Projects


Spare time stuff, research, etc.

Open source tools for open data

Louhos: Since 2011 I have been developing open source tools for processing, analyzing and visualizing open data with a few Finnish friends in the Louhos project. It all started with our sorvi R package winning the Apps4Finland 2011 data opening category. Since then, our blog (in Finnish; migrated from Wordpress in June 2014) has received more than 30000 views and we’ve won also other prices in Apps4Finland.

rOpenGov: Currently we are actively developing the rOpenGov R ecosystem for open goverment data. We already have a lot of packages involved all around Europe and the US, and even more are being developed. In Finland, the original sorvi package has been split to several more focused packages. Personally I am most actively developing the helsinki and gisfin packages.

R packages for open data

  • helsinki - Helsinki open data R tools
  • gisfin - Finland GIS R tools
  • sorvi - Finnish open government data R tools

Check out R-bloggers for interesting blogs related to the R language!

Achievements

Open knowledge

Open knowledges cover a wide set of topics from open data and science to democracy. Open Knowledge Finland (OKFFI) was founded few years ago to represent the emerging Finnish openness community. It works through working groups, and I’m also actively involved in some of these as listed below.

My Data has emerged as an important topic on the side of open data. The working group recently produced a My data survey that clarifies the related concepts nicely. An English version is coming in the future. I have also developed some code for analyzing personal data from various sources.

Open science - the openness of research publications, data and code - is a really hot topic now. Problems in research reproducibility have raised the need for better and more open ways to conduct science.

Research on machine learning and bioinformatics

I finished my PhD studies in Aalto University in 2014. In my thesis I developed machine learning methods for molecular biology and medicine applications.

Software

Publications

Here some selected publications. See all of my publications in Google Scholar.

Cross-organism toxicogenomics with group factor analysis
Tommi Suvitaival, Juuso A Parkkinen, Seppo Virtanen, and Samuel Kaski
Systems Biomedicine 2014; 2:e29291
DOI | code

Probabilistic drug connectivity mapping
Juuso A Parkkinen and Samuel Kaski
BMC Bioinformatics 2014, 15:113
DOI | code

Comprehensive data-driven analysis of the impact of chemoinformatic structure on the genome-wide biological response profiles of cancer cells to 1159 drugs
Suleiman A Khan, Ali Faisal, John P Mpindi, Juuso A Parkkinen, Tuomo Kalliokoski, Antti Poso, Olli P Kallioniemi, Krister Wennerberg and Samuel Kaski
BMC Bioinformatics 2012, 13:112
DOI

Graph Visualization With Latent Variable Models
Juuso A Parkkinen, Kristian Nybo, Jaakko Peltonen and Samuel Kaski
In MLG ‘10: Proceedings of the Eighth Workshop on Mining and Learning with Graphs. Washington, D.C. 2010
DOI

Searching for functional gene modules with interaction component models
Juuso A Parkkinen and Samuel Kaski
BMC Systems Biology 2010, 4:4
DOI | code

Theses

Probabilistic components of molecular interactions and drug responses
Doctoral thesis
Aalto University School of Science, Department of Information and Computer Science, September 2014
online | PDF

Generative probabilistic models of biological and social network data
Master’s thesis
Helsinki University of Technology, Department of Information and Computer Science, September 2009
online | PDF

Äänenkorkeuden havaitsemisen hermostollinen perusta
Bachelor’s thesis (in Finnish)
Helsinki University of Technology, Department of Electrical and Communications Engineering
online