PhD Position F/M Artificial intelligence tools for clinical data warehouses in neuroimaging
il y a 1 mois
Contexte et atouts du poste
You will work within the ARAMIS Lab (
The PhD thesis will be co-directed by Ninon Burgos (Research Scientist, HDR) and Olivier Colliot (Research Director). The position is funded through the GALAN project, a large-scale national grant in collaboration between the ARAMIS Lab, the Lille Neurosciences and Cognition Research Team, the departments of neuroradiology of the Pitié-Salpêtrière hospital and of the CHU of Lille, and the teams in charge of the CDWs of AP-HP and CHU of Lille. You will be involved in these collaborations and interact with the different partners.
Mission confiée
In recent years, very large clinical data warehouses (CDW) have been created containing the medical data of millions of patients. The AP-HP (Assistance Publique-Hôpitaux de Paris) CDW brings together data from multiple hospitals in the Paris region, including clinical data, diagnoses, medical reports and medical imaging data. CDWs provide fantastic opportunities to revolutionize digital healthcare. However, harnessing CDWs for research raises major challenges, among which controlling for data quality, biases and dealing with the full range of possible disorders and medical conditions.
Our team is a pioneer on the topic of neuroimaging in CDWs. We have built the first automatic quality control system for T1-weighted brain MRI of CDWs [1,2], that we subsequently extended to FLAIR MRI [3]. We have demonstrated that AI models trained on research data failed to generalize to clinical routine data and that, when data quality is not adequately taken into account, this leads to the catastrophic phenomenon of “short-cut” learning where the AI model learns to recognize image quality in place of the radiological features of the disorders [4].
The general objective of this PhD thesis project is to develop AI-based tools to harness the full potential of neuroimaging data in CDWs and to demonstrate that they can be used to develop trustworthy and unbiased AI-assisted reading systems for neuroradiology. Specific objectives are:
Objective 1: build AI-based quality control (QC) tools for different types of MRI sequences, including T2-weighted, T2*-weighted, susceptibility weighted imaging and diffusion weighted imaging. To that purpose, we will develop new approaches based on transfer learning and synthetic data generation. Objective 2: build a proof-of-concept unbiased AI-assisted reading system for neuroradiology. To that purpose, we will develop unsupervised anomaly detection to assist the detection of lesional areas, leveraging previous work from the team [5,6] while exploring new approaches such as diffusion models.The work will also include data management and preparation tasks, installation of code and dependencies in specific environments, and performance benchmarking. The methodological developments will be integrated into ClinicaDL (
This project is expected to have a major impact on several aspects. It will allow researchers to fully exploit the very rich but complex neuroimaging data in CDWs, potentially leading to major new discoveries in various fields such as a better understanding of the factors influencing healthy and pathological brain aging. The project will result in next generation AI-based diagnostic tools that are expected to generalize well and thus have a high potential for translation to the clinic.
[1] Simona Bottani, Ninon Burgos, Aurélien Maire, Adam Wild, Sébastian Ströer, Didier Dormont, Olivier Colliot. Automatic quality control of brain T1-weighted magnetic resonance images for a clinical data warehouse. Medical Image Analysis, 2021. [2] Sophie Loizillon, Simona Bottani, Aurélien Maire, Sebastian Ströer, Didier Dormont, Olivier Colliot, Ninon Burgos, APPRIMAGE Study Group. “Automatic motion artefact detection in brain T1-weighted magnetic resonance images from a clinical data warehouse using synthetic data”. Medical Image Analysis, 2024. [3] Sophie Loizillon, Olivier Colliot, Lydia Chougar, Sebastian Stroer, Yannick Jacob, Aurélien Maire, Didier Dormont and Ninon Burgos. Semi-supervised Domain Adaptation for Automatic Quality Control of FLAIR MRIs in a Clinical Data Warehouse. In DART 2023 - 5th MICCAI Workshop on Domain Adaptation and Representation Transfer, 2023 [4] Simona Bottani, Ninon Burgos, Aurélien Maire, Dario Saracino, Sebastian Stroer, Didier Dormont, Olivier Colliot. Evaluation of MRI-based machine learning approaches for computer-aided diagnosis of dementia in a clinical data warehouse. Medical Image Analysis, 2023. [5] Sophie Loizillon, Yannick Jacob, Aurélien Maire, Didier Dormont, Olivier Colliot, Burgos Ninon “Detecting Brain Anomalies in Clinical Routine with the beta-VAE: Feasibility Study on Age-Related White Matter Hyperintensities.” 2024. [6] Ravi Hassanaly, Maëlys Solal, Olivier Colliot, and Ninon Burgos. Pseudo-healthy image reconstruction with variational autoencoders for anomaly detection: A benchmark on 3D brain FDG PET, 2024.
Principales activités
Main activities:
researchwrite scientific paperspresent work at scientific conferencesprogrammingdata managagement and curationinteract with partners (clinicians, scientists, engineers)
Compétences
Master’s degree or engineering degree with computer science, signal/image analysis and/or applied mathematics profile Strong interest for medical applications Knowledge of deep learning Knowledge in digital image processing and medical imaging Good programming skills in Python Good writing skills Good relational and communication skills to interact with professionals from various backgrounds Proficient in French language
Avantages
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 and flexible organization of working hours (after 12 months of employment) Professional equipment available (videoconferencing, loan of computer equipment, etc.) Social, cultural and sports events and activities Access to vocational training Social security coverage-
Clinical Data Manager
il y a 4 semaines
Paris, France Excelya Temps pleinCreated in 2014, Excelya is a people-centered Contract Research Organization (CRO) that excels with care. We offer a personal and authentic experience within a young, ambitious health company on the path to becoming the clinical research leader in Europe thanks to our 800 Excelyates. Our unique one-stop provider service model - leveraging full-service,...
-
Artificial Intelligence Engineering Executive Manager
il y a 2 semaines
Paris, Ile-de-France AXA Group Operations Temps pleinOur ambition is to be a major catalyst for AXA’s transformation into a tech-led company.Officially launched in January 2019, AXA Group Operations’ goal is to support AXA entities around the world in empowering people to live better lives. As AXA’s ‘engine’, Group Operations is responsible for making the business run on a day-to-day basis, as well...
-
Artificial Intelligence Engineering Executive Manager
il y a 1 mois
Paris, France AXA Group Operations Temps pleinOur ambition is to be a major catalyst for AXA’s transformation into a tech-led company.Officially launched in January 2019, AXA Group Operations’ goal is to support AXA entities around the world in empowering people to live better lives. As AXA’s ‘engine’, Group Operations is responsible for making the business run on a day-to-day basis, as well...
-
Artificial Intelligence Engineering Executive Manager
il y a 2 semaines
Paris, France AXA Group Operations Temps pleinOur ambition is to be a major catalyst for AXA’s transformation into a tech-led company.Officially launched in January 2019, AXA Group Operations’ goal is to support AXA entities around the world in empowering people to live better lives. As AXA’s ‘engine’, Group Operations is responsible for making the business run on a day-to-day basis, as well...
-
Artificial Intelligence Engineering Executive Manager
il y a 1 mois
Paris, France AXA Group Temps pleinOur ambition is to be a major catalyst for AXA’s transformation into a tech-led company. Officially launched in January 2019, AXA Group Operations’ goal is to support AXA entities around the world in empowering people to live better lives. As AXA’s ‘engine’, Group Operations is responsible for making the business run on a day-to-day basis, as...
-
Informatiker/in, Data Engineer,Wirtschaftsinformatiker/in
il y a 2 jours
Paris, France Duisburger Hafen AG Temps pleinIT, Data Engineering, Azure Data Factory, Informatik,Microsoft Azure, Data Warehousing, Business Intelligence, CloudComputing Data Engineer (m/f/d) Duisburg Type of employment: salaried employee Job ID: 357 Perspectivesthat move. By water, rail and road - we getthe flow of goods moving. As the leading logistics hub in CentralEurope, the duisport...
-
Artificial Intelligence Solutions Architect
il y a 1 mois
Paris, France INTEL Temps pleinThe European, Middle East and Africa (EMEA) Sales and Marketing Group (SMG) is an international team of sales and marketing professionals spanning both commercial and technical sales, Industry Centre of Excellence teams, marketing, and sales operations. It's a very fast paced, dynamic, and exciting environment. We are looking for technical and architectural...
-
Data Warehouse Aas
il y a 4 semaines
Paris, France Ardemis Partners Temps plein**Localisation**: Velizy **Métier**: Data **Type de contrat**: mission **Salaire**: Selon Profil **Type d'entreprise**: **Compétences**: Data #Business Analyst #Business Intelligence #anglais Description de poste As a member of the DWH as a Service Squad for a Specific Domain, Within IDS (IS Data & Digital Services) Tribe, you will actively...
-
Post-Doctoral Research Visit F/M EICACS
il y a 1 mois
Paris, France INRIA Temps pleinContexte et atouts du poste This position contributes to a European project which involves partners from both industry and academia of various European countries. The goal of the project include: The promotion or development of design rules and interoperability standards, to ensure the interoperability of collaborative heterogeneous assets to...
-
Post-doctoral position in the “Immunity and Cancer”
il y a 1 mois
Paris, France Institut Curie Temps pleinThe department of Immunology headed by Ana-Maria Lennon-Duménil is actively looking for a Post-doc motivated to work on an ambitious project in translational Immunology. Institut Curie ( is one of the most renowned European institutions for cancer research with a strong interdisciplinary tradition. It is located in the center of Paris, in a culturally and...
-
Clinical Trial Associate
il y a 2 heures
Paris 4e, France Cmed Temps pleinCmed occupies a unique position in the clinical research industry, not only as an expert in the operational delivery of clinical trials but also as a developer of its own technologies for managing clinical data. Over the last 16 years this has included Timaeus® and now encapsia, a new game changing Cloud based Clinical Data Suite. This is a very exciting...
-
senior data scientist
il y a 5 jours
Paris, France Aijobs Temps pleinData is at the core of PriceHubble. We process a wide variety of data from multiple sources. As a data scientist in the data-intelligence team, you will have three main missions: First, to augment the data we have via machine learning prediction. Second, to develop techniques to measure, assert, and improve the quality of the data we have. Third, to...
-
Research Engineer Position
il y a 3 jours
Paris 13e, France INSERM U1135 CIMI Temps plein**RESEARCH ENGINEER POSITION in TEAM 2 of INSERM UMR 1135-Cimi-Paris (Paris, France)** **for the RespiriTB and RespiriNTM EU IMI H2020 Program** **for 2.5 years starting 2023** In the context of a **European IMI AMR** **project** (innovative medicines initiative, antimicrobial resistance), we are offering a **research engineer position** for a project...
-
Clinical Research Associate
il y a 4 semaines
Paris, France Institut de Myologie Temps pleinLocated in Paris at the heart of Europe’s largest hospital, the Pitié-Salpêtrière, the Institute of Myology was created in 1996 under the impetus of an association of patients and parents of patients, the AFM-Telethon. Its objective is to promote the existence, recognition and development of myology as a clinical and scientific discipline in its own...
-
Clinical Trial Ambassador
il y a 1 mois
Paris, France Syneos Health Commercial Solutions Temps plein**Overview** The Clinical Trial Ambassador will establish, cultivate, and maintain scientific relationships with investigators and study coordinators to support enrollment while developing a strong understanding of clinical practice as it relates to areas of interest. This position interacts with various internal and external stakeholders, with a focus on...
-
Data Science Intern
il y a 4 semaines
Paris 4e, France Scienta Lab Temps plein**Company overview** Created in 2021 by Camille Bouget, Vincent Bouget et Julien Duquesne, Scienta Lab is a deeptech company harnessing artificial intelligence to transform the drug discovery and development process in immunology and inflammation. With its unique and proprietary technology based on a foundation model, Scienta Lab leverages multimodal data...
-
(H/F) Clinical Director
il y a 4 semaines
Paris, France Wandercraft Temps pleinOur Clinical Director will manage a skilled clinical team. He/she will be responsible for the following duties (list not exhaustive): **Clinical strategy** - Definition and execution of the clinical strategy and roadmap: - Leading the design and execution of clinical studies promoted by Wandercraft and/or our partners in France and internationally,...
-
Clinical Research Director
il y a 1 mois
Paris, France Proclinical Staffing Temps pleinClinical Research Director - Paris, France - PermanentProclinical is seeking a dedicated and experienced Clinical Research Director (CRD) to manage the clinical activities of a range of products. This is a permanent position located in Paris, France.Primary Responsibilities:The ideal candidate will have a strong background in designing and monitoring...
-
Sr Clinical Research Associate Home-based in France
il y a 1 mois
Paris, France Novasyte Temps pleinWe have a vacancy within our Clinical Monitoring Team for experienced permanent Clinical Research Associates II or Senior CRA, to join our Single sponsor team in France. - Essential Functions - Perform site monitoring visits (selection, initiation, monitoring and close-out visits) in accordance with contracted scope of work and Good Clinical Practice. -...
-
Associate/Senior professor in law
il y a 1 mois
Paris, France KEDGE Business School Temps pleinAssociate/Full Professor in Business Law, preferably with some knowledge in the fields of:Company Law, Corporate governance and Corporate Social Responsibility (CSR)OrNew technologies, IT Law, Personal Data Law and Artificial Intelligence (Campus of Paris, France)Accounting, Finance & Economics departmentKEDGE Business School is a vibrant business school...
