SARAO hosts 4th Big Data Africa School drawing synergies between radio astronomy and biomedical imaging

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This year has seen the return of SARAO’s hosting of the Big Data Africa School after a pause of more than three years due to the Covid-19 pandemic. The 4th Big Data Africa School was funded by the UK Newton Fund under the Development in Africa with Radio Astronomy (DARA) Big Data project.

This year’s school hosted 25 participants in Cape Town from 5 to 11 March 2023, with participants hailing from diverse regions in Africa. The participants ranged in age between 19 and 39 years of age with 7 Doctoral degree students, 10 Masters degree students and 8 Bachelor of Science (Honours) / Engineering students. The countries represented at the 4th Big Data Africa School are South Africa, Namibia, Madagascar, Zimbabwe, Mozambique, Zambia, Malawi, Lesotho, Ghana, Morocco, Kenya, Algeria, Ethiopia and Uganda.

The aim of the Big Data Africa School is to introduce fundamental data science tools and techniques to science and engineering graduates at various academic levels of their studies. Apart from introductory lectures in data science, the focus of the school is on students getting hands-on experience by working on real-life data sets which forms a large component of the school’s programme.

The thematic area for the 4th Big Data Africa School was selected as healthcare / biomedical imaging with SARAO joining forces with experts in this area from partnering institutions IBM Research Africa, University of Barcelona, Namibia University of Science & Technology (NUST), African Network for Artificial Intelligence in Biomedical Imaging (AFRICAI), University of Basel and the University of Cape Town (UCT), who provided the relevant projects and data sets, as well as the mentors who worked continuously with groups of participants throughout the week. Partner, the Inter-University Institute for Data Intensive Astronomy (IDIA) provided the Cloud infrastructure and computational resources needed for carrying out the projects.

This year’s school offered a range of exciting projects in the healthcare domain, which included detecting of out of distribution samples in healthcare: Malaria as a use case (IBM Research Africa); 3D Vertebrae reconstruction from 2D X-ray imaging (University of Basel, UCT); Explainable AI of medical images using SHAP and LIME (NUST); Combating data scarcity in medical imaging – using AI to generate synthetic images using breast mammograms as a use case (University of Barcelona); and the application of deep learning techniques to automate the process of cardiac disease diagnosis which can be generalised across different clinical centres, imaging conditions and scanner vendors (University of Barcelona).

Carla Sharpe, SARAO Africa Programme Manager, said at the welcoming ceremony: “I am always blown away at how these young people use their very advanced skills and brilliant minds and solve really basic on-the-ground problems. It really moves me and sticks in my mind.”

Invited speakers at this year’s school included Prof. Yves Wiaux from Heriot-Watt University in Edinburgh who serves as the Head of the Biomedical and Astronomical Signal Processing (BASP) Group. Prof. Wiaux’s presentation focused on data calibration techniques used in radio astronomy imaging which can be applied to medical imaging, drawing synergies between the radio astronomy and biomedical imaging communities. His presentation was complemented by invited guest speaker, Prof. Tinashe Mutsvangwa, from UCT who presented on 3D bone reconstruction from 2D X-ray images. Prof. Mutsvangwa also gave an overview of the South African environment for his work and its challenges within an African setting.

The participants were given guidance in formulating their final presentations by Mark Johnson from SARAO’s Commercialisation unit. Johnson undertook the “Skills for Industry” component of the school giving participants insight to formulating a pitch for a panel of potential funders and how to view their projects as a potential business. These sessions with invaluable insight from SARAO’s Commercialisation unit were offered to students in the evenings in preparation of their final presentations.

Another important activity at this year’s school included the celebration of International Women’s Day on Wednesday, 8 March 2023. “It is the first time we are running the Big Data Africa School with a predominantly female majority,” commented Dr Bonita de Swardt, Programme Manager: Strategic Partnerships for Human Capital Development at SARAO. The women participants at this year’s school comprised 18 out of the 25 participants, making over 70% of participants female. De Swardt further added: “It will be interesting to observe the team and overall dynamics of participants in an environment not commonly seen in STEM. We will continue to strive including women and girls in our initiatives to ensure that they are not left behind in the digital revolution.”

Participants were treated with a cake that celebrated the anniversary of the publication of SARAO’s Women in Data Science report and its achievement in attaining the first school with an apparent gender equity. In addition, the in-country Director for Women in Tech South Africa, Melissa Slaymaker, joined participants on Friday, 10 March 2023 as part of the week’s Women’s Day celebrations. Slaymaker presented the work being carried out by Women in Tech in Africa and globally, and informed participants how they can become part of the network of women making a difference in access and participation in STEM activities.

The final group presentations were held on Friday, 10 March 2023, which was followed by a social networking evening and prize-giving dinner. The panel of judges included Dr Nikhita Madhanpall (OAD), Prof. Karim Lekadir (University of Barcelona), Prof. Wiaux, Prof. Mutsvangwa, Nathi Ndlovu (CSIR), Johnson and Sharpe.

The group and individual prizes were announced in the evening with the OOD Red Star team (out of distribution samples in healthcare: Malaria as a use case) taking first place, followed by the Golden GANS (Combating data scarcity in medical imaging – using AI to generate synthetic images using breast mammograms as a use case) being runners up.

Individual prizes went to Refiloe Shabe from Lesotho for showing the best team leadership; Rancy Chepchirchir from Kenya for showing the most progression during the week of the school; and Emmanuel Hansingo from Zambia for embodying the ‘spirit of the school’.

The prize-giving dinner was attended by Chris Austin, Development Director at the British High Commission in Pretoria, who added “There is no right way or wrong way to approach problems, but the collective way, thinking about what evidence there is, what data there is and what you can do with it is super exciting. It is fantastic to hear what you have been working on through this programme, bringing some clever people together from all over Africa. The UK government has been delighted to support the DARA programme over several years and I hope that this legacy will continue”.

“What makes running these schools successfully is great partnerships” adds De Swardt. “It is fantastic that SARAO, a radio astronomy observatory, can host these skills training events in scientific areas that are broader than our mandate as an organisation. Thank you to all our partnering institutions for their commitment to these programmes.”

The final day of the school involved a scenic tour of the Cape Peninsula where participants got to see some of Cape Town’s iconic marine life and landscape such as the African penguins, Cape Point Nature Reserve and seal island.

4th Big Data Africa School participant, Maziko Mphepo from Malawi, provided his thoughts on the school from the perspective of a student: “From the informative and engaging sessions to the well-planned social activities, everything was flawlessly executed. I particularly enjoyed the opportunity to connect with other like-minded individuals and learn from industry experts in such an immersive and inspiring environment.

I am deeply grateful for the opportunity to attend this year’s school and gain new skills and knowledge in my field of interest. The efforts and hard work SARAO and its partners have made a significant impact on my personal and professional development, and I cannot thank you enough.

I truly appreciate SARAO’s hard work and commitment to providing a top-notch educational experience. I am grateful for the opportunity to have been a part of this program, and I’m sure that all the students share my sentiments.”