{"id":7763,"date":"2021-11-29T19:17:52","date_gmt":"2021-11-29T17:17:52","guid":{"rendered":"https:\/\/clients.triloogia.ee\/proekspert\/wp-new\/?p=7763"},"modified":"2023-08-11T09:44:44","modified_gmt":"2023-08-11T07:44:44","slug":"ai-in-biochemistry-proeksperts-man-on-the-scene","status":"publish","type":"post","link":"https:\/\/clients.triloogia.ee\/proekspert\/wp-new\/blog\/in-the-spotlight\/ai-in-biochemistry-proeksperts-man-on-the-scene\/","title":{"rendered":"AI in biochemistry: Proekspert’s man on the scene"},"content":{"rendered":"\n

\u200b\u200bData scientist T\u00f5nis Laasfeld won Estonia\u2019s Ustus Agur stipend. We talked to him about the intersection of chemistry and data in academia and industry.<\/p>\n\n\n\n

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Foto: Joanna J\u00f5hvikas<\/figcaption><\/figure>\n\n\n\n

Congratulations on being awarded the Ustus Agur stipend. Let\u2019s start by asking what everyone\u2019s wondering: Who is Ustus Agur?<\/strong><\/h4>\n\n\n\n

He is the founding father of information technology in Estonia. Since 2003, the Estonian Association of Information Technology and Telecommunications<\/a> has given an annual stipend in his name for the investment toward scientific education.<\/p>\n\n\n\n

But you\u2019re getting a PhD in chemistry. How is that related to IT?<\/strong><\/h4>\n\n\n\n

The stipend is for those who use information technology in other areas. In some cases, chemistry and IT are even more closely connected than two areas within chemistry. Even my thesis advisors come from two different areas, Ago Rinken<\/strong> from biochemistry and pharmacology, and Leopold Parts<\/strong> from genomics and deep learning.<\/p>\n\n\n\n

How do chemistry and data science intersect in your work?<\/strong><\/h4>\n\n\n\n

I develop software, called Aparecium, for pharmacologists who need to analyze data. Many of their experiments are done with microscopes, which make beautiful images of samples. But to analyze data quantitatively, those images must be turned into numbers that correspond to biochemical processes.<\/p>\n\n\n\n

I have applied the software in three areas. First, data can be analyzed to study whether a combination of chemotherapies works better than using a single agent. Second, labeled drug molecules can be used to measure how regular drug molecules point to drug targets. This is useful to screen a huge number of candidates for a drug and measure which of them it would bond best with. A third application is to study how viral infections happen over time and take temporal measurements. In our lab, we study baculoviruses this way. Novavax, the American biotech company developing a new Covid vaccine, uses baculovirus technology in their vaccines.<\/p>\n\n\n\n

Pharmacological research is of course very international, but the field\u2019s historical connection to Estonia is quite interesting. Experimental pharmacology was developed at Tartu University<\/a> in the 1800s, which was then known as Dorpat University. There were two German pharmacologists, Rudolf Buchheim and Oswald Schmiedeberg, who later trained most other pharmacology professors in Europe. In their work they studied muscarine which is found in the redcap mushroom and works by activating muscarinic acetylcholine receptors. Today, I\u2019m studying the very same receptors that they studied 150 years ago. (And a fun fact if you\u2019re into trivia: muscarine was extracted in the same year of Estonia\u2019s first song festival, which is also the year Mendeleev published the periodic table of the elements.)<\/p>\n\n\n\n

So how is your research relevant to Proekspert and the work done here?<\/strong><\/h4>\n\n\n\n

What I do at the university is directly applicable to the data science industry. For example, a cell seen under a microscope and an object on earth seen from space are quite similar in relative scale. The artificial intelligence algorithms you need to apply are the same.<\/p>\n\n\n\n

One project I can talk about is a project Proekspert did for the European Space Agency<\/a> where we created an algorithm to screen satellite images, detect football fields, and determine whether they\u2019re natural grass or artificial turf. The app we developed gives governments and other organizations information that\u2019s critical in city planning, helping them make informed environmental decisions. Where can you place new fields so they\u2019ll be environmentally safe \u2013 to avoid runoff of herbicides or keep those black rubber particles from washing into rivers? Or since artificial turf generates heat pockets in summer, where can we put new fields to not exacerbate the problem? Or maybe an artificial turf company wants information about sector growth. Another app can show the condition of artificial turf, which a turf company might use to know where to direct its sales efforts.<\/p>\n\n\n\n

There are lots of applications for our work, but the ESA<\/a> wanted to demonstrate that their satellites have commercial applications beyond just the scientific ones. The ESA funded part of that work, and Proekspert<\/a> funded part, as well.<\/p>\n\n\n\n

What about a project you\u2019re not allowed to talk about?<\/strong><\/h4>\n\n\n\n

I can describe in vague terms one we did for cardiovascular diagnoses, helping a client automate the decision process for its medical personnel. There is an imaging measurement they need from the patient that required manual adjustment of equipment before the image went into a processing pipeline. The doctor taking the measurement could not be certain whether the measurement was good enough for analysis, so we created a solution to determine that. By improving the diagnostic tool, we saved the manpower of medical professionals, since they could determine immediately whether their measurement was good enough.<\/p>\n\n\n\n

How have you arranged it with Proekspert so that you\u2019re able to work both in academia and business?<\/strong><\/h4>\n\n\n\n

For the last year and a half I\u2019ve worked part time as a data scientist at Proekspert<\/a>, and I should complete my PhD in August 2023. What I\u2019ll do after I get my degree is hard to say. I may do post-doc work at an institution abroad, but I would eventually return to Estonia. I like both academia and the industry side, and Proekspert is good about letting me balance them.<\/p>\n\n\n\n

You\u2019re probably not the only one at Proekspert with a foot in both worlds?<\/strong><\/h4>\n\n\n\n

There are others at Proekspert who are also PhD students. I know two personally \u2013 a chemist and a physicist who are also connected to Tartu University, and working with computational methods. Estonia\u2019s Masters programs are also fairly science-heavy, and these students are also involved with Proekspert<\/a>.<\/p>\n\n\n\n

So the academic-industry partnership is a productive combination?<\/strong><\/h4>\n\n\n\n

Yes, it\u2019s useful for both parties. At first glance, you\u2019d think you\u2019d have to split your time, and your efficiency would be reduced. But in reality, the academic world moves slower, and it\u2019s not so likely to adapt to new project management systems. But companies are ready to try things out. So I can learn from industry and apply it in the university to make my work there more efficient. The software development skills help me to analyze huge datasets in a few hours that would otherwise take days or weeks of manual labor.<\/p>\n\n\n\n

And the skills transfer the other direction, too. An academic background is important in industry, because data science often focuses on data. It\u2019s data science, not just data analysis. Academia teaches us to think about our assumptions, how to run tests \u2013 these things you can miss if you don\u2019t have a good grasp of scientific method. Those without an academic background can make a solution, but it may not be the solution.<\/p>\n\n\n\n

This is understood at Proekspert. If you want to learn something, then the teams and people in the organization get that this is useful in the long run. The team compensates and covers for you in your absence so there aren\u2019t hiccups in the processes. It\u2019s a great environment for those of us who straddle the two worlds, or really for anybody who likes to learn.<\/p>\n\n\n\n

T\u00f5nis Laasfeld (27)<\/h2>\n\n\n\n