Publications

Scientific publications

This section contains all scientific publications produced by the project.

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Utility-Oriented Knowledge Graph Accuracy Estimation with Limited Annotations: A Case Study on DBpedia.

Stefano Marchesin, Gianmaria Silvello, and Omar Alonso.  Accepted to AAAI HCOMP 2024.

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BIDSAlign: a library for automatic merging and preprocessing of multiple EEG repositories”

 Andrea Zanola, Federico Del Pup, Camillo Porcaro and Manfredo Atzori. JNE 2024.

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Content-Based Dataset Retrieval Methods: Reproducibility of the ACORDAR Test Collection.

Laura Menotti, Manuel Barusco, Riccardo Forzan, and Gianmaria Silvello. Accepted to TPDL 2024. 
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Veracity Estimation for Entity-Oriented Search with Knowledge Graphs.

Stefano Marchesin, Gianmaria Silvello, and Omar Alonso. Accepted at CIKM 2024.

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SelfEEG: A Python library for Self-Supervised Learning in Electroencephalography.

Federico Del Pup, Andrea Zanola, Louis Fabrice Tshimanga, Paolo Emilio Mazzon and Manfredo Atzori. Journal of Open Source Software, 9(95), 6224.
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Efficient and Reliable Estimation of Knowledge Graph Accuracy.

Added to the the CC: Stefano Marchesin and Gianmaria Silvello. Proc. of the VLDB Endowment, Vol. 17, No. 9, 2024,

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MetaTron: advancing biomedical annotation empowering relation annotation and collaboration.

Added to the the CC: Ornella Irrera, Stefano Marchesin, and Gianmaria Silvello. BMC Bioinformatics, Vol. 25, No. 112, 2024.

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Publishing CoreKB Facts as Nanopublications.

Added to the the CC: Fabio Giachelle, Stefano Marchesin, Laura Menotti, and Gianmaria Silvello. In Proc. of the 20th Italian Research Conference on Digital Libraries (IRCDL 2024). CEUR-WS Proceedings vol. 3643, pp. 16-24, Open Access, 2024.

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Exploring the Role of Generative AI in Constructing Knowledge Graphs for Drug Indications with Medical Context.

Reham Alharbi, Umair Ahmed, Daniil Dobriy, Weronika Łajewska, Laura Menotti, Mohammad Javad Saeedizade, and Michel Dumontier. In Proc. of the 15th International Semantic Web Applications and Tools for Health Care and Life Science conference (SWAT4HCLS 2024), CEUR-WS Proceedings, Open Access, 2024. To appear.
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Spirochetosis detection in colon histopathology images via fine-tuning and boosting techniques using foundation models

Agata Polejowska, Fazael Ayatollahi, Ayse Selcen Oguz Erdogan, Francesco Ciompi, Annemarie Boleij.  Medical Imaging with Deep Learning 2024 Short Paper Submission
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Histopathobiome – integrating histopathology and microbiome data via multimodal deep learning.

Agata Polejowska, Annemarie Boleij, Francesco Ciompi. MICCAI COMPAYL 2024 Workshop.
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An extensible and unifying approach to retrospective clinical data modeling: the BrainTeaser Ontology

Guglielmo Faggioli, Laura Menotti1, Stefano Marchesin1, Adriano Chió, Arianna Dagliati, Mamede de Carvalho, Marta Gromicho, Umberto Manera, Eleonora Tavazzi, Giorgio Maria Di Nunzio, Gianmaria Silvello1, Nicola Ferro.  Journal of Biomedical Semantics 2024. 
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DROPLETS: A Marker Design for visually enhancingLocal Cluster Association

Stefan Lengauer, Peter Waldert, and Tobias Schreck. Bio+MedVis Workshop @ IEEE VIS 2024
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UNIPD@SimpleText2024: A Semi-Manual Approach on Prompting ChatGPT for Extracting Terms and Write Terminological Definitions

Giorgio Maria Di Nunzio, Elena Gallina, Federica Vezzani. Notebook for the SimpleText Lab at CLEF 2024.
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Overview of the CLEF 2024 SimpleText Task 2: Identify and Explain Difficult Concepts

Giorgio Maria Di Nunzio, Federica Vezzani, Vanessa Bonato, Hosein Azarbonyad, Jaap Kamps, Liana Ermakova. Notebook for the SimpleText Lab at CLEF 2024.
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Toward improving reproducibility in neuroimaging deep learning studies

Federico Del Pup, Manfredo Atzori. Opinion article published at Frontiers.
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Stakeholders' engagement for improved health outcomes: a research brief to design a tool for better communication and participation

Giuseppe Pellegrini, Chiara Lovati. Brief Research Report published at Frontiers.
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Extending Nanopublications with Knowledge Provenance for Multi-Source Scientific Assertions

Fabio Giachelle, Stefano Marchesin, Laura Menotti, Gianmaria Silvello. In Proc. of the 21st conference on Information and Research science Connecting to Digital and Library science.
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The more, the better? Evaluating the role of EEG preprocessing for deep learning applications

Federico Del Pup, Andrea Zanola, Louis Fabrice Tshimanga, Alessandra Bertoldo, Manfredo Atzori. Article published at the IEEE Transactions on Neutral Systems and Rehabilitation Engineering journal.
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Exploring Publicly Accessible Optical Coherence Tomography Datasets A Comprehensive Overview

Anastasiia Rozhyna, Gábor Márk Somfai, Manfredo Atzori, Delia Cabrera Debuc, Amr Saad, Jay Zoellin, Henning Müller. Article published at Diagnostics journal.
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MetaTron: Streamlining Collaborative Annotation for Biomedical Documents

Ornella Irrera, Stefano Marchesin, Gianmaria Silvello. Presented at the SWAT4HCLS 2025: 16th International SWAT4HCLS Conference.
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Reproducibility and Analysis of Dataset Recommendation Methods

Ornella Irrera, Gianmaria Silvello, Matteo Lissandrini, Daniele Dell’Aglio. Presented at the RecSys 2024 international forum.
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When LMF and TMF meet: towards a Unified Markup Framework (UMF)

Federica Vezzani, Giorgio María Di Nunzio, Ana Salgado, Rute Costa. Published on the Computational Terminology journal. 

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Credible Intervals for Knowledge Graph Accuracy Estimation

Stefano Marchesin, Gianmaria Silvello. Presented at the SIGMOD 2025 Conference.
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Binomial Confidence Intervals for Knowledge Graph Accuracy Estimation (Extended Abstract)

Stefano Marchesin, Gianmaria Silvello. Presented at SEBD 2025: 33rd Symposium On Advanced Database Systems.

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Le rôle du référent en terminologie: enquête sur la perception du trouble dysmorphique corporel

Federica Vezzani, Rute Costa. Published at the Roczniki Humanistyczne Journal.
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A Novel Approach to Semic Analysis: Extraction of Atoms of Meaning to Study Polysemy and Polyreferentiality

Vanessa Bonato, Giorgio Maria Di Nunzio, Federica Vezzani. Published at MDPI-Languages journal.

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Behavioral Clusters and Lesion Distributions in Ischemic Stroke, Based on NIHSS Similarity Network

Louis Fabrice Tshimanga, Andrea Zanola, Silvia Fachini, Antonio Luigi Bisogno, Lorenzo Pini, Manfredo Atzori, Maurizio Corbetta. Published at the Jouernal of Healtcare Informatics Research.
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Can We Measure the Impact of a Database?

Peter Buneman, Dennis Dosso, Matteo Lissandrini, Gianmaria Silvello, Sun He. Published at the Communications ACM Journal.

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Exploring Terminological Collocations in Biomedical Texts

Rute Costa, Margarida Ramos, Matilde Canelas, Ana Mouro. Presented at the 4th International Conference on “Multilingual digital terminology today. Design, representation formats and management systems”.
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The Elephant in the Room: The Impact of Domain-Expert (Dis)agreement. A Case Study on Cryptic Species

Giorgio Maria Di Nunzio, Lucia Manni, Emanuela De Lisa, Federica Vezzani. Presented at the 4th International Conference on “Multilingual digital terminology today. Design, representation formats and management systems”

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HERO-Genomics: An Ontology for Integration and Access of Multicenter Genomic Data

Laura Menotti, Gianmaria Silvello, Mirco Cazzaro, Ivo G. Gut, Manuel Rueda. Presented at the SWAT4HCLS ’25: The 16th International SWAT4HCLS conference.

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Reusability of Biomedical Annotations for Gut-Brain Interplay Information Extraction as Terminological Data

Vanessa Bonato. Presented at the 4th International Conference on “Multilingual digital terminology today.

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BioASQ at CLEF2025: The thirteenth edition of the Large-scale biomedical semantic indexing and question answering challenge

Giorgio Maria Di Nunzio, Nicola Ferro, Stefano Marchesin, Laura Menotti, Gianmaria Silvello. BioASQ task for CLEF2025.

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Doctron: A web-based collaborative annotation tool for ground truth creation in IR

Irrera Ornella, Stefano Marchesin, Farzad Shami, Gianmaria Silvello. In Proceedings of the 48th International ACM SIGIR Conference on Research and Development in Information Retrieval (SIGIR’25), July 13–18, 2025, Padua, Italy.

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Fact Verification in Knowledge Graphs Using LLMs

Farzad Shami, Stefano Marchesin, Gianmaria Silvello. In Proceedings of the 48th International ACM SIGIR Conference on Research and Development in Information Retrieval (SIGIR ’25), July 13–18, 2025, Padua, Italy.

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FAIR Terminology Meets CLEAR Global

Giorgio Maria Di Nunzio, Eszter Papp, Federica Vezzani, Ellie Kemp. 

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OnSET: Ontology and Semantic Exploration Toolkit

Benedikt Kantz, Stefan Lengauer, Kevin Innerebner, Elisabeth Lex, Peter Waldert, Tobias Schreck. In Proceedings of The 48th International ACM SIGIR Conference on Research and Development in Information Retrieval (SIGIR 2025)

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Variation in Psychopathological Terminology. A Case Study on Body-Dismorphic Disorder

Federica Vezzani, Rute Costa. 

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The role of data partitioning on the performance of EEG-based deep learning models in supervised cross-subject analysis: a preliminary study

Federico Del Pup, Andrea Zanola, Louis Fabrice Tshimanga, Alessandra Bertoldo, Livio Finos, Manfredo Atzori.

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Changes to Average Survival of Patients With Amyotrophic Lateral Sclerosis (1995–2018)

Rosario Vasta, Filippo De Mattei, Salvatore Tafaro, Antonio Canosa, Umberto Manera, Maurizio Grassano, Francesca Palumbo, Sara Cabras, Enrico Matteoni, Francesca Di Pede, Grazia Zocco, Giorgio Pellegrino, Emilio Minerva, Daniela Pascariu, Barbara Iazzolino, Stefano Callegaro, Giuseppe Fuda, Paolina Salamone, Fabiola De Marchi, Letizia Mazzini, Cristina Moglia, Andrea Calvo, Adriano Chio. At Neurology ® 2025

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Phosphatemia is an Independent Prognostic Factor in Amyotrophic Lateral Sclerosis

Rosario Vasta, Emanuele Koumantakis, Antonio Canosa, Umberto Manera, Maurizio Grassano, Francesca Palumbo, Sara Cabras, Enrico Matteoni, Francesca Di Pede, Filippo De Mattei, Filippo Vergnano, Jessica Mandrioli, Cecilia Simonini, Ilaria Martinelli, Fabiola De Marchi, Letizia Mazzini, Cristina Moglia, Andrea Calvo, Adriano Chió. Annals of Neurology published by Wiley Periodicals LLC on behalf of American Neurological Association

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Uncertainty-Aware Training for Ophthalmic Segmentation Using MedSAM

Nebbia, G., McNamara, S., Clark, C. W., Kinder, S., Veturi, Y. A., Manoharan, N., Forest, T., Kahook, M., Mandava, N., Singh, P., & Kalpathy-Cramer, J. In Translational Vision Science & Technology journal (Vol. 15, N.2). 

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Scaling Trust: Veracity-Driven Defect Detection in Entity Search

Ornella Irrera, Stefano Marchesin, Gianmaria Silvello, Omar Alonso. Proceedings of the 34th ACM International Conference on Information and Knowledge Management, 1001-1012.

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A Review of Privacy Metrics for Privacy-Preserving Synthetic Data Generation

Frederik Marinus Trudslev, Matteo Lissandrini, Juan Manuel Rodriguez, Martin Bøgsted, Daniele Dell’Aglio.

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Constrained Linked Entity ANnotation using RAG (CLEANR)

Benedikt Kantz, Peter Waldert, Stefan Lengauer, Tobias Schreck. CEUR Workshop Proceedings.

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Brain Metabolic Features of FUS-ALS: A 2-[18F]FDG-PET Study

Antonio Canosa, Umberto Manera, Rosario Vasta, Grazia Zocco, Francesca Di Pede, Sara Cabras, Filippo De Mattei, Francesca Palumbo, Barbara Iazzolino, Emilio Minerva, Luca Sbaiz, Maura Brunetti, Salvatore Gallone, Maurizio Grassano, Enrico Matteoni, Giulia Polverari, Giuseppe Fuda, Federico Casale, Paolina Salamone, Giovanni De Marco, Giulia Marchese, Cristina Moglia, Andrea Calvo, Marco Pagani, Adriano Chiò. Annals of Neurology, 97(6), 1134-1143.

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Mapping the natural history of amyotrophic lateral sclerosis: time-to-event analysis of clinical milestones in the pan-European, population-based PRECISION-ALS cohort

Alejandro Caravaca Puchades, Harry E. McDonough, Ammar Al-Chalabi, Adriano Chiò, Philippe Corcia, Miriam Galvin, Orla Hardiman, Mark Heverin, Frederik Hobin, Oskar Holmdahl, Caroline Ingre, Nikita Lamaire, Éanna Mac Domhnaill, Umberto Manera, Robert McFarlane, Mohammed Mouzouri, Fouke Ombelet, Sarah Opie-Martin, Stefan Sennfält, Cristina Terrafeta Pastor, Jan H. Veldink, Philip Van Damme, Leonard van den Berg, Ruben P.A. van Eijk, Rosario Vasta, Daphne N. Weemering, Pamela Shaw, Christopher J. McDermott & Mónica Povedano Panadés. Amyotrophic Lateral Sclerosis and Frontotemporal Degeneration, 26, 8-19.

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Clinical trajectories of genetic variants in ALS: a European observational study within PRECISION-ALS

Robert McFarlane, Sarah Opie-Martin, Alejandro Caravaca, Adriano Chiò, Philippe Corcia, Miriam Galvin, Mark Heverin, Frederik Hobin, Oskar Holmdahl, Caroline Ingre, Nikita Lamaire, Éanna Mac Domhnaill, Umberto Manera, Christopher McDermott, Harry McDonough, Mohammed Mouzouri, Fouke Ombelet, Mónica Povedano, Stefan Sennfält, Pamela Shaw, Cristina Terrafeta, Jan Veldink, Philip Van Damme, Leonard Van der Berg,  Ruben Van Eijk, Rosario Vasta, Daphne Weemering, Ammar Al-Chalabi, Orla Hardiman. Amyotrophic Lateral Sclerosis and Frontotemporal Degeneration, 26, 41-49

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Exploring the phenotypic fingerprints of ANXA11 variants in ALS: a population‑based study in an European cohort

Francesca Palumbo, Barbara Iazzolino, Cristina Moglia, Umberto Manera, Enrico Matteoni, Sara Cabras, Maura Brunetti, Salvatore Gallone, Stefano Callegaro, Rosario Vasta, Gabriele Mora, Fabiola De Marchi, Lucia Corrado, Sandra D’Alfonso, Letizia Mazzini, Antonio Canosa, Maurizio Grassano, Andrea Calvo, Adriano Chiò. Journal of NEUROLOGY, 272, 524.

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Respiratory function, survival, and NIV prevalence over time in ALS - a PRECISION ALS study

Robert McFarlane, Sarah Opie-Martin, Alejandro Caravaca, Adriano Chiò, Philippe Corcia, Miriam Galvin, Mark Heverin, Frederik Hobin, Oskar Holmdahl, Caroline Ingre, Nikita Lamaire, Éanna Mac Domhnaill, Umberto Manera, Christopher McDermott, Harry McDonough, Mohammed Mouzouri, Fouke Ombelet, Mónica Povedano, Stefan Sennfält, Pamela Shaw, Cristina Terrafeta, Jan Veldink, Philip Van Damme, Leonard Van der Berg,  Ruben Van Eijk, Rosario Vasta, Daphne Weemering, Ammar Al-Chalabi, Orla Hardiman. Amyotrophic Lateral Sclerosis and Frontotemporal Degeneration, 26, 61-72.

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Benchmarking Large Language Models for Knowledge Graph Validation

Farzad Shami, Stefano Marchesin, Gianmaria Silvello. EDBT ’26, Tampere (Finland).

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A Cost-Effective Framework to Evaluate LLM-Generated Relevance Judgements

Simone Merlo, Stefano Marchesin, Guglielmo Faggioli, Nicola Ferro. CIKM ’25: Proceedings of the 34th ACM International Conference on Information and Knowledge Management (November 2025)

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Overview of GutBrainIE@CLEF 2025: Gut-Brain Interplay Information Extraction

Marco Martinelli, Gianmaria Silvello, Vanessa Bonato, Nicola Ferro, Giorgio Maria Di Nunzio, Ornella Irrera, Stefano Marchesin, Laura Menotti, Federica Vezzani. CLEF 2025 Working Notes, 9 – 12 September 2025, Madrid, Spain

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PrivEval: a tool for interactive evaluation of privacy metrics in synthetic data generation

Fredrik Marinus Trudslev, Matteo Lissandrini, Juan Manuel Rodriguez, Martin Bøgsted, Daniele Dell’Aglio. Proceedings of the VLDB Endowment, Vol. 18, No. 12 

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Provenance-driven nanopublications: representing source lineage and trust networks for multi-source assertions

Gianmaria Silvello, Stefano Marchesin, Laura Menotti, Fabio Giachelle. International Journal on Digital Libraries (2025)