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PhD Connect Conference

Posted on 10 December 202411 December 2024 by kerry.turcsi

Our Turing Liaison team recently funded a number of PhD students to go to the 2024 Alan Turing PhD Connect Conference. This is one of the range of approaches we are taking to bridging the gap between the Turing’s goals and the University’s research and academics who reflect these goals.

Attendees sat around circular tables with sheets of paper and pens on the table — *Attendees at a PhD Connect conference. Photo provided by Jingrong Bai*.

Supporting PhD students to make connections and discover new collaborations through the Turing will hugely benefit students and the wider data science and AI community, and is an important part of our objective. Below are some statements from the students we funded about their experience at the conference.

Damien Wang

I am Damien, a first-year PhD student from University of Bristol and SWDTP who specializing in psychology and artificial intelligence. The past two days at PhD Connect 2024 have been incredibly fulfilling. I had the opportunity to explore a wide range of PhD projects in AI and data science, engaging in discussions with other attendees and collaboratively tackling problems by leveraging our diverse backgrounds.

Conversations with peers and insights from the panel discussions were truly enlightening. I was also fortunate to represent my group during the Mini-DSG session and deliver my own poster presentation. These experiences have boosted my confidence and skills in presenting, and I’m grateful for the valuable feedback I received on my research.

This two-day journey has inspired me to push forward with even greater motivation. A heartfelt thanks to the Alan Turing Institute and everyone I met along the way!

Ming Chen

The PhD Connect 2024 conference was an incredible opportunity to engage with peers, learn from industry experts, and explore real-world applications of data science and AI. My research interests include learning sciences and emerging technologies in language learning. I would say that one of the highlights for me was participating in group research discussions, which broadened my understanding of AI’s role in addressing societal challenges.

I also appreciated the networking opportunities and the chance to discuss my research with fellow attendees and professionals from diverse sectors. Another interesting part of the conference is the Research Karaoke, which is a great experience for people to have fun and practise doing presentations.

Jizhao Niu

I am grateful to The Jean Golding Institute for funding my attendance at the conference. It was a fantastic opportunity to meet many PhD students from Bristol and beyond, engaging in discussions on health sciences-related projects.

A highlight for me was the training session on how to pitch research effectively, which provided valuable insights and practical skills. We worked as a team to sell an item to other groups, which was both enjoyable and educational.

I learned the importance of tailoring research presentations to audiences with diverse backgrounds — a skill I look forward to applying in the future!

Jingrong Bai

During the conference, we got insightful points on AI-human by Piotr Mirowski from DeepMind. Then, we interacted with the group work and presented karaoke, which was good for us to connect with other PhD students across the UK, also, learned how to prepare a good presentation by Beatriz Costa Gomes. Last but not the least, we shared our research ideas through the poster session. All in all, it is a valuable experience for me to know the AI field and meet all of the awesome people, really appreciate all of the speakers, organizers and students.

Jingrong Bai (left) standing in front of a poster with two other individuals discussing the posters on display — *Jingrong Bai (second on the left) with other PhD students at a networking sessio*n.

Zia Saylor

Zia Taylor (left), Kerstin Nothnagel (centre) and Michael Rumbelow (right) at PhD Connect — *Zia Saylor (left), Kerstin Nothnagel (centre) and Michael Rumbelow (right) at PhD Connect*.

Perhaps my favorite session was the one on day 2 morning of the conference when we discussed the principles of a good academic presentation. Focusing on basics like practice, maintaining relevancy to the audience, and ensuring that materials were packaged in an alluring way were key methods discussed. Looking at the AI aspect of our learning opportunities, much of the conference consisted of hands-on opportunities to engage with the materials, from designing a workflow that would integrate AI into academia without infringing on the rights and words of academics to developing a mechanism to integrate data on building pricing into an AI cost estimation algorithm that could be made. This enabled us as students to learn more about AI in its many forms and potential for interdisciplinary applications.

Jay Liu

It has been a wonderful journey for me to attending the 2024 Alan Turing AI PhD Conference at Horizon Leeds. It is my first time travelling to Leeds, a fantastic city with fancy malls and restaurants. I am grateful for the great opportunity and generous funding for the program!

I am a PhD student in Finance at the University of Bristol Business School, focusing on understanding the effects of AI and algorithmic decision making in the financial markets. I believe the conference can further improve my understanding on AI and the application of AI on interdisciplinary research!

Jay Liu standing in front of a digital screen showing a slide titled 'Welcome to the PhD Connect' — *Jay Liu standing in front of a digital screen at PhD Connect*.

Alan Turing Institute tote bag (right) featuring Alan Turing's face on it and Jay Liu's name badge (left) for PhD Connect — *Jay Liu standing in front of a digital screen at PhD Connect*.

Zhengzhe Peng

Numerous speakers standing at the front of the room in front of a slideshow projected on a wall — *Session from PhD connect with multiple speakers*.

Attending the PhD Connect Conference organized by the Alan Turing Institute was an enriching experience. I particularly appreciated the diverse perspectives shared during interdisciplinary discussions on data science applications. The keynote sessions inspired new ideas for integrating AI into my research, while the networking opportunities allowed me to connect with peers tackling similar challenges. I gained valuable insights into emerging methodologies and practical approaches that will enhance my PhD work.

Boyang Yu

This conference let me engage with the Mini-data group to explore data science applications in real-world challenges, which is what I’m doing as a PhD. I enhanced my presentation skills and learned to communicate complex ideas to a broader audience, inspired by a standout example from the presenter (Dr Beatriz Costa Gomes). I saw some very nice posters and great to have a picture with one of my most favourite poster (and its owner).

Female speaker on stage behind a lectern with a projected slide behind them showing 'Today's agenda' with timings and session titles — *Damien Wang (left) and Boyang Yu (right) at a poster session at PhD Connect*.

Ding Li

Attending the 2024 Turing Phd connect conference is such an unforgettable experience. I have met a bunch of bioinformatics students from various universities and institutions sharing their research with AI and Machine Learning. The poster and presentation session left me with impression on how research from other fields could help with my own PhD project. During the session, I discussed with Mr Muizz who is also from University of Bristol, but another school of Engineering Mathematics, and heard about how he applied AI on topology of insects’ wings in traditional species classification and phylogeny. It would never happen if there were no such an opportunity.

Ding Li standing in front of a poster with two other male individuals conversing about the poster — *Ding Li (Left) listening to talks given by data scientist Dr Piotr Mirowskifrom Google Deepmind*.

Kerstin Nothnagel

Attending the Alan Turing Institute PhD Connect Conference was an incredible experience. Highlights included Dr Piotr Mirowski’s inspiring keynote on human-machine collaboration and the ‘Mini Data Study Group,’ where we tackled real-world challenges like ICU surge prediction and cancer forecasting.

This event was a perfect prelude to my upcoming ATI funded UK-Italy Trustworthy AI Visiting Researcher Programme in Milan, where I’ll collaborate with global researchers to explore ‘Global AI Policies and Regulations and Their Impact on Healthcare.’ The project is reinforced by the importance of unifying AI policies to ensure technology benefits everyone equally, closing economic gaps rather than widening them.

Foodscapes: visualizing dietary practices on the Roman frontiers

Posted on 26 September 202426 September 2024 by kerry.turcsi

JGI Seed Corn Funding Project Blog 2023/24: Lucy Cramp, Simon Hammann & Martin Pitts

*Table laid out with Roman pottery from Vindolanda ready for sampling for organic residue analysis as part of our ‘Roman Melting Pots’ AHRC-DFG funded project*

The extraction and molecular analysis of ancient food residues from pottery enable us to reconstruct the actual uses of vessels in the past. This means we can start to build up pictures of dietary patterns in the past, including foodways at culturally diverse communities such as the Roman frontiers. However, there remains a challenge in how we can interpret these complex residues, and both visualise and interrogate these datasets to explore use of resources in the past.

Nowadays, it is commonplace to extract organic residues from many tens, if not hundreds, of potsherds; within each residue, and especially using cutting-edge high-resolution mass spectrometric (HRMS) techniques, there might be several hundred compounds present, including some at very low abundance. Using an existing dataset of gas chromatography-high resolution mass spectrometric data from the Roman fort and associated settlement at Vindolanda, this project aimed to explore methods through which these dietary information could be spatially analysed across an archaeological site, with a view to developing methods that could be applied on a range of scales, from intra-site through to regional and even global. It was hoped that it would be possible to display the presence of different compounds in potsherds recovered from different parts of a site that are diagnostic of particular foodstuffs, in order to spatially analyse the distribution of particular resources within and beyond sites.

*A fragment from a Roman jar that was sampled from Vindolanda for organic residue analysis as part of our ‘Roman Melting Pots’ AHRC-DFG funded project*

The project started by processing a pilot dataset of GC-HRMS data from the site of Vindolanda, following a previously-published workflow (Korf et al. 2020). These pottery sherds came from different locations at the fort, occupied by peoples of different origins and social standings. This included the praetorium (commanding officer’s house), schola (‘officers’ mess’), infantry barracks (occupied by Tungrians, soldiers from modern-day Belgium and Netherlands), and the non-military ‘vicus’ outside of the fort walls likely occupied by locals, traders and families. Complex data, often containing several hundred compounds per residue were re-integrated using open-source mass spectrometry data processing software MZ Mine, supported by our collaborator from MZ IO gmbh, Dr Ansgar Korf. This produced a ‘feature list’ of compounds and their intensities across the sample dataset. This feature list was then presented to Emilio Romero, a PhD student in Translational Health Sciences, who worked as part of the Ask-JGI helpdesk to support academic researchers on projects such as these. Emilio developed data matrices and performed statistical analyses to identify significant compounds of interest that were driving differences between the composition of organic residues from different parts of the settlement. This revealed, for example, that biomarkers of plant origin appear to be more strongly associated with pottery recovered from inside the fort compared with the vicus outside the fort walls. He was then able to start exploring ways to spatially visualize these data, with input from Léo Gorman, a data scientist from the JGI, and Levi Wolf from the School of Geographical Sciences. Emilio says:

‘Over the past year, my experience helping with the Ask-JGI service has been truly rewarding. I was very excited to apply as I wanted to gain more exposure to the world of research in Bristol, meet different researchers and explore with them different ways of working and approaching data.

One of the most challenging projects was working with chemometric concentrations of different chemical compound residues extracted from vessels used in ancient human settlements. This challenge allowed me to engage in dialogue with specialists in the field and work in a multidisciplinary way in developing data matrices, extracting coordinates and creating maps in R. The most rewarding part was being able to use a colour scale to represent the variation in concentration of specific compounds in settlements through the development of a Shiny application in R. It was certainly an invaluable experience and a technique I had never had the opportunity to practice before.’

This work is still in progress, but we have planned a final workshop that will take place in mid-November. Joining us will be our project partners from the Vindolanda Trust, as well as colleagues from across the Roman Melting Pots project, the JGI and the University of Bristol. A funding application to develop this exploratory spatial analysis has been submitted to the AHRC.

Contact details and links

You can find out more about our AHRC-DFG funded project ‘Roman Melting Projects’ and news from this season’s excavations at Vindolanda and its sister site, Magna.

A real-time map-based traffic and air-quality dashboard for Bristol

Posted on 24 September 202426 September 2024 by kerry.turcsi

JGI Seed Corn Funding Project Blog 2023/24: James Matthews

Example screenshot of the Bristol Air Quality and Traffic (AQT) Dashboard with Key — *Example of the dashboard in use.*

A reduction in urban air quality is known to be a detrimental to health, affecting many conditions including cardiorespiratory health. Sources of poor air quality in urban areas include industry, traffic and domestic wood burning. Air quality can be tracked by many government, university and citizen held pollution sensors. Bristol has implemented a clean air zone, but non-traffic related sources, such as domestic wood burning, are not affected.

The project came about through the initiative of Christina Biggs who approached academics in the school of Engineering Mathematics and Technology (Nikolai Bode) and the School of Chemistry (James Matthews and Anwar Khan) with a vision for an easy to use data dashboard that could empower citizens by drawing data from citizen science, university and council air quality and traffic sensors in order to better understand the causes of poor air quality in their area. The aims were to (1) work with community groups to inform the dashboard design (2) create an online dashboard bringing together air quality and traffic data (3) use council air quality sensors to enable comparison with citizen science sensors for validation and (4) to use this to identify likely sources of poor air quality.

An online dashboard was created using R with Shiny and Leaflet, collecting data using API code, and tested offline. The latest version of the dashboard has been named the Bristol Air Quality and Traffic (AQT) dashboard. The dashboard allows PM_2.5 data and traffic numbers to be investigated in specific places and plotted as a time series. We are able to compare citizen sensor data to council and government data, and we can compare to known safety limits.

The dashboard collates traffic data from several sources including Telraam traffic report and Vivacity traffic data which provide information on car numbers from local sensors; and PM_2.5 data from different sources including Defra air quality stations and SensorCommunity (previously named as Luftdaten) citizen air quality stations. Clicking onto a data point provides the previous 24 hour time series of measurements. For example, in the screenshots below, one Telraam sensor shows a clear PM2.5 peak during the morning rush hour of 26^th June 2024 (a) which is likely related to traffic, while the second shows a higher PM2.5 peak in the evening (b) which could be related to domestic field burning, such as an outdoor barbecue. A nearby traffic sensor shows that the morning peak and smaller afternoon peak do agree with traffic numbers (c), but the evening peak might be unrelated. Data can be selected from historic data sets and is available to download for future interrogation.

Example of data output from the dashboard showing PM2.5 midnight to midnight on 26/06/2024 — *Figure (a) Example of data output from the dashboard showing PM_2.5*

*Figure (c) Example of data output from the dashboard showing traffic measured using local Bristol sensors*

It is a hope that these snapshots might provide an intuitive way for communities to understand the air quality in their location. Throughout the project, the project team held regular meetings with Stuart Phelps from Baggator, a community group based in Easton, Bristol, so that community needs were put to the forefront of the dashboard design.

We are currently planning a demonstration event with local stakeholders to allow them to interrogate the data and provide feedback that can be used to add explanatory text to the dashboard and enable easy and intuitive analysis of the data. We will then engage with academic communities to consider how to use the data on the dashboard to answer deeper scientific questions.

Contact details and links

Details of the dashboard can be found at the link below, and further questions can be sent to James Matthews at j.c.matthews@bristol.ac.uk

https://github.com/christinabiggs/Bristol-AQT-Dashboard/tree/main

Ask JGI Student Experience Profiles: Rachael Laidlaw

Posted on 14 August 202414 August 2024 by kerry.turcsi

Rachael Laidlaw (Ask-JGI Data Science Support 2023-24)

I first came into contact with the Jean Golding Institute last year at The Alan Turing Institute’s annual AI UK conference in London, and then again in the early stages of the DataFace project in collaboration with Cheltenham Science Festival. This meant that before I officially joined the team back in October, I already knew what a lovely group of people I’d be getting involved with! Having nice colleagues, however, was not my only motivation for applying to be an Ask-JGI student. On top of that, I’d decided that whilst starting out in my ecological computer-vision PhD niche, I didn’t want to forget all of the statistical skills that I’d developed back in my MSc degree. Plus, it sounded really fun to keep myself on my toes by exercising my mind tackling a variety of data-oriented requests from across the university’s many departments.

Rachael Laidlaw in centre with two JGI staff members to the left and one JGI staff member to the right pointing towards a Data pin board at the JGI stall — *Rachael Laidlaw (centre)*, second-year PhD student in Interactive Artificial Intelligence, and other JGI staff members at the JGI stall

During the course of my academic life, I’ve taken the plunge of changing disciplines twice, moving from pure mathematics to applied statistics and then again to computer science, and I liked the idea of supporting others to potentially do the same thing as they looked to enhance their work by delving into data. Through Ask-JGI, I kept my weeks interesting by having something other than my own research to sometimes switch my focus to, and it felt very fulfilling to be able to offer useful technical advice to those who were in the same position that I myself had been in not so long ago too! I therefore got stuck in with anything and everything, from training CNNs for rainfall forecasting or performing statistical tests to compare the antibiotic resistance of different bacteria, to modelling the outcomes of university spinouts or advising on the ethical considerations and potential bias present when designing and deploying a questionnaire-based study. And, of course, by exposing myself to these problems (alongside additional outreach initiatives and showcase events), I also learned a lot along the way, both from my own exploration and from the rest of the team’s insights.

One especially exciting query revolved around automating the process of identifying from images which particular underground printing presses had been used to produce various historical political pamphlets, based on imperfections in the script. This piqued my interest immediately as it drew parallels with my PhD project, highlighting the copious amount of uses of computer vision and how it can save us time by speeding up traditionally manual processes: from the monitoring of animal biodiversity to carrying out detective work on old written records.

All in all, this year has broadened my horizons by giving me great consultancy-style work experience through the opportunity to share my expertise and help a wide range of researchers. I would absolutely encourage other curious PhD students to apply and see what they can both give to and gain from the role!

Ask JGI Student Experience Profiles: Mike Nsubuga

Posted on 5 August 20247 August 2024 by kerry.turcsi

Mike Nsubuga (Ask-JGI Data Science Support 2023-24)

Embarking on a New Path

In the early days at Bristol, even before I began my PhD, I stumbled upon something extraordinary. AskJGI, a university initiative that provides data science support to researchers from all disciplines, caught my attention through a recruitment advert circulated by my PhD supervisor for support data scientists.

My journey started with hesitation. As a brand-new PhD student, who had just relocated to the UK, I questioned whether I was ready or suitable for such a role. Despite my reservations, my supervisor saw potential in me and encouraged me to seize this opportunity. Yielding to their encouragement, I applied, not fully realizing then how this decision would profoundly shape both my academic and professional paths.

A World of Opportunities

Joining AskJGI opened a door to a dynamic world brimming with ideas and innovations. My background in bioinformatics and computational biology meant that working on biomedical queries was particularly rewarding. These projects varied from analyzing protein expression data to studying infectious diseases, allowing me to use data science in meaningful ways.

Among the initiatives I was involved in was developing models to predict protein production efficiency in cells from their genetic sequences. Our goal was clear yet impactful: to identify patterns in genetic sequences that indicate protein production efficiency. We employed advanced data analysis and machine learning techniques to achieve effective predictions.

Additionally, I contributed to a project analyzing the severity of dengue infections by using statistical models to identify key biological markers. We pinpointed certain markers as critical for distinguishing between mild and severe cases of the infection.

These projects showcased the transformative power of data science in understanding and potentially managing diseases, directly impacting public health strategies.

Making Science Accessible: Community Engagement at City Hall

A highlight of my tenure with AskJGI was participating in Data Science Week at bustling Bristol City Hall. The event was not merely a showcase of data science but an opportunity to demystify complex concepts for the public. Engaging in lively discussions and simplifying intricate algorithms for curious visitors was incredibly fulfilling, especially seeing their excitement as they understood the concepts that are often discussed in our professional circles.

Audience sitting in City Hall. Some audience members are raising there hand. There is a projector and a speaker at the front of the hall — AI and the Future of Society event as part of Bristol Data Week 2024

Fostering Connections and Gaining Insights

AskJGI enhanced my technical skills and broadened my understanding of the academic landscape at the University of Bristol. The connections I forged were invaluable, sparking collaborations that would have been unthinkable in the more isolated environment of my earlier academic career. Reflecting on my transformative journey with AskJGI, I am convinced more than ever of the importance of interdisciplinary collaboration and the critical role of data science in tackling complex challenges. I encourage any researcher at the University of Bristol who is uncertain about their next step to explore what AskJGI has to offer. For PhD students looking to get involved, it represents not just a learning opportunity but a chance to make a significant societal impact.

24/25 Ask-JGI Application