PhD Position in Computer Science/Machine Learning

at The University of Southern Denmark
Published September 25, 2023
Location Odense, Denmark
Category Machine Learning  
Job Type Scholarship  


We are looking for PhD candidates to join the TACsy (Training Alliance for Computational Systems Chemistry) Marie-Skłodowska-Curie Joint Doctoral Network. This network consists of fifteen (15) highly interlinked PhD projects, of which this particular call is for project DC 13: Computational Lipidomics and Mass Spectrometry – Learning Mechanistical Models. The application deadline is 23 October 2023. The anticipated start date is 1 January 2024, but flexibility in both directions is possible.

Several approaches developed within TACsy are based on a graph transformation language which is used to expand chemical spaces, similarly to how production rules in formal languages are used to derive words of a formal language. Both metabolic networks and the fragmentation process within a mass spectrometer can be modelled as a rule-based system. The latter has the advantage that the combinatorics are far less dramatic, since fragmentation only splits (never merges) chemical compounds. Modelling fragmentation patterns as graph transformation rules, however, is a challenge and requires automation.

Within this project the PhD student will develop novel machine learning algorithms for automated rule inference in the mass spectrometer setting. For the subsequent spectrum prediction these results will be integrated with approaches that stochastically simulate the fragmentation process in a mass spectrometer. The PhD student will have a 12 month research stay with our industry partner Thermo Fisher Scientific, a world leader in instrumentation and mass spectrometry.

In addition to developing novel algorithms for rule inference and mass spectrum prediction, the PhD student will have the chance to apply them in a flagship project of TACsy (in collaboration with our scientific partner EMBL): After modelling lipid metabolic networks as graph transformations, the computational framework developed will support our partner’s functional studies of how the lipid metabolic networks of mouse embryonic stem cells are remodelled during cell fate acquisition.

We are seeking an excellent and highly motivated individual with either an MSc degree in computer science, an MSc degree in Applied Mathematics, or an MSc degree in chemistry/physics with a strong focus on computational methods. The ideal candidate has familiarity with one or more of the following areas: machine learning, data mining, knowledge discovery, stochastic simulations, algorithmics, graph theory, graph transformation, algorithm engineering. Proven competences in programming and ease with formal thinking are a necessity.

This PhD project is a joint degree between University of Southern Denmark (Daniel Merkle, Rolf Fagerberg) and Technical University of Vienna (Thomas Gärtner). Additionally, the student will have a twelve months internship at Thermo Fisher Scientific GMBH (Christoph Henrich).

The TACsy consortium encompasses 11 partners across six countries in Europe and North America, including both academic institutions and industrial partners. The consortium consists of world-class scientists with competences spanning chemistry, biochemistry, computer science, and machine learning. All fifteen doctoral candidates will work with two research groups, and will obtain a degree from both host institutions, and complete research stays either at world-leading industry partners or at prestigious non-European academic partners:

  • University of Southern Denmark (DK)
  • University of Vienna (AT)
  • Leipzig University (DE)
  • Friedrich-Schiller-University Jena (DE)
  • TU Vienna (AT)
  • The University of Sheffield (UK)
  • European Molecular Biology Laboratory (EMBL)
  • BASF SE (DE)
  • Fluigent SA (FR)
  • Thermo Fisher Scientific GMBH (DE)
  • Harvard Medical School (US)

The candidates will all be part of a strong joint PhD training programme, with a focus on career development, application writing, communication skills, and community building through scientific summer schools.

All candidates will be expected to:

  • Have potential for conducting outstanding research, as demonstrated by scientific accomplishments (in particular quality of thesis, but also publications, code repositories, conference presentations, outreach activities, etc.).
  • Be interested in working in a multidisciplinary and international research environment.
  • Have excellent communication skills in English, verbally as well as in scientific writing.
  • Be willing to undertake international research stays, internships, and travels.

See details about the network as a whole, its scientific content, and the application and selection process here.

Salary, working conditions, application process, etc.

All positions are fully funded, with very competitive salaries. More information on funding from the MSCA programme can be found here (beginning on page 78). Please note that a country correction coefficient (page 109) applies to the living allowance in order to ensure equal treatment and purchasing power parity for all researchers. Salary rules apply to the doctoral candidates hosted in the European Union and will change depending on the host institution.

The TACsy project wishes our staff to reflect the diversity of society and thus welcomes applications from all qualified candidates regardless of personal background. We are searching for a diverse group of candidates with very different backgrounds and qualities, who inspire and motivate each other. We want every talent to feel at home in our organisations and to have the same career opportunities. The position of working hours is flexible in order to accommodate individual needs and allow for the best possible work-life balance for each candidate.

The guaranteed Doctoral Candidate PhD funding from the European Commission is for 36 months. Therefore, appointment as a PhD Research Fellow is for three years. Employment stops automatically at the end of the period. The holder of the scholarship is not allowed to have other paid employment during the three-year period. Additional funding may be possible, depending on the local supervisor and in accordance with the regular PhD time in the country of origin.

Applications must be in English and must include the following:

  • A research proposal/description of your approach to the project in question (max one page excluding references). This should be attached under the “Project description” option.
  • A letter stating your specific interest, motivation, and qualifications for the project (max. two pages). This letter should be attached under the "Application form" option. (There is no application form.)
  • Detailed CV, including personal contact information of two or three references. This should be attached under the “CV” option.
  • Copies of diplomas, Bachelor as well as Master’s degree, including transcript of notes/grades. This should be collated into one document and attached under the “Certificates” option.
  • At least two signed reference letters. These should be combined into one file and attached under the “References” option. Should your referees wish to send their letters directly to us, please have them send these to mentioning your name and the title of the position in the subject line. And please note that these also need to reach us before the deadline.

Applications must be submitted electronically using the link “Apply online”. Attached files must be in Adobe PDF or Word format. Each box can only contain a single file of max. 10 Mb. We strongly recommend that you read “How to apply” before you apply.

Incomplete applications and applications received after the deadline will neither be considered nor evaluated. This also applies to reference letters.

Details on the selection process can be found here. Please note that the recruitment team reserves the right to conduct a second interview. Shortlisting may be used in the assessment process.

Please note that there are two limitations to apply for this programme, as specified in the MSCA regulations. Applicants must:

  • Not be in possession of a PhD degree at the date of recruitment.
  • Meet the Marie-Curie mobility rule (see pages 81-82 here). In TACsy, this means the applicants are not eligible for a specific position if it is true for both host institutions of the position that the applicant for more than 12 of the last 36 months has resided or performed a main activity (work, studies, etc.) in the country of that host institution. The host institutions relevant to this rule are for the present call located in (DC 1: Denmark and Germany), (DC 3: Austria and Germany), (DC 6: Austria and Germany), (DC 12: Austria and Denmark), (DC 13: Austria and Denmark).

Contact Information
For further information please contact Daniel Merkle, tel.: +45 6550 2322, e-mail:

The successful applicant will, if employed at SDU, be employed in accordance with the agreement on salaried PhD scholars between the Ministry of Finance and AC (the Danish Confederation of Professional Associations).

The successful candidate will, if employed at SDU, be enrolled at this university in accordance with faculty regulations and the Danish Ministerial Order on the PhD Programme at the Universities (PhD order).

These positions are subject to the entry into force of grant agreement no 101072930 by and between the European Research Executive Agency and University of Southern Denmark and thereby funded by the European Union’s Horizon Europe Research and Innovation Programme.

Further information about the PhD-study can be found at the homepage of the University.

Further information for international applicants considering applying for a job at the University of Southern Denmark. Please take a look at the webpage from our International Staff Office (ISO) at The University of Southern Denmark. Campus: Flere tjenestesteder Application deadline: 23/10/2023