arXiv subjects

Benjamin Navet

Publications and source records attributed to Benjamin Navet.

4 recordsLinked to original sources

arXiv2026

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↗

arXiv2026

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↗

arXiv2025

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↗

arXiv2025

Merging Embedded Topics with Optimal Transport for Online Topic Modeling on Data Streams

Topic modeling is a key component in unsupervised learning, employed to identify topics within a corpus of textual data. The rapid growth of social media generates an ever-growing volume of textual data daily, making online topic modeling methods essential for managing these data streams that continuously arrive over time. This paper introduces a novel approach to online topic modeling named StreamETM. This approach builds on the Embedded Topic Model (ETM) to handle data streams by merging models learned on consecutive partial document batches using unbalanced optimal transport. Additionally, an online change point detection algorithm is employed to identify shifts in topics over time, enabling the identification of significant changes in the dynamics of text streams. Numerical experiments on simulated and real-world data show StreamETM outperforming competitors. We provide the code publicly available at https://github.com/fgranese/StreamETM.

cs.LG↗