PhD Position Privacy for Crop Breeding

Do you want to contribute to privacy-preserving models for crop breeding? Join the Pattern Recognition and Bioinformatics section and work at the interface of model design and biological applications.

Job description

Genome sequence models are increasingly used in plant breeding and crop improvement pipelines. But training such models on private genomic data carries a risk: rather than learning general rules of sequence-function relationships, a model may simply memorize segments of the genomes it was trained on and later reproduce these. Since training data may be commercially sensitive, we need to understand when and why sequence models reproduce their training data and how to prevent it.

This project aims to characterize and mitigate memorization risk in sequence models to ensure privacy of training data. The PhD student will develop methods to quantify the degree to which a trained model reproduces specific training sequences, investigate how properties specific to plant genomes shape memorization behavior, design strategies that prevent leakage, and translate these findings into practical guidance.

The student will be embedded in the Pattern Recognition and Bioinformatics section, INSY department, TU Delft. In this project we work together with KeyGene, a research company for the development of breakthrough technology innovation for crop improvement.

Job requirements

To be considered for the position you must:

• have a master’s degree (or equivalent) in Computer Science.
• have proven affinity with (and preferably a degree in) Biology.
• have strong computational skills in model design, implementation and testing.
• have experience with courses and projects in Bioinformatics.
• have good communication skills in English (both verbal and written).
• be eager to push yourself to learn new skills, exchange knowledge and collaborate where possible.
• be willing to teach and guide students. Prior teaching experience is appreciated.

To thrive as a PhD candidate, it’s crucial to have a strong research mindset driven by curiosity and passion for your topic. Reflecting on your motivation for pursuing a PhD trajectory is essential, as this path involves unique challenges and uncertainties inherent to scientific exploration. Success requires dedication, adaptability, the ability to analyze complex problems, manage your time effectively, innovate and stay resilient under pressure. Combined with the ability and willingness to work independently and collaborate well, these qualities are indispensable for a fulfilling PhD journey. These experiences will build you as an independent researcher, expand your professional network, and pave the way for diverse career paths, inside or outside academia.

TU Delft (Delft University of Technology)

Working at TU Delft means contributing to solutions that really make a difference.

At TU Delft, our people make the difference. With their knowledge and curiosity, our staff provide a high-quality education and conduct pioneering research that extends beyond the campus. You will have the opportunity to take the initiative, work with others, and grow as a professional.

Working at TU Delft means joining an international community of professionals and students. Together, we create knowledge, innovations, and solutions that help move the world forward.

Faculty of Electrical Engineering, Mathematics and Computer Science

The Faculty of Electrical Engineering, Mathematics and Computer Science (EEMCS) brings together three scientific disciplines. Combined, they reinforce each other and are the driving force behind the technology we all use in our daily lives. At the same time, the faculty is developing the chips and sensors of the future and setting the foundations for the software technologies to run on this new generation of equipment, including AI. There is plenty of room at the faculty for ground-breaking research. We educate innovative engineers and have excellent labs and facilities that underline our strong international position. In total, more than 1000 employees and 4,000 students work and study in this innovative environment.

Conditions of employment

Doctoral candidates will be offered a 4-year period of employment in principle, but in the form of 2 employment contracts. An initial 1.5 year contract with an official go/no go progress assessment within 15 months, followed by an additional contract for the remaining 2.5 years assuming everything goes well and performance requirements are met.

As a PhD candidate you will be enrolled in the TU Delft Graduate School. The TU Delft Graduate School provides an inspiring research environment with an excellent team of supervisors, academic staff and a mentor. The Doctoral Education Programme is aimed at developing your transferable, discipline-related and research skills.

The TU Delft offers a customisable compensation package, discounts on health insurance, and a monthly work costs contribution. Flexible work schedules can be arranged.

As part of knowledge security, TU Delft conducts a risk assessment during the recruitment of personnel to prevent the unwanted transfer of sensitive knowledge and technology. The assessment is based on information provided by candidates, such as their motivation letter and CV, and takes place at the final stages of the selection process. When the outcome of the assessment is negative, the candidate will be informed. The processing of personal data in the context of the risk assessment is carried out on the legal basis of the GDPR: performing a public task in the public interest.