PhD Project in AI for Analytical Chemistry

PhD fellowship in Computer Science, Department of Computer Science, SCIENCE, University of Copenhagen

Department of Computer Science invites applicants for a PhD fellowship in AI for Analytical Chemistry. The project is part of the research project “Chemical foundation models for small molecule detection and identification from environmental samples”, which is financed by Novo Nordisk Foundation.

Start date is (expected to be) 1 September 2026 or as soon as possible thereafter.

The project
We are seeking a motivated PhD student to work on deep learning methods for automated detection and identification of small molecules from chromatography and mass spectrometry data. The project combines self-supervised segmentation models for signal detection in chemical data with probabilistic generative models for de novo molecular structure prediction from mass spectra, with emphasis on uncertainty quantification in low-annotation regimes. The segmentation component focuses on learning to detect chemical signals across diverse instrument platforms directly from unlabeled data, without relying on manual parameter tuning. The generative modeling direction treats structure elucidation as a conditional generation problem over a vast chemical space, where the key challenge is not only accuracy but producing calibrated uncertainty estimates when labeled spectrum-structure pairs are scarce. Both directions involve methodological contributions to deep learning in semi-supervised and self-supervised representation learning, grounded in a high-impact application domain.

The work is motivated by pressing non-target screening problems in environmental water analysis and is carried out in close collaboration with analytical chemistry experts at the University of Copenhagen. This gives the project direct access to large-scale experimental datasets from wastewater and drinking water monitoring and provides real-world evaluations.

Who are we looking for?
We are looking for candidates within the field(s) of Computer Science, Applied Mathematics, Bioinformatics, or related field. Background in analytical chemistry or cheminformatics is beneficial, but it is not a hard requirement.

Our group and research- and what do we offer?
You will be a part of a newly established research group led by Assistant Professor Svetlana Kutuzova, whose primary research focus is deep learning research with applications to life science. The group collaborates closely with the research group of Professor Mads Nielsen, a world-class expert in computer vision and healthcare informatics. Both groups co-locate in the Pioneer Centre for Artificial Intelligence and are a part of Department of Computer Science, Faculty of SCIENCE, University of Copenhagen. We are located in Copenhagen.

We offer creative and stimulating working conditions in dynamic and international research environment.

1. Principal supervisor is Professor Mads Nielsen, Department of Computer Science, E-mail madsn@di.ku.dk, Direct Phone: +4524600599
2. Co-supervisor is Assistant Professor Svetlana Kutuzova, Department of Computer Science, Email svegal@di.ku.dk
3. Co-supervisor is Professor Jan Christensen, Department of Plant and Environmental Sciences, Email jch@plen.ku.dk

The PhD programme
A PhD programme is a three year full-time study within the framework of the regular PhD programme (5+3 scheme).

Qualifications needed for the regular programme
To be eligible for the regular PhD programme, you must have completed a degree programme, equivalent to a Danish master’s degree (180 ECTS/3 FTE BSc + 120 ECTS/2 FTE MSc) related to the subject area of the project, e.g. Computer Science, Applied Mathematics or Bioinformatics. For information of eligibility of completed programmes, see General assessments for specific countries and Assessment database.

Terms of employment in the regular programme
Employment as PhD fellow is full time and for maximum 3 years.

Employment is conditional upon your successful enrolment as a PhD student at the PhD School at the Faculty of SCIENCE, University of Copenhagen. This requires submission and acceptance of an application.

Terms of appointment and payment accord to the agreement between the Danish Ministry of Taxation and The Danish Confederation of Professional Associations on Academics in the State. The position is covered by the Protocol on Job Structure.

Responsibilities and tasks in the PhD programme

• Carry through an independent research project under supervision
• Complete PhD courses corresponding to approx. 30 ECTS / ½ FTE
• Participate in active research environments, including a stay at another research institution, preferably abroad
• Teaching and knowledge dissemination activities
• Write scientific papers aimed at high-impact journals and computer science conferences
• Write and defend a PhD thesis on the basis of your project

We are looking for the following qualifications:

• Professional qualifications relevant to the PhD project
• Relevant publications
• Relevant work experience
• Other relevant professional activities
• Curious mind-set with a strong interest in AI for science
• Full working proficiency in English language

Application and Assessment Procedure
Your application including all attachments must be in English and submitted electronically by clicking APPLY NOW below.

Please include: 

1. Motivated letter of application (max. one page)
2. Curriculum vitae including information about your education, experience, language skills and other skills relevant for the position
3. Original diplomas for Bachelor or Master and transcript of records in the original language, including an authorized English translation if issued in another language than English or Danish. If not completed, a certified/signed copy of a recent transcript of records or a written statement from the institution or supervisor is accepted.
4. Publication list (if possible)
5. Reference letter

Application deadline: The deadline for applications is 20 May 2026, 23:59 GMT +2.

We reserve the right not to consider material received after the deadline, and not to consider applications that do not live up to the abovementioned requirements.

The further process
After deadline, a number of applicants will be selected for academic assessment by an unbiased expert assessor. You are notified whether you will be passed for assessment.

The assessor will assess the qualifications and experience of the shortlisted applicants with respect to the above-mentioned research area, techniques, skills and other requirements. The assessor will conclude whether each applicant is qualified and, if so, for which of the two models. The assessed applicants will have the opportunity to comment on their assessment. You can read about the recruitment process at https://employment.ku.dk/faculty/recruitment-process/.

Interviews with selected candidates are expected to be held in week 25 -26.

Questions
For specific information about the PhD fellowship, please contact the principal supervisor.

General information about PhD study at the Faculty of SCIENCE is available at the PhD School’s website: https://www.science.ku.dk/phd/

The University of Copenhagen wishes to reflect the surrounding community and invites all regardless of personal background to apply for the position.