Newly conferred Honorary Doctor, algorithmics pioneer Esko Ukkonen: ”Computation will become like electricity”

Ukkonen, a Professor at University of Helsinki and Docent at Aalto University, is a prominent forerunner of computer science and algorithmics in Finland.

Several algorithms that Ukkonen has developed have become standard material in academic textbooks and they are widely applied. He has also led two Centres of Excellence funded by the Academy of Finland and supervised 27 doctoral dissertations to this day. For instance Aalto University Professor of computer science Pekka Orponen and the current President of the Academy of Finland Heikki Mannila have received their doctorates under Ukkonen’s tutelage.

– It does appear that I have trained the best computer science professors in Finland, Ukkonen laughs.

In his own doctoral dissertation in 1978 Ukkonen studied round-off errors in numerical analysis but took on algorithmics soon after. Algorithmics is basic research that studies the power of computers. It strives to find out which computational problems have a fast solution algorithm – and those that have not. This study produces algorithms that may be widely applicable.

– The whole field was still taking shape when I was starting my career, so you can say I had my part in creating the foundations of computer science in Finland. I have helped to develop machine learning in University of Helsinki. In Helsinki University of Technology, now within Aalto University, there was already then remarkable work done on the field, initiated by Academician Teuvo Kohonen, Ukkonen recalls.

Algorithmics revolutionised biological data

Bioinformatics is a cross-disciplinary science in which the fundamentals of life – the sequencing, structure and operation of genes and proteins – are modelled with algorithms. Professor Ukkonen became enthralled by the prospects of this line of research early in the 1980s.

– Sequencing DNA had become possible in the late 1970s, and molecular biology became very intriguing indeed to computer scientists. A watershed for me was a meeting with biotechnicians of VTT Technical Research Centre of Finland in 1980. Fittingly enough, the person to call this meeting to order was Tuula Teeri, now President of Aalto University.

– DNA
analysis suits us algorithmics researchers well, because the essential structure, the nucleobases of the DNA molecule, can be described with four characters A, C, G and T. It’s exactly the kind of character string data that we know how to analyse, and of course I wanted to make myself useful, Ukkonen recalls his initial interest in bioinformatics.

In 1990, the Human Genome Project launched with the goal of determining the entire DNA sequence and mapping the roughly 30 000 genes in the human genome. Unprecedented amounts of DNA data became available, and understanding the “programme of life” coded in the DNA strings of the genome became then a central issue in science.

– I studied and developed string searching algorithms for DNA analysis already in the 1980s, but felt a bit enclosed in an esoteric niche. Nowadays bioinformatics has established itself and amasses a surprisingly large share of the funding in computer science.

Now Ukkonen and his group look for patterns in strings of DNA that code biological signals. This enables them to predict, for instance, the root causes for different diseases. Many of the models Ukkonen and his colleagues have developed have been proven to be biologically precise.

– Thanks to our models, biologists have for instance been able to confirm a certain gene mutation to cause colorectal cancer, tells Ukkonen.

From cutting-edge basic research to popularising science

From 2002 through 2013 Ukkonen led two Centres of Excellence in data analysis appointed by the Academy of Finland. They were preceded by a doctoral programme in bioinformatics in Aalto University and the University of Helsinki. In the turn of the millennium, Ukkonen co-founded a joint venture of Aalto University and University of Helsinki: Helsinki Institute for Information Technology HIIT. In 2004–2008 he was also the Director of HIIT’s Basic Research Unit.

– HIIT has been a wonderful success: Finland needed and still needs intensive research environments like this to instigate critical mass. HIIT has also succeeded in securing long-term funding and with it the ability to flexibly hire researchers.

Ukkonen still supervises four doctoral students. With two of them, he has endeavoured to music: they apply algorithmics to the analysis of musical notation.

– Music can be conceived of as a string of characters not at all unlike texts and DNA. Musical notation is even more complicated, though, as it is two-dimensional.

Ukkonen has also throughout his career tried to popularise a science quite often beyond lay understanding. He says computer scientists should talk about issues in every-day life: information security, social media and cloud services.

– Computation is rapidly becoming a public utility just like electricity, and scientists should be able to explain what this enables and also how to keep the development in check.