Publications

Papers by group members since the group started in 2019.

2026

CANE is a Format: Rethinking Output Formats for Few-Shot LLM-Based Named Entity Recognition
Joseph Cornelius, Kei K Ito, Fabio Rinaldi
EMNLP 2026, 2026
Measuring the gap: correlating synthetic-to-real drift with PHI de-identification performance
Joseph Cornelius, Fabio Rinaldi
Genomics & Informatics, 2026 · DOI
Automatic Medical Discharge Summary Evaluation
Andrea Franchini, Lorenzo Ruinelli, Amos Colombo, Samuel Corecco, Behnaz Rezaeifar, Sotirios Georgios Popeskou, Mathilde Marie Rochat, Dimitrios Christoforidis, Nicolò Saverio Centemero, Matteo Cerina, Fabio Rinaldi
Building Commons for Clinical LLMs, Paris 2026 International Conference, 2026
Credal Ensembles for Uncertainty Quantification in LLMs
Vani Kanjirangat, Oscar William Lithgow-Serrano, Alessandro Antonucci
The Proceedings of the Third Workshop on Uncertainty-Aware NLP, 2026 · DOI
Evaluating Multilingual Tokenization under Worst-N Parity-Aware BPE
Vani Kanjirangat, David Kletz, Tanja Samardžić, Ljiljana Dolamic, Fabio Rinaldi
Proceedings of the 1st Workshop on Multilinguality in the Era of Large Language Models (MeLLM 2026), 2026 · DOI
Are Language Models Script-Aware?
David Kletz, Sandra Mitrović, Ljiljana Dolamic, Fabio Rinaldi
AACL-IJCNLP 2026, 2026
Script Choice in LLMs: Evidence for Late-Layer Commitment
David Kletz, Sandra Mitrović, I. Sabato, Ljiljana Dolamic, Fabio Rinaldi
Findings of EMNLP 2026, Budapest, Hungary, 2026
Are the LLMs Capable of Maintaining at Least the Language Genus?
Sandra Mitrović, David Kletz, Ljiljana Dolamic, Fabio Rinaldi
Proceedings of the Thirty-Second Language Resources and Evaluation Conference (LREC 2026), 2026

2025

From literature to biodiversity data: mining arthropod organismal traits with machine learning
Joseph Cornelius, Harald Detering, Oscar William Lithgow-Serrano, Donat Agosti, Fabio Rinaldi, Robert Waterhouse
Biodiversity Data Journal, 2025 · DOI
Zero-Shot Cross-Sentential Scientific Relation Extraction via Entity-Guided Summarization
Vani Kanjirangat, Fabio Rinaldi
Proceedings of the Third Workshop for Artificial Intelligence for Scientific Publications, 2025 · DOI
Tokenization and Representation Biases in Multilingual Models on Dialectal NLP Tasks SAC Award
Vani Kanjirangat, Tanja Samardžić, Ljiljana Dolamic, Fabio Rinaldi
Proceedings of the 2025 Conference on Empirical Methods in Natural Language Processing, 2025 · DOI
Better Together: Towards Localizing Fact-Related Hallucinations using Open Small Language Models
David Kletz, Sandra Mitrović, Ljiljana Dolamic, Fabio Rinaldi
Proceedings of the 1st Workshop on Confabulation, Hallucinations and Overgeneration in Multilingual and Practical Settings (CHOMPS 2025), 2025 · DOI
Polarity inversion operators in PLM
David Kletz, Pascal Amsili, Marie Candito
Proceedings of the 29th Conference on Computational Natural Language Learning, 2025 · DOI
Causal Understanding by LLMs: The Role of Uncertainty
Oscar William Lithgow-Serrano, Vani Kanjirangat, Alessandro Antonucci
Proceedings of the 2nd Workshop on Uncertainty-Aware NLP (UncertaiNLP 2025), 2025 · DOI
Assessing RAG System Capabilities on Financial Documents
Oscar William Lithgow-Serrano, David Kletz, Vani Kanjirangat, David Adametz, Marzio Lunghi, Claudio Bonesana, Matilde Tristany-Farinha, Yuntao Li, Detlef Repplinger, Marco Pierbattista, Stefania Stan, Oleg Szehr
Proceedings of The 10th Workshop on Financial Technology and Natural Language Processing, 2025 · DOI
Swushroomsia at SemEval-2025 Task 3: Probing LLMs' Collective Intelligence for Multilingual Hallucination Detection
Sandra Mitrović, Joseph Cornelius, David Kletz, Ljiljana Dolamic, Fabio Rinaldi
Proceedings of the 19th International Workshop on Semantic Evaluation (SemEval-2025), 2025
Presenting LLMs' Collective Intelligence Approach for Multilingual Hallucination Detection
Sandra Mitrović, Joseph Cornelius, David Kletz, Ljiljana Dolamic, Fabio Rinaldi
Proceedings of the 9th edition of the Swiss Text Analytics Conference, 2025
Enhancing the study of historical figures through AI-powered interactive data visualizations
Giovanni Profeta, Joseph Cornelius, Fabio Rinaldi
DH2025 - Digital Heritage International Congress, Siena, 2025 · DOI
Health-related NLP activities at IDSIA
Fabio Rinaldi, Andrea Franchini, R. Noseda, Oscar William Lithgow-Serrano, Joseph Cornelius, Lorenzo Ruinelli, Amos Colombo, Sandra Mitrović, A. Ceschi
Joint Proceedings of the Thematic Workshops at Ital-IA 2025, Trieste, Italy, June 23-24, 2025, 2025

2024

Pre-Gamus: Reducing Complexity of Scientific Literature as a Support against Misinformation
Nico Colic, Jin-Dong Kim, Fabio Rinaldi
Proceedings of the Workshop on DeTermIt! Evaluating Text Difficulty in a Multilingual Context @ LREC-COLING 2024, 2024
BUST: Benchmark for the evaluation of detectors of LLM-Generated Text
Joseph Cornelius, Oscar William Lithgow-Serrano, Sandra Mitrović, Ljiljana Dolamic, Fabio Rinaldi
Proceedings of the 2024 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies (Volume 1: Long Papers), 2024 · Code · DOI
NLP\_DI at NADI 2024 shared task: Multi-label Arabic Dialect Classifications with an Unsupervised Cross-Encoder
Vani Kanjirangat, Tanja Samardžić, Ljiljana Dolamic, Fabio Rinaldi
Proceedings of the Second Arabic Natural Language Processing Conference, 2024 · DOI
On the Limitations of Zero-Shot Classification of Causal Relations by LLMs (Work in Progress)
Vani Kanjirangat, Alessandro Antonucci, Marco Zaffalon
CEUR Workshop Proceedings, 2024
Experiments in Automated Generation of Discharge Summaries in Italian
Lorenzo Ruinelli, Amos Colombo, Mathilde Rochat, Sotirios Georgios Popeskou, Andrea Franchini, Sandra Mitrović, Oscar William Lithgow-Serrano, Joseph Cornelius, Fabio Rinaldi
Proceedings of the First Workshop on Patient-Oriented Language Processing (CL4Health) @ LREC-COLING 2024, 2024

2023

Classification of cancer TNM stage from Japanese radiology report using on-premise LLM at NTCIR-17 MedNLP-SC RR-TNM subtask
Koji Fujimoto, Mizuho Nishio, Chikako Tanaka, Morteza Rohanian, Farhad Nooralahzadeh, Michael Krauthammer, Fabio Rinaldi
Proceedings of the 17th NTCIR Conference on Evaluation of Information Access Technologies, December 12-15, 2023, Tokyo, Japan, 2023 · DOI
Proceedings of the Swiss Text Analytics Conference 2022, Lugano, Switzerland, June 8-10, 2022
Manuela Hürlimann, Roberto Mastropietro, Daniele Puccinelli, Fabio Rinaldi, Mark Cieliebak (eds.)
Edited proceedings (CEUR-WS.org), 2023
Optimizing the Size of Subword Vocabularies in Dialect Classification
Vani Kanjirangat, Tanja Samardžić, Ljiljana Dolamic, Fabio Rinaldi
Tenth Workshop on NLP for Similar Languages, Varieties and Dialects (VarDial 2023), 2023 · DOI
Edge Labelling in Narrative Knowledge Graphs
Vani Kanjirangat, Alessandro Antonucci
The 6th International Workshop on Narrative Extraction from Texts: Text2Story 2023, co-located with the 45th European Conference on Information Retrieval (ECIR 2023), Dublin, Ireland, April 2-6, 2023, 2023
Boosting Radiology Report Generation by Infusing Comparison Prior
Sanghwan Kim, Farhad Nooralahzadeh, Morteza Rohanian, Koji Fujimoto, Mizuho Nishio, Ryo Sakamoto, Fabio Rinaldi, Michael Krauthammer
Proceedings of the 22nd Workshop on Biomedical Natural Language Processing and BioNLP Shared Tasks, 2023 · DOI
Zero-shot classification of TNM staging for Japanese radiology report using ChatGPT at RR-TNM subtask of NTCIR-17 MedNLP-SC
Mizuho Nishio, Hidetoshi Matsuo, Takaaki Matsunaga, Koji Fujimoto, Morteza Rohanian, Farhad Nooralahzadeh, Fabio Rinaldi, Michael Krauthammer
Proceedings of the 17th NTCIR Conference on Evaluation of Information Access Technologies, December 12-15, 2023, Tokyo, Japan, 2023 · DOI
Challenges and best practices for digital unstructured data enrichment in health research: A systematic narrative review
Jana Sedlakova, Paola Daniore, Andrea Horn Wintsch, Markus Wolf, Mina Stanikic, Christina Haag, Chloé Sieber, Gerold Schneider, Kaspar Staub, Dominik Alois Ettlin, Oliver Grübner, Fabio Rinaldi, Viktor von Wyl
PLOS Digital Health, 2023 · DOI
Exploring the Latest Highlights in Medical Natural Language Processing across Multiple Languages: A Survey
Anastassia Shaitarova, Jamil Zaghir, Alberto Lavelli, Michael Krauthammer, Fabio Rinaldi
Yearbook of Medical Informatics, 2023 · DOI
AGRONER: An unsupervised agriculture named entity recognition using weighted distributional semantic model
G. Veena, Vani Kanjirangat, Deepa Gupta
Expert Systems with Applications, 2023 · DOI
Semi-supervised Bootstrapped Syntax-Semantics based Approach for Agriculture Relation Extraction for Knowledge Graph Creation and Reasoning
G. Veena, Deepa Gupta, Vani Kanjirangat
IEEE Access, 2023 · DOI

2022

Leveraging Token-Based Concept Information and Data Augmentation in Few-Resource NER: ZuKyo-EN at the NTCIR-16 Real-MedNLP task
Joseph Cornelius, Oscar William Lithgow-Serrano, Vani Kanjirangat, Fabio Rinaldi, K. Fujimoto, M. Nishio, O. Sugiyama, Farhad Nooralahzadeh, A. Horvath, Michael Krauthammer
The 16th NTCIR Conference on Evaluation of Information Access Technologies, 2022
Approach for Named Entity Recognition and Case Identification Implemented by ZuKyo-JA Sub-team at the NTCIR-16 Real-MedNLP Task
K. Fujimoto, M. Nishio, O. Sugiyama, K. Ichikawa, Joseph Cornelius, Oscar William Lithgow-Serrano, Vani Kanjirangat, Fabio Rinaldi, A. Horvath, Farhad Nooralahzadeh, Michael Krauthammer
The 16th NTCIR Conference on Evaluation of Information Access Technologies, 2022
SwissMADE study Automatic Detection of Adverse Drug Events in Geriatric Care: Study Proposal
Frederic Gaspar, Monika Lutters, Patrick Emanuel Beeler, Pierre Olivier Lang, Bernard Burnand, Fabio Rinaldi, Christian Lovis, Chantal Csajka, Marie-Annick Le Pogam
JMIR Research Protocols, 2022 · DOI
Early Guessing for Dialect Identification
Vani Kanjirangat, Tanja Samardžić, Fabio Rinaldi, Ljiljana Dolamic
Findings of the Association for Computational Linguistics: EMNLP 2022, 2022 · DOI
NLP DI at NADI Shared Task Subtask-1: Sub-word Level Convolutional Neural Models and Pre-trained Binary Classifiers for Dialect Identification
Vani Kanjirangat, Tanja Samardžić, Ljiljana Dolamic, Fabio Rinaldi
Proceedings of the Seventh Arabic Natural Language Processing Workshop (WANLP), 2022 · DOI
Proceedings of the 13th International Workshop on Health Text Mining and Information Analysis (LOUHI 2022)
Alberto Lavelli, Eben Holderness, Antonio Jimeno Yepes, Anne-Lyse Minard, James Pustejovsky, Fabio Rinaldi (eds.)
Edited proceedings (Association for Computational Linguistics), 2022 · DOI
mattica@SMM4H'22: Leveraging sentiment for stance & premise joint learning
Oscar William Lithgow-Serrano, Joseph Cornelius, Fabio Rinaldi, Ljiljana Dolamic
Proceedings of the Seventh Workshop on Social Media Mining for Health Applications, Workshop & Shared Task, 2022
An annotated dataset for extracting gene-melanoma relations from scientific literature
Roberto Zanoli, Alberto Lavelli, Theresa Löffler, Nicolas Andres Perez Gonzalez, Fabio Rinaldi
Journal of Biomedical Semantics, 2022 · DOI

2021

Automated Detection of Adverse Drug Events from Older Patients' Electronic Medical Records Using Text Mining
Nico Colic, Patrick Beeler, Chantal Csajka, Vasiliki Foufi, Frederic Gaspar, Marie-Annick Le Pogam, Angela Lisibach, Christian Lovis, Monika Lutters, Fabio Rinaldi
Pattern Recognition. ICPR International Workshops and Challenges (International Workshop on Artificial Intelligence for Healthcare Applications), 2021 · DOI
Approaching SMM4H with auto-regressive language models and back-translation
Joseph Cornelius, Tilia Ellendorff, Fabio Rinaldi
Proceedings of the Sixth Social Media Mining for Health (\#SMM4H) Workshop and Shared Task, 2021 · DOI
MultiGBS: A multi-layer graph approach to biomedical summarization
Ensieh Davoodijam, Nasser Ghadiri, Maryam Lotfi Shahreza, Fabio Rinaldi
Journal of Biomedical Informatics, 2021 · DOI
Lisen&Curate: A platform to facilitate gathering textual evidence for curation of regulation of transcription initiation in bacteria
Martín Díaz-Rodríguez, Oscar William Lithgow-Serrano, Francisco Guadarrama-García, Víctor H. Tierrafría, Socorro Gama-Castro, Hilda Solano-Lira, Heladia Salgado, Fabio Rinaldi, Carlos-Francisco Méndez-Cruz, Julio Collado-Vides
Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, 2021 · DOI
Real-time geospatial surveillance of localized emotional stress responses to COVID-19: A proof of concept analysis
Tamar Edry, Nason Maani, Martin Sykora, Suzanne Elayan, Yulin Hswen, Markus Wolf, Fabio Rinaldi, Sandro Galea, Oliver Gruebner
Health & Place, 2021 · DOI
Parallel sequence tagging for concept recognition
Lenz Furrer, Joseph Cornelius, Fabio Rinaldi
BMC Bioinformatics, 2021 · DOI
Proceedings of the 12th International Workshop on Health Text Mining and Information Analysis (LOUHI 2021)
Eben Holderness, Antonio Jimeno Yepes, Alberto Lavelli, Anne-Lyse Minard, James Pustejovsky, Fabio Rinaldi (eds.)
Edited proceedings (Association for Computational Linguistics), 2021
Enhancing Biomedical Relation Extraction with Transformer Models using Shortest Dependency Path Features and Triplet Information
Vani Kanjirangat, Fabio Rinaldi
Journal of Biomedical Informatics, 2021 · DOI
Editor's introduction to the special section on the 7th Biomedical Linked Annotation Hackathon (BLAH7)
Jin-Dong Kim, Kevin Bretonnel Cohen, Fabio Rinaldi, Zhiyong Lu, Hyun-Seok Park
Genomics & Informatics, 2021 · DOI
The Gene Regulation Knowledge Commons: the action area of GREEKC
Martin Kuiper, Joseph Bonello, Jesualdo T. Fernández-Breis, Philipp Bucher, Matthias E. Futschik, Pascale Gaudet, Ivan V. Kulakovskiy, Luana Licata, Colin Logie, Ruth C. Lovering, Vsevolod J. Makeev, Sandra Orchard, Simona Panni, Livia Perfetto, David Sant, Stefan Schulz, Steven Vercruysse, Daniel R. Zerbino, Astrid Lægreid
Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, 2021 · DOI
Learning adaptive representations for entity recognition in the biomedical domain
Ivano Lauriola, Fabio Aiolli, Alberto Lavelli, Fabio Rinaldi
Journal of Biomedical Semantics, 2021 · DOI
Improving classification of low-resource COVID-19 literature by using Named Entity Recognition
Oscar William Lithgow-Serrano, Joseph Cornelius, Vani Kanjirangat, Carlos-Francisco Méndez-Cruz, Fabio Rinaldi
Genomics & Informatics, 2021 · DOI
Revisiting the decay of scientific email addresses
Raul Rodriguez-Esteban, Dina Vishnyakova, Fabio Rinaldi
Journal of the Association for Information Science and Technology, 2021 · DOI
Negation typology and general representation models for cross-lingual zero-shot negation scope resolution in Russian, French, and Spanish
Anastassia Shaitarova, Fabio Rinaldi
Proceedings of the 2021 Conference of the North American Chapter of the Association for Computational Linguistics: Student Research Workshop, 2021 · DOI
Factors associated with cattle necropsy submissions in Switzerland, and their importance for surveillance
Irene Zühlke, John Berezowski, Michèle Bodmer, Susanne Küker, Anne Göhring, Fabio Rinaldi, Céline Faverjon, Corinne Gurtner
Preventive Veterinary Medicine, 2021 · DOI

2020

Annotating the Pandemic: Named Entity Recognition and Normalisation in COVID-19 Literature
Nico Colic, Lenz Furrer, Fabio Rinaldi
Proceedings of the 1st Workshop on NLP for COVID-19 (Part 2) at EMNLP 2020, 2020 · DOI
COVID-19 Twitter Monitor: Aggregating and Visualizing COVID-19 Related Trends in Social Media
Joseph Cornelius, Tilia Ellendorff, Lenz Furrer, Fabio Rinaldi
Proceedings of the Fifth Social Media Mining for Health Applications Workshop & Shared Task, 2020
Proceedings of the 11th International Workshop on Health Text Mining and Information Analysis (LOUHI 2020)
Eben Holderness, Antonio Jimeno Yepes, Alberto Lavelli, Anne-Lyse Minard, James Pustejovsky, Fabio Rinaldi (eds.)
Edited proceedings (Association for Computational Linguistics), 2020 · DOI
Temporal Embeddings and Transformer Models for Narrative Text Understanding Best Paper Award
Vani Kanjirangat, Simone Mellace, Alessandro Antonucci
Proceedings of the Text2StoryIR'20 Workshop at ECIR, 2020
Semantically Corroborating Neural Attention for Biomedical Question Answering
Marilena Oita, Vani Kanjirangat, Fatma Oezdemir-Zaech
Machine Learning and Knowledge Discovery in Databases: International Workshops of ECML PKDD 2019, W\"urzburg, Germany, September 16-20, 2019, Proceedings, Part II, 2020 · DOI
Cross-lingual Transfer-learning Approach to Negation Scope Resolution
Anastassia Shaitarova, Lenz Furrer, Fabio Rinaldi
Proceedings of the 5th Swiss Text Analytics Conference (SwissText) & 16th Conference on Natural Language Processing (KONVENS), Zurich, Switzerland, June 23-25, 2020, 2020
Temporal Word Embeddings for Narrative Understanding
Claudia Volpetti, Vani Kanjirangat, Alessandro Antonucci
Proceedings of the 2020 12th International Conference on Machine Learning and Computing (ICMLC), 2020 · DOI

2019

Improving spaCy dependency annotation and PoS tagging web service using independent NER services
Nico Colic, Fabio Rinaldi
Genomics & Informatics, 2019 · DOI
Approaching SMM4H with Merged Models and Multi-task Learning
Tilia Ellendorff, Lenz Furrer, Nico Colic, Noëmi Aepli, Fabio Rinaldi
Proceedings of the Fourth Social Media Mining for Health Applications (\#SMM4H) Workshop & Shared Task, 2019 · DOI
OGER++: hybrid multi-type entity recognition
Lenz Furrer, Anna Jancso, Nico Colic, Fabio Rinaldi
Journal of Cheminformatics, 2019 · DOI
Proceedings of the Tenth International Workshop on Health Text Mining and Information Analysis (LOUHI 2019)
Eben Holderness, Antonio Jimeno Yepes, Alberto Lavelli, Anne-Lyse Minard, James Pustejovsky, Fabio Rinaldi (eds.)
Edited proceedings (Association for Computational Linguistics), 2019
NOVEL2GRAPH: Visual Summaries of Narrative Text Enhanced by Machine Learning
Vani Kanjirangat, Alessandro Antonucci
Text2Story@ECIR, 2019
Introduction to BLAH5 special issue: recent progress on interoperability of biomedical text mining
Jin-Dong Kim, Kevin Bretonnel Cohen, Nigel Collier, Zhiyong Lu, Fabio Rinaldi
Genomics & Informatics, 2019 · DOI
Natural Language Processing of Clinical Notes on Chronic Diseases: Systematic Review
Seyedmostafa Sheikhalishahi, Riccardo Miotto, Joel T Dudley, Alberto Lavelli, Fabio Rinaldi, Venet Osmani
JMIR Medical Informatics, 2019 · DOI
A new approach and gold standard toward author disambiguation in MEDLINE
Dina Vishnyakova, Raul Rodriguez-Esteban, Fabio Rinaldi
Journal of the American Medical Informatics Association, 2019 · DOI