Internship - Machine learning for prediction of response to immunotherapy in lung cancer

2022-05572 - Internship - Machine learning for prediction of response to immunotherapy in lung cancer

Level of qualifications required : Master's or equivalent

Fonction : Internship Research

About the research centre or Inria department

The Inria Sophia Antipolis - Méditerranée center counts 34 research teams as well as 8 support departments. The center's staff (about 500 people including 320 Inria employees) is made up of scientists of different nationalities (250 foreigners of 50 nationalities), engineers, technicians and administrative staff. 1/3 of the staff are civil servants, the others are contractual agents.

Context

The internship position will take place in the environment of the Inria-Inserm team COMPO (COMputational Pharmacology in Oncology), located in the University Hospitals of Marseille (AP-HM). The team is composed of mathematicians, pharmacists and clinicians and is a unique multidisciplinary environment focused on developing novel computational tools for decision- making in clinical oncology.

The intern will join the QUANTIC project, which consists in the statistical and machine learning analysis of the large scale, multi-modal data collected within the national PIONeeR clinical study 1. The project aims at predicting response/resistance to immune-checkpoint inhibitors for patients with advanced non-small cell lung carcinoma. The data consists of multi-modal and high-dimensional features from quantitative digital pathology, lesions sizes, pharmacokinetics, immunoprofiling, soluble biomarkers and sequencing data.

1 https: // marseille-immunopole.org/the-pioneer-project/

Assignment

Despite the large number of variables (1167), multiple variables have missing values, at possibly high (>50%) level. The inter will be in charge of exploring the missingness pattern of the data (missing at/completely at/not at random) and assessing state-of-the art machine learning methods for missing values imputation in this concrete application.

In addition, he/she will explore methods for data augmentation, with a focus on large-dimensional longitudinal data.

Keywords: Machine learning; clinical oncology; data imputation; data augmentation

Main activities

Literature review

Data visualization

Exploratory data analysis

Statistical analysis

Programming (R/python)

Implementation of machine learning algorithms for data imputation

Implementation of machine learning algorithms for data augmentation

Skills

Technical skills and level required :

Data analysis

Statistics

Computer programming (R/python)

Basic knowledge of cancer biology, immunology and/or medicine is a plus

Other valued appreciated : motivation to develop computational tools for concrete clinical applications, general enthusiasm to work in a team

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.)

Professional equipment available (videoconferencing, loan of computer equipment, etc.)

Social, cultural and sports events and activities

Access to vocational training

Social security coverage

Remuneration

The amount of the stipend is based on the hourly rate in effect within public institutions and indexed to changes in the maximum hourly rate fixed by the social security

General Information

Theme/Domain : Computational Neuroscience and Medicine Statistics (Big data) (BAP E)

Town/city : Marseille

Inria Center : Centre Inria d'Université Côte d'Azur

Starting date : 2022-02-01

Duration of contract : 6 months

Deadline to apply : 2023-01-08

Contacts

Inria Team : COMPO

Recruiter : Benzekry Sebastien / [email protected]

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.