School of Electrical Engineering and Computer Science at KTH

Project description

Third-cycle subject: Computer Science

Variational autoencoders (VAEs), the newest version of the Variational inference (VI) methodology, is becoming increasingly important in analysis of large single-cell and spatial biological data. Yet, employing them for posterior approximations in Bayesian phylogenetics is a difficult problem, and clear examples of successful applications are still outstanding. Following the recent trends in VAE research, one may hypothesize that this may be addressed by incorporating inductive biases, modeling more advanced prior distributions, and/or via architecture design.

The aim of this project is to explore the possibility of employing VAEs, or other deep generative models, in the setting of somatic cancer evolution and Bayesian phylogenetics. By doing so, the successful applicant will simultaneously contribute to two highly impactful scientific fields: computational biology/cancer and approximate Bayesian inference in deep learning.

Our group teaches and produces cutting-edge research in VAEs, VI and approximate Bayesian inference in general (e.g., sequential Monte Carlo, MCMC, importance sampling). We are especially interested in the development of inference methods for phylogenetics and single-cell data. As such, the group provides a fertile environment for the Ph.D. student’s development. Additionally, the group has an excellent national and international network, including both methodological and cancer-research groups.

This project is funded by WASP, as such the Ph.D. student will be a part of the WASP Graduate School, which is dedicated to provide the skills needed to analyze, develop, and contribute to the interdisciplinary area of artificial intelligence, autonomous systems and software. The WASP Graduate School assists in forming a Strong Professional Network and its curriculum provides the foundations, perspectives, and state-of-the-art knowledge in the different disciplines taught by leading researchers in the field. The WASP Graduate School provides added value on top of the existing PhD programs at the partner universities, providing unique opportunities for students who are dedicated to achieve international research excellence with industrial relevance.

Supervision: Jens Lagergren is proposed to supervise the doctoral student. Decisions are made on admission

What we offer

Admission requirements

To be admitted to postgraduate education (Chapter 7, 39 § Swedish Higher Education Ordinance), the applicant must have basic eligibility in accordance with either of the following:

  • passed a second cycle degree (for example a master's degree), or
  • completed course requirements of at least 240 higher education credits, of which at least 60 second-cycle higher education credits, or
  • acquired, in some other way within or outside the country, substantially equivalent knowledge

In addition to the above, there is also a mandatory requirement for English equivalent to English B/6, read more here


In order to succeed as a doctoral student at KTH you need to be goal oriented and persevering in your work. During the selection process, candidates will be assessed upon their ability to:

  • have excellent programming skills,
  • have a solid background in machine learning,
  • have excellent skills in mathematics,
  • independently pursue his or her work,
  • collaborate with others,
  • have a professional approach and
  • analyse and work with complex issues.

After the qualification requirements, great emphasis will be placed on personal skills. 

Target degree: Doctoral degree

Information regarding admission and employment

Only those admitted to postgraduate education may be employed as a doctoral student. The total length of employment may not be longer than what corresponds to full-time doctoral education in four years ' time. An employed doctoral student can, to a limited extent (maximum 20%), perform certain tasks within their role, e.g. training and administration. A new position as a doctoral student is for a maximum of one year, and then the employment may be renewed for a maximum of two years at a time. In the case of studies that are to be completed with a licentiate degree, the total period of employment may not be longer than what corresponds to full-time doctoral education for two years.

Union representatives

You will find contact information for union representatives on KTH's website.

Doctoral section (Students’ union on KTH Royal Institute of Technology)

You will find contact information for doctoral section on the section's website.

To apply for the position

Apply for the position and admission through KTH's recruitment system. It is the applicant’s responsibility to ensure that the application is complete in accordance with the instructions in the advertisement.

Applications must be received at the last closing date at midnight, CET/CEST (Central European Time/Central European Summer Time).

Applications must include the following elements:

  • CV including your relevant professional experience and knowledge.
  • Application letter with a brief description of why you want to pursue research studies, about what your academic interests are and how they relate to your previous studies and future goals. (Maximum 2 pages long)
  • Copies of diplomas and grades from previous university studies and certificates of fulfilled language requirements (see above). Translations into English or Swedish if the original document is not issued in one of these languages.Copies of originals must be certified.
  • Representative publications or technical reports. For longer documents, please provide a summary (abstract) and a web link to the full text.

Other information

Striving towards gender equality, diversity and equal conditions is both a question of quality for KTH and a given part of our values.

For information about processing of personal data in the recruitment process please read here.

We firmly decline all contact with staffing and recruitment agencies and job ad salespersons.

Disclaimer: In case of discrepancy between the Swedish original and the English translation of the job announcement, the Swedish version takes precedence.


Type of employment Temporary position
Contract type Full time
First day of employment According to agreement
Salary Monthly salary according to KTH's doctoral student salary agreement
Number of positions 1
Full-time equivalent 100%
City Stockholm
County Stockholms län
Country Sweden
Reference number J-2023-1767
  • Jens Lagergren,
Published 21.Jun.2023
Last application date 15.Aug.2023 11:59 PM CEST

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