Machine learning for Brain Neuroimaging

Inria

France

February 9, 2022

Description

2022-04340 - Machine learning for Brain Neuroimaging

Level of qualifications required : Graduate degree or equivalent

Fonction : Temporary scientific engineer

About the research centre or Inria department

Located at the heart of the main national research and higher education cluster, member of the Université Paris Saclay, a major actor in the French Investments for the Future Programme (Idex, LabEx, IRT, Equipex) and partner of the main establishments present on the plateau, the centre is particularly active in three major areas: data and knowledge; safety, security and reliability; modelling, simulation and optimisation (with priority given to energy).

The 450 researchers and engineers from Inria and its partners who work in the research centre's 28 teams, the 60 research support staff members, the high- level equipment at their disposal (image walls, high-performance computing clusters, sensor networks), and the privileged relationships with prestigious industrial partners, all make Inria Saclay Île-de-France a key research centre in the local landscape and one that is oriented towards Europe and the world.

Context

Working at Inria

Established in 1967, Inria is the only public research body fully dedicated to computational sciences. Combining computer sciences with mathematics, Inria's 3,900 researchers and engineers strive to invent the digital technologies of the future. Educated at leading international universities, they creatively integrate basic research with applied research and dedicate themselves to solving real problems, collaborating with the main players in public and private research in France and abroad and transferring the fruits of their work to innovative companies. The researchers at Inria published over 4,500 articles in 2019. They are behind over 300 active patents and 120 start- ups.The 172 project teams are distributed in ten research centers located throughout France.

Working with Parietal team

Besides permanent researchers, the developer will be in contact with PhD students that do software development as part of their PhD contract, and with the developer team that contributes to scikit-learn and Joblib, supported by the scikit-learn consortium. He or she will also be in contact with cognitive and clinical neuroscientists at NeuroSpin. Parietal researchers use English as a common language for their activities (daily interactions, weekly meetings, yearly retreats).

Assignment

We are looking for a programmer to join our research group, Parietal team, at INRIA, to work on Nilearn, a library applying advanced machine learning and signal processing to functional brain imaging. As a programmer, you will be developing tools for the analysis of cognitive neuroscience and "functional connectivity" –brain connectivity inferred using functional MRI. Large databases have been made available with these types of data and require powerful data analysis software. The project unites neuroscientists, data- miners, statisticians and clinical researchers to transfer recent advances in basic neuroscience to clinical diagnostic tools. Your duties will be to work hand in hand with the computer science and statistics researchers to turn the research code into a solid and well documented Python library usable by clinical researchers. In particular, to make the core data-processing routines more usable, the project will develop specific data visualization. The technologies used rely on the scientific Python stack and scikit-learn machine learning library.

Main activities

• Improvement and homogenization of the library API, generation of automated reports for group analyses, facilitation of statistical analyses (contrast specification).

• Integration within the EBRAINS (Human Brain Project) platform users to run connectivity analyses (estimation, visualization, population modeling) there.

This involves the following steps:

  • Integration of Nilearn into EBRAINS.
  • Development of new functionalities for manipulation of brain regions, integrated in the EBRAINS atlas viewer.
  • • Depending on the engineer's profile and tastes, she/he will work on some of Nilearn's long-term development directions such as: – Improving support for surface data (visualization, processing operations). – Improving the reporting capabilities (interactivity, extending reports to more estimators). – Improving the integration of the BIDS standard. – Improving Nilearn's website.

    • Animation of the developers community. Organization and participation to: – Weekly office hours. – Monthly Nilearn's core-developer meeting. – Occasional social events: Nilearn dev-days (2020 edition, 2021 edition), brainhack, coding sprints, training on software development.

    Skills

    • Love high-quality code and open source.

    • Worry about users and like to communicate.

    • Be curious about data (i.e. like looking at data and understanding it).

    • Have an affinity for problem-solving tradeoffs.

    • Good scientific Python coders.

    • Enjoy interacting with a community of developers.

    • Interest in brain imaging and its applications.

    Benefits package
  • Restauration subventionnée
  • Transports publics remboursés partiellement
  • Congés: 7 semaines de congés annuels + 10 jours de RTT (base temps plein) + possibilité d'autorisations d'absence exceptionnelle (ex : enfants malades, déménagement)
  • Possibilité de télétravail (après 6 mois d'ancienneté) et aménagement du temps de travail
  • Équipements professionnels à disposition (visioconférence, prêts de matériels informatiques, etc.)
  • Prestations sociales, culturelles et sportives (Association de gestion des œuvres sociales d'Inria)
  • Accès à la formation professionnelle
  • Sécurité sociale
  • Remuneration

    Remuneration in regards to professional experiences.

    General Information
  • Theme/Domain : Computational Neuroscience and Medicine Software engineering (BAP E)

  • Town/city : Palaiseau

  • Inria Center : CRI Saclay - Île-de-France
  • Starting date : 2022-02-01
  • Duration of contract : 1 year, 1 month
  • Deadline to apply : 2022-02-09
  • Contacts
  • Inria Team : PARIETAL
  • Recruiter : Thirion Bertrand / Bertrand.Thirion@inria.fr
  • About Inria

    Inria is the French national research institute dedicated to digital science and technology. It employs 2,600 people. Its 200 agile project teams, generally run jointly with academic partners, include more than 3,500 scientists and engineers working to meet the challenges of digital technology, often at the interface with other disciplines. The Institute also employs numerous talents in over forty different professions. 900 research support staff contribute to the preparation and development of scientific and entrepreneurial projects that have a worldwide impact.

    Instruction to apply

    Defence Security : This position is likely to be situated in a restricted area (ZRR), as defined in Decree No. 2011-1425 relating to the protection of national scientific and technical potential (PPST).Authorisation to enter an area is granted by the director of the unit, following a favourable Ministerial decision, as defined in the decree of 3 July 2012 relating to the PPST. An unfavourable Ministerial decision in respect of a position situated in a ZRR would result in the cancellation of the appointment.

    Recruitment Policy : As part of its diversity policy, all Inria positions are accessible to people with disabilities.

    Warning : you must enter your e-mail address in order to save your application to Inria. Applications must be submitted online on the Inria website. Processing of applications sent from other channels is not guaranteed.

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