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Project Description

PhD Subject: Computer Science

The project focuses on improving species delimitation in biodiversity conservation through modern methods in artificial intelligence (AI).

Traditional methods for species delimitation, based on morphological characteristics, struggle to handle groups such as bacteria and mosses, where morphology is either highly plastic or non-existent. To document and conserve the many yet unidentified species, many of which are close to extinction, the project proposes to leverage AI advancements for improved species delimitation.

Large-scale initiatives such as the International Barcode of Life and the Earth Biogenome Project are already working on characterizing and sequencing DNA from millions of species. However, there are computational challenges in using these extensive genomic datasets for species delimitation. The multispecies coalescent (MSC) model offers a framework for understanding genealogical relationships and genetic divergence between species, but its complexity requires new methods for effective analysis.

This project aims to utilize methods in variational inference (VI), enhanced by AI technologies such as normalizing flows, graph neural networks, and transformer models, to represent probability distributions over trees and improve MSC estimation. These technologies have shown significant improvements in phylogenetic analysis compared to traditional Bayesian methods, and this capacity for enhancements will have an even greater impact on the more complex MSC model.

The project will develop an efficient framework for constructing species and gene trees under the MSC model. The goal is to achieve genome-level analysis capacity, including all gene families for the studied species and a large number of species. Finally, a framework utilizing the coalescent model for species delimitation will be developed and applied.

Supervision: Jens Lagergren is proposed to supervise the PhD student. A decision will be made upon admission.

We Offer

• The opportunity to pursue a PhD in a dynamic, international research environment in collaboration with industry and leading universities worldwide.
• A workplace with many employment benefits and a monthly salary according to KTH's agreement for doctoral salaries.
• Research education at an institution that is active and supportive in matters such as working conditions, equality and diversity, and study environment.
• Work and study in Stockholm with proximity to nature and the sea.

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 degree at advanced level, or
• fulfilled course requirements of at least 240 higher education credits, of which at least 60 higher education credits at advanced level, or
• acquired equivalent knowledge in some other way, within or outside the country.

In addition to the above, there is also a mandatory requirement for English equivalent to English B/6.

Selection

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

• independently drive your work forward,
• collaborate with others,
• have a professional approach, and
• analyze and work with complex issues.

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

Target Degree: Doctoral Degree

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 within, for example, education and administration. A new employment as a PhD student is valid for a maximum of one year, and the employment may thereafter 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.

Union Representatives

Contact information for union representatives.

PhD Section (Student Union of the Royal Institute of Technology)

Contact information for the PhD section.

Application

You apply via KTH's recruitment system. As an applicant, you are primarily responsible for ensuring that your application is complete when submitted.

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

The application must include the following content:

• CV with relevant professional experiences and skills.
• Application 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 degree certificates and transcripts from previous university studies and certificates of fulfilled language requirements (see above). Translations into English or Swedish if the original document is not issued in one of these languages. Copies of originals must be certified.
• Representative publications or technical reports. For longer documents, please attach a summary (abstract) and a web link to the full text.

Other

The pursuit of equality, diversity, and equal opportunities is both a quality issue and an obvious part of KTH's core values.

For information on the processing of personal data in connection with recruitment.

It may occur that an employment at KTH is classified in a security class. If this is the case for this particular employment, a security review of the applicant will be conducted in accordance with the Security Protection Act (2018:585) after consent. In these cases, a condition 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 sellers of job advertisements.

About KTH

KTH is one of Europe's leading technical universities and an important arena for knowledge development. As Sweden's largest university for technical research and education, we gather students, researchers, and faculty from all over the world. Our research and education encompass both natural sciences and all branches of engineering, as well as architecture, industrial economics, urban planning, history, and philosophy. https://www.kth.se/om/om-kth-1.885102 (https://www.kth.se/om/om-kth-1.885102)