Fabio Rinaldi

Table of Contents

Short Bio

f2-small.jpg Currently I am responsible for NLP research at IDSIA (Dalle Molle Institute for Artificial Intelligence), in Southern Switzerland. Until 2019 I was a lecturer and senior researcher at the University of Zurich, as well as PI in a number of research projects. I co-authored more than 100 scientific papers (including more than 30 journal papers), dealing with topics such as Ontologies, Entity Extraction, Answer Extraction, Text Classification, Document and Knowledge Management, Language Resources and Terminology.

I acquired and managed numerous projects, with funding from the European Union, the Swiss National Science Foundation (which funds basic research), InnoSuisse (a Swiss agency which funds applied research), large companies (in particular the Pharmaceutical Industry), and private research-funding foundations. The total funding acquired so far for my group is close to 3 million Swiss Francs. For additional information about my projects, please consult my website http://www.ontogenesis.org/

I have an academic background in computational sciences and more than 25 years experience in NLP research. In recent years my major focus of interest has been applications in the biomedical domain, such as automatic analysis of the scientific literature, of clinical reports, and health-related social media discussions.


External links

International collaborations

fabio-zapata.jpg I have numerous international collaborations, and I am keen to establish new ones. As an example, I established a collaboration with the RegulonDB group at the National University of Mexico, and was a visiting research professor there for four years (visiting a few weeks each year). RegulonDB is one of the major life sciences databases, well-known in the bioinformatics community, and funded by the US National Institute of Health.

fabio-yukata.jpg I have also lived and worked as a researcher in Italy (2 years), the UK (3 years), in Japan (about 1 year), in Germany (about 5 months), and in the US (about two months).

Recent publications

  • Joseph Cornelius, Tilia Ellendorff, Lenz Furrer, Fabio Rinaldi (2020). 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. Check here the preprint
  • Lenz Furrer, Joseph Cornelius, Fabio Rinaldi (2020). Parallel sequence tagging for concept recognition. arXiv:2003.07424
  • 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. https://www.zora.uzh.ch/id/eprint/173922/
  • 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
  • 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


E-Mail: fabio AT idsia.ch
Tel: +41 (0)58 666 67 14
Fax: +41 (0)58 666 66 61

Postal address:

Dr.  Fabio  Rinaldi
Dalle Molle Institute for Artificial Intelligence Research (IDSIA)
Galleria 2, Via Cantonale 2c
CH-6928 Manno (Lugano, Switzerland)

My previous affiliation (until the end of 2019):

Institute of Computational Linguistics. University of Zurich
Tel.: +41 44 635 7132
Fax: +41 44 635 6809
fabio.rinaldi AT uzh.ch

NLP group page

How to find me

Notice that while the postal address indicates "Galleria 2", my office is at "Galleria 1".

Dalle Molle Institute for Artificial Intelligence Research (IDSIA)
Galleria 1, Via Cantonale 
CH-6928 Manno (Lugano, Switzerland)

Author: Fabio Rinaldi

Created: 2020-10-06 Tue 19:12