PhD on AI-driven multimodal data fusion models in rare diseases

KU LEUVEN; Belgique; Sur place; EUR 32 000 - 42 000; Plein temps

Résumé du poste

KU Leuven in Belgium invites applications for a Doctoral Researcher position focused on developing and benchmarking multimodal AI methods for disease prediction. The project combines histopathology with multi-omics data to learn robust cross-modal representations in an international consortium.

The MSCA SPACE-MEL network funds the 48-month program, with an intended start in 2027, offering a competitive salary and family allowances where applicable. English proficiency required.

Qualifications

• Master's degree in Bioinformatics, Computer Science, AI, Bioscience Engineering or related field.
• Applicants must be doctoral candidates admitted to KU Leuven Doctoral School of Biomedical Sciences.
• Mobility rule: no residence in Belgium >12 months in the last 36 months before recruitment.

Responsabilités

• Develop and benchmark zero-shot multimodal fusion models for rare disease prediction.
• Integrate spatial and single-cell multi-omics with histopathology and clinical data for robust cross-modal representations.
• Advance ML strategies for multimodal representation learning and data integration within an international consortium.

Connaissances

Python

PyTorch

Machine learning

Multimodal learning

Linux & HPC

Git

Workflow tools

English proficiency

Formation

Master's degree in Bioinformatics/CS/AI/Bioscience Eng

Outils

Snakemake

Nextflow

Conda

Docker

Git

Description du poste

Organisation/Company KU LEUVEN Research Field Computer science » Informatics Engineering » Biomedical engineering Engineering » Computer engineering Biological sciences » Biology Researcher Profile First Stage Researcher (R1) Application Deadline 15 Oct 2026 - 23:59 (UTC) Country Belgium Type of Contract Temporary Job Status Full-time Offer Starting Date 1 Jan 2027 Is the job funded through the EU Research Framework Programme? Other EU programme Reference Number BAP-2026-557 Is the Job related to staff position within a Research Infrastructure? No

Offer Description

The candidate will develop and benchmark zero-shot multimodal fusion models for rare disease prediction, using melanoma as a use case. The project integrates spatial and single-cell multi-omics data with histopathology and clinical information to learn robust cross-modal representations for diagnostic prediction. It pursues two integrated objectives: (i) to develop generative and explainable AI approaches for multimodal data fusion; and (ii) to extend existing multimodal frameworks with additional omics layers and evaluate their performance across heterogeneous datasets. At KU Leuven, the candidate will develop machine-learning strategies for multimodal representation learning and for the integration of the complex biological datasets generated within the consortium.

Duration and start date: 48 months, full-time. The first 36 months are funded by the MSCA Doctoral Network SPACE-MEL; the appointment is extended to a full four-year doctoral trajectory at KU Leuven. Intended start date: begin 2027.

Eligibility conditions

• Master's degree in Bioinformatics, Computer Science, Artificial Intelligence, Bioscience Engineering or a related field, obtained by the start date of the contract.
• Applicants must be doctoral candidates, i.e. not already in possession of a doctoral degree, and must be admissible to the KU Leuven Doctoral School of Biomedical Sciences.
• Mobility rule: applicants must not have resided or carried out their main activity (work, studies) in Belgium for more than 12 months in the 36 months immediately before the recruitment date.

Required skills

• Strong programming skills in Python, and experience with at least one deep-learning framework (PyTorch preferred).
• A solid grounding in machine learning. Experience with representation learning, generative models, foundation models or multimodal integration is a strong asset.
• Experience in the analysis of high-dimensional biological data (single-cell or spatial transcriptomics, digital pathology or biomedical imaging) is an advantage.
• Comfortable working on Linux and HPC/GPU systems, with version control (git) and reproducible workflows (conda or containers, Snakemake or Nextflow).
• Able to work independently as well as within an interdisciplinary, international consortium.
• Proficiency in the English language is required, as well as good communication skills, both oral and written. Successful candidates will need to provide an English test (e.g. IELTS, TOEFL, Cambridge English). You may be exempt if you are a national of a majority native-English speaking country, or have qualifications / degree that has been taught and assessed in English. The supervisor may also confirm that a candidate has the required level of English.

Secondments

• 4 months at University of Manchester, United Kingdom (supervisor: Dr. Martin Fergie)
• 3 months at Spotlight Pathology Ltd., United Kingdom (supervisor: Dr. Samantha Perona)

The doctoral candidate will receive a competitive salary in accordance with the MSCA Doctoral Networks program, comprising a living allowance and a mobility allowance. A family allowance is foreseen where applicable. KU Leuven additionally offers holiday pay, hospitalization insurance, reimbursement of certain commuting costs and access to its sports and childcare facilities.

For more information please contact Prof. dr. Alejandro Sifrim, mail: [e-mail].

Required documents:

• Statement of interest (limit of 2,500 characters) explaining why you wish to be considered for the fellowship and which qualities and experience you will bring to the role.
• Curriculum vitae.
• A certificate of University examinations taken (with marks).
• A final degree certificate translated in English. If, at the time of application, candidates should not be yet in possession of a degree certificate, they can submit it at the time of the examination. However, if successful, the candidate will be required to provide a translated and legalised certificate as proof of eligibility for doctoral admission.
• A limited number of applicants will be invited for an interview and will be asked to provide the contact details of up to two referees.

The doctoral candidate will receive a competitive salary in accordance with the MSCA Doctoral Networks program, comprising a living allowance and a mobility allowance. A family allowance is foreseen where applicable. KU Leuven additionally offers holiday pay, hospitalization insurance, reimbursement of certain commuting costs and access to its sports and childcare facilities.

Eligibility criteria

Eligibility conditions

• Master's degree in Bioinformatics, Computer Science, Artificial Intelligence, Bioscience Engineering or a related field, obtained by the start date of the contract.
• Applicants must be doctoral candidates, i.e. not already in possession of a doctoral degree, and must be admissible to the KU Leuven Doctoral School of Biomedical Sciences.
• Mobility rule: applicants must not have resided or carried out their main activity (work, studies) in Belgium for more than 12 months in the 36 months immediately before the recruitment date.

Selection process

For more information please contact Prof. dr. Alejandro Sifrim, mail: [e-mail].

Required documents:

• Statement of interest (limit of 2,500 characters) explaining why you wish to be considered for the fellowship and which qualities and experience you will bring to the role.
• Curriculum vitae.
• A certificate of University examinations taken (with marks).
• A final degree certificate translated in English. If, at the time of application, candidates should not be yet in possession of a degree certificate, they can submit it at the time of the examination. However, if successful, the candidate will be required to provide a translated and legalised certificate as proof of eligibility for doctoral admission.
• A limited number of applicants will be invited for an interview and will be asked to provide the contact details of up to two referees.