Courses in previous years: [ 2006 ]
Lecturer  Prof. Sami
Kaski, Laboratory of Computer and Information Science, Helsinki
University of Technology 

Assistant  M.Sc. Arto Klami 
Credits (ECTS)  5 or 7 
Semester  Spring 2007 (periods III and IV) 
Sessions  On Fridays at 1012 in room A328 (at the Computer Science and Engineering building). 
Registration  TKK students: WebTopi, others: send mail to t616070@cis.hut.fi. The course started on Friday 19.1. 2007, but it is still possible to join (please send email if you are planning to do this). 
t616070@cis.hut.fi 
Modeling of networks is a rich research area joining modern computational modeling approaches with timely applications in diverse fields including the WWW and biological networks. The common denominator is that the goal is to model the link structure between items. In biological systems, which is the application area of this course, the items are typically genes or biological molecules, and links are interactions between them. The data may be in the form of direct measurements of the links, and the task is then to directly model the link structure, for instance searching for hubs or clusters. Alternatively, the data may be about the nodes, and the task is to infer the underlying link structure. This has been studied a lot when inferring gene regulatory networks from gene expression data, for instance.
In this course we will discuss the modeling methods and the biological applications together, by studying a set of recent papers and relevant background material. The applications give the necessary context for appreciating the models, and the methods give a rigorous background for modeling of biological networks. From the modeling perspective, modeling and inference of graphs is a very active research area in which spectral methods, kernel methods, cooccurrence data, Bayesian networks, graphical models, and causal models are some of the relevant keywords. In bioinformatics some relevant research areas are protein interaction networks (interactomics), regulation of gene expression, and more generally systems biology.
The course will be most useful for graduatelevel (after bachelor) or doctoral students of bioinformatics or related fields. Mathematically oriented biology and medical students are very welcome as well. The modeling methodologies are very general, and useful also for other students of computer science, mathematics and physics.
The course is held as a seminar course, where every participant gives one lecture/presentation of a chosen topic. Passing the course with 7 credit points requires performing the following tasks:
Instructions for the individual tasks are given here, and the exercise problems are also on a separate page. Leaving out the project work but passing the first three requirements results to 5 credit points. The course will be graded so that 60% of the grade is based on the presentation (including the exercise task) and 40% on the project work. If one solves almost all (90%) exercise problems then they have a weight of 10% towards the best grade, and solving at least half of them is required for passing.
Some basic course on machine learning helps significantly in understanding the models, but sufficient knowledge of mathematics (probabilities, statistics, linear algebra etc) should also be enough. Basic knowledge of bioinformatics or computational biology is strongly advisable.
Below is a preliminary schedule for the course. The topics and the material of the remaining presentations will be added when they have been fixed. The schedule may still change if there are new participants. There will be email notification if a significant change is made.
The first two presentations are tutorials given by the course staff, and the papers mentioned should be read before the sessions.
The slides of the presentations have restricted access. The password required for downloading them has been sent to the course participants.
Time  Lecturer  Subject and material 

19.1.  Sami Kaski 

16.2.  Sami Kaski 
Overview of biological network modeling

23.2.  Arto Klami  Tutorial on Bayes networks 
2.3.  Cancelled  No session 
9.3.  Jarkko Miettinen  Kernel methods for link prediction 
16.3.  Mikko Kivelä  Analysis of network structure 
23.3.  Erno Lindfors  Topology analysis of complex biological networks 
30.3.  Jenni Hulkkonen  Advanced Bayes networks 
6.4.  No meeting  Easter 
13.4.  Janne Toivola  Dynamic Bayes networks 
20.4.  Antti Ajanki & Abhishek Tripathi 
Recent advances in network modeling

27.4.  Ilkka Huopaniemi & Andrey Erlmolov  Metabolic networks 
4.5.  Cancelled 
Visualization of biological networks

The topics and material for the presentations will be decided directly with each participant. Background material will be added here to the degree that it is needed.
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