The Netherlands Cancer Institute (NKI ) & University of Amsterdam,
are recruiting a researcher for a PhD or postdoctoral position
PhD/postdoc in integrated diagnostics with deep learning techniques for cancer treatment
Project
Precise risk assessment of disease recurrence in women with breast and ovarian cancer is of utmost importance to predict who will benefit from systemic therapy. The semi-quantitative morphological interpretation of histological sections of carcinomas is still the cornerstone of diagnosis and assessing cancer prognosis and response to treatment. In the last decade, molecularly based personalized treatment strategies are gradually used more often in daily clinical practice. They have been shown to improve the prediction of clinical outcome in women's cancers, and their use as a prognostic and predictive biomarker has been extensively validated. Although these molecular techniques result in invaluable information for specific patient groups, optimization of risk assessment might benefit from further improvement. We want to optimize the treatment decisions with the help of artificial intelligence (AI). Using AI, we will address the problem at two levels; Although, however, morphological parameters such as tumour-stroma ratio and tumour-infiltrating lymphocytes can be directly assessed from H&E slides, these have not been implemented in pathology reports as this information is hard to extract and is therefore subject to substantial inter-rater variability. In the first part of the project, we intend to alleviate this problem using medical imaging and computer vision algorithms to quantify these morphological parameters on H&E slides accurately. Secondly, as the primary goal of all these analyses is to predict disease outcome, we will also consider the problem from a knowledge discovery perspective which biomarkers are responsible for this specific outcome? Therefore, this project will need to develop deep learning techniques for detection, classification, and outcome prediction in multidisciplinary data. Additionally, we will design novel self-supervised contrastive learning techniques and combine these with model interpretability techniques to discover new knowledge about breast and ovarium cancer. Ultimately, we want to improve the risk assessment in women's cancer to detect women who might be spared systemic therapy or need it the most.
What are you going to do?
As a PhD candidate or postdoctoral researcher, you will be responsible for developing and evaluating state-of-the-art deep learning techniques in multidisciplinary data. In addition, you will validate these algorithms in independent cases to ensure the devised AI algorithms' applicability in clinical practice. You are embedded in the Horlings Lab at the Netherlands Cancer Institute and the NKI-UvA ICAI AI for Oncology Lab. You will discuss results with our team, publish your work in artificial intelligence / medical journals, and present it at international conferences. What do we require? We are looking for an enthusiastic PhD student or postdoctoral researcher who will develop novel deep learning algorithms and shape the research in collaboration with the project leaders, AI, and medical experts. We are looking for a motivated, goal-oriented, independent, and proactive PhD candidate or postdoc who is enthusiastic about working in a multidisciplinary setting. Preferably you have a Master's degree in Artificial Intelligence, Computer Science, Physics, Mathematics, or equivalent inexperience. In any case, you should have experience with deep learning and have excellent programming skills. Affinity with deep learning and the other required techniques should be clear from your materials submitted, including courses followed and your GitHub account.
Your working environment
The Netherlands Cancer Institute - Antoni van Leeuwenhoek (NKI-AvL) is a leading Comprehensive Cancer Center with more than 100 years of history and employs high-performance multidisciplinary teams consisting of scientists, clinicians, laboratory specialists, bioinformaticians, software developers, security and privacy experts, data managers, and other staff. In the next decade, NKI-AvL aims to leverage the value of Artificial Intelligence in Oncology (AI in Oncology) for its scientific research and healthcare activities. This covers applications in fundamental research, screening, diagnostics, treatment and quality of life. Increasing numbers of workers: students (PhDs, postdocs), scientific staff, treating physicians, conduct AI-related research and implement algorithmic diagnostic and clinical support. In addition to these developments, there is a growing focus on knowledge centralisation and collaboration with external parties.
About the Faculty of Science and the NKI-UvA ICAI AI for Oncology Lab
The Faculty of Science has a student body of around 7,000 and 1,600 members of staff working in education, research or support services. Researchers and students at the Faculty of Science are fascinated by every aspect of how the world works, be it elementary particles, the birth of the universe, or the brain's functioning. The Horlings' lab focuses on developing 'Computational Pathology' approaches that combine clinical, pathology, and genomics data with image analysis of the tumour to find the balance between over- and under-treatment of women's ovarian and breast cancer. Thus, to get the right treatment for the right woman at the right time. The NKI-UvA ICAI AI for Oncology Lab is a collaboration between the Netherlands Cancer Institute and the Informatics Institute of the University of Amsterdam. The lab's mission is to develop innovations in artificial intelligence for the improvement of diagnosis and therapy of cancer. Job application The position will be filled at the Netherlands Cancer Institute. Your application letter and resume can be attached to the application form on their website. Applications with no letter of interest or course list will be desk rejected. This application will remain open until the position has been filled. Applications are processed immediately upon receipt.
Your career opportunities and terms of employment
You will join a dynamic international research group. You will collaborate with scientists and clinicians with expertise in different disciplines. You will have the opportunity to follow high-quality courses offered by the NKI career development program. Amsterdam is a very livable city with many cultural amenities. The institute is located within a 20-minute tram or bicycle ride from the centre of Amsterdam and within 20-minutes from Schiphol airport by car, bus or bicycle.
Our offer
We offer a temporary contract for 36 hours a week at the Netherlands Cancer Institute. For a PhD student, the employment will be for a period of 4 years. According to the standard PhD scales, the gross salary per month for our PhD will range from €2,884 to a maximum of €3,322. The terms of employment will be following the CAO Ziekenhuizen (Collective Labor Agreement for Hospitals). For the postdoctoral position, the employment will be for a period of 3 years. The gross salary will range from €3,447 and €4,077 per month for a full-time position, according to the FWG-function group 55 (postdoc), depending on previous experience as a postdoc. The terms of employment will be following the CAO Ziekenhuizen (Collective Labour Agreement for Hospitals). In addition, you will receive a fixed end-of-year bonus in December (8,33%), and in May, you will receive 8,33% holiday pay. The terms of employment will be following the CAO Ziekenhuizen (Collective Labor Agreement for Hospitals).
Interested?
Send us your CV and motivation letter. You are more than welcome to send inquiries to
Dr Jonas Teuwen or Dr Hugo Horlings . Jonas Teuwen j.teuwen@nki.nl, or Hugo Horlings, +31(0)20 512 2765, h.horlings@nki.nl (www.cpath.nl)
