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):
- 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
Other writings
- 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!
Public presentations
- 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)
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
- 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.
Software
- 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
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