PhD position Organ-Specific Embedding Models for Computational Pathology

PhD position Organ-Specific Embedding Models for Computational Pathology

Are you passionate about advancing AI in digital pathology? At the Pathology department of Amsterdam UMC, we are seeking a motivated PhD candidate to develop organ-specific foundation models that will transform histopathological image analyses and clinical research.

The project

As a PhD candidate, you will establish and benchmark self-supervised learning (SSL) pipelines tailored to specific organs, enabling accurate whole slide image (WSI) classification and downstream predictive tasks. You will lead the design, implementation, and evaluation of novel organ-specific embedding models — experimenting with contrastive objectives, innovative embedding strategies, and feature aggregation methods — and validate their performance in clinically relevant applications. The explainability of the learned models will also be thoroughly investigated.

About your role

• Innovative Model Research: Formulate and test self-supervised objectives (e.g., DINOv2, Barlow Twins) and model architectures, exploring novel approaches to capture organ-specific histological features;
• Experimental Design & Analysis: Lead hypothesis-driven experiments, define evaluation metrics, conduct rigorous ablation studies, and interpret model behaviour to uncover biological insights from WSIs;
• Dataset Creation: Collaborate with IT and data management teams to centralize and index thousands of WSIs across organ groups, maintaining a robust database with redundancy and secure backups;
• Cross-Organ Benchmarking: Systematically benchmark your models against general-purpose foundational models.
• Interdisciplinary Collaboration: Work closely with clinicians, molecular pathologists, and bioinformaticians to integrate AI models into clinical practice;
• Scholarly Dissemination: Author high-impact publications, present at top-tier conferences, and contribute to grant and project proposals that extend your research vision.

About you

You are a proactive, analytical thinker with a strong background in computer science, machine learning, or a related discipline, and an interest in medical AI. You thrive in an interdisciplinary environment and are eager to push the boundaries of computational pathology.

You have:

• A Master’s degree in Computer Science, Artificial Intelligence, Biomedical Engineering, or a related field (with outstanding grades);
• Hands-on experience with Python and deep learning frameworks (e.g., PyTorch, TensorFlow);
• Familiarity with self-supervised learning techniques and multiple instance learning, or a strong willingness to learn. A strong mathematical background is preferred;
• Knowledge of containerization (Docker/Kubernetes), distributed computing, and version control (Git), or a willingness to learn;
• Excellent communication skills and the ability to collaborate effectively with researchers, clinicians, and IT specialists.

Our offer

• A flying start to your career in scientific research.
• Plenty of room for your drive to shape tomorrow's healthcare.
• Working on large-scale and in-house research, with motivated colleagues from all over the world.
• You will be employed by Amsterdam UMC Research BV.
• A contract for 12 months, with the intention to extend for a total of 4 years. The Guideline PhD contract applies to this vacancy.
• Salary scale OIO: € 3.108 to € 3.939 gross based on full-time employment (depending on education and experience) and a year-end bonus of 8.3%.
• Holiday hours: 190,4 per year for fulltime and a possibility to save additional hours.
• Pension accrual with BeFrank, a modern, comprehensible and fairly priced pension.
• For >7 km each way, 100% reimbursement for public transport travel costs and, for private transport, €0.18 per km up to a maximum of 40 km each way.
• Do you prefer walking or cycling? Take advantage of our good bike scheme. Moreover, you will receive a reimbursement of €0.18 per km.

About your workplace

You will be embedded in the Multimodal AI group in the Pathology department, working alongside five principal investigators, other PhD candidates, and research staff. This dynamic, multidisciplinary team fosters innovation and open exchange of ideas.

Amsterdam UMC Research BV supports non-profit scientific research. In doing so, we provide researchers with everything they need to excel. Our principal investigators (PIs) and project leaders offer support in the field of project management, finance and human resources. In medical scientific research projects, legal support is also provided.

Amsterdam UMC has an open culture. This means that we hope that everyone feels welcome in our organization and that we strive to offer equal opportunities to everyone. We therefore cordially invite all interested parties to respond to this vacancy.

If you have any questions about this position, please feel free to contact Richard Schoonhoven, Assistant Professor, via r.a.schoonhoven@amsterdamumc.nl.