Doctoral Research Fellow (PhD) in Artificial Intelligence for Personalized Medicine

Bård Halvorsen
19th April 2024
Languages
English

• English

English
Digitalisation and Society
Doctoral Research Fellow (PhD) in Artificial Intelligence for Personalized Medicine
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About the position 

A Doctoral Research Fellowship in Artificial Intelligence for Personalized Medicine is available at the Faculty of Computer Sciences, Engineering and Economics at Østfold University College (ØUC).

The Doctoral Research Fellowship is associated with the PhD project “Transfer Retrieval: A new paradigm for Personalized Medicine through AI-driven genomic database search” funded by Østfold University College (ØUC).

The doctoral position is part of the research initiative “The Digital Society ” at ØUC

Project description 

A key challenge in current healthcare arises from the ineffective medications among a significant portion of patients. The increasing costs associated with these ineffective treatments have become a pressing concern for governments. Personalized medicine emerges as a promising solution to address these issues by enabling a medical treatment that tailors prevention, diagnosis and medication strategies for an individual patient. The emergence of -omics and single cell technologies has created new opportunities for the diagnosis and treatment of complex diseases such as cancer. Integrating information from multiple sources, e.g. proteins, RNAs and clinical/environmental factors, makes it possible to understand disease mechanisms, find biomarkers and therapeutic agents. The effective integration and utilization of vast amounts of such publicly available data is an important challenge in the implementation of personalized medicine.

The main objective of this PhD project is to build a generic solution for the content-based search of relevant genomic profiles in large, clinically-annotated databases, which, in turn, may foster personalized medicine through similarity assessment between diagnosis and treatment of different cancer samples. To this end, the project will develop a machine-learning-based information retrieval framework for a data-driven but biologically-guided representation of gene expression profiling experiments.

We particularly aim to propose a new architecture for cross-technology and cross-modality retrieval of similar profiling experiments using both clinical annotations and data representations that will be learned from large compendium of publicly available datasets. This includes both the development of novel computational models to represent transcriptome data and building biological models to map raw expression measurements to cellular networks and activities associated with certain diseases. The project will then follow a multi-disciplinary approach to derive and integrate data-driven models and biological mapping functions. We further plan to assess the clinical significance of the proposed solution using a number of down-stream tasks with expert-annotated real-world data, including cancer type/subtype identification and genetic perturbation prediction. The project is eventually expected to deliver explainable AI models that will support the diagnosis and treatment of cancers.

About Research fellowship  

The Doctoral Research Fellowship is a full time (100%) fixed term position for 3 years funded by Østfold University College. 

The candidate will be employed at Østfold University College. The candidate is expected to apply and be accepted in our Doctoral Programme “Digitalisation and Society”. Read more on our website: Digitalisation and Society  

Estimated starting date: 1st of September 2024

The candidate is expected to:

• actively take part in inter- and multi-disciplinary research activities relevant to AI Hub hosted by Østfold University College.

• design, develop, implement and test novel computational models for intelligent analysis and retrieval of transcriptomic data during their PhD studies.

• disseminate research results on the project through high-quality scientific publications.

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Qualification requirements 

The successful candidate is required to have 

• completed a master's degree or second degree (equivalent to 120 credits according to Norwegian standard definitions) within the field of Computer Science or similar. Candidates that are close to completion may also be evaluated. Documentation of the completed master’s degree must be submitted within three weeks after the application deadline.  
• been awarded the grade B or better for the Master thesis - in terms of the Norwegian grading scale. If the research summary is of excellent quality, grade C candidates can be considered.  
• excellent oral and written communication skills in English and sufficient oral and written communication skills in a Scandinavian language. For international candidates (outside of EU/EEA area), approved TOEFL English proficiency test with min score 90 or IELTS test with min. score 7.5. 
•  solid programming skills.

Desired qualifications

We would like you to have

• an average grade point for courses included in the Master’s degree of B or better in terms of the Norwegian grading scale. 
• relevant work and/or academic experience.
• prior knowledge and/or experience in tools and databases in bioinformatics and computational biology.
• experience in installing, training and using large foundation/language models
• relevant background in machine learning, deep learning, bioinformatics and computational biology.

Personal qualifications

The successful candidate has

• motivation and potential in the field of research.
• the ability to work in a project team and take responsibility for own research goals.
• good communication and collaboration skills and the ability to join interdisciplinary academic communities.

Emphasis will be placed on the following

In the evaluation of the applicants, emphasis will be placed on education, experience and personal and interpersonal qualities. Motivation, ambitions, and potential will also count in the assessment of the candidates.

Furthermore, emphasis will be placed on the following:

• quality of the research experience and publications
• prior academic output and/or research performance (Master thesis and papers in journals/conferences and citations)
• the applicant’s own ideas of research themes and research design that would be relevant for the project, and the quality and relevance of the project sketch

We offer

• a gross annual salary of minimum NOK 532 200,- and automatically development with a 3 % annual increase during the period. In addition to taxes, a further 2% is deducted for the Norwegian Public Service Pension Fund. 
• an exciting job opportunity at Østfold University College. 
• participation in a new interdisciplinary doctoral program and a research group where the project is located. 
• beneficial pension arrangements with the Norwegian State Pension Fund. 
• good employee welfare arrangements. 
• working locations at Østfold University College, Halden (Norway).
• a vibrant AI community, see https://www.hiof.no/english/research/ai-hub/

Submitting an application  

Please submit your application electronically via our recruitment system Jobbnorge.no. All attached documentation must be in a Scandinavian language or in English.

Application must include the following: 

• A short (1-2 page) cover letter describing your motivation, your suitability, relevant qualifications and research interests for this position. The cover letter must also state your reasons for applying to the project and what makes you particularly qualified to carry out this PhD work.  
• A brief high-level project sketch/project description (maximum 2 pages) for a PhD project according to the project description above.
• A copy of your CV.
• A list of publications (if applicable). Include a short description of your contribution in multi-authored publications.
• Copies of degree certificates and transcripts of academic records. Higher education taken outside the Nordic countries must be documented by the submission of a dated and signed diploma/certificate and a transcript of grades in the original language. If the original language is not English or a Nordic language, you must also enclose an official translation. Foreign applicants must attach an explanation of their university’s grading system.
• A copy of your master thesis.
• Names and contact details of 2-3 references (name, relation to candidate, e-mail and telephone number). 

All attachments should be included electronically within the application deadline. Other documentation may be claimed at a later stage, e.g., proof of claimed English proficiency.

Documents to be sent as hard copies by post
Applicants with degrees from: Cameroon, Canada, Ethiopia, Eritrea, Ghana, Nigeria, the Philippines and the USA must send their transcripts and diploma of master’s and bachelor’s education as hard copies directly from the relevant college/university, in addition to uploading them online. The hard copies must be received by us within four weeks after the application deadline expires. 

To send hard copies to HiØ, please use the following address:

Høgskolen i Østfold
HR-section
Postboks 700
1757 HALDEN

Please note that incomplete applications will not be considered.

Admission and appointment 

Admission to the doctoral programme Digitalisation and Society is a condition for appointment as a research fellow. The final plan for research training shall be approved and regulated by contract at the latest three months after the appointment is taken up.

The successful candidate will receive assistance in the application process to the PhD programme Digitalisation and Society at Østfold University College when starting in the position.  

The appointment is to be made in accordance with the State Employees law, the act relating to Universities and Universities Colleges and the national guidelines for appointment as a PhD student, a postdoctoral fellow or a research assistant. 

Contact persons 

You are strongly encouraged to contact the main supervisor for a discussion about the position, relevant references and the project. For other information, please contact the Vice-Dean or the advisors:

• Main supervisor: Associate Professor Hasan Ogul, +47 462 15 195, e-mail: [email protected]
• Vice-Dean of Research: Tore Gimse, +47 69 60 80 58, e-mail: [email protected]
• Advisor for the PhD programme: Liv Simensen, +47 69 60 85 61, e-mail: [email protected]  
• HR Senior Advisor: Hilde Gunn Avløyp, +47 69 60 82 97, e-mail: [email protected]

Other information

The university college is committed to fostering a diverse and gender-balanced workforce. We seek employees with diverse skills, academic backgrounds, life experiences, and perspectives. If there are qualified applicants with disabilities, gaps in their CVs, or immigrant backgrounds, we will invite at least one applicant from each of these groups for an interview.

In accordance with the Norwegian Freedom of Information Act § 25, paragraph 2, information about the applicant may be disclosed even if the applicant has requested not to be included on the list of applicants.

If you disclose that you have an immigrant background, disability, or gaps in your CV, this information, in anonymized form, may be used for statistical purposes.

About us

Through education, research, and artistic development of national and international quality and relevance, and through our contribution to public discourse and knowledge dissemination, we create a better and more sustainable society. We aim to have international engagement while also strengthening our visibility and focus on the local community. Through interaction and dialogue with regional businesses and society, we take an active role as a societal developer. We are looking for individuals who are passionate about their field and who want to contribute to the development of Østfold University College, building an attractive, competent, and forward-thinking institution.Become one of us!

The Digital Society is our largest priority area of research, where we explore the interaction between digitalisation and society from various theoretical perspectives and develop new responsible digital technology.

Our other priority area of research is Language in Learning, which aims to enhance collaboration across language disciplines and create conditions for a diverse research and teaching environment.

Questions about the position

Hasan Ogul

Associate Professor

+4746215195

[email protected]

Tore Gimse

Vice-Dean of Research

+47 69608058

[email protected]

Apply for this job
Deadline

19th April 2024

Employer

About Østfold University College

Municipality

Halden

Scope

Fulltime (1 positions) Fulltime (%)

Duration

Engagement

Place of service
B R A veien 4, 1783 Halden

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