PhD in GenAI for Scientific Workflow Reconstruction and FAIR Publication

This is a challenging research project at the intersection of AI, NLP, and software engineering, with applications in life sciences and beyond.

Job Description

Reproducibility of scientific analyses is often limited by incomplete documentation of workflows in publications. This PhD project will develop a Generative AI-assisted platform to rebuild such workflows and make them FAIR, reusable, and executable. The project is situated at the intersection of AI, NLP, and software engineering, with broad applications in life sciences and beyond.

We are seeking highly motivated applicants for a PhD position to strengthen our research teams. The successful candidate will work within two research groups from our Computer Science department: Bioinformatics and User Centric Data Science. The focus will be on exploring the potential of applying Generative AI for reproducing, modularizing, and FAIR publication of existing research.

The reproducibility of scientific findings often depends on access to workflows and code used in original analyses. However, many publications lack complete, structured representations of their computational processes. This PhD project involves a GenAI-based approach to replicate and rebuild scientific data analysis workflows (such as for longitudinal, genomics, imaging, etc. data) using platforms like Snakemake and Nextflow.

By combining prompt engineering, modular workflow synthesis, and open-source pipeline deployment, the project aims to reduce technical barriers to reproducibility and promote the reuse of computational methods. The interaction with GenAI is not straightforward, and the quality of the output is highly dependent on the input from the human expert. Investigating the interaction process will play an important role in this research by determining the best ways of interaction in various scenarios and facilitating experts with intuitive interfaces, templates, and training materials.

If you are inspired by the FAIR principles and Open Science, have a strong background in programming and AI, and want to work with bioinformatics research publications, please apply!

Your Profile

Required:

• BSc and MSc in Computer Science, Artificial Intelligence, or a related field.
• Solid programming and development skills (Python, Git, Bash).
• Experience with machine learning (e.g., PyTorch/TensorFlow).
• Strong interest in generative AI and prompt engineering.
• Strong interest in data (genomics, imaging, etc.) analysis for Bioinformatics.

Nice-to-have:

• Scientific publications on applications of generative AI
• Interest in Bioinformatics software development
• Familiarity with workflow systems (e.g., Snakemake, Nextflow, Galaxy)

What We Offer

A challenging position in a socially engaged organisation. At VU Amsterdam, you contribute to education, research, and service for a better world. In return for your efforts, we offer you:

• A salary of minimum €3.059,00 (PhD) and maximum €3.881,00 (PhD) gross per month, on a full-time basis, based on the UFO profile PhD candidate. The exact salary depends on your education and experience.
• A position for at least 1 FTE. Your employment contract will initially last 18 months. After a satisfactory evaluation of the initial appointment, the contract will be extended for an additional 3 years, making it 4 years in total.

We also offer attractive fringe benefits and regulations, such as:

• A full-time 38-hour working week comes with a holiday leave entitlement of 232 hours per year. If you choose to work 40 hours, you have 96 extra holiday leave hours on an annual basis. For part-timers, this is calculated pro rata.
• 8% holiday allowance and 8.3% end-of-year bonus
• Contribution to commuting expenses
• Optional model for designing a personalized benefits package
• Hybrid working enables a good work-life balance

About Us

Faculty of Science
Researchers and students at VU Amsterdam’s Faculty of Science tackle fundamental and complex scientific problems to help pave the way for a sustainable and healthy future. From forest fires to big data, from obesity to malnutrition, and from molecules to the moon: we cover the full spectrum of the natural sciences. Our teaching and research have a strong experimentally technical, computational, and interdisciplinary nature.

We work on new solutions guided by value-driven, interdisciplinary methodologies. We are committed to research, valorisation, and training socially engaged citizens of the world who will make valuable contributions to a sustainable, healthy future.

Are you interested in joining the Faculty of Science? You will join undergraduate students, PhD candidates, and researchers at the biggest sciences faculty in the Netherlands. You will combine a professional focus with a broad view of the world. We are proud of our collegial working climate, characterised by committed staff, a pragmatic attitude, and engagement in the larger whole. The faculty is home to over 11,000 students enrolled in 40 study programmes and employs over 1,600 professionals spread across 10 academic departments.

Vrije Universiteit Amsterdam
Vrije Universiteit Amsterdam stands for values-driven education and research. We are open-minded experts with the ability to think freely—a broader mind. Maintaining an entrepreneurial perspective and concentrating on diversity, significance, and humanity, we work on sustainable solutions with social impact. By joining forces across the boundaries of disciplines, we work towards a better world for people and planet. Together we create a safe and respectful working and study climate, and an inspiring environment for education and research.

We are located on one physical campus, in the heart of Amsterdam's Zuidas business district, with excellent location and accessibility. Over 6,150 staff work at the VU and over 31,000 students attend academic education.