PhD student in Machine Learning with a focus on probabilistic models in microbial and cellular ecology

Are you interested in working with probabilistic models in microbial and cellular ecology, with the support of competent and friendly colleagues in an international environment? Are you looking for an employer that invests in sustainable employeeship and offers safe, favorable working conditions? We welcome you to apply for a PhD position at Uppsala University. 

Uppsala University has a long tradition of successful research – among its alumni are 16 Nobel Prize laureates, including, most recently, Svante Pääbo. The University is unique when it comes to combining IT with wider research, from life sciences to the humanities, and this collaboration is currently facilitated by AI4Research and the Centre for Interdisciplinary Mathematics.

The Department of Information Technology holds a leading position in both research and education at all levels. We are currently Uppsala University's third largest department, have around 350 employees, including 120 teachers and 120 PhD students. Approximately 5,000 undergraduate students take one or more courses at the department each year. You can find more information about us on the Department of Information Technology website.

At the Division of Systems and Control, we develop both theory and concrete tools to design systems that learn, reason, and act in the real world based on a seamless combination of data, mathematical models, and algorithms. Our research integrates expertise from machine learning, optimization, control theory, and applied mathematics, spanning diverse application domains such as medicine, energy systems, biomedical systems, neuroscience, and safety and security.

The Division of Systems and Control enjoys a wide network of strong international collaborators all around the world, for example at the University of Cambridge, University of Oxford, Imperial College, University of Sydney, University of Newcastle and Aalto University. We strive for all PhD students to get a solid international experience during their PhD.

The position is a part of the Beijer Laboratory for Artificial Intelligence Research, funded by Kjell and Märta Beijer Foundation. The Beijer Laboratory for Artificial Intelligence Research was established in 2023 at Uppsala University with an ambition to grow activities within the subject of AI, focusing on applications in the life sciences and questions related to societal development.

Project description
All ecological systems, including ecologies of cells, consist of interacting parts. Cell imaging data, which hold rich information about how cells act and interact with each other, can be translated into spatio-temporal point patterns in which points represent cell locations. In this project, the doctoral student will develop mathematical models and machine learning methods that probabilistically infer information about microbial and cellular ecologies from the point patterns that they generate. During the process, the student will learn how to combine mathematical models (based e.g., point processes and differential equations) with machine learning methods (e.g., Hamiltonian Monte Carlo sampling and neural networks) to solve research problems in microbial and cellular ecology. The doctoral student will join the Artificial Intelligence and Mathematics for Oncology (AIMOn) group and work closely with experts in applied mathematics, statistics, machine learning and experimental cell and microbiology. The project is funded by a grant from the Swedish Research Council.

Duties
A Ph.D. student is expected to devote their time to graduate education mainly. The rest of the duties may involve teaching at the Department, including also some administration, to at most 20%.

Requirements
To meet the entry requirements for doctoral studies, you must

• hold a Master’s (second-cycle) degree in engineering physics, applied mathematics, physics, computer science, machine learning, or in a similar research field, or
• have completed at least 240 credits in higher education, with at least 60 credits at Master’s level including an independent project worth at least 15 credits, or
• have acquired substantially equivalent knowledge in some other way.

We are looking for candidates with

• a strong interest in developing probabilistic mathematical models and machine learning methods to understand microbial and cellular ecologies,
• good communication skills and sufficient proficiency in oral and written English,
• excellent study results, 
• programming experience,
• creativity, thoroughness, and a structured approach to problem-solving,
• a collaborative mindset and enthusiasm for interdisciplinary work.

Additional qualifications
Experience with calculus, linear algebra and programming is required. Prior knowledge of ecology or microecology is not required. Experience with one or more of the following subjects is meriting:

• mathematical biology,
• Bayesian statistics,
• probability theory,
• machine learning.

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

For special entry requirements, please see the subject’s general study plan.

Application
The application must include:

1. a cover letter (at most 1 page) outlining the applicant’s motivation for applying for this position, including a self-assessment on why you would be the right candidate for this position, and your expected earliest starting date (a starting date between March and August 2025 is expected);
2. a CV;
3. degrees and transcript of records with grades (translated to English or Swedish);
4. the Master’s thesis (or a draft thereof, and/or some other self-produced technical or scientific text), publications, and other relevant documents;
5. references with contact information (names, emails and telephone number) and up to two letters of recommendation. 

Applicants who fulfill at least one of the eligibility requirements are strongly encouraged to apply. All applicants should indicate their earliest possible start date.

About the employment
The employment is a temporary position according to the Higher Education Ordinance chapter 5 § 7. Scope of employment 100 %. Starting date August 1st 2025 or as agreed. Placement: Uppsala.

For further information about the position, please contact: Assistant Professor Sara Hamis, e-mail: sara.hamis@it.uu.se. 

Please submit your application by 31 December 2024, UFV-PA 2024/3935.

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