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S-114.4220 Research Seminar on Computational Science

The topic of the course in fall 2005 is

Modeling in spatial epidemiology and spreading of contagious disease (3 p) L

Teachers: Prof. Jouko Lampinen, Dr.Tech. Aki Vehtari, Dr.Tech. Jari Saramäki

Place and time:

1) Spatial epidemiology (chronic disease)

Prof. Jouko Lampinen, Dr.Tech. Aki Vehtari

Spatial epidemiology is defined by Ellit and Wartenberg as "the description and analysis of geographic variations in disease with respect to demographic, environmental, behavioral, socioeconomic, genetic and infectious risk factors.". Common for spatial models is that they include some kind of explicit or implicit spatial correlation part, which can be formed in many ways. There exist many computational methods to obtain estimates of the interesting quantities in the studies. Presentation of summaries of the estimation results is also important topic.

Topics in this seminar include

2) Spreading of contagious disease (infectious disease)

Dr.Tech. Jari Saramäki

The second part of the seminar will focus on modelling the spreading of contagious disease. Lately, it has become evident that instead of relying on traditional assumptions of full mixing, where disease transmission takes place between random individuals, contact patterns between susceptible and infected individuals have to be taken into account. On the other hand, during the last years, the theoretical and methodological framework of complex networks has proven to be extremely fruitful in understanding networked systems, such as technological networks or networks of social interactions.

It is then rather natural to utilize the complex networks framework in modelling the contact patterns between individuals. Key questions such as epidemic thresholds, above which the disease will infect a substantial fraction of a population, can then be addressed using methods from statistical physics, such as percolation theory. In addition to the complex networks framework, there is currently interest in designing agent-based models where the contact patterns emerge from spatial simulations of the mobility of individuals. This topic will also be addressed briefly.

Topics to be covered include:

Course requirements:

Exercise instructions

Exercise is divided in two parts. Everyone makes both parts.

1) Spatial epidemiology with CAR model
Will be announced 8th December

2) Simulations of SIR spreading on networks
Matlab codes


Date Talker Subject
3.11. Jouko Lampinen Introduction to spatial epidemiology
3.11. Jari Saramäki Introduction to spreading of contagious disease
10.11. 12:30-> Aki Vehtari Introduction to Bayesian analysis
10.11. 13:15-> Jari Saramäki Introduction to complex networks
17.11. Markus Siivola Visualization of spatial data (slides,handout)
17.11. Jaakko Riihimäki Explorative methods for spatial data (slides,handout)
17.11. Jussi Kumpula Disease spreading in small world networks (slides,handout)
24.11. Abhishek Paliwal Epidemic spreading in Scale-Free Networks (slides,handout)
24.11. Riitta Toivonen Two models of pandemic influenza spread and strategies for containing the disease at the source (slides,handout)
24.11. Tapio Heimo The generating function approach to spreading and percolation
1.12. Seminar starts 12:00!  
1.12. Aki Havulinna Spatial CAR-models
1.12. Jarno Vanhatalo Spatial point processes
1.12. Jarkko Miettinen Spatial cluster models
1.12. Janne Paanajärvi Spatio-temporal models
8.12. Antti Yli-Krekola Epidemic Threshold in Structured Scale-Free Networks (slides,handout)
8.12. Matti Helin  
8.12. Matti Peltomäki Threshold effects for two pathogens spreading on a network (slides,handout)

General instructions

To simulate scientific writing, for every talk there is first author and second author. Every student is first author for one talk and second author for another talk. First author first writes the paper, second author gives comments and helps to improve it and both authors discuss about the presentation with teachers. The first author prepares the talk and second author again gives comments and helps to improve the presentation. First author presents the talk. Names of both authors are shown in the paper and in the slides. Normal talk is 25 minutes.


Prof. Jouko Lampinen

Dr.Tech. Aki Vehtari

Dr.Tech. Jari Saramäki

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Sivua on viimeksi päivitetty 4.11.2005