Sydney Precision Data Science Centre
Sydney Data Science Insights
Edition 4, December 2024
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Message from the Director - Professor Jean Yang
Dear Colleagues,
After another busy year, it was exciting to host the ABACBS conference in Sydney in early November. Many of our centre members were involved in supporting the delivery of the conference especially my co-convener Ellis Patrick who ensured the week-long conference ran smoothly.
It is always inspiring to learn about the new engagement opportunities created by our ECR community, which this year included hackathons and workshops. In addition, many of our ECRs provided mentoring to students through the SUDATA mentoring program.
Once again, I am impressed and delighted by the awards and honours received by our students and researchers. Please see the news section for all the details and check out our final two events this year.
As the year draws to a close, I wish everyone a happy and restful holiday and look forward to what the next year brings.
Best wishes,
Jean
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Researcher Spotlight: Dr Alistair Senior
In this newsletter, we are delighted to spotlight Dr Alistair Senior, a member of our executive committee and one of the recipients of the University’s Horizon Fellowships. Part of a new multidisciplinary initiative the Horizon Fellowships support EMCRs to unlock solutions to the complex problems of climate change, health and sustainability. Alistair’s fellowship focuses on healthy ageing through sustainable nutrition. Learn about Alistair’s involvement in SPDS in this spotlight feature.
What excites you about data science?
I like that data science allows us to ask and answer new questions from existing data. There’s something really appealing to me about learning or developing a new method and then seeing all the new potential applications for that, particularly in biology.
What is keeping you busy at the moment?
At the moment I’m being kept busy with 2 PhD students who are completing their projects; one in nutritional data science and one in evolutionary theory. On top of that, I have a few new students starting, thanks to funding from my recent Horizon fellowship from the University.
How long have you been working with the SPDS?
I have been working with SPDS since its inception, including working on the application to establish the centre.
What’s next for you at the SPDS?
Up next we have our strategic planning day for the centre leadership. In particular, I’m interested in thinking about how we can promote SPDS around the wider university, and how to build more links with researchers who could benefit from collaborating with us.
Where could we find you when you’re not working?
At the moment I’m kept busy with my family. We seem to spend a lot of time at our local park and pool in Petersham.
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Feature method: TOP (Transfer-learning Omics Prediction) framework
In this issue, we present the TOP (Transferable Omics Prediction) framework, an innovative approach to integrating information from diverse omics datasets while addressing unknown variations. Large-scale omics research often involves data from multiple technologies, environments, or populations, each contributing unique biases. Identifying biologically meaningful signals amidst this complexity is a significant challenge.
TOP introduces a reference-free paradigm, bypassing traditional batch correction methods for combining datasets that rely on predefined standards. Instead, it identifies "self-normalising" features—markers that are robust to both technical and biological confounding factors. This approach ensures robust predictions without dataset-specific adjustments making the models appealing to clinical applications.
Key features of TOP include:
- Balanced Data Integration: TOP carefully weights contributions from each dataset, ensuring that large datasets do not overshadow smaller ones. This preserves biological diversity and highlights subtle patterns.
- Interpretability: By using log-ratios of critical features and weighted lasso regression, TOP simplifies model interpretation, prioritising the most relevant signals for downstream validation and hypothesis testing.
- Scalability and Flexibility: TOP's platform-agnostic methodology supports a range of data types, from gene expression to imaging, making it applicable across fields with complex sources of variation.
The TOP framework was developed to assess the potential for a blood test for acute organ rejection in transplant recipients. TOP made it possible to construct a model using gene expression measurements from multiple cohorts and multiple organ types. In addition to this, the predictive model it constructed can be applied to a single patient sample without requiring normalisation or standardisation, making it clinically applicable.
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Workflow of the Transferable Omics Prediction (TOP) framework utilised to build a regression model across multiple datasets
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Mentoring program sucess
Over the course of Semester 2 2024, SPDS and SUDATA ran a research mentoring program. Thank you to our ECR mentors Matthew Shu, Lijia Yu, Mohammad Davoudabadi, and Pratibha Panwar, who guided 12 undergraduate students through projects of their choosing. Dr Mohammad Javad Davoudabadi's group, Jack Li, Tobit Louis, and Aniket Sinha, have had their project work accepted as a poster at the 12th Australasian Council for Undergraduate Research Conference in December 2024, which is an excellent outcome for the students and program.
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News & updates
June 2024
- PhD student, Farhan Ameen was awarded the Best Poster Prize at the Single Cell Biology conference at the Wellcome Genome Campus in Cambridge.
July 2024
- Congratulations to PhD student Harry Robertson for leading a study published in Nature Medicine! In collaboration with Westmead Institute for Medical Research, our researchers have identified molecular biomarkers for transplant rejection that are common to all the major transplanted organs, hearts, lungs, livers, and kidneys. Read the news story and see a clip from Channel 7 News on our website.
- PhD student Manoj Wagle was awarded the Philipp Hofflin International Research Travel Scholarship. Manoj will be travelling to the Computer Science and Artificial Intelligence Laboratory at MIT and Broad Institute of MIT and Harvard in early 2025 to conduct research as part of his PhD. The research will focus on developing Interpretable deep-learning-based approaches with application to neuroscience.
- We hosted the Centre’s second annual Winter Data Analysis Challenge from 22 to 24 July 2024. For this year’s challenge, participants were provided with one large dataset on human lifespans over different geopolitical entities and time periods and asked to explore the phenomenal gains in human lifespan that have occurred within the last 150 years.
August 2024
- Dr Shila Ghazanfar was interviewed by AMSI BioSummer as an alumnus of the program. Having first attended AMSI BioInfoSummer in 2013 as a PhD student, she has since returned frequently as a guest speaker. Read more about Shila's research and career on the AMSI website.
- The Centre’s ECRs collaborated with SUDATA, COMBINE and GraftAI to deliver the 2024 Bioinformatics Data Analysis Hackathon on Saturday 17 August. A total of 72 contestants spent the day coding and learning.
October 2024
- Centre Director, Professor Jean Yang, was named one of SUPRA’s Supervisors of the Year in 2024. Jean was nominated by her students and was one of several supervisors recognised in the 2024 awards.
November 2024
- Associate Professor Ellis Patrick and Professor Jean Yang co-convened the 2024 ABACBS Conference supported by the University of Sydney as a Platinum Sponsor and hosted in the Abercrombie Building. This year ABACBS welcomed 400 attendees with two international keynotes. The event included 16 sessions and 83 speakers across the 2 days. It was a busy week for the bioinformatics community as the COMBINE Symposium hosted 200 attendees the day before, and the BioC Asia conference followed the conference to wrap up the week.
- PhD student Jackson Zhou won the Statistical Society of Australia's JB Douglas Award for his talk titled Fast Expectation Propagation Regression Models.
Decemeber 2024
- Congratulations to PhD student Daniel Kim on winning the GovHack challenge. A great way to end the year.
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Images: Left - Ellis Patrick, Natasha Rogers, Harry Roberston and Jean Yang at Westmead before their Nature Medicine article was published; Centre - Jackson Zhou delivering his winning JB Douglas talk; Right - Shila Ghazanfar and Alistair Senior presenting first place award in the Winter Data Analysis Challenge to Jey Son Chuah.
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Upcoming events
We have two special end-of-year seminars being held in December with visiting speakers.
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Wrap-up of the 2024 Statistical Bioinformatics Seminar Series
The Centre's seminar coordinator, Lijia Yu, reflects on the seminar series after she took over coordination in Semester 2.
Our Statistical Bioinformatics Seminar Series delivered each Monday during the semester features a range of speakers, and includes four Judith & David Coffey invited speakers per year. This semester’s series brought together national and international experts from Asia and North America, who shared insights on topics such as AI in biotechnology, digital pathology, genetics, spatial and single-cell omics. Our speakers represented various career stages, from postdocs to professors, with an equal representation of five female and five male speakers.
This semester, we had the great honour of hosting Prof David Ascher, as a Judith & David Coffey invited speaker, for his talk titled "Harnessing the Power of AI in Biotechnology, Personalized Medicine, Drug Development, and Beyond". Professor Ascher discussed the evolution of variant interpretation, highlighting the transition from traditional statistical methods to advanced AI techniques. Tools like AlphaFold, which apply deep learning to predict protein structures, are now transforming the field. With this year's Nobel Prize in Chemistry awarded to scientists working in the AI field, we were all deeply attuned to the revolutionary impact of AI on biomedical and data science research. We are also grateful to our North American speakers, Assoc Profs Lulu Shang and Chang Su, Dr Laura Luebbert, and Dr Drew Williamson, who presented late on their Sunday nights. We were also pleased to have Assoc Prof Joshua Ho from Hong Kong, along with Dr Clara Jiang, Dr Aishwarya Bhaskaran, and Dr Xufeng Lin, who joined us from across Australia. Their participation brought valuable insights to our series and enriched our understanding of various topics.
Many of our seminars are recorded. To access the seminar videos, please visit our YouTube page. Lastly, I would like to extend my gratitude to all our audience members - your participation has been invaluable to the success of this seminar series. The series will resume in Semester 1, 2025 and we look forward to welcoming you next year.
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ECR Update
Chair of the ECR Committee. Dr Helen Fu provides and update on ECR activities in 2024.
This year, the Early Career Researcher (ECR) community of SPDS Centre organised and enjoyed a wide range of events that supported our professional growth and strengthened our connections, thanks to the support of the Centre and research leaders. The year kicked off with a cross-cluster development retreat at Willow Tree Estate, where ECRs from across our Centre came together for workshops, team building, and a little friendly competition on the go-kart track.
Among the many highlights of 2024, we ran our Hackathon with SUDATA and COMBINE. Our ECRs also led workshops like "What is Bioinformatics?" alongside SUDATA, contributing to UNSW BINFSOC's educational seminars, and playing an active role as mentors in the SUDATA mentoring program. Several ECRs played key roles in organising this year's major conferences—COMBINE and ABACBS. Special thanks go to Andy and Farhan for their leadership in making COMBINE a success. We had the pleasure of organising a memorable birthday celebration for our Centre Director, Jean, and it was a wonderful time. We also hosted farewell lunches for Nick, Helen, and Daniel M. Additionally, we had the pleasure of hosting A/Prof Yingying Wei from The Chinese University of Hong Kong. Outside of the research setting, we enjoyed rock climbing and badminton outings. It's been a fantastic year for the ECR community of SPDS Centre.
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Images: Left - the Hackathon in action, Centre - the COMBINE organising committee, Right - another successful ECR social dinner
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Australian Data Science Network Conference
In October or November 2025, SPDS will host the fourth annual conference of the Australian Data Science Network (ADSN). This relatively small-scale conference brings together people across the full spectrum of data science, including industry participants. The 2024 conference was held in early December at Curtin University. Over three days, the 2024 conference attracted 136 attendees from 41 organisations roughly equally divided between university, government and industry sectors.
We're looking for enthusiastic local organising committee members. If you're interested in contributing please send an email to data-science.admin@sydney.edu.au
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