How I ended up in the ACM SRC grand finals

[Editor’s Note: This is an invited post from Hasindu, who is one of the winners of the 2020 ACM Student Research Competition and the winner of 2019 SIGBED Student Research Competition, on his experience and research.]

 

How I ended up in the ACM SRC grand finals

My PhD research project targeted publications in leading bioinformatics and science journals. I was very keen to witness a mainstream computer science conference since I had never been to one.  Last year, one of our collaborative papers got accepted into ESWEEK 2019. I was planning on taking this opportunity and attending the conference when my labmate, Hassaan Saadat, who had experienced the ins and outs of ACM/IEEE conferences knew of the ACM SRC at ESWEEK (through one of his colleagues at Arizona State University – Sumit Kumar Mandal) and encouraged my participation. This itself was a sufficient reason for me to attend ESWEEK 2019, and without any delay, I  prepared and submitted the required abstract.  

The abstract got in, my poster was shortlisted for presentation, I gave a talk to the judges in the finals, and won first place in the ACM SIGBED SRC. Things did not end there, as my paper (which was requested of all the winners of the SRC competition of the SIGs) won the third place in the ACM SRC grand finals from amongst winners from many other ACM conferences.

ACM SIGBED SRC and ESWEEK experience

ACM SIGBED SRC was a great experience. It was incredibly well organized, and the organizing committee and the judges were highly encouraging.  It was also a great opportunity for a young researcher like me to network with experts in embedded systems at ESWEEK, witness a great conference, and enjoy the heart of New York – Manhattan! The SRC competition undoubtedly polished my presentation skills, boosted my confidence, gave recognition to my work, and fine-tuned my research direction for the computer science and embedded system community. This competition is something I would highly recommend to other PhD candidates in the future. Although getting a visa to enter the USA while possessing a Sri Lankan passport was probably the only thing I found more challenging than the competition,  I am extremely delighted that the effort was so well rewarded.

PhD thesis project – embedded systems for ultra-portable DNA data analysis

My PhD thesis project – the one that won the above award – is primarily focused on designing and developing embedded systems to perform ultra-portable DNA data analysis. DNA data analysis has revolutionary implications in healthcare, epidemiological, and forensic applications. DNA sequencers – the devices that read the DNA from biological tissue samples on to the computer – have become ultra-portable (e.g, Nanopore MinION). Taking full advantage of such ultra-portable sequencers requires ultra-portable embedded systems capable of analysing terabytes of data coming from the devices to enable point-of-care or in-the-field DNA data analysis. During the ACM SIGBED presentation, I stated the Ebola virus outbreak in West Africa as a critical real-world problem that would have benefitted from such ultra-portable analytics. The scientists could generate the sequenced DNA data in-the-field but faced tremendous troubles and delays when transferring the data over the mobile internet to be processed in high-performance computers in the UK. Today with the COVID-19 pandemic, the importance of such ultra-portable analytics has become even more evident where rapid tracking of the virus spread is crucial in controlling the situation.

Doing an impactful multi-disciplinary project also has its challenges. I started my PhD with no background of genomics. My primary supervisor, Sri Parameswaran who is the head of the embedded systems groups at UNSW Sydney (one of the finest research groups to work on the earth in my opinion), used to say that this project involves being thrown in at the deep-end to learn. Genomics is a huge field with massive domain knowledge and combining that with embedded systems is not for the faint-hearted but my great interest in the two fields,  thirst for new knowledge and the motivation to serve gave me the energy to overcome all the challenges and obstacles. I was also fortunate to get the opportunity to work in collaboration with the Garvan Institute of Medical Research,  one of the largest medical research centres in Australia, where I found my co-supervisor Martin A. Smith and this collaboration was vital to the success of this project.

What is next?

The prototype embedded systems we built are not limited to simulations or constrained data sets, but in fact, they are real prototypes that work on real datasets. From here, it is only a matter of converting these working prototypes into a product with an appealing user-friendly design and interface so that people in the medical or biological field can easily use them without needing the facility of high-performance computers or networks. Yet, genomics is a huge field and there is a plethora of workflows, and the prototype we built covers only a few. So, there is still plenty of research work and ground to cover for us and anyone interested in taking the challenge. I believe that our work –being the first of its kind– opens the door to such future research directions.

More details of the project can be found in the following publications: acm, nature, bmcbioinformatics

Author bio: Hasindu Gamaarachchi is a final-year PhD candidate at School of Computer Science and Engineering, University of New South Wales, Sydney, Australia. He received his bachelor degree with first-class honours for Computer Engineering from the University of Peradeniya, Sri Lanka in 2015. His research interests are in embedded systems, GPGPU computing and bioinformatics.

DisclaimerAny views or opinions represented in this blog are personal, belong solely to the blog post authors and do not represent those of ACM SIGBED or its parent organization, ACM.

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