arXiv subjects

Gianmaria Silvello

Publications and source records attributed to Gianmaria Silvello.

At least 19 recordsLinked to original sources

arXiv2026

Overview of BioASQ 2026: The fourteenth BioASQ Challenge on Large-Scale Biomedical Semantic Indexing and Question Answering

This paper presents an overview of the fourteenth edition of the BioASQ challenge, organized in the context of the Conference and Labs of the Evaluation Forum (CLEF) 2026. BioASQ is an international challenge series that supports progress in biomedical language processing tasks ranging from semantic indexing and information extraction to question answering and summarization. In 2026, BioASQ included six shared tasks: a) Task 14b on biomedical semantic question answering. b) Task Synergy14 on question answering for developing biomedical top- ics. c) Task MultiClinSum-2 on multilingual clinical summarization. d) Task BioNNE-R on extracting relations between nested named entities in Russian and English. e) Task ELCardioCC on clinical coding in cardiology. f) Task GutBrainIE on gut-brain interplay information extrac- tion. Across these six tasks, 87 distinct teams participated, submitting more than 1000 runs overall. As in previous editions, several submissions reached competitive performance, reflecting the continued progress of state-of-the-art methods across biomedical language processing tasks.

cs.CL↗

arXiv2026

Efficient Dense Vector Search within Knowledge Graph Content Embeddings

Knowledge graphs are a core component of today's knowledge infrastructure, supporting reasoning and anchoring knowledge systems to verifiable facts. RDF stores and SPARQL engines fulfill this function, enabling a range of retrieval and inference tasks on structured knowledge. Coupling them with Language Models (LMs) extends RAG toward neurosymbolic reasoning, where structured queries gate or re-rank generative outputs. This line of reasoning requires that SPARQL evaluation natively support tensor operations on dense embeddings, enabling multimodal querying and learned similarity-based ranking to be expressed together with graph-structural constraints. This approach is feasible only if the engine can efficiently perform dense vector search. We present QLever-Unified Indexed Vector Embedding Retrieval (QUIVER), an extension to QLever that adds native support for dense vector retrieval within RDF knowledge graphs. It implements three optimizations: engine-level registration of tensor functions, vocabulary-time parsing of JSON-encoded vectors, and a virtual SERVICE that exposes a vector index inside the query. We propose two new benchmarks: an extension of Berlin Sparql Benchmark (BSBM) with text embeddings and an extension of DBpedia with image embeddings. Against the baselines, vocabulary-time parsing alone yields median speedups of up to 41.9x on BSBM and 20x on DBpedia for single-type ranking; adding an approximate nearest-neighbor index yields speedups of 355x on BSBM and 97.8x on DBpedia. The index further makes cross-modal vector joins on DBpedia feasible in seconds, whereas all non-indexed configurations time out.

cs.DB↗

arXiv2026

Data Citation for Large Language Models: A Challenge

Large language models increasingly mediate access to information, and a growing body of work asks whether they cite the sources behind their outputs. That work treats citation as a verification device and applies it to textual documents. Scholarly citation serves two further functions, credit and provenance, and it applies to data as much as to text. This paper argues that data citation for large language models is an open challenge, distinct from document-level citation grounding and harder to solve. We ask how such models should cite data so that outputs stay verifiable, provenance stays traceable, and credit reaches data creators and curators. We set out three research directions. Training data attribution has to turn influence estimates into references for corpora absorbed into model parameters. Data citation at inference time has to identify datasets, subsets, and query results at the right granularity and fixity. Citing knowledge graph facts has to define what a reference to a single triple denotes and how credit propagates along provenance. Progress on all three depends on joint work across the database, information retrieval, knowledge representation, and artificial intelligence communities.

cs.IR↗

arXiv2026

Ontology-Driven Structural Regularization for Document-Level Relation Extraction

Document-Level Relation Extraction (DocRE) relies heavily on costly manually annotated datasets, while large distant supervision resources such as DocRED distant remain underexploited due to noise. We show that a critical yet overlooked source of noise lies in structural inconsistencies within relational triples, including violations of ontology constraints and logical contradictions. We introduce an ontology-driven framework to quantify and enforce structural consistency in DocRE datasets. Our analysis reveals substantial structural noise in DocRED distant and demonstrates that such inconsistencies propagate to model predictions. Enforcing structural well-formedness during training significantly reduces logical contradictions and consistently improves generalization performance. These findings establish structural consistency as a missing axis of supervision in DocRE and highlight structural regularization as an effective strategy for leveraging distant data at scale.

cs.CL↗

arXiv2026

Benchmarking Large Language Models for Knowledge Graph Validation

Knowledge Graphs (KGs) store structured factual knowledge by linking entities through relationships, crucial for many applications. These applications depend on the KG's factual accuracy, so verifying facts is essential, yet challenging. Expert manual verification is ideal but impractical on a large scale. Automated methods show promise but are not ready for real-world KGs. Large Language Models (LLMs) offer potential with their semantic understanding and knowledge access, yet their suitability and effectiveness for KG fact validation remain largely unexplored. In this paper, we introduce FactCheck, a benchmark designed to evaluate LLMs for KG fact validation across three key dimensions: (1) LLMs internal knowledge; (2) external evidence via Retrieval-Augmented Generation (RAG); and (3) aggregated knowledge employing a multi-model consensus strategy. We evaluated open-source and commercial LLMs on three diverse real-world KGs. FactCheck also includes a RAG dataset with 2+ million documents tailored for KG fact validation. Additionally, we offer an interactive exploration platform for analyzing verification decisions. The experimental analyses demonstrate that while LLMs yield promising results, they are still not sufficiently stable and reliable to be used in real-world KG validation scenarios. Integrating external evidence through RAG methods yields fluctuating performance, providing inconsistent improvements over more streamlined approaches -- at higher computational costs. Similarly, strategies based on multi-model consensus do not consistently outperform individual models, underscoring the lack of a one-fits-all solution. These findings further emphasize the need for a benchmark like FactCheck to systematically evaluate and drive progress on this difficult yet crucial task.

cs.DB↗

arXiv2026

A Domain-Specific Curated Benchmark for Entity and Document-Level Relation Extraction

Information Extraction (IE), encompassing Named Entity Recognition (NER), Named Entity Linking (NEL), and Relation Extraction (RE), is critical for transforming the rapidly growing volume of scientific publications into structured, actionable knowledge. This need is especially evident in fast-evolving biomedical fields such as the gut-brain axis, where research investigates complex interactions between the gut microbiota and brain-related disorders. Existing biomedical IE benchmarks, however, are often narrow in scope and rely heavily on distantly supervised or automatically generated annotations, limiting their utility for advancing robust IE methods. We introduce GutBrainIE, a benchmark based on more than 1,600 PubMed abstracts, manually annotated by biomedical and terminological experts with fine-grained entities, concept-level links, and relations. While grounded in the gut-brain axis, the benchmark's rich schema, multiple tasks, and combination of highly curated and weakly supervised data make it broadly applicable to the development and evaluation of biomedical IE systems across domains.

cs.CL↗

arXiv2026

DOREMI: Optimizing Long Tail Predictions in Document-Level Relation Extraction

Document-Level Relation Extraction (DocRE) presents significant challenges due to its reliance on cross-sentence context and the long-tail distribution of relation types, where many relations have scarce training examples. In this work, we introduce DOcument-level Relation Extraction optiMizing the long taIl (DOREMI), an iterative framework that enhances underrepresented relations through minimal yet targeted manual annotations. Unlike previous approaches that rely on large-scale noisy data or heuristic denoising, DOREMI actively selects the most informative examples to improve training efficiency and robustness. DOREMI can be applied to any existing DocRE model and is effective at mitigating long-tail biases, offering a scalable solution to improve generalization on rare relations.

cs.CL↗

arXiv2026

From Single to Multi-Agent Reasoning: Advancing GeneGPT for Genomics QA

Comprehending genomic information is essential for biomedical research, yet extracting data from complex distributed databases remains challenging. Large language models (LLMs) offer potential for genomic Question Answering (QA) but face limitations due to restricted access to domain-specific databases. GeneGPT is the current state-of-the-art system that enhances LLMs by utilizing specialized API calls, though it is constrained by rigid API dependencies and limited adaptability. We replicate GeneGPT and propose GenomAgent, a multi-agent framework that efficiently coordinates specialized agents for complex genomics queries. Evaluated on nine tasks from the GeneTuring benchmark, GenomAgent outperforms GeneGPT by 12% on average, and its flexible architecture extends beyond genomics to various scientific domains needing expert knowledge extraction.

cs.AI↗

arXiv2026

Efficient and Reliable Estimation of Named Entity Linking Quality: A Case Study on GutBrainIE

Named Entity Linking (NEL) is a core component of biomedical Information Extraction (IE) pipelines, yet assessing its quality at scale is challenging due to the high cost of expert annotations and the large size of corpora. In this paper, we present a sampling-based framework to estimate the NEL accuracy of large-scale IE corpora under statistical guarantees and constrained annotation budgets. We frame NEL accuracy estimation as a constrained optimization problem, where the objective is to minimize expected annotation cost subject to a target Margin of Error (MoE) for the corpus-level accuracy estimate. Building on recent works on knowledge graph accuracy estimation, we adapt Stratified Two-Stage Cluster Sampling (STWCS) to the NEL setting, defining label-based strata and global surface-form clusters in a way that is independent of NEL annotations. Applied to 11,184 NEL annotations in GutBrainIE -- a new biomedical corpus openly released in fall 2025 -- our framework reaches a MoE $\leq 0.05$ by manually annotating only 2,749 triples (24.6%), leading to an overall accuracy estimate of $0.915 \pm 0.0473$. A time-based cost model and simulations against a Simple Random Sampling (SRS) baseline show that our design reduces expert annotation time by about 29% at fixed sample size. The framework is generic and can be applied to other NEL benchmarks and IE pipelines that require scalable and statistically robust accuracy assessment.

cs.CL↗

arXiv2025

Overview of BioASQ 2025: The Thirteenth BioASQ Challenge on Large-Scale Biomedical Semantic Indexing and Question Answering

This is an overview of the thirteenth edition of the BioASQ challenge in the context of the Conference and Labs of the Evaluation Forum (CLEF) 2025. BioASQ is a series of international challenges promoting advances in large-scale biomedical semantic indexing and question answering. This year, BioASQ consisted of new editions of the two established tasks, b and Synergy, and four new tasks: a) Task MultiClinSum on multilingual clinical summarization. b) Task BioNNE-L on nested named entity linking in Russian and English. c) Task ELCardioCC on clinical coding in cardiology. d) Task GutBrainIE on gut-brain interplay information extraction. In this edition of BioASQ, 83 competing teams participated with more than 1000 distinct submissions in total for the six different shared tasks of the challenge. Similar to previous editions, several participating systems achieved competitive performance, indicating the continuous advancement of the state-of-the-art in the field.

cs.CL↗

arXiv2025

Credible Intervals for Knowledge Graph Accuracy Estimation

Knowledge Graphs (KGs) are widely used in data-driven applications and downstream tasks, such as virtual assistants, recommendation systems, and semantic search. The accuracy of KGs directly impacts the reliability of the inferred knowledge and outcomes. Therefore, assessing the accuracy of a KG is essential for ensuring the quality of facts used in these tasks. However, the large size of real-world KGs makes manual triple-by-triple annotation impractical, thereby requiring sampling strategies to provide accuracy estimates with statistical guarantees. The current state-of-the-art approaches rely on Confidence Intervals (CIs), derived from frequentist statistics. While efficient, CIs have notable limitations and can lead to interpretation fallacies. In this paper, we propose to overcome the limitations of CIs by using \emph{Credible Intervals} (CrIs), which are grounded in Bayesian statistics. These intervals are more suitable for reliable post-data inference, particularly in KG accuracy evaluation. We prove that CrIs offer greater reliability and stronger guarantees than frequentist approaches in this context. Additionally, we introduce \emph{a}HPD, an adaptive algorithm that is more efficient for real-world KGs and statistically robust, addressing the interpretive challenges of CIs.

cs.DB↗

arXiv2025

Testing software for non-discrimination: an updated and extended audit in the Italian car insurance domain

Context. As software systems become more integrated into society's infrastructure, the responsibility of software professionals to ensure compliance with various non-functional requirements increases. These requirements include security, safety, privacy, and, increasingly, non-discrimination. Motivation. Fairness in pricing algorithms grants equitable access to basic services without discriminating on the basis of protected attributes. Method. We replicate a previous empirical study that used black box testing to audit pricing algorithms used by Italian car insurance companies, accessible through a popular online system. With respect to the previous study, we enlarged the number of tests and the number of demographic variables under analysis. Results. Our work confirms and extends previous findings, highlighting the problematic permanence of discrimination across time: demographic variables significantly impact pricing to this day, with birthplace remaining the main discriminatory factor against individuals not born in Italian cities. We also found that driver profiles can determine the number of quotes available to the user, denying equal opportunities to all. Conclusion. The study underscores the importance of testing for non-discrimination in software systems that affect people's everyday lives. Performing algorithmic audits over time makes it possible to evaluate the evolution of such algorithms. It also demonstrates the role that empirical software engineering can play in making software systems more accountable.

cs.SE↗

arXiv2024

Can we measure the impact of a database?

In disseminating scientific and statistical data, on-line databases have almost completely replaced traditional paper-based media such as journals and reference works. Given this, can we measure the impact of a database in the same way that we measure an author's or journal's impact? To do this, we need somehow to represent a database as a set of publications, and databases typically allow a large number of possible decompositions into parts, any of which could be treated as a publication. We show that the definition of the h-index naturally extends to hierarchies, so that if a database admits some kind of hierarchical interpretation we can use this as one measure of the importance of a database; moreover, this can be computed as efficiently as one can compute the normal h-index. This also gives us a decomposition of the database that might be used for other purposes such as giving credit to the curators or contributors to the database. We illustrate the process by analyzing three widely used databases.

cs.DB↗

arXiv2024

Automatic Labels are as Effective as Manual Labels in Biomedical Images Classification with Deep Learning

The increasing availability of biomedical data is helping to design more robust deep learning (DL) algorithms to analyze biomedical samples. Currently, one of the main limitations to train DL algorithms to perform a specific task is the need for medical experts to label data. Automatic methods to label data exist, however automatic labels can be noisy and it is not completely clear when automatic labels can be adopted to train DL models. This paper aims to investigate under which circumstances automatic labels can be adopted to train a DL model on the classification of Whole Slide Images (WSI). The analysis involves multiple architectures, such as Convolutional Neural Networks (CNN) and Vision Transformer (ViT), and over 10000 WSIs, collected from three use cases: celiac disease, lung cancer and colon cancer, which one including respectively binary, multiclass and multilabel data. The results allow identifying 10% as the percentage of noisy labels that lead to train competitive models for the classification of WSIs. Therefore, an algorithm generating automatic labels needs to fit this criterion to be adopted. The application of the Semantic Knowledge Extractor Tool (SKET) algorithm to generate automatic labels leads to performance comparable to the one obtained with manual labels, since it generates a percentage of noisy labels between 2-5%. Automatic labels are as effective as manual ones, reaching solid performance comparable to the one obtained training models with manual labels.

eess.IV↗

arXiv2022

Algorithmic Fairness Datasets: the Story so Far

Data-driven algorithms are studied in diverse domains to support critical decisions, directly impacting people's well-being. As a result, a growing community of researchers has been investigating the equity of existing algorithms and proposing novel ones, advancing the understanding of risks and opportunities of automated decision-making for historically disadvantaged populations. Progress in fair Machine Learning hinges on data, which can be appropriately used only if adequately documented. Unfortunately, the algorithmic fairness community suffers from a collective data documentation debt caused by a lack of information on specific resources (opacity) and scatteredness of available information (sparsity). In this work, we target data documentation debt by surveying over two hundred datasets employed in algorithmic fairness research, and producing standardized and searchable documentation for each of them. Moreover we rigorously identify the three most popular fairness datasets, namely Adult, COMPAS and German Credit, for which we compile in-depth documentation. This unifying documentation effort supports multiple contributions. Firstly, we summarize the merits and limitations of Adult, COMPAS and German Credit, adding to and unifying recent scholarship, calling into question their suitability as general-purpose fairness benchmarks. Secondly, we document and summarize hundreds of available alternatives, annotating their domain and supported fairness tasks, along with additional properties of interest for fairness researchers. Finally, we analyze these datasets from the perspective of five important data curation topics: anonymization, consent, inclusivity, sensitive attributes, and transparency. We discuss different approaches and levels of attention to these topics, making them tangible, and distill them into a set of best practices for the curation of novel resources.

cs.CY↗

arXiv2022

Learning to Rank from Relevance Judgments Distributions

Learning to Rank (LETOR) algorithms are usually trained on annotated corpora where a single relevance label is assigned to each available document-topic pair. Within the Cranfield framework, relevance labels result from merging either multiple expertly curated or crowdsourced human assessments. In this paper, we explore how to train LETOR models with relevance judgments distributions (either real or synthetically generated) assigned to document-topic pairs instead of single-valued relevance labels. We propose five new probabilistic loss functions to deal with the higher expressive power provided by relevance judgments distributions and show how they can be applied both to neural and GBM architectures. Moreover, we show how training a LETOR model on a sampled version of the relevance judgments from certain probability distributions can improve its performance when relying either on traditional or probabilistic loss functions. Finally, we validate our hypothesis on real-world crowdsourced relevance judgments distributions. Overall, we observe that relying on relevance judgments distributions to train different LETOR models can boost their performance and even outperform strong baselines such as LambdaMART on several test collections.

cs.IR↗

arXiv2021

Incentives for Item Duplication under Fair Ranking Policies

Ranking is a fundamental operation in information access systems, to filter information and direct user attention towards items deemed most relevant to them. Due to position bias, items of similar relevance may receive significantly different exposure, raising fairness concerns for item providers and motivating recent research into fair ranking. While the area has progressed dramatically over recent years, no study to date has investigated the potential problem posed by duplicated items. Duplicates and near-duplicates are common in several domains, including marketplaces and document collections available to search engines. In this work, we study the behaviour of different fair ranking policies in the presence of duplicates, quantifying the extra-exposure gained by redundant items. We find that fairness-aware ranking policies may conflict with diversity, due to their potential to incentivize duplication more than policies solely focused on relevance. This fact poses a problem for system owners who, as a result of this incentive, may have to deal with increased redundancy, which is at odds with user satisfaction. Finally, we argue that this aspect represents a blind spot in the normative reasoning underlying common fair ranking metrics, as rewarding providers who duplicate their items with increased exposure seems unfair for the remaining providers.

cs.CY↗

arXiv2021

Algorithmic Audit of Italian Car Insurance: Evidence of Unfairness in Access and Pricing

We conduct an audit of pricing algorithms employed by companies in the Italian car insurance industry, primarily by gathering quotes through a popular comparison website. While acknowledging the complexity of the industry, we find evidence of several problematic practices. We show that birthplace and gender have a direct and sizeable impact on the prices quoted to drivers, despite national and international regulations against their use. Birthplace, in particular, is used quite frequently to the disadvantage of foreign-born drivers and drivers born in certain Italian cities. In extreme cases, a driver born in Laos may be charged 1,000 euros more than a driver born in Milan, all else being equal. For a subset of our sample, we collect quotes directly on a company website, where the direct influence of gender and birthplace is confirmed. Finally, we find that drivers with riskier profiles tend to see fewer quotes in the aggregator result pages, substantiating concerns of differential treatment raised in the past by Italian insurance regulators.

cs.CY↗