Projects


Blogs, presentations, open knowledege, research.

Blogs

In addition to my personal blog, I’ve been contributing to these other blogs (some pieces published in multiple blogs):

Reaktor’s blog

Medium

Other writings

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

Public presentations

  • Learnings from a company-wide Fitbit experiment in Quantified Employee seminar, 28.3.2017 (slideshare)
  • Data-driven leadership culture in DataBusiness challenge event, 20.1.2017 (slideshare)
  • Hosting the Challenges in Big / Small Personal Data Analytics -session in the Mydata2016 conference, 2.10.2016.
  • Probabilistic programming for understanding regional trends in apartment prices in ICCSS2015, 11.5.2015. (slides)
  • Lecture on data science in Tampere Technical University, 28.4.2015 (slides, blog)
  • Kohti älykkäämpää fillarikaupunkia HSY:n paikkatietoseminaarissa, 11.3.2015 (slides)

Open knowledge

I am a big fan of all things open, including open data, open source, and open science. Recently I’ve also been active in the MyData community. Below I have listed some open stuff that I’ve been involved in.

Open data science at Reaktor

Open source projects and tools for open data

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

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. Currently we are 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.

Achievements related to open data

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.

A transcriptomics data-driven gene space accurately predicts liver cytopathology and drug-induced liver injury
Pekka Kohonen, Juuso A. Parkkinen, Egon L. Willighagen, Rebecca Ceder, Krister Wennerberg, Samuel Kaski & Roland C. Grafström
Nature Communications 8, 15932 (2017)
DOI | code | blog

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