Novel semi-supervised Bayesian learning to rapidly screen new oligonucleotide drugs for impurities.
This is an exciting opportunity to join Compass’ 4-year programme with integrated training in the statistical and computational techniques of Data Science. You will be part of a dynamic cohort of PhD researchers hosted in the historic Fry Building, which has recently undergone a £35 million refurbishment as the new home for Bristol’s School of Mathematics.
This fully-funded 4 year studentship covers:
- tuition fees at UK rate
- tax-free stipend of up £19,609 per year for living expenses and
- equipment and travel allowance to support research related activities.
This opportunity is open to UK, EU, and international students.
AstraZeneca is a global, science-led biopharmaceutical business whose innovative medicines are used by millions of patients worldwide. Oligonucleotide-based therapies are advanced novel interventions with the potential to provide a step-change in treatment for many. Nevertheless, as oligonucleotides are large complex molecules they are currently very difficult to profile for impurities, as the analysis is labour intensive and the data complexity is high.
About the Project
The aim of this PhD is to develop Bayesian data science methodology that does this automatically, accurately, and delivers statistical measures of certainty. The challenge is a mathematical one, and no chemistry, biology or pharmacological background is expected of the student. More specifically, we have large batches of mass spectrometry data that will enable us to learn how to characterise the known oglionucleotide signal and deconvolute it from a number of known and unknown impurities longitudinally, in a semi-supervised learning framework. This will allow us to confirm the overall consistency of the profile, identify any change patterns, trends over batches, and any correlation between impurities.
The end goal is to establish a data analytics pipeline and embed it as part of routine analysis in AstraZeneca, so impurities can be monitored more closely and more precisely. The knowledge can then be used to identify possible issues in manufacturing and improve process chemistry by pinpointing impurities associated with different steps of the drug synthesis. This project would also improve the overall understanding of oligonucleotides and therefore, serve as a key step towards establishing an advanced analytical platform.
The PhD will be supervised by statistical data scientist Prof Andrew Dowsey at Bristol in collaboration with AstraZeneca. Prof Dowsey’s group has extensive expertise and experience in Bayesian mass spectrometry analytics (e.g. Nature Comms Biology 2019; Nature Scientific Reports 2016) and leads the development of the seaMass suite of tools for quantification and statistical analyses in mass spectrometry.
Application Deadline is 5.00pm Friday 18 June 2021. Please quote ‘Compass/ AstraZeneca’ in the funding section of the application form and in your Personal Statement to ensure your application is reviewed correctly. Please follow the Compass application guidance.
Interviews are expected to be held in the week commencing 12 July.
We are excited to share Dr Daniel Lawson’s (Compass CDT Co-Director) latest video where he will tell you about the Data Science behind Bristol’s COVID Modelling.
To acknowledge the variety of sectors where data science research is relevant, in March 2021, the Compass students are undertaking a series of workshops led by the Bristol Doctoral College to explore Skills for Interdisciplinary Research. Using the Vitae framework for researcher development, our colleague at BDC will introduce Compass students to the following topics:
Workshop 1: What is a doctorate? A brief history of doctorates in the UK, how they have changed in the past two decades, why CDTs?, what skills are needed now for a doctorate?
Workshop 2: Interdisciplinarity – the foundations. A practical case study on interdisciplinary postgraduate research at Bristol.
Workshop 3: Ways of knowing, part 1 – Positivism and ‘ologies! Deconstructing some of the terminology around knowledge and how we know what we know. Underpinning assumption – to know your own discipline, you need to step outside of it and see it as others do.
Workshop 4: Ways of knowing, part 2 – Social constructionism and qualitative approaches to research. In part 1 of ways of knowing, the ideal ‘science’ approach is objective and the researcher is detached from the subject of study; looking at other approaches where the role of research is integral to the research.
Workshop 5: Becoming a good researcher – research integrity and doctoral students. A look at how dilemmas in research can show us how research integrity is not just a case of right or wrong.
Workshop 6: Getting started with academic publishing. An introduction on the scholarly publishing pressure in contemporary research and it explores what that means in an interdisciplinary context.
This February our 2nd year Compass students will attend workshops in responsible innovation.
Run in partnership with the School of Management, the structured module constitutes Responsible Innovation training specifically for research in Data Science.
Taking the EPSRC AREA (Anticipate, Reflect, Engage, Act) framework for Responsible Innovation as it’s starting point, the module will take students through a guided process to develop the skills, knowledge and facilitated experience to incorporate the tenets of the AREA framework in to their PhD practice. Topics covered will include:
· Ethical and societal implications of data science and computational statistics
· Skills for anticipation
· Reflexivity for researchers
· Public perception of data science and engagement of publics
· Regulatory frameworks affecting data science
A post by Mauro Camara Escudero, PhD student on the Compass programme.
Last December the first Compass cohort partook a 3-day entrepreneurship training with SpinUp Science. Keep reading and you might just find out if the Silicon Gorge life is for you!
The Ambitious Project of SpinUp Science
SpinUp Science’s goal is to help PhD students like us develop an entrepreneurial skill-set that will come in handy if we decide to either commercialize a product, launch a start-up, or choose a consulting career.
I can already hear some of you murmur “Sure, this might be helpful for someone doing a much more applied PhD but my work is theoretical. How is that ever going to help me?”. I get that, I used to believe the same. However, partly thanks to this training, I changed my mind and realized just how valuable these skills are independently of whether you decide to stay in Academia or find a job at an established company.
Anyways, I am getting ahead of myself. Let me first guide you through what the training looked like and then we will come back to this!
Day 1 – Meeting the Client
The day started with a presentation that, on paper, promised to be yet another one of those endless and boring talks that make you reach for the Stop Video button and take a nap. The vague title “Understanding the Opportunity” surely did not help either. Instead, we were thrown right into action!
Ric and Crescent, two consultants at SpinUp Science, introduced us to their online platform where we would be spending most of our time in the next few days. Our main task for the first half-hour was to read about the start-up’s goals and then write down a series of questions to ask the founders in order to get a full picture.
Before we knew it, it was time to get ready for the client meeting and split tasks. I volunteered as Client Handler, meaning I was going to coordinate our interaction with the founders. The rest of Compass split into groups focusing on different areas: some were going to ask questions about competitors, others about the start-up product, and so on.
As we waited in the ZOOM call, I kept wondering why on earth I volunteered for the role and my initial excitement was quickly turning into despair. We had never met the founders before, let alone had any experience consulting or working for a start-up.
Once the founders joined us, and after a wobbly start, it became clear that the hard part would not be avoiding awkward silences or struggling to get information. The real challenge was being able fit all of our questions in this one-hour meeting. One thing was clear: clients love to talk about their issues and to digress.
After the meeting, we had a brief chat and wrote down our findings and thoughts on the online platform. I wish I could say we knew what we were doing, but in reality it was a mix of extreme winging and following the advice of Ric and Crescent.
Last on the agenda, was a short presentation where we learned how to go about studying the market-fit for a product, judge its competitors and potential clients, and overall how to evaluate the success of a start-up idea. That was it for the day, but the following morning we would put into practice everything we had learned up to that point.
Day 2 – Putting our Stalking Skills to good use
The start-up that we were consulting for provides data analysis software for power plants and was keen to expand in a new geographical area. Our goal for the day was therefore to:
understand the need for such a product in the energy market
research what options are available for the components of their product
find potential competitors and assess their offering
find potential clients and assess whether they already had a similar solution implemented
study the market in the new geographical area
This was done with a mix of good-old Google searches and cold-calling. It was a very interesting process as in the morning we were even struggling to understand what the start-up was offering, while by late afternoon we had a fairly in-depth knowledge of all the points above and we had gathered enough information to formulate more sensible questions and to assess the feasibility of the start-up’s product. One of the things I found most striking about this supervised hands-on training is that as time went on I could clearly see how I was able to filter out useless information and go to the core of what I was researching.
To aid us in our analyses, we received training on various techniques to assess competitors, clients and the financial prospect of a start-up. In addition, we also learned about why the UK is such a good place to launch a start-up, what kind of funding is available and how to look for investors and angels.
Exhausted by a day of intense researching, we knew the most demanding moments were yet to come.
Day 3 – Reporting to the Client
The final day was all geared towards preparing for our final client meeting. Ric and Crescent taught us how to use their online platform to perform PESTEL and SWOT analyses efficiently based on the insights that we gathered the day before. It was very powerful seeing a detailed report coming to life using inputs from all of our researches.
With the report in hand, several hours of training under our belt, and a clearer picture in our head, we joined the call and each one of us presented a different section of the report, while Andrea was orchestrating the interaction. Overall, the founders seemed quite impressed and admitted that had not heard of many of the competitors we had found. They were pleased by our in-depth research and, I am sure, found it very insightful.
So, was it useful?
I believe that this training gave us a glimpse of how to go about picking up a totally new area of knowledge and quickly becoming an expert on it. The time constraint allowed us to refine the way in which we filter out useless information, to get to the core of what we are trying to learn about. We also worked together as a team towards a single goal and we formulated our opinion on the start-up. Finally, we had two invaluable opportunities to present in a real-world setting and to handle diplomatically the relationship with the client.
In the end, isn’t research all about being able to pickup new knowledge quickly, filter out useless papers, working together with other researchers to develop a method and present such results to an audience?
Find out more about Mauro Camara Escudero and his work on his profile page.
The Compass Seminars will be starting next week with an exciting talk by Yuege Xie, a PhD student at UT Austin. You might wonder why we need another seminar series and how this will differ from the Data Science or Statistics Seminars. You can find out more below.
To start off, the primary audience will be the two cohorts of PhD students in the Compass CDT, although anyone is welcome and, in fact, encouraged to attend. The aim is to take advantage of the current situation and attract speakers whose work is closely related to the students’ research areas. Each speaker will be encouraged not only to provide an exhaustive background on the talk but also to structure the talk as a tutorial, where possible. This practical and workshop-like approach differs from the other two seminars and it has been designed to keep PhD students engaged and allow them to explore different research areas in a more accessible way.
For the last month of TB1, one of the main goals will be to get the series up-and-running by establishing a line-up of speakers that has been suggested by the first cohort of Compass students, so keep an eye out on our calendar!
As the series gains momentum, the vision that we have for this seminar series is to be a platform for PhD students in Statistics, Data Science and Machine Learning across the UK to network with fellow researchers, to get exposed to different research areas in an accessible way, and to participate in collaborative tasks and challenges such as Hackathons and Kaggle-like competitions. By building a strong national community of young data scientists we will be able to attract important industry speakers and professors from around the world.
At the moment, work is underway to expand the audience of this seminar series and we will surely keep you updated! Come join us next Thursday and get a Deliveroo voucher after completing a feedback survey at the end!
Upcoming seminars (if you are interested in attending you can sign up with Eventbrite using the links below):
- A picture is worth a thousand words. But what does it say? 19 November 2020, 11.00 AM – 19 November 2020, 12.00 PM Merve Alanyali, LV= via Zoom
- Detecting Local and Global Changes in Terrorism Incidence and the Effects of the COVID-19 Pandemic 3 December 2020, 11.00 AM – 3 December 2020, 2.00 PM Dr Sam Tickle, Data Science Heilbronn Research Fellow, University of Bristol via Zoom
- The Interface of Reinforcement Learning and Planning 17 December 2020, 11.00 AM – 17 December 2020, 12.00 PM Aviv Tamar, Technion – Israel Institute for Technology via Zoom