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Department of Computer Science (DIKU), Faculty of Science at University of Copenhagen is offering two PhD scholarships within the PHYLORAMA research project commencing 1 April 2021 or as soon as possible thereafter.


Description of the scientific environment
The two PhD scholarships are part of a collaborative research project entitled “Expanding the Tree of Life through a digital view of museum collections (PHYLORAMA)” between the Department of Computer Science (DIKU) and Natural History Museum of Denmark (NHMD) at University of Copenhagen. As part of this project, NHMD will also offer an additional PhD scholarship within entomology with a focus on the phylogeny of rove beetles (Staphylinidae). Although each of the PhD projects of PHYLORAMA have certain foci within their respective domains, we expect applicants with the desire to go beyond their domain limits. Interactions and synergy among supervisors and students from the computer science and entomology domains are at the core of PHYLORAMA. All PhD projects will contribute to the digitalization of the NHMD collections. 

The two PhD scholarships offered here will have main employment at DIKU and be embedded in the Section for Image Analysis, Computational Modelling and Geometry (IMAGE), but some time will also be spend at NHMD. The IMAGE section aspires to be a top research environment that bridges theory and applications of image analysis, computer, vision and machine learning. We offer laboratory and workshop facilities that will be used as part of the PhD projects.

Project description
The Tree of Life (Phylogeny) is a fundamental concept of biology to understand the biodiversity of our planet. Species are represented as ‘leaves’ and their evolutionary relationships as tree branches. Yet the position of more than one million+ species of insects remain poorly resolved within the Tree of Life, or even completely unknown. This is partly because of the extreme diversity of insects as a lineage. Automated pipelines of phylogenomics cannot overcome this so-called ‘Linnean shortfall’ because 1) the majority of insect species are available as legacy specimens from natural history museum collections only and thus contain DNA of low quality, and 2) DNA is not available in fossils which are crucial for the Tree of Life reconstruction. By combining computer vision with entomology, we will explore a possibility of a high throughput ‘phylophenomic’ pipeline that 1) rapidly acquire and manage images of millions of specimens, both recent and fossil, in the museum collections; and 2) identify taxa from images and cluster them via interpretable deep learning models into the Tree of Life clades either based on phenotypes or in combination with genomic data. The PHYLORAMA research project is a blend of systematic entomology and computer science, with classical elements from both domains and a shot for innovation aiming a boost in phylogenetic research in entomology by computer science.


The PHYLORAMA project seeks highly motivated applicants for two PhD scholarships:

  1. Automated taxonomic identification and clustering: This PhD project will focus on development of novel methods and algorithms for automated taxonomic identification and clustering of rove beetles (Staphylinidae) from images using interpretable deep learning. Furthermore, an experimental setup for massive digital image data acquisition must be build.
     
  2. 3D reconstruction with refraction: This PhD project will focus on development of methods for 3D reconstruction of insects enclosed in amber by extending Multi-view and photometric stereo methods to handle refraction of light as it passes through amber and combining these two approaches in a unified photogeometric model. Methods for recovery of the amber surface geometry need to be developed and an experimental setup must be built containing camera and lighting that will generate data to be used in the PHYLORAMA project. This will be a joint PhD with DIKU and the Institut National Polytechnique de Toulouse, INPT, France, leading to a dual degree PhD from these two institutions. Consequently, the PhD student will spent her/his stay abroad at INPT.

Principal supervisor for PhD project 1 is Associate Professor, PhD., Kim Steenstrup Pedersen, Department of Computer Science, kimstp@di.ku.dk, Direct Phone: +45 61 37 45 29. Principal supervisor for PhD project 2 is Associate Professor, PhD., Francois Lauze, Department of Computer Science, francois@di.ku.dk, Direct Phone: + 45 35 33 56 71.

Job description
The position is available for a 3-year period and your key tasks as a PhD student at SCIENCE are:

  • To manage and carry through your research project
  • Attend PhD courses
  • Write scientific articles and your PhD thesis
  • Teach and disseminate your research
  • To stay at an external research institution for a few months, preferably abroad
  • Work for the department

Formal requirements
Applicants should hold an MSc degree in Computer Science, Engineering, Mathematics or other relevant field with a focus on image analysis, computer vision and machine learning. The successful applicant is expected to have obtained outstanding grades during the MSc studies, and to be proficient in spoken and written English. As criteria for the assessment of your qualifications emphasis will also be put on previous publications (if any) and relevant work experience.

Terms of employment
The position is covered by the Memorandum on Job Structure for Academic Staff.

Terms of appointment and payment accord to the agreement between the Ministry of Finance and The Danish Confederation of Professional Associations on Academics in the State.

The starting salary is currently at a minimum DKK 331,125 (approx. €43,750) including annual supplement (+ pension at a minimum DKK 53,811). Negotiation for salary supplement is possible.

Application Procedure
The application, in English, must be submitted electronically by clicking APPLY NOW below.

Please include

  • Cover Letter, stating which PhD project you are applying for and detailing your motivation and background for applying for the specific PhD project.
  • CV
  • Diploma and transcripts of records (BSc and MSc)
  • Other information for consideration, e.g. list of publications (if any)
  • 1-3 reference letters (if any)

Reference letters must be uploaded by the applicant him/herself. The recruiting person must NOT  obtain reference letters which content is not known to the applicant him/herself. This is against Danish law.

The University wishes our staff to reflect the diversity of society and thus welcomes applications from all qualified candidates regardless of personal background.

The deadline for applications is 7 February 2021, 23:59 GMT +1.

After the expiry of the deadline for applications, the authorized recruitment manager selects applicants for assessment on the advice of the Interview Committee. Afterwards an assessment committee will be appointed to evaluate the selected applications. The applicants will be notified of the composition of the committee and the final selection of a successful candidate will be made by the Head of Department, based on the recommendations of the assessment committee and the interview committee.

The main criterion for selection will be the research potential of the applicant and the above mentioned skills. The successful candidate will then be requested to formally apply for enrolment as a PhD student at the PhD school of Science. You can read more about the recruitment process at https://employment.ku.dk/faculty/recruitment-process/.


Questions
For specific information about the PhD scholarship, please contact the principal supervisors Associate Professor, PhD, Kim Steenstrup Pedersen, Department of Computer Science, kimstp@di.ku.dk, Direct Phone: +45 61 37 45 29 and Associate Professor, PhD, Francois Lauze, Department of Computer Science, francois@di.ku.dk, Direct Phone: + 45 35 33 56 71.

General information about PhD programmes at SCIENCE is available at https://www.science.ku.dk/phd.

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