In addition to my personal blog, I’ve been contributing to these other blogs (some pieces published in multiple blogs):
- What did we learn from using Fitbits for a year?
- Using visualizations to communicate data science – Case cancer risk analysis
- More privacy and better personalization – a mission impossible?
- Exploring the future of occupational healthcare
- Ethics and MyData — from theory to practice
- Is Your Personal Data Used to Influence Your Actions?
- Openness Empowers Individuals and Societies
- BioDI: Mitä yliopisto ei opettanut minulle? - Kirjoitus Aalto-yliopiston Bioinformaatioteknologian kilta Inkubion lehdessä S’napsissa 3/2015.
Check out R-bloggers for interesting blogs related to the R language!
- How can we make personalised medicine a reality while ensuring data protection? in MyData 2019, Helsinki, 27.9.2019 (slides)
- From academia to industry, reflections on a career in data science in HICT S5, Aalto University, 25.4.2019 (slideshare)
- Modern, citizen-centred data stewardship for the common good: why do we have to go beyond the GDPR? in BeyondRCT, Amsterdam, 25.9.2018 (slides)
- Avoimen datan ja omadatan mahdollisuudet terveysalalla, SOSTE Järjestöjohdon tammifoorumi, 31.1.2018 (slides)
- Opportunities for Life After PhD in Helsinki Life Science Day, 9.11.2017 (slideshare, blog)
- Hosting the Ethics of MyData and AI session in MyData 2017 conference, 30.8.2017
- 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)
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
- GIST cancer risk calculator: web service, blog post
- Kannattaakokauppa.fi (apartment price modeling and visualisation): web service, blog post, interviews in Finnish: HS, Iltasanomat
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.
More open data stuff
- Pyöräily on arkista touhua data journalism piece (in Finnish) about statistical modelling of bicycle traffic in Helsinki. See also code.
- Datademo funding for the helsinki and gisfin packages. Details (in Finnish) here and here. I was also interviewed in Citiscope and in a video.
- Apps4Finland 2013: Third place in the visualization category with the Alueellinen hyvinvointi-visualization that was developed together with Juha Leppänen and Satu Korhonen from Demos Helsinki think tank. Details (in Finnish).
- Apps4Finland 2012: Victory in the data opening category (official and audience votes): Data elections (Datavaalit). Details (in Finnish).
- Apps4Finland 2012: Victory in the data guide category (audience votes): Finnish data wiki. Details (in Finnish).
- Apps4Finland 2011: Victory in the data opening category (both official and audience votes): sorvi - R toolbox for open data. Details (in Finnish).
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.
- ProbCMap - Source code related to article Probabilistic drug connectivity mapping
- ICMg - Interation component model for gene modules. R packge related to article Searching for functional gene modules with interaction component models. ICMg is also included in the Netresponse package.
- Eyediagram - Code for creating eyediagram visualizations
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
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
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
Äänenkorkeuden havaitsemisen hermostollinen perusta
Bachelor’s thesis (in Finnish)
Helsinki University of Technology, Department of Electrical and Communications Engineering