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).


  • 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


  • 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: 10.1007/978-3-030-68763-215



  • 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

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.

Back to home page

Author: Fabio Rinaldi

Created: 2022-03-30 Wed 14:18