Research Engineer F/M – Aligning medical foundation models across histology, spatial transcriptomics and MRI

Research Engineer F/M – Aligning medical foundation models across histology, spatial transcriptomics and MRI Download job offer in PDF format Level of qualifications required : Graduate degree or equivalent Fonction : Temporary scientific engineer Context The position is in the ARAMIS project-team (Inria, CNRS, Inserm, Sorbonne Université), at the Paris Brain Institute (ICM) on the Pitié-Salpêtrière hospital campus. ARAMIS develops computational and statistical methods for multimodal patient data in brain disorders. The engineer will be supervised by Reuben Dorent (Inria research scientist), whose work focuses on multimodal representation learning and statistical inference from incomplete medical data. Assignment Assignments : With the help of Reuben Dorent, the recruited person will be taken to: • Build a reproducible pipeline that extracts and stores representations from several foundation models per modality (histology, spatial transcriptomics, MRI) on public multimodal datasets; • Set up an evaluation protocol for alignment from few pairs, using datasets in which the true correspondences are known but only a few hundred of them are revealed during training; • Extend the team's two-modality alignment method [1] to a first setting with three modalities, and compare it with existing baselines; • Support a PhD student of the team working on histology-spatial transcriptomics integration, by providing shared tools for data preprocessing, feature extraction and evaluation. For a better knowledge of the proposed research subject : [1] J. Kordes, R. Dorent. Representation Alignment from a Few Paired Data via Distilled Optimal Transport. arXiv:2610.12781, 2026. [2] S. Ruyter, R. Dorent et al. Program-space Diffusion for Morphology-to-Transcriptomics Prediction. COMPAYL workshop, MICCAI 2026. [3] J. Ostermaier, S. Ruyter, R. Dorent et al. Disentangled shared representations improve morpho-transcriptomic integration. COMPAYL workshop, MICCAI 2026. Collaboration : The recruited person will be working closely with a PhD student of the ARAMIS team. Responsibilities : • Write data loaders and preprocessing for public datasets such as HEST-1k (paired histology and spatial transcriptomics), TCGA (MRI, histology and clinical data), Ivy GAP and the Allen Human Brain Atlas. • Extract embeddings from several pretrained foundation models per modality (e.g. pathology, single-cell / spatial transcriptomics and 3D MRI models) and organise them in a common, documented format. • Implement the evaluation protocol: train/test splits that reveal only a few hundred pairs, retrieval and matching metrics, and robustness to the choice of paired samples. • Implement and run baselines and the extension of the team's alignment method to three modalities; analyse the results. • Package the code (tests, documentation, example notebooks) so that it can be reused by the PhD students of the team and released as open-source software. • Take part in team meetings, present results and contribute to the writing of technical reports and, where results allow, scientific publications. Main activities • Analyse and implement related work. • Design novel innovative solutions. • Write progress reports and papers. • Communicate advancement to the team. Skills Technical skills and level required : • Solid Python programming and experience with PyTorch. • Practical experience in deep learning; knowledge of representation learning or self-supervised learning.Good software practices: git, code review, testing, documentation, use of GPU clusters (SLURM). Languages :English Relational skills : Good communication skills Other valued appreciated : 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 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 Apply for this position Share • Facebook • Linkedin • Twitter • Email General Information • Theme/Domain : Computational Neuroscience and Medicine Biologie et santé, Sciences de la vie et de la terre (BAP A) • Town/city : Paris • Inria Center : Centre Inria de Paris • Starting date : 2026-01-01 • Duration of contract : 6 months • Deadline to apply : 2026-11-22 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. 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. Contacts • Inria Team : ARAMIS • Recruiter : Dorent Reuben / reuben.dorent@inria.fr The keys to success There you can provide a "broad outline" of the collaborator you are looking for what you consider to be necessary and sufficient, and which may combine : • tastes and appetencies, • area of excellence, • personality or character traits, • cross-disciplinary knowledge and expertise... This section enables the more formal list of skills to be completed and 'lightened' (reduced) : • "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 Ruby on Rails development and strong influencing skills. A thesis in the field of **** is a real asset." About Inria Inria, the French national institute for research in digital science and technology, supports the French government in national research and innovation strategies in the digital field, acting as Digital Programs Agency. Inria leads over 300 research and innovation projects with its 3,500 scientists, engineers, and support staff, in partnership with universities and the digital ecosystem (businesses, entrepreneurs, and public stakeholders). Together, we explore strategic fields such as artificial intelligence, cybersecurity, quantum computing, cloud technologies, digital transformation in healthcare, digital twins, and digital technologies for defence. We develop practical solutions such as software, tech startups, partnerships with national companies, and cutting-edge training programmes. Our goal is to drive scientific, technological, and industrial excellence to ensure France’s digital sovereignty.