PhD fellow in Computer Science (211-0333/19-2H)

DIKU is offering two Ph.D. scholarships in deep probabilistic programming (DPP) and protein structure prediction, commencing April 1st, 2020, or as soon as possible thereafter. The scholarships are made possible by a grant from the Independent Research Fund Denmark.

The overall objective of DPP is to predict the structure of proteins from their amino acid sequence (protein folding), one of the great scientific challenges of our times, by combining and advancing Bayesian statistics, deep learning and functional programming language technology and, conversely, advance high-performance deep probabilistic programming driven by protein folding.

The specific aims of this PhD project are the development of probabilistic models of protein structure for protein structure prediction using deep probabilistic programming.

Description of the scientific environment

The Department of Computer Science at University of Copenhagen (DIKU) is the first computer science department in Denmark, established by Peter Naur in 1970. Since then, our researchers and graduates have formed the basis for society’s accelerating technological transformation, and our research environment and results have made us one of Europe’s leading and most attractive computer science departments. The PhD will be part of the research group of Assoc. Prof. Thomas Hamelryck (, which focusses on probabilistic machine learning and protein structure prediction. The PhD position is part of a collaborative project involving Prof. Fritz Henglein (DIKU), Prof. Gabrielle Keller (Utrecht University, The Netherlands) and Prof. Christophe Ley (University Gent, Belgium).

Project description

The so-called “protein folding problem” - predicting the structure of proteins from their amino acid sequence - is one of the great scientific challenges of our times. The PhD position is part of a project that focuses on probabilistic protein structure prediction using deep probabilistic programming, an important emerging paradigm in machine learning that brings together Bayesian statistics, deep learning and programming language implementation. Conversely, we also use the protein folding problem as a challenge to drive the development of high-performance deep probabilistic programming. This results in an integrated multi-level approach - from developing a deep model of protein structure over efficient, tailored inference algorithms to fast, tailored execution on GPUs. The project brings together a multi-disciplinary team covering machine learning, statistics, protein structure and computer science.

Principal supervisor is Assoc. Prof. Thomas Hamelryck, Department of Computer Science,, Tel: +45 23960613

Job description

The position is available for a 3-year period and your key tasks as a PhD student at SCIENCE are:

  • To manage and carry through your research project
  • Attend PhD courses
  • Write scientific articles and your PhD thesis
  • Teach and disseminate your research
  • To stay at an external research institution for a few months, preferably abroad
  • Work for the department

Formal requirements

Applicants should hold an MSc degree related to computer science, physics or statistics with good results and good English skills. As criteria for the assessment of your qualifications emphasis will also be laid on experience in computer science, machine learning, previous publications (if any) and relevant work experience. Knowledge of protein structure or molecular biology is not required.

Terms of employment

The position is covered by the Memorandum on Job Structure for Academic Staff.

Terms of appointment and payment accord to the agreement between the Ministry of Finance and The Danish Confederation of Professional Associations on Academics in the State.

The starting salary is currently at a minimum DKK 328.355 (approx. €43,750) including annual supplement (+ pension at a minimum DKK 53,360). Negotiation for salary supplement is possible.

Integrated MSc and PhD Scheme

The position is also available for candidates who are (or are eligible to be) enrolled at one of the faculty’s master programmes in Computer Science, psysics or statistics. The duration of the integrated programme depends on the amount of credits that you have passed on your MSc programme. For further information about the study programme please see:, “Study Structures”.

Scholarship and terms of employment for integrated MSc and PhD

PhD grant portions (Ph.D.‐SU klip)
In the period up to the completion of the MSc programme (up to three years), the student is entitled to so-called PhD grant portions. The grant portions are financed by the grant donor but not by the Danish State Educational Grant and Loan Scheme Agency (as is the case for the ordinary study grant portions on the BSc and MSc programmes). They are called PhD grant portions because this kind of remuneration is regulated and described in the Executive Order on the State Educational Grant and Loan Scheme in Denmark (SU‐bekendtgørelsen), and because the value of a PhD grant portion corresponds to the value of an ordinary Danish study grant portion. Students are awarded 48 PhD grant portions during the period of their MSc and PhD studies. 48 PhD grant portions at DKK

'Duty work'

As a supplement to the PhD grant portions, the student may, in accordance with the collective agreement of the Danish Confederation of Professional Associations (AC), be offered 'duty work'. In the period up to the completion of the MSc programme, students performing 'duty work' are paid by the hour. UCPH has decided to offer students on integrated MSc and PhD schemes 150 hours of 'duty work' per year during Part A of the programme (until two years of the combined programme of study remain). 'Duty work' during Part A if it has a duration of three years: 450 hours at a rate of DKK 217,95 (+ 12.5% holiday pay).

For further information about Part A please see:

Salary in accordance with the collective agreement with the Danish Confederation of Professional Associations (AC)

In the period after the completion of the MSc programme, the student is employed as a PhD scholar and is remunerated in accordance with the collective agreement with the Danish Confederation of Professional Associations (AC). The scheme is arranged in such a way that students graduate from the MSc programme at a time when there are two years left of the integrated programme. For this reason, the salary must be paid for a period of two years in accordance with the collective agreement with the Danish Confederation of Professional Associations (AC).

Application Procedure

The application, in English, must be submitted electronically by clicking APPLY NOW below.

Please include

  • Cover Letter, stating which PhD project you are applying for and detailing your motivation and background for applying for the specific PhD project.
  • CV
  • Diploma and transcripts of records (BSc and MSc)
  • Acceptance Letter for the relevant MSc Programme at SCIENCE, if any
  • Other information for consideration, e.g. list of publications (if any), 

The University wishes our staff to reflect the diversity of society and thus welcomes applications from all qualified candidates regardless of personal background.

The deadline for applications is 15 January 2020, 23:59 GMT +1.

After the expiry of the deadline for applications, the authorized recruitment manager selects applicants for assessment on the advice of the Interview Committee. Afterwards an assessment committee will be appointed to evaluate the selected applications. The applicants will be notified of the composition of the committee and the final selection of a successful candidate will be made by the Head of Department, based on the recommendations of the assessment committee and the interview committee.
The main criterion for selection will be the research potential of the applicant and the above mentioned skills. The successful candidate will then be requested to formally apply for enrolment as a PhD student at the PhD school of Science. You can read more about the recruitment process at


For specific information about the PhD scholarship, please contact the principal supervisor Assoc. Prof. Thomas Hamelryck,, tel. +45 23960613.

General information about PhD programmes at SCIENCE is available at


Part of the International Alliance of Research Universities (IARU), and among Europe’s top-ranking universities, the University of Copenhagen promotes research and teaching of the highest international standard. Rich in tradition and modern in outlook, the University gives students and staff the opportunity to cultivate their talent in an ambitious and informal environment. An effective organisation – with good working conditions and a collaborative work culture – creates the ideal framework for a successful academic career.