*NLP and deep learning against pandemics* (2 year postdoc)
Collaborative project "ComCorText"

*Keywords:* NLP, AI, deep learning, epidemiology, risk factors,
outbreak detection.

*Host lab**:*
Imaging and Modeling Unit
(https://research.pasteur.fr/en/team/imaging-and-modeling/),
Institut Pasteur (https://www.pasteur.fr/en), Paris, France

Collaboration with the Epidemiology of Emerging Diseases Unit
https://research.pasteur.fr/en/team/epidemiology-of-emerging-diseases/
(Institut Pasteur) and Sanofi

The COVID-19 pandemic has abundantly illustrated the importance of
quickly identifying the factors that increase or decrease pathogen
transmission. An early understanding of the airborne nature of
SARS-CoV-2 transmission, for example, could have helped slow down the
pandemic and reduce its human burden. In this project, we will explore
the potential of natural language processing (NLP) methods to
automatically identify risk factors and protective factors by analyzing
large corpora of unstructured text.
This project takes advantage of the unique resource provided by the
ComCor study, which contains free text descriptions of suspected
circumstances of contamination from >50,000 individuals tested positive
for COVID-19, totaling well over 500,000 words. The proposed project
will mobilize state-of-the-art NLP techniques based on deep learning,
such as contextualized word embeddings learned by transformer models
(e.g. BERT).
Methods developed in this project will be tested and validated
primarily (but not exclusively) on the ComCor data set in collaboration
with the Epidemiology of Emerging Disease Unit of A. Fontanet.

Once validated, we will also explore applications of these methods to
other text data sets, including social media and data obtained in the
framework of the AIOLOS project. AIOLOS is a French-German research
program, that aims at supporting decision-making by integrating
information from various to detect early signs of a new outbreak,
monitor its spread and derive appropriate response measures. A total of
17 partners (5 main partners, including Sanofi and Fraunhofer and 12
associated partners, including Institut Pasteur) are involved in this
project.


*We are looking for a highly motivated and autonomous candidate with a
solid background in NLP or related fields to lead this project.*
Please send applications (motivation letter + CV with names of 2-3
references) to Ch. Zimmer (czimmer@pasteur.fr) and Tiffany Charmet
(tiffany.charmet@pasteur.fr)