Scientific Engineer F/M Unveiling Neuroscience with a Domain-Specific Probabilistic Logic Language

Inria
September 22, 2022
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2022-05285 - Scientific Engineer F/M Unveiling Neuroscience with a Domain- Specific Probabilistic Logic Language

Renewable contract : Oui

Level of qualifications required : PhD 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

Neuroscience is at an inflection point. The 150-year old cortical specialization paradigm, in which cortical brain areas have a distinct set of functions, is experiencing an unprecedented momentum with over 1000 articles being published every year. However, this paradigm is reaching its limits. Recent studies show that current approaches to atlas brain areas, like relative location, cellular population type, or connectivity, are not enough on their own to characterize a cortical area and its function unequivocally. This hinders the reproducibility and advancement of neuroscience.

Neuroscience is thus in dire need of a universal standard to specify neuroanatomy and function: a novel formal language allowing neuroscientists to simultaneously specify tissue characteristics, relative location, known function and connectional topology for the unequivocal identification of a given brain region.

The vision of NeuroLang is that a unified formal language for neuroanatomy will boost our understanding of the brain. By defining brain regions, networks, and cognitive tasks through a set of formal criteria, researchers will be able to synthesize and integrate data within and across diverse studies. NeuroLang will accelerate the development of neuroscience by providing a way to evaluate anatomical specificity, test current theories, and develop new hypotheses.

NeuroLang will lead to a new generation of computational tools for neuroscience research. In doing so, we will be shedding a novel light onto neurological research and possibly disease treatment and palliative care. Our project complements current developments in large multimodal studies across different databases. This project will bring the power of Domain Specific Languages to neuroscience research, driving the field towards a new paradigm articulating classical neuroanatomy with current statistical and machine learning-based approaches.

This job takes part within the Neurolang ERC-Stg project. The candidate will integrate the MIND team condicting collaborative reserach with institutions such as NeuroSpin, the Brain and Spine institute at Paris, the Pasteur Institute, Université de Paris, Stanford, and Harvard. If the current world situation allows it, travelling will be involved.

Assignment

Assignments : With the help of D. Wassermann, PI of the ERC grant NeuroLang, the recruited person will be taken to drive and develop neuroscience applications of the probabilistic logic language NeuroLang (neurolang.github.io). This will entail driving collaborations between cognitive neuroscientist and computerscientists and conduct independent research in evidence-driven neuroscience.

Some example pubications DSL-based programming applied to neuroscience and its uses and applications.

  • Gallardo, G., Wassermann, D. & Anwander, A. Bridging the Gap: From Neuroanatomical Knowledge to Tractography of Brain Pathways. https:// biorxiv.org/lookup/doi/10.1101/2020.08.01.232116 (2020) doi:10.1101/2020.08.01.232116.
  • Dadi, K. et al. Fine-grain atlases of functional modes for fMRI analysis. NeuroImage 221 , 117126 (2020).
  • Menon, V. et al. Microstructural organization of human insula is linked to its macrofunctional circuitry and predicts cognitive control. eLife 9 , e53470 (2020).
  • Chen, L. et al. The visual word form area (VWFA) is part of both language and attention circuitry. Nat Commun 10 , 5601 (2019).
  • Sydnor, V. J. et al. A comparison of three fiber tract delineation methods and their impact on white matter analysis. NeuroImage 178 , 318–331 (2018).
  • Main activities

    Examples of activities:

  • Analyse the requirements of our congitive neuroscience partners, specifically in the area of cortical specialization and systems neuroscience.
  • Propose original cognitive neuroscience research which can be formalised into a logical protocol to imporve its reproducibility
  • Co-advise a team of PhD students developing methodological resarch in neuroscience applications.
  • Skills

    Technical skills and level required : Analysis of neuroimaging data, knowledge in neuroanatomy,

    Desired skills: Machine Learning, discrete mathematics, programming language theory, data analytics, databases. Python programming and version control through Git/Github will be appreciated

    Languages : Good English conversational and written skills

    Relational skills : good Interpersonal Abilities and Problem- Solving/Reasoning/Creativity

    Benefits package
  • Subsidized meals
  • Partial reimbursement of public transport costs
  • Leave: 7 weeks of annual leave + 10 extra days off due to RTT (statutory reduction in working hours) + possibility of exceptional leave (sick children, moving home, etc.)
  • Possibility of teleworking (after 6 months of employment) and flexible organization of working hours
  • Professional equipment available (videoconferencing, loan of computer equipment, etc.)
  • Social, cultural and sports events and activities
  • Access to vocational training
  • Social security coverage
  • Remuneration

    2653 € / month gross salary

    General Information
  • Theme/Domain : Data and Knowledge Representation and Processing Biologie et santé, Sciences de la vie et de la terre (BAP A)

  • Town/city : Palaiseau

  • Inria Center : CRI Saclay - Île-de-France
  • Starting date : 2023-01-01
  • Duration of contract : 12 months
  • Deadline to apply : 2022-09-22
  • Contacts
  • Inria Team : MIND
  • Recruiter : Wassermann Demian / demian.wassermann@inria.fr
  • The keys to success

    The ideal candidate will have

  • Prior work in the field of neuroimaging
  • Good skills in computer science and or statistics
  • Teamwork preference,
  • Vocation for cross-disciplinary work
  • Essential qualities in order to fulfil this assignment are feeling at ease in an environment of scientific dynamics and wanting to learn and listen.
  • Passionate about innovation, with expertise in Python development and strong influencing skills.
  • 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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