PhD fellowship in Computer Science

PhD Project in shape statistics and stochastic processes for phylogenetic analysis
Department of Computer Science
Faculty of SCIENCE
University of Copenhagen

The IMAGE section at the department of computer science (DIKU) invites applicants for a PhD fellowship in in stochastic shape statistics and stochastic processes for phylogenetic analysis. The project is part of the research project “Stochastic Morphometry: Evolutionary Modelling of Whole Shape Data”.

Start date is (expected to be) 1 February 2022 or as soon as possible thereafter.

The project
Organismal morphology is studied in biology to decode evolutionary relationships among species and test hypotheses about the evolutionary tree. The Stochastic Morphometry project aims for developing statistical models of morphological change through evolution, thereby making phylogenetic inference tools applicable for studying shape evolution. The aim is to revolutionize how evolutionary analyses of morphological data are performed to fully take advantage of the rich information of changes in complex biological structures. The developed models will be applied to studies of a rich set of biological data. The project is lead by Stefan Sommer (UCPH), Rasmus Nielsen (UCPH, Berkeley), Mads Nielsen (UCPH) and Christy Hipsley (UCPH).

The PhD project will focus stochastic evolution of shapes in infinite dimensions, and inference in such models, for example by simulation of stochastic processes conditional on reaching observed shapes at the leafs of the evolutionary tree. The project will thereby span differential geometry, stochastic analysis, numerical computations, and statistics: We will create tools that give new biological insight, but in order to reach this use an extremely exiting mix of advanced mathematics, statistics, and computer science at the very forefront of the state-or-the-art.

The project is physically located in Copenhagen, but with strong links to University of California, Berkeley. The project participants should expect to participate in visits and research stays in Berkeley.

Who are we looking for?
We are looking for excellent candidates within the fields of statistics, mathematics, computer science, physics or related fields. Applicants can have an MSc from one of these fields, and in addition have

• solid programming experience
• solid mathematical training and interest, for example in differential geometry, stochastic processes, probability theory, statistics, or theoretical computer science
• have a wish to apply advanced mathematics, statistics and computer science techniques in biology
• be creative, solution oriented and able to work both independently and in research teams
• be ambitious and have a wish to work with a world-leading team in Copenhagen and Berkeley

Our group and research- and what do we offer?
The stochastic morphometry research project comprises leading experts in phylogenetic analysis, shape modelling and stochastics of shapes, image analysis, and biology. In addition to senior researchers, the group will host multiple junior researchers (PhDs and postdocs), and master students. We offer an exciting research environment where you will get the chance to apply mathematical and computational tools to solve important problems in biology and thereby change the way animal morphology is used in phylogenetic analyses in the future.

The group is a part of department of Computer Science, Faculty of SCIENCE, University of Copenhagen. We are primarily located in Copenhagen but the project has strong links to University of California, Berkeley and visits and research stays in Berkeley should be expected.

We offer creative and stimulating working conditions in dynamic and international research environment.

Principal supervisor is Professor Stefan Sommer, DIKU, E-mail: [email protected] , Direct Phone: +45 21179128.

The PhD programme
Depending of your level of education, you can undertake the PhD programme as either:

Option A:
A three year full-time study within the framework of the regular PhD programme (5+3 scheme), if you already have an education equivalent to a relevant Danish master’s degree.

Option B:
An up to five year full-time study programme within the framework of the integrated MSc and PhD programme (the 3+5 scheme), if you do not have an education equivalent to a relevant Danish master ́s degree – but you have an education equivalent to a Danish bachelors ́s degree.

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Option A: Getting into a position on the regular PhD programme

Qualifications needed for the regular programme
To be eligible for the regular PhD programme, you must have completed a degree programme, equivalent to a Danish master’s degree (180 ECTS/3 FTE BSc + 120 ECTS/2 FTE MSc) related to the subject area of the project (see above). For information of eligibility of completed programmes, see General assessments for specific countries and Assessment database.

Terms of employment in the regular programme
Employment as PhD fellow is full time and for maximum 3 years.

Employment is conditional upon your successful enrolment as a PhD student at the PhD School at the Faculty of SCIENCE, University of Copenhagen. This requires submission and acceptance of an application for the specific project formulated by the applicant.

The terms of employment and salary are in accordance to the agreement between the Ministry of Finance and The Danish Confederation of Professional Associations on Academics in the State (AC). The position is covered by the Protocol on Job Structure.

Salary range starts at DKK 27,588.59 per month incl. PhD supplement (1 April 2021 level).

Option B: Getting into a position on the integrated MSc and PhD programme

Qualifications needed for the integrated MSc and PhD programme

If you do not have an education equivalent to a relevant Danish master ́s degree, you might be qualified for the integrated MSc and PhD programme, if you have an education equivalent to a relevant Danish bachelor ́s degree. Here you can find out, if that is relevant for you: General assessments for specific countries and Assessment database.

Terms of the integrated programme
To be eligible for the integrated scholarship, you are (or are eligible to be) enrolled at one of the faculty’s master programmes in Computer Science.

Students on the integrated programme will enroll as PhD students simultaneously with completing their enrollment in this MSc degree programme.

The duration of the integrated programme is up to five years, and depends on the amount of credits that you have passed on your MSc programme. For further information about the study programme, please see: www.science.ku.dk/phd , “Study Structures”.

Until the MSc degree is obtained, (when exactly two years of the full 3+5 programme remains), the grant will be paid partly in the form of 48 state education grant portions (in Danish: “SU-klip”) plus salary for work (teaching, supervision etc.) totalling a workload of at least 150 working hours per year. A PhD grant portion is DKK 6,243. Salary is DKK 221.34 per working hour (+ 12.5% holiday pay).(1 April 2021 level)

When you have obtained the MSc degree, you will transfer to the salary-earning part of the scholarship for a period of two years. At that point, the terms of employment and payment will be according to the agreement between the Ministry of Finance and The Danish Confederation of Professional Associations on Academics in the State (AC). The position is covered by the Protocol on Job Structure. Salary range starts at DKK 27,568.13 per month incl. PhD supplement.

Responsibilities and tasks in both PhD programmes

• Complete and pass the MSc education in accordance with the curriculum of the MSc programme (ONLY when you are attending the integrated MSc and PhD programme)
• Carry through an independent research project under supervision
• Complete PhD courses corresponding to approx. 30 ECTS / ½ FTE
• Participate in active research environments, including a stay at another research institution, preferably abroad
• Teaching and knowledge dissemination activities
• Write scientific papers aimed at high-impact journals
• Write and defend a PhD thesis on the basis of your project

We are looking for the following qualifications:

• Solid programming experience
• Solid mathematical training and interest, for example in differential geometry, stochastic processes, probability theory, statistics, or theoretical computer science
• A wish to apply advanced mathematics, statistics and computer science techniques in biology
• Creative, solution oriented and able to work both independently and in research teams
• Ambitious and have a wish to work with a world-leading team in Copenhagen and Berkeley
• Good language skills, both orally and written

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Application and Assessment Procedure

Your application including all attachments must be in English and submitted electronically by clicking APPLY NOW below.

Please include:

1. Motivated letter of application (max. one page)
2. Your motivation for applying for the specific PhD project
3. Curriculum vitae including information about your education, experience, language skills and other skills relevant for the position
4. Original diplomas for Bachelor of Science or Master of Science and transcript of records in the original language, including an authorized English translation if issued in another language than English or Danish.If not completed, a certified/signed copy of a recent transcript of records or a written statement from the institution or supervisor is accepted.
5. Documented examples of computer code you have written (if possible) (e.g. links to Github repository)
6. Publication list (if possible)
7. Reference letters (if available)

Application deadline:
The deadline for applications is 31 October 2021, 23:59 GMT +1.

We reserve the right not to consider material received after the deadline, and not to consider applications that do not live up to the abovementioned requirements.

The further process
After deadline, a number of applicants will be selected for academic assessment by an unbiased expert assessor. You are notified, whether you will be passed for assessment.

The assessor will assess the qualifications and experience of the shortlisted applicants with respect to the above mentioned research area, techniques, skills and other requirements. The assessor will conclude whether each applicant is qualified and, if so, for which of the two models. The assessed applicants will have the opportunity to comment on their assessment. You can read about the recruitment process at https://employment.ku.dk/faculty/recruitment-process/ .

Interviews with selected candidates are expected to be held in week 49.

Questions
For specific information about the PhD fellowship, please contact the principal supervisor.General information about PhD study at the Faculty of SCIENCE is available at the PhD School’s website: https://www.science.ku.dk/phd/ .

The University of Copenhagen wishes to reflect the surrounding community and invites all regardless of personal background to apply for the position.

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.