Project Description

PhD Subject: Computer Science

Cryo-EM is an imaging method that uses images from electron microscopes to reconstruct the 3D structure of biological molecules.

However, the images from the electron microscope are very noisy, which is compensated by collecting a large amount of data, leading to high collection costs.

This project proposes a new method for reconstructing 3D structures of molecules from cryo-EM images using generative models. The prospective student will join this link (https://www.csc.kth.se/~azizpour/) and develop new generative models of biomolecular structures to be used by other project members as a starting point in Bayesian inference of protein dynamics to construct more reliable 3D structures.

The project constitutes a collaboration within Digital Futures between the Departments of Mathematics and Intelligent Systems at KTH and the Department of Biochemistry and Biophysics at SU.

Another PhD position in generative modeling for biology can be found here (https://www.kth.se/lediga-jobb/899298?l=en).

Supervision

Hossein Azizpour is proposed to supervise the PhD student. Decisions will be made upon admission.

Eligibility for Admission

To be admitted to doctoral education (Chapter 7, Section 39 of the Higher Education Ordinance), the applicant must have basic eligibility:

• completed a master's degree, or
• completed course requirements of at least 240 higher education credits, of which at least 60 higher education credits at the master's level, or
• acquired equivalent knowledge in some other way, within or outside the country.
• strong programming skills, especially experience in deep learning programming,
• previous education and research experience in machine learning.

In addition to the above, there is also a document (https://www.kth.se/studies/phd/entry-requirements-for-doctoral-studies-1.520175).

Selection

To succeed in your PhD studies at KTH, you need to be goal-oriented and persistent in your work. In the selection of applicants, the ability to:

• independently drive their work forward,
• collaborate with others,
• maintain a professional attitude, and
• analyze and work with complex issues.
• demonstrate research experience and education in both theory and practice of machine learning, particularly deep generative modeling,
• research experience or education in life science data, particularly MSI data, and
• previous experience with remote GPU and HPC services.

After the eligibility requirements, great importance will be placed on personal qualities.

Target Degree

Doctorate

Information on Admission and Employment

Only those who have been admitted to doctoral education may be employed as PhD students. The total employment period may not exceed what corresponds to full-time doctoral education for four years. An employed PhD student may, to a limited extent (maximum 20%), perform certain tasks in e.g. education and administration. A new employment as a PhD student is valid for a maximum of one year, after which the employment may be renewed for a maximum of two years at a time. For studies that will conclude with a licentiate degree, the total employment period may not exceed what corresponds to full-time doctoral education for two years.

As a PhD student, you will benefit from benefits (https://www.kth.se/om/jobba-pa-kth/kth-en-arbetsplats-med-manga-formaner-1.467932) and have a monthly salary according to salary structure (https://intra.kth.se/anstallning/anstallningsvillkor/lon/doktorandstegen-1.572915). Read more about doctoral studies (https://www.kth.se/studies/phd/doctoral-studies-phd-1.9318).

Union Representatives

Contact information for union representatives (https://intra.kth.se/administration/rekrytering/annonsering/fackrepresentanter-1.500898).

The Doctoral Section (Student Union of the Royal Institute of Technology) contact information can be found here (https://www.dr.kth.se/).

Application

You apply via KTH's recruitment system. As an applicant, you have the main responsibility for ensuring that your application is complete when submitted.

The application must be received by KTH no later than the last application date at midnight, CET/CEST (Central European Time/Central European Summer Time).

The application should include the following content:

• CV with relevant professional experiences and skills.
• Cover letter with a brief account of why you want to pursue doctoral studies, your academic interests, and how they relate to your previous studies and future goals. (Max 2 pages)
• Copies of diplomas and transcripts from previous university studies and certificates of fulfilled requirements (https://www.kth.se/en/studies/phd/admission-requirements-1.520175). Translations into English or Swedish if the original document is not issued in one of these languages. Copies of originals should be verified (https://www.kth.se/student/studier/examen/vidimering-av-handlingar-1.55190).
• Representative publications or technical reports. For longer documents, please attach a summary (abstract) and a web link to the full text.

Other

For processing of personal data (https://www.kth.se/om/work-at-kth/processing-of-personal-data-in-the-recruitment-process-1.823440) in connection with recruitment.

It may occur that a position at KTH is classified. If so, a security review of the applicant will be conducted in accordance with the Security Protection Act (2018:585) after consent. In these cases, a prerequisite for employment is that the applicant is approved after the security review.

We kindly ask for no direct contact with staffing and recruitment companies or advertisers of job postings.

Become a part of KTH

KTH shapes the future through education, research, and innovation. As a leading international technical university, we play an active role in driving and participating in the transition to a sustainable society. Here you are offered the opportunity to grow and develop in a creative and dynamic workplace with good working conditions and benefits. Equality, diversity, and equal opportunities are quality issues and an obvious part of KTH's values as a university and government agency.

Read more about working at KTH (https://www.kth.se/om/jobba-pa-kth).