Mots-Clés

Bioinformatique - Traitement automatique des langues

Description

Université Paris-Saclay is opening an attractive position in biomedical language processing and data integration with research in the LISN laboratory.

 

Deadline for applications: 19 Apr 2022, 4:00pm Paris time Position start: 1 Sep 2022

 

This is a new type of "tenure track" position started this year in France: a special Associate Professor position, called "Chaire Professeur Junior", with a fast track to tenured, Full Professor within about 5 years.  The general objective of the project of which this position is part is to build bridges between two areas: natural language processing of biomedical texts and integration of biological data.

 

This new type of Associate Professor position has a reduced teaching load of 64 hours a year, compared to the standard 192 hours of usual positions.  The research environment is that of the natural language processing team of the LISN Language Sciences and Technologies department and/or the Bioinformatics team of the LISN Data Science department.  LISN is the Interdiscplinary Laboratory for Digital Sciences, a computer science research center with five departments, created in January 2021 from the teams of two former research centers: LIMSI and LRI.

 

Additionally, the Junior Professor will automatically receive a one-shot 200 k€ research grant from the National Research Agency (typically to hire a post-doc or doctoral student, for travel expenses, etc.).

 

About language in a French environment: interaction in the research team can be performed in English.  Teaching is in French or in English depending on the classes.  If needed, the successful candidate can teach entirely in English initially, but is expected to be able to teach in French too after a couple of years.

 

Université Paris-Saclay is among the top 20 universities in the Shanghai Jiao Tong ranking, and the first in continental Europe.

 

APPLICATION INSTRUCTIONS

 

Interested candidates should contact the following people before applying:

- Research: Pierre Zweigenbaum <pz@lisn.fr> (BioNLP) and Sarah Cohen-Boulakia <cohen@lri.fr> (Bioinformatics)

- Teaching: Computer Science Department <presidence-dept-info.sciences@u-psud.fr>

 

- Official job description: job 188, https://www.galaxie.enseignementsup-recherche.gouv.fr/ensup/ListesPostesPublies/FIDIS/0912408Y/FOPC_0912408Y_188.pdf

 

Application is then through the Galaxie server (FIDIS):

- https://galaxie.enseignementsup-recherche.gouv.fr/antares/can/index.jsp

Deadline for applications: 19 Apr 2022, 4:00pm Paris time Position start: 1 Sep 2022

 

FROM THE OFFICIAL JOB DESCRIPTION

 

TAL-BIOInfo

Computer Science:

Biomedical langage processing, Analysis and integration of biological data

 

** Research activities

The LISN laboratory is a multidisciplinary research laboratory in Orsay, France. It is composed of five departments and 17 teams. The recruited person will work at the interface of the Information, Written and Signed Language (ILES: Natural Language Processing) team of the Language Sciences and Technologies department and of the Bioinformatics team of the Data Science department. They will work primarily on the themes of biomedical natural language processing and/or analysis and integration of biological data. They will bring skills that may include (non-exhaustive list) natural language processing, knowledge representation, machine learning, algorithmics, statistics.

 

We will also consider profiles of people who fit more generally into the Information, Written and Signed Language (ILES) team or into the Bioinformatics team, as well as profiles with a strong interest in natural language processing and bioinformatics and who fit into the Language Sciences and Technologies or Data Science departments.

 

The general objective of the project of which this position is part is to build bridges between two areas: natural language processing of biomedical texts and integration of biological data. The problem of analyzing and integrating data and scientific knowledge, in the form of both structured data and texts, is particularly relevant in the biomedical field where the production of data (biological experiments, clinical trials, medical records) and knowledge (publications) has accelerated over the last few years. A recurrent challenge to obtain a relevant interpretation of the content of these specialized texts is to know how to embed words, data and structured knowledge into a common space. One line of research is representation learning with neural network architectures. Biological data integration aims at exploiting the complementarity of datasets to allow the discovery of new knowledge from multiple massive and highly heterogeneous datasets. This need was recently highlighted again in the COVID-19 pandemic.

 

Data integration increasingly requires natural language processing methods to automatically extract information that is only contained in text, such as drugs tested in clinical trials or gene-disease relationships in scientific abstracts. Natural language processing and biological data integration also share a common need to design FAIR, transparent and reproducible processing pipelines. The bioinformatics community is strongly structured around such good practices, which could benefit natural language processing to better reproduce an experiment over time and thanks to the notion of provenance, trace the data used, the parameterization of the tools, build robust and transparent scientific platforms. The challenge of this project is therefore to mutually fertilize the fields of biological data integration and biomedical text analysis: the needs of each field can find solutions in the other, the solutions of each field can give rise to new problems in the other

 

** Teaching

Teaching is one of the University's foundational missions. As such, the recruited person will demonstrate their ability to link teaching sequences and pedagogical modalities to explicit learning and skill acquisition objectives.

 

The recruited person may teach in all the fields of study of the Computer Science Department of the Orsay Faculty of Sciences, at Bachelor and Master levels (traditional and apprenticeship).

 

They will teach in their areas of expertise, but may also be called upon to strengthen the teaching potential of the department in basic computer science.

 

They may be required to provide part of their teaching in English, in particular in the context of Masters courses but also in Bachelor's courses.

 

During their career, the recruited person will also be required to participate in the life of the Computer Science Department and assume leadership positions (management of "filières", participation in the government structures of the Faculty of Sciences and of the University, contribution to project steering).

 

** LISN

LISN was created on 1 Jan 2021 and currently hosts 163 faculty members.

https://www.lisn.upsaclay.fr/

See also:

- https://www.limsi.fr/en/research/iles/

- https://www.lri.fr/equipe.php?eq=4