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MRC DiMeN Doctoral Training Partnership: Diagnosing by eye: using machine learning to unlock the power of retinal imaging for improving healthcare


MRC DiMeN Doctoral Training Partnership

, , Dr Jeffry Hogg Wednesday, January 27, 2021 Competition Funded PhD Project (Students Worldwide)
Newcastle United Kingdom Data Analysis Neurology Neuroscience Ophthalmology Software Engineering Statistics

About the Project

The retina of the eye can now be scanned in microscopic detail, quickly and non-invasively, using optical coherence tomography (OCT). The most common treatable medical retinal diseases –  age-related macular degeneration, diabetic macular oedema, retinal vein occlusion and myopic macular degeneration –  are now all diagnosed with the help of OCT images and treated with a course of injections into the eye (anti-VEGF therapy). However, success is variable and clinicians are not currently able to predict which patients will benefit. One problem is that the massive data stacks generated by OCT cannot be fully interpreted by humans.

The overall aim of our work is to improve prognostic forecasting for these diseases, using supervised machine learning on OCT images plus patient demographics & baseline.  Specific objectives are to train machine learning models to: (1) automatically extract both physiological (e.g. neural layers) and pathological (e.g. sub/intra-retinal fluid) features of the retina; (2) use these to classify eyes as (not) having particular retinal diseases; (3) predict outcome measures or recommend treatment options such as visual acuity capacity or the required number of injections, respectively. This requires large amounts of data, but Newcastle upon Tyne Hospitals Trust has large established clinical databases of all these diseases, along with OCT scans of the eyes. 

This is an iCASE PhD where you will benefit from three months interning with the Neura Health Group start-up, gaining valuable industrial experience in the growing area of AI in healthcare. iCASE students also benefit from an enhanced stipend, £2500 per year above the standard rate.

The supervisory team form part of a group which has won one of the first NIHR AI awards to work in a related area: using retinal scans to diagnose neurological disorders such as Parkinson’s disease (OCTAHEDRON: Optical Coherence Tomography Automated Heuristics for Early Diagnosis via Retina in Ophthalmology and Neurology; see https://www.nihr.ac.uk/documents/ai-in-health-and-care-awards-funded-projects-2020/25625 and https://youtu.be/9FkZF0LHKuQ ). By working alongside a larger team, in Neura Health and the OCTAHEDRON project, you will benefit from exposure to a wider range of issues than you could feasibly handle on your own; for example patient involvement, IP, clinical constraints, ethics, data governance, MHRA approvals, equipping you for a successful career within this complex field. The group also has a strong collaboration with the manufacturer providing the major share of UK OCT equipment, Heidelberg Engineering, and there may be opportunities to visit them too.

The project will deliver training in all 3 MRC Skills Priority Areas: Quantitative skills (specifically mathematics, statistics, computation, data analytics and informatics, machine learning and Artificial Intelligence, developing digital and technology excellence); Interdisciplinary skills (at the interfaces between engineering/computational, biological/neuroscientific and clinical); and Whole organism physiology (translational medicine).

You will be supported by a multidisciplinary supervisory team, including Jeffry Hogg, a clinical academic fellow in ophthalmology (https://orcid.org/0000-0001-8044-7790) , visual neuroscientist Jenny Read, http://jennyreadresearch.com , and  machine learning expert Jaume Bacardit, http://homepages.cs.ncl.ac.uk/jaume.bacardit/.

iCASE Partner

You will have a degree in computer science, mathematics, physics or similar, with strong programming skills and a desire to use these to make a difference in healthcare.

This project is part of the Discovery Medicine North Doctoral Training Partnership (DiMeN DTP), a diverse community of PhD students across the North of England researching the major health problems facing the world today. Our partner institutions (Universities of Leeds, Liverpool, Newcastle and Sheffield) are internationally recognised as centres of research excellence and can offer you access to state-of the-art facilities to deliver high impact research.

We are very proud of our student-centred ethos and committed to supporting you throughout your PhD. As part of the DTP, we offer bespoke training in key skills sought after in early career researchers, as well as opportunities to broaden your career horizons in a range of non-academic sectors.

Being funded by the MRC means you can access additional funding for research placements, international training opportunities or internships in science policy, science communication and beyond. See how our current DiMeN students have benefited from this funding here: http://www.dimen.org.uk/overview/student-profiles/flexible-supplement-awards

Further information on the programme and how to apply can be found on our website:

https://bit.ly/3lQXR8A 


Funding Notes

Funded by the MRC for 3.5yrs, including a minimum of 3 months working within the industry partner.

Funding will cover UK tuition fees and an enhanced stipend (around £17,785) only. We aim to support the most outstanding applicants from outside the UK. We are able to offer a limited number of bursaries that will enable full studentships to be awarded to international applicants. These full studentships will only be awarded to exceptional quality candidates, due to the competitive nature of this scheme. Please read additional guidance here: View Website
Studentships commence: 1st October 2021.
Good luck!

References

Bacardit: “Automatic recognition of feeding and foraging behaviour in pigs using deep learning” Biosystems Engineering (2020) 197: 91-104 https://doi.org/10.1016/j.biosystemseng.2020.06.013
Hogg: “Ranibizumab and aflibercept intravitreal injection for treatment naïve and refractory macular oedema in branch retinal vein occlusion. Eur J Ophthalmol (2020) https://doi.org/10.1177/1120672120945103
Read: “ASTEROID: a new clinical Stereotest on an autostereo 3D tablet” Translational vision science & technology 8 (1), 25-25 https://doi.org/10.1167/tvst.8.1.25

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