Natural Language Processing (NLP) for Healthcare

We apply advanced NLP methodologies to the problem of extraction of information from health-related textual documents.

We have considerable prior expertise in the extraction of information from the scientific literature, built through more than a decade of research projects, supported by the Swiss National Science Foundation, InnoSuisse and other research funding agencies.

Key Projects

MelanoBase


Extract disease information from literature

SwissMADE


Swiss Monitoring of Adverse Drug Events (clinical text processing)

Twitter monitor


Social-media health-related conversations

Biomedical Entity Recognition


OntoGene entity recognition and Bio Term Hub

 

Selected Publications

  • Donald C. Comeau, Rezarta Islamaj Doğan, Paolo Ciccarese, Kevin Bretonnel Cohen, Martin Krallinger, Florian Leitner, Zhiyong Lu, Yifang Peng, Fabio Rinaldi, Manabu Torii, Alfonso Valencia, Karin Verspoor, Thomas Wiegers, Cathy Wu, and W. John Wilbur. “BIoC: A Minimalist Approach to Interoperability for Biomedical Text Processing.” The Journal of Biological Databases and Curation. Database 2013: bat064 doi:10.1093/database/bat064 published online September 18, 2013

  • Donald C. Comeau, Riza Theresa Batista-Navarro, Hong-Jie Dai, Rezarta Islamaj Doğan, Antonio Jimeno, Ritu Khare, Zhiyong Lu, Hernani Marques, Carolyn J. Mattingly, Mariana Neves, Yifan Peng, Rafal Rak, Fabio Rinaldi, Richard Tzong-Han Tsai, Karin Verspoor, Thomas C. Wiegers, Cathy H. Wu, and W. John Wilbur. “BioC Interoperability Track Overview”. The Journal of Biological Databases and Curation, Database 2014, doi: 10.1093/database/bau053

  • Fabio Rinaldi,Tilia Renate Ellendorff, Sumit Madan, Simon Clematide, Adrian van der Lek, Theo Mevissen, Juliane Fluck. “BioCreative V Track 4: A Shared Task for the Extraction of Causal Network Information in Biological Expression Language.” The Journal of Biological Databases and Curation, 2016, baw067. doi:10.1093/database/baw067

  • Lenz Furrer, Fabio Rinaldi. “OGER: OntoGene’s Entity Recogniser in the BeCalm TIPS Task.” Proceedings of the BioCreative V.5 Challenge Evaluation Workshop. Barcelona, Spain, 26–27 April 2017, pg. 175–182.

  • 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

  • Lenz Furrer, Anna Jancso, Nicola Colic, Fabio Rinaldi. “OGER++: Hybrid multi-type entity recognition”. Journal of Cheminformatics (2019) 11:1. doi:10.1186/s13321-018-0326-3

  • 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

  • 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

  • Joseph Cornelius, Tilia Ellendorff, Lenz Furrer, Fabio Rinaldi (2020). “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.

  • 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.

  • Ivano Lauriola, Fabio Aiolli, Alberto Lavelli, Fabio Rinaldi. “Learning adaptive representations for entity recognition in the biomedical domain.” Journal of Biomedical Semantics (2021), accepted for publication.

  • Lenz Furrer, Joseph Cornelius, Fabio Rinaldi. “Parallel sequence tagging for concept recognition.” BMC Bioinformatics, 2022 (accepted for publication, preprint: 2003.07424).

  • 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

Contact

Dr. Fabio Rinaldi

Senior Researcher at IDSIA

Personal website