subtasks through code-generating agents that invoke available tools and scientific software libraries, and scores executions with an LLM-based judge whose feedback drives workflow refinement. On ScienceAgentBench, Mimosa achieves a success rate of 43.1% with DeepSeek-V3.2, surpassing both single-agent baselines and static multi-agent configurations. Our results further reveal that models respond heterogeneously to multi-agent decomposition and iterative learning, indicating that the benefits of workflow evolution depend on the capabilities of the underlying execution model. Beyond these benchmarks, Mimosa modular architecture and tool-agnostic design make it readily extensible, and its fully logged execution traces and archived workflows support auditability by preserving every analytical step for inspection and potential replication. Combined with domain-expert guidance, the framework has the potential to automate a broad range of computationally accessible scientific tasks across disciplines. Released as a fully open-source platform, Mimosa aims to provide an open foundation for community-driven ASR.

cs.AI

Overcoming the Generalization Limits of SLM Finetuning for Shape-Based Extraction of Datatype and Object Properties

Small language models (SLMs) have shown promises for relation extraction (RE) when extracting RDF triples guided by SHACL shapes focused on common datatype properties. This paper investigates how SLMs handle both datatype and object properties for a complete RDF graph extraction. We show that the key bottleneck is related to long-tail distribution of rare properties. To solve this issue, we evaluate several strategies: stratified sampling, weighted loss, dataset scaling, and template-based synthetic data augmentation. We show that the best strategy to perform equally well over unbalanced target properties is to build a training set where the number of occurrences of each property exceeds a given threshold. To enable reproducibility, we publicly released our datasets, experimental results and code. Our findings offer practical guidance for training shape-aware SLMs and highlight promising directions for future work in semantic RE.

cs.CL

OLIVAW: ACIMOV's GitHub robot assisting agile collaborative ontology development

Agile and collaborative approaches to ontologies design are crucial because they contribute to making them userdriven, up-to-date, and able to evolve alongside the systems they support, hence proper continuous validation tooling is required to ensure ontologies match developers' requirements all along their development. We propose OLIVAW (Ontology Long-lived Integration Via ACIMOV Workflow), a tool supporting the ACIMOV methodology on GitHub. It relies on W3C Standards to assist the development of modular ontologies through GitHub Composite Actions, pre-commit hooks, or a command line interface. OLIVAW was tested on several ontology projects to ensure its usefulness, genericity and reusability. A template repository is available for a quick start. OLIVAW is

cs.SE

MetaboT: An LLM-based Multi-Agent Frameworkfor Interactive Analysis of Mass SpectrometryMetabolomics Knowledge Graphs

Mass spectrometry-based metabolomics generates complex, high-dimensional data that holds vast potential for biological discovery but remains difficult to integrate and interpret. Knowledge graphs (KGs) unify this heterogeneous information by representing spectra, annotations, taxa, chemical classes, and biological activities as a single interoperable network; however, their practical use is limited by the steep learning curve of corresponding specialized representation and query languages. Here we introduce MetaboT, an open-source multi-agent Large Language Model (LLM) framework that translates natural-language questions into executable SPARQL queries over metabolomics knowledge graphs. MetaboT mitigates the hallucination and schema-compliance limitations of single-model approaches through a modular architecture in which specialised agents handle scope validation, entity resolution against authoritative resources, schema-aware query generation, iterative refinement, and result interpretation. We validated MetaboT on the Experimental Natural Products Knowledge Graph (ENPKG), using an expert-authored benchmark of natural-language questions paired with reference SPARQL queries, and demonstrate its ability to answer complex questions about plant--metabolite relationships and biological activities. MetaboT lowers the technical barrier for metabolomics researchers and enables semantic data mining without specialised programming expertise.

cs.AI

No Such Thing as Free Brain Time: For a Pigouvian Tax on Attention Capture

In our age of digital platforms, human attention has become a scarce and highly valuable resource, rivalrous, tradable, and increasingly subject to market dynamics. This article explores the commodification of attention within the framework of the attention economy, arguing that attention should be understood as a common good threatened by over-exploitation. Drawing from philosophical, economic, and legal perspectives, we first conceptualize attention not only as an individual cognitive process but as a collective and infrastructural phenomenon susceptible to enclosure by digital intermediaries. We then identify and analyze negative externalities of the attention economy, particularly those stemming from excessive screen time: diminished individual agency, adverse health outcomes, and societal and political harms, including democratic erosion and inequality. These harms are largely unpriced by market actors and constitute a significant market failure. In response, among a spectrum of public policy tools ranging from informational campaigns to outright restrictions, we propose a Pigouvian tax on attention capture as a promising regulatory instrument to internalize the externalities and, in particular, the social cost of compulsive digital engagement. Such a tax would incentivize structural changes in platform design while preserving user autonomy. By reclaiming attention as a shared resource vital to human agency, health, and democracy, this article contributes a novel economic and policy lens to the debate on digital regulation. Ultimately, this article advocates for a paradigm shift: from treating attention as a private, monetizable asset to protecting it as a collective resource vital for humanity.

cs.SI

Eat your own KR: a KR-based approach to index Semantic Web Endpoints and Knowledge Graphs

Over the last decade, knowledge graphs have multiplied, grown, and evolved on the World Wide Web, and the advent of new standards, vocabularies, and application domains has accelerated this trend. IndeGx is a framework leveraging an extensible base of rules to index the content of KGs and the capacities of their SPARQL endpoints. In this article, we show how knowledge representation (KR) and reasoning methods and techniques can be used in a reflexive manner to index and characterize existing knowledge graphs (KG) with respect to their usage of KR methods and techniques. We extended IndeGx with a fully ontology-oriented modeling and processing approach to do so. Using SPARQL rules and an OWL RL ontology of the indexing domain, IndeGx can now build and reason over an index of the contents and characteristics of an open collection of public knowledge graphs. Our extension of the framework relies on a declarative representation of procedural knowledge and collaborative environments (e.g., GitHub) to provide an agile, customizable, and expressive KR approach for building and maintaining such an index of knowledge graphs in the wild. In doing so, we help anyone answer the question of what knowledge is out there in the world wild Semantic Web in general, and we also help our community monitor which KR research results are used in practice. In particular, this article provides a snapshot of the state of the Semantic Web regarding supported standard languages, ontology usage, and diverse quality evaluations by applying this method to a collection of over 300 open knowledge graph endpoints.

cs.IR

Q${}^2$Forge: Minting Competency Questions and SPARQL Queries for Question-Answering Over Knowledge Graphs

The SPARQL query language is the standard method to access knowledge graphs (KGs). However, formulating SPARQL queries is a significant challenge for non-expert users, and remains time-consuming for the experienced ones. Best practices recommend to document KGs with competency questions and example queries to contextualise the knowledge they contain and illustrate their potential applications. In practice, however, this is either not the case or the examples are provided in limited numbers. Large Language Models (LLMs) are being used in conversational agents and are proving to be an attractive solution with a wide range of applications, from simple question-answering about common knowledge to generating code in a targeted programming language. However, training and testing these models to produce high quality SPARQL queries from natural language questions requires substantial datasets of question-query pairs. In this paper, we present Q${}^2$Forge that addresses the challenge of generating new competency questions for a KG and corresponding SPARQL queries. It iteratively validates those queries with human feedback and LLM as a judge. Q${}^2$Forge is open source, generic, extensible and modular, meaning that the different modules of the application (CQ generation, query generation and query refinement) can be used separately, as an integrated pipeline, or replaced by alternative services. The result is a complete pipeline from competency question formulation to query evaluation, supporting the creation of reference query sets for any target KG.

cs.DB

Pay Attention: a Call to Regulate the Attention Market and Prevent Algorithmic Emotional Governance

Over the last 70 years, we, humans, have created an economic market where attention is being captured and turned into money thanks to advertising. During the last two decades, leveraging research in psychology, sociology, neuroscience and other domains, Web platforms have brought the process of capturing attention to an unprecedented scale. With the initial commonplace goal of making targeted advertising more effective, the generalization of attention-capturing techniques and their use of cognitive biases and emotions have multiple detrimental side effects such as polarizing opinions, spreading false information and threatening public health, economies and democracies. This is clearly a case where the Web is not used for the common good and where, in fact, all its users become a vulnerable population. This paper brings together contributions from a wide range of disciplines to analyze current practices and consequences thereof. Through a set of propositions and principles that could be used do drive further works, it calls for actions against these practices competing to capture our attention on the Web, as it would be unsustainable for a civilization to allow attention to be wasted with impunity on a world-wide scale.

cs.SI

Love Me, Love Me, Say (and Write!) that You Love Me: Enriching the WASABI Song Corpus with Lyrics Annotations

We present the WASABI Song Corpus, a large corpus of songs enriched with metadata extracted from music databases on the Web, and resulting from the processing of song lyrics and from audio analysis. More specifically, given that lyrics encode an important part of the semantics of a song, we focus here on the description of the methods we proposed to extract relevant information from the lyrics, such as their structure segmentation, their topics, the explicitness of the lyrics content, the salient passages of a song and the emotions conveyed. The creation of the resource is still ongoing: so far, the corpus contains 1.73M songs with lyrics (1.41M unique lyrics) annotated at different levels with the output of the above mentioned methods. Such corpus labels and the provided methods can be exploited by music search engines and music professionals (e.g. journalists, radio presenters) to better handle large collections of lyrics, allowing an intelligent browsing, categorization and segmentation recommendation of songs.

cs.CL

Graph Data on the Web: extend the pivot, don't reinvent the wheel

This article is a collective position paper from the Wimmics research team, expressing our vision of how Web graph data technologies should evolve in the future in order to ensure a high-level of interoperability between the many types of applications that produce and consume graph data. Wimmics stands for Web-Instrumented Man-Machine Interactions, Communities, and Semantics. We are a joint research team between INRIA Sophia Antipolis-M{\'e}diterran{\'e}e and I3S (CNRS and Universit{\'e} C{\^o}te d'Azur). Our challenge is to bridge formal semantics and social semantics on the web. Our research areas are graph-oriented knowledge representation, reasoning and operationalization to model and support actors, actions and interactions in web-based epistemic communities. The application of our research is supporting and fostering interactions in online communities and management of their resources. In this position paper, we emphasize the need to extend the semantic Web standard stack to address and fulfill new graph data needs, as well as the importance of remaining compatible with existing recommendations, in particular the RDF stack, to avoid the painful duplication of models, languages, frameworks, etc. The following sections group motivations for different directions of work and collect reasons for the creation of a working group on RDF 2.0 and other recommendations of the RDF family.

cs.DB