PhD Position in Clinical Data Engineering and Privacy-Preserving Machine Learning 100%

Department of Clinical Research
Employment upon agreement
The Faculty of Medicine at the University of Bern is an environment for high-quality, future-oriented research. Strong connections between basic research, engineering sciences, and university hospitals enable a unique setting for translational and patient-centered clinical research. The faculty prioritizes cross-disciplinary research and digitalization , fostering innovation in medical science. It is one of the largest medical faculties in Switzerland and is affiliated with the country's largest hospital complex.

The Department of Clinical Research (DCR) is a joint initiative of the University of Bern's Faculty of Medicine and its university hospitals, including Inselspital and the University Psychiatric Services (UPD). It supports and professionalizes clinical and translational research collaborations.
Our specialized divisions assist researchers throughout the entire research process, from project conception to result dissemination. We provide tailored educational programs and events on all aspects of clinical research, equipping researchers and students with the skills to conduct efficient and impactful studies. Our mission prioritizes patient-centered research, ensuring that patient perspectives are integral to our work.

The Medical Data Science group, led by Assistant Professor Benjamin Ineichen, a medical doctor with a PhD in neuroscience/pharmacology, is part of the DCR at the University of Bern. The group, known as the STRIDE-Lab , is a multidisciplinary team with expertise in medicine, neuroscience, statistics, and computer science. It focuses on bridging the gap between preclinical and clinical research and eventually drug approval, to advance therapy development for human diseases, with a focus on neuroscience. Using evidence synthesis and data science, the lab aims to improve experimental animal welfare while also contributing to better patient treatments.

Developing drugs for clinical applications is challenging, with only about 5% of therapies receiving regulatory approval ( Ineichen et al., PLoS Biology, 2024 ). While some failures are due to the complexity of innovative therapies, others stem from adjustable factors in drug testing, such as outcome measures, trial duration, and model selection (Berg et al., eBiomedicine, 2024) . The impact of these factors is difficult to assess in individual trials but can be uncovered through large-scale clinical trial data analysis (Ineichen et al., Nature Reviews, 2024) .

Our approach combines expertise in medicine, evidence synthesis, and natural language processing (NLP) (Doneva et al., EMNLP, 2024) with Bern's extensive clinical trial landscape and modern data science infrastructure. The goal is to identify the key factors driving successful drug approvals and use this knowledge to optimize clinical trial design. This shall be achieved by developing TrialSim, a digital platform that integrates deep learning to curate, integrate, and analyze large-scale clinical trial data.

For your PhD project, you will build the clinical trial arm of the TrialSim platform: a secure and scalable clinical data pipeline. Your main tasks include:

1. Establish privacy-compliant electronic health records (EHR) data pipelines in collaboration with hospital IT systems. For this, we will leverage the modern data infrastructure in Bern.
2. Design data access, cleaning, linking and structured data integration workflows using LLMs.
3. Integrate curated data into an agentic LLM framework and apply machine learning or deep learning to identify factors associated with successful drug development.

You will work at the interface of medicine and computer science, leveraging the large volume of clinical data available in Bern. Additionally, you will:

• Contribute to ongoing teaching efforts in the group/at the Department
• Contribute to publications and (inter)national conferences
• Contribute to a positive and collaborative team culture

We are looking for candidates with a high enthusiasm for the projects we work on, including for drug development, clinical trials, health data, and statistical modelling, enjoying interdisciplinary work at the intersection of medicine and computer science.

Required academic qualifications:

• Master degree in computer science/informatics, medical data science, health informatics, statistics, mathematics, software engineering, or a related field.

Required technical qualifications:

• Expertise in Python programming and machine learning skills, including MLOps, MLflow and/or Docker
• Experience in data engineering and building data pipelines
• Exposure to health data, preferably clinical data such as EHRs / unstructured text

Nice to have: Experience with transformer models (e.g., BERT) or generative LLMs for data curation and extraction. Experience with data privacy methods for sensitive patient data.

Additionally required soft skills:

• Excellent organizational and planning skills
• Strong team spirit - you value collaboration, shared goals, and respectful communication
• Motivation and commitment for topics such as drug development, clinical trials, health data, and statistical modeling as well as interdisciplinary work at the intersection of medicine and computer science

• Purposeful work aimed at improving animal welfare and advancing treatment for neurological (and other) diseases
• A small multidisciplinary team with expertise in medicine, neuroscience, statistics, and computer science
• Flexible working hours
• Opportunities for first- and co-authorships on peer-reviewed scientific articles whenever possible
• Access to a dynamic machine learning community at the University of Bern, with a strong emphasis on digitalization
• Collaboration within Switzerland's largest medical faculty and hospital complex, offering extensive networking opportunities
• Bern, the capital of Switzerland, is a lively city with rich cultural offerings and easy access to Switzerland's most stunning natural landscapes
• We are committed to diversity and inclusion, valuing different perspectives to drive innovation. We welcome applicants from all backgrounds and ensure a respectful, supportive environment where everyone can thrive

If you have any inquiries, please contact Prof. Ineichen Benjamin, at E-Mail schreiben.

Are you interested? Then please send us your complete application to HR Administration
(E-Mail schreiben) by (October 10th, 2025), at the latest.

Required application documents:

• CV, including publications
• Motivation letter explaining your interest in this particular project and environment
• Academic transcript/record of grades

Note: Only complete applications will be considered. We will invite promising candidates for an interview.