PhD student in Scientific Computing focusing on Deep Learning for Cryo-Electron Microsopy - Hiring in process/Finished, not possible to apply

The Department of Information Technology has a leading position in research and all levels of higher education. Today the department has 280 employees, including 120 academic staff and 110 full-time PhD students. The Department comprises research and education in a spectrum of areas within Computer Science, Information Technology and Scientific Computing. More than 4000 students take one or several courses offered by the Department each year.

The position is hosted by the Division of Scientific Computing within the Department of Information Technology. As one of the world’s largest focused research environments in Scientific Computing the research and education has a unique breadth, with large activities in classical scientific computing areas such as mathematical modeling, development and analysis of algorithms, scientific software development and high-performance computing. The division is currently in an expansive phase in new emerging areas such as cloud and fog computing, data science, and artificial intelligence, where it plays key roles in several new strategic initiatives at the University.

Our PhD programs in scientific computing has resulted in over 80 completed PhD theses over the years. Several PhD alumni in Scientific Computing from Uppsala University are successful practitioners in the field, in industry as well as in academia.

Project description: The PhD position offered is connected to a project grant to Prof. Ozan Öktem. The project focus is the development and usage of artificial intelligence models for recovering the 3D structure and dynamics of isolated protein molecules in aqueous buffer from cryo-electron microscopy data. The project is an independent component of a larger collaboration that includes SciLifeLab, University of Cambridge, MRC Laboratory of Molecular Biology in Cambridge, and Thermo Fischer Scientific.

We create our own models for these applications, see the following paper for an example approach. This is an interdisciplinary project. Previous knowledge of structural biology/microscopy is not a requirement, but the successful completion of the project will require an interest in the application area. Interest and knowledge relating to neural network models, statistical learning, and numerical optimization are crucial to the project.

Duties: The duties of a PhD student are primarily directed at their own research education, which lasts four years. The work may also involve, to a limited extent (maximum 20%) other departmental duties, such as teaching undergraduate courses and administrative tasks – in which case the position may be extended to a maximum of five years.

Requirements: A PhD position at the Division requires a Master of Science or equivalent in a field that is relevant to the topic of the PhD thesis, good communication skills and excellent study results, as well as sufficient proficiency in oral and written English. Knowledge and experience in mathematical analysis, numerical optimization, statistical learning, deep learning, and scientific programming are of additional importance.

Additional qualifications: Basic knowledge of algebraic geometry and combinatorics is an advantage.

Application: Your application should include

• a personal letter describing your background, relevant qualification, research interests and how you see that your background would contribute to the specific project,
• Curriculum Vitae,
• degree documents (for any completed degree) and transcript of records (including completed courses and grades) to support that you’re qualified for admission to education at the PhD level,
• list of publications (if any),
• copy of your master thesis, or a detailed description of the ongoing thesis work, including a plan for its completion, if not fully complete at the end of the application period,
• list of reference persons with contact details,
• any other supporting documentation demonstrating your suitability for the position.

It is not a strict requirement for the relevant pre-requisite degree to be completed when the application is made. All applicants should state when they would be able to fulfill all requirements and be ready to assume the position. 

Rules governing PhD students are set out in the Higher Education Ordinance chapter 5, §§ 1-7 and in Uppsala University's rules and guidelines.

Salary: According to local agreement for PhD students.
 
Starting date: As soon as possible, preferably no later than 1 September.

Type of employment: Temporary position according to the Higher Education Ordinance chapter 5 § 7.

Scope of employment: 100 %

For further information about the position please contact: Project leader Professor Ozan Öktem, ozan.oktem@it.uu.se; ozan@oktem.se, Head of Division Emanuel Rubensson emanuel.rubensson@it.uu.se.

Please submit your application by 15 June 2021, UFV-PA 2021/2355.

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