Publication list

Table of Contents

This page lists recent publications of the members of the NLP Team at IDSIA. NLP Team at IDSIA (Swiss AI Lab / Istituto Dalle Molle per l'Intelligenza Artificiale).


  • Anastassia Shaitarova, Jamil Zaghir, Alberto Lavelli, Michael Krauthammer, Fabio Rinaldi. Exploring the Latest Highlights in Medical Natural Language Processing across Multiple Languages: A Survey. IMIA Yearbook of Medical Informatics, 2023 December 2023 Yearbook of Medical Informatics 32(01):230-243 doi: 10.1055/s-0043-1768726
  • 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 and Michael Krauthammer. Proceedings of the 17th NTCIR Conference on Evaluation of Information Access Technologies, December 12-15, 2023, Tokyo, Japan. doi: 10.20736/0002001283
  • 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 and Fabio Rinaldi. Proceedings of the 17th NTCIR Conference on Evaluation of Information Access Technologies, December 12-15, 2023, Tokyo, Japan. doi: 10.20736/0002001299
  • Sanghwan Kim, Farhad Nooralahzadeh, Morteza Rohanian, Koji Fujimoto, Mizuho Mizuho, Ryo Sakamoto, Fabio Rinaldi, Michael Krauthammer. (2023). Boosting Radiology Report Generation by Infusing Comparison Prior. The 22nd Workshop on Biomedical Natural Language Processing and BioNLP Shared Tasks. 50-61. doi: 10.18653/v1/2023.bionlp-1.4
  • Vani Kanjirangat, Tanja Samardžić, Ljiljana Dolamic, Fabio Rinaldi (2023). Optimizing the Size of Subword Vocabularies in Dialect Classification. In Tenth Workshop on NLP for Similar Languages, Varieties and Dialects (VarDial 2023) (pp. 14-30). doi: 10.18653/v1/2023.vardial-1.2
  • Manuela Hürlimann, Roberto Mastropietro, Daniele Puccinelli, Fabio Rinaldi, Mark Cieliebak. Proceedings of the Swiss Text Analytics Conference 2022, Lugano, Switzerland, June 8-10, 2022. CEUR Workshop Proceedings 3361, 2023.
  • Kanjirangat, V. and Antonucci, A., 2023. Edge Labelling in Narrative Knowledge Graphs. The 6th International Workshop on Narrative Extraction from Texts: Text2Story 2023, co-located with 45th European Conference on Information Retrieval, ECIR 2023, Dublin, Ireland, April 2–6, 2023.
  • Veena, G., Kanjirangat, V. and Gupta, D., 2023. AGRONER: An unsupervised agriculture named entity recognition using weighted distributional semantic model. Expert Systems with Applications, p.120440.
  • Veena, G., Gupta, D. and Kanjirangat, V., 2023. Semi-supervised Bootstrapped Syntax-Semantics based Approach for Agriculture Relation Extraction for Knowledge Graph Creation and Reasoning. IEEE Access.


  • Cornelius, J., Oscar Lithgow-Serrano, Kangirangat, V., Rinaldi, F., Fujimoto, K., Nishio, M., Sugiyama, O., Nooralahzadeh, F., Horvath, A., Krauthammer, M. (2022). Leveraging Token-Based Concept Information and Data Augmentation in Few-Resource NER : ZuKyo-EN at the NTCIR-16 Real-MedNLP task. The 16th NTCIR Conference Evaluation of Information Access Technologies, 316–321. ISBN 978-4-86049-082-9
  • Fujimoto, K., Nishio, M., Sugiyama, O., Ichikawa, K., Cornelius, J., Lithgow-Serrano, O., Kanjirangat, V., Rinaldi, F., Horvath, A., Nooralahzadeh, F., Krauthammer, M. (2022). Approach for Named Entity Recognition and Case Identification Implemented by ZuKyo-JA Sub-team at the NTCIR-16 Real-MedNLP Task. The 16th NTCIR Conference Evaluation of Information Access Technologies, 322–329. ISBN 978-4-86049-082-9
  • Lithgow-Serrano, O., Cornelius, J., Rinaldi, F., Dolamic, L. (2022). mattica@SMM4H’22: Leveraging sentiment for stance & premise joint learning. Proceedings of The Seventh Workshop on Social Media Mining for Health Applications, Workshop and Shared Task, 75–77.
  • Kanjirangat,V., Samardzic,T., Rinaldi,Fabio., Dolamic,Ljiljana. (2022). Early Guessing for Dialect Identification. In Findings of the 2022 Conference on Empirical Methods in Natural Language Processing (EMNLP 2022), pp. 6417-6426.
  • Kanjirangat,V., Samardzic,T., Dolamic,Ljiljana., Rinaldi,Fabio. (2022). NLP_DI at NADI Shared Task Subtask-1: Sub-word Level Convolutional Neural Models and Pre-trained Binary Classifiers for Dialect Identification. Proceedings of the NADI Shared Task, The Seventh Arabic Natural Language Processing Workshop (WANLP) at The 2022 Conference on Empirical Methods in Natural Language Processing.
  • Lenz Furrer, Joseph Cornelius, Fabio Rinaldi. Parallel sequence tagging for concept recognition. BMC Bioinformatics volume 22, Article number: 623 (2021). doi: 10.1186/s12859-021-04511-y
  • Roberto Zanoli, Alberto Lavelli, Theresa Löffler, Nicolas Andres Perez Gonzalez, Fabio Rinaldi. An annotated dataset for extracting gene-melanoma relations from scientific literature. Journal of Biomedical Semantics, volume 13, Article number: 2 (2022). doi: 10.1186/s13326-021-00251-3
  • Sedlakova, Jana & Daniore, Paola & Horn, Andrea & Wolf, Markus & Stanikić, Mina & Haag, Christina & Sieber, Chloé & Schneider, Gerold & Staub, Kaspar & Ettlin, Dominik & Gruebner, Oliver & Rinaldi, Fabio & von Wyl, Viktor. (2022). Challenges and best practices for digital unstructured data enrichment in health research: a systematic narrative review. doi: 10.1101/2022.07.28.22278137
  • Gaspar F, Lutters M, Beeler PE, Lang PO, Burnand B, Rinaldi F, Lovis C, Csajka C, Le Pogam M. SwissMADE study Automatic Detection of Adverse Drug Events in Geriatric Care: Study Proposal. JMIR Res Protoc 2022;11(11):e40456 doi: 10.2196/40456
  • Proceedings of the 13th International Workshop on Health Text Mining and Information Analysis, LOUHI@EMNLP 2022, Abu Dhabi, United Arab Emirates (Hybrid), December 7, 2022. Association for Computational Linguistics 2022, ISBN 978-1-959429-13-5. Editors: Alberto Lavelli, Eben Holderness, Antonio Jimeno-Yepes, Anne-Lyse Minard, James Pustejovsky, Fabio Rinaldi.


  • Vani Kanjirangat, Fabio Rinaldi. Enhancing Biomedical Relation Extraction with Transformer Models using Shortest Dependency Path Features and Triplet Information. Journal of Biomedical Informatics, Oct 2021. doi: 10.1016/j.jbi.2021.103893
  • Carlos-Francisco Méndez-Cruz, Martín Díaz-Rodríguez, Oscar Lithgow-Serrano, Francisco Guadarrama-García, Víctor H. Tierrafría, Socorro Gama-Castro, Hilda Solano-Lira, Fabio Rinaldi, Julio Collado-Vides. Lisen&Curate: A platform to facilitate gathering textual evidence for curation of regulation of transcription initiation in bacteria. BBA - Gene Regulatory Mechanisms, August 2021. doi: 10.1016/j.bbagrm.2021.194753 Early access link:
  • Oscar William Lithgow-Serrano, Joseph Cornelius, Vani Kanjirangat, Carlos Francisco Méndez-Cruz, Fabio Rinaldi. “Improving Classification of Low-Resource COVID-19 Literature by Using Named Entity Recognition.” Genomics & Informatics 2021; 19(3): e22. doi: 10.5808/gi.21018
  • Raul Rodriguez-Esteban, Dina Vishnyakova, Fabio Rinaldi. Revisiting the decay of scientific email addresses. Journal of the Association for Information Science and Technology. June 2021. doi: 10.1002/asi.24545
  • Tamar Edry, Nason Maani, Martin Sykora, Suzanne Elayan, Yulin Hswen, Markus Wolf, Fabio Rinaldi, Sandro Galea, Oliver Gruebner. Real-time geospatial surveillance of localized emotional stress responses to COVID-19: A proof of concept analysis. Health Place. 2021 Jul; 70: 102598. doi: 10.1016/j.healthplace.2021.102598
  • Joseph Cornelius, Tilia Ellendorff, Fabio Rinaldi. Approaching SMM4H with auto-regressive language models and back-translation. Proceedings of the Sixth Social Media Mining for Health (#SMM4H) Workshop and Shared Task. NAACL 2021. doi: 10.18653/v1/2021.smm4h-1.32
  • Ivano Lauriola, Fabio Aiolli, Alberto Lavelli, Fabio Rinaldi. Learning adaptive representations for entity recognition in the biomedical domain Journal of Biomedical Semantics, volume 12, Article number: 10 (2021). doi: 10.1186/s13326-021-00238-0
  • Anastassia Shaitarova, Fabio Rinaldi. Negation typology and general representation models for cross-lingual zero-shot negation scope resolution in Russian, French, and Spanish. Proceedings of the 2021 Conference of the North American Chapter of the Association for Computational Linguistics: Student Research Workshop. doi: 10.18653/v1/2021.naacl-srw.3
  • Ensieh Davoodijam, Nasser Ghadiri, Maryam Lotfi Shahreza, Fabio Rinaldi. MultiGBS: A multi-layer graph approach to biomedical summarization. Journal of Biomedical Informatics. Volume 116, April 2021, 103706. doi: 10.1016/j.jbi.2021.103706 preprint:
  • Irene Zühlke, John Berezowski, Michèle Bodmer, Susanne Küker, Anne Göhring, Fabio Rinaldi, Céline Faverjon, Corinne Gurtner. Factors associated with cattle necropsy submissions in Switzerland, and their importance for surveillance. Preventive Veterinary Medicine, Volume 187, 2021, 105235, ISSN 0167-5877. doi: 10.1016/j.prevetmed.2020.105235
  • Nico Colic, Patrick Beeler, Chantal Csajka, Vasiliki Foufi, Frederic Gaspar, Marie-Annick Le Pogam, Angela Lisibach, Christian Lovis, Monika Lutters and Fabio Rinaldi. Automated detection of adverse drug events from older patients’ electronic medical records using text mining. The international Workshop on Artificial Intelligence for Healthcare applications, January 2021. doi: 10.1007/978-3-030-68763-2_15
  • Kim, Jin-Dong, Cohen, Kevin, Rinaldi, Fabio, lu, Zhiyong, Park, Hyun-Seok. (2021). Editor’s introduction to the special section on the 7th Biomedical Linked Annotation Hackathon (BLAH7). Genomics & Informatics. 19. e20. doi: 10.5808/gi.19.3.e1
  • Kuiper, Martin, Bonello, Joseph, Fernandez-Breis, Jesualdo, Bucher, Philipp, Futschik, Matthias, Gaudet, Pascale, Kulakovskiy, Ivan, Licata, Luana, Logie, Colin, Lovering, Ruth, Makeev, Vsevolod, Orchard, Sandra, Panni, Simona, Perfetto, Livia, Sant, David, Schulz, Stefan, Zerbino, Daniel, Lægreid, Astrid, Bock, Christoph, Eibeck, Karen. (2021). The Gene Regulation Knowledge Commons. Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms. 1865. 194768. doi: 10.1016/j.bbagrm.2021.194768
  • 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. Association for Computational Linguistics, Online, April 2021


  • Joseph Cornelius, Tilia Ellendorff, Lenz Furrer, Fabio Rinaldi. COVID-19 Twitter Monitor: Aggregating and visualizing COVID-19 related social media mining. In: Proceedings of the 5th Social Media Mining for Health Applications (#SMM4H) Workshop & Shared Task, Barcelona, Spain, 8-13. December 2020. paper
  • Nico Colic, Lenz Furrer, Fabio Rinaldi. Annotating the Pandemic: Named Entity Recognition and Normalisation in COVID-19 Literature. Proceedings of the 1st Workshop on NLP for COVID-19 (Part 2) at EMNLP 2020. doi: 10.18653/v1/2020.nlpcovid19-2.27
  • Anastassia Shaitarova, Lenz Furrer, Fabio Rinaldi. Cross-lingual Transfer-learning Approach to Negation Scope Resolution Proceedings of the 5th Swiss Text Analytics Conference (SwissText) & 16th Conference on Natural Language Processing (KONVENS). Zurich, Switzerland, June 23-25, 2020. paper
  • Lenz Furrer, Joseph Cornelius, Fabio Rinaldi (2020). Parallel sequence tagging for concept recognition. arXiv:2003.07424
  • Vani, K., Mellace, S., & Antonucci, A. (2020). Temporal Embeddings and Transformer Models for Narrative Text Understanding. In Proceedings of the Text2StoryIR'20 Workshop @ ECIR. arXiv:2003.08811 [BEST PAPER AWARD!]
  • Oita, M., Vani, K., & Oezdemir-Zaech, F. (2020). Semantically Corroborating Neural Attention for Biomedical Question Answering. In Machine Learning and Knowledge Discovery in Databases: International Workshops of ECML PKDD 2019, Würzburg, Germany, September 16–20, 2019, Proceedings, Part II (pp. 670-685). Springer International Publishing. doi: 10.1007/978-3-030-43887-6_60
  • Volpetti, C., Vani, K, and Antonucci, A (2020). Temporal Word Embeddings for Narrative Understanding. ICMLC.
  • 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. Association for Computational Linguistics, Online, November 2020.


  • Vani, K., and Antonucci, A (2019). NOVEL2GRAPH: Visual Summaries of Narrative Text Enhanced by Machine Learning. Text2Story@ ECIR.
  • Ellendorff, Tilia; Furrer, Lenz; Colic, Nicola; Aepli, Noëmi; Rinaldi, Fabio (2019). Approaching SMM4H with Merged Models and Multi-task Learning. In: Proceedings of the 4th Social Media Mining for Health Applications (#SMM4H) Workshop & Shared Task, Florence, Italy, 2 August 2019 - 2 August 2019, 58-61. doi: 10.18653/v1/W19-3208
  • Raul Rodriguez-Esteban, Dina Vishnyakova, Fabio Rinaldi (2019). Revisiting the decay of scientific email addresses. bioRxiv 633255; doi: 10.1101/633255
  • Vishnyakova, D., Rodriguez-Esteban, R., Rinaldi, F. (2019). A new approach and gold standard toward author disambiguation in MEDLINE. J Am Med Inform Assoc 26(10), pp. 1037–1045. doi: 10.1093/jamia/ocz028
  • Natural Language Processing of Clinical Notes on Chronic Diseases: Systematic Review. Seyedmostafa Sheikhalishahi, Riccardo Miotto, Joel T Dudley, Alberto Lavelli, Fabio Rinaldi, Venet Osmani (2019). JMIR Med Inform, vol. 7, iss. 2. doi: 10.2196/12239
  • Kim, J.D., Cohen, K.B., Collier, N., Lu, Z., Rinaldi, F. (2019). Introduction to BLAH5 special issue: recent progress on interoperability of biomedical text mining. Genomics Inform 17(2), pp. E12. doi: 10.5808/GI.2019.17.2.e12
  • Colic, N. and Rinaldi, F. Improving spaCy dependency annotation and PoS tagging web service using independent NER services. Genomics Inform. 2019;17(2):e21. doi: 10.5808/GI.2019.17.2.e21
  • Furrer, Lenz; Jancso, Anna; Colic, Nicola; Rinaldi, Fabio (2019). OGER++: hybrid multi-type entity recognition. Journal of Cheminformatics, 11(1):7. doi: 10.1186/s13321-018-0326-3
  • 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. Association for Computational Linguistics, Hong Kong, November 2019.

Previous publications

  • Susanne Küker, Celine Faverjon, Lenz Furrer, John Berezowski, Horst Posthaus, Fabio Rinaldi and Flavie Vial. The value of necropsy reports for animal health surveillance. BMC Veterinary Research (2018) 14:191. doi: 10.1186/s12917-018-1505-1
  • Marco Basaldella, Lenz Furrer, Carlo Tasso, Fabio Rinaldi. Entity Recognition in the Biomedical domain using a hybrid approach. Journal of Biomedical Semantics (2017), 8:51. doi: 10.1186/s13326-017-0157-6
  • Balderas-Martínez YI, Rinaldi F, Contreras G, Solano-Lira H, Sánchez-Pérez M, Collado-Vides J, Selman M, Pardo A; Improving biocuration of microRNAs in diseases: a case study in idiopathic pulmonary fibrosis. Database (Oxford) 2017; 2017 (1): bax030. doi: 10.1093/database/bax030
  • Fabio Rinaldi, Oscar Lithgow, Socorro Gama-Castro, Hilda Solano, Alejandra Lopez, Luis José Muñiz Rascado, Cecilia Ishida-Gutiérrez, Carlos-Francisco Méndez-Cruz, Julio Collado-Vides; Strategies towards digital and semi-automated curation in RegulonDB. Database (Oxford) 2017; 2017 (1): bax012. doi: 10.1093/database/bax012

Note: Only a few selected publications are mentioned here. For a more complete list of previous publications of Dr. Rinaldi, see here.

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Author: Fabio Rinaldi

Created: 2024-01-04 Thu 11:59