The course consists of the following components:

Lectures

Preliminary schedule:

• Monday 16.1.  Introduction (Heinonen)
• Thursday 19.1. Network models (Salmela)
• Monday 23.1. Network clustering (Salmela) Note: This lecture will be given in the exercise slot 10-12!
  • Hartuv, E. Shamir, R.: A clustering algorithm based on graph connectivity. Information Processing Letters Volume 76, Issues 4-6, 31 December 2000, Pages 175-181
• (Thursday 26.1. Presentation of group work)
• Monday 30.1. Motif discovery (Salmela)
  • FPF algorithm: Schreiber & Schwöbbermeyer: Frequency concepts and Pattern Detection for the Analysis of Motifs in Networks. Transactions on Computational Systems Biology III. Lecture Notes in Computer Science, 2005, Volume 3737/2005, 89-104
• Thursday 2.2. Transcriptional regulation networks I (Salmela)
• Monday 6.2. Transcriptional regulation networks II (Salmela)
• Thursday 9.2. Network inference I (Heinonen) (revised the covariance slides sligthly)
  • CLR algorithm: Faith et al: Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles. PLoS Biology (2007) 5(1):e8
• Monday 13.2. Network inference II (Heinonen)
• Thursday 16.2. Support vector machines and diffusion kernel (Heinonen)
• Monday 20.2. Metabolic networks I (Heinonen)
• Thursday 23.2. Metabolic networks II (Heinonen)

Group work

• 10% of the grade
• Completed during the group work session
• Monday 23.1. 12-14: Preparation of a short presentation (ca. 15 min) of a network analysis paper
• Thursday 26.1.  Presentations of group work
• Network analysis papers:
  • Jian Hou, Chunxiang Li, Roman Sirokov, Marcus Söderholm: Zhang & Zhang: A big world inside small world networks
  • Mohammad Islam, Andres Levitski, Anna Kuosmanen, Johannes Ylinen: Ravasz & Barabasi: Hierarchical organization in complex networks
  • Himanshu Chedda, Hailin Lei, Shewangizaw Sore, Teemu Summanen: Small et al: Scale-free networks which are highly assortative but not small world
  • (Callaway et al: Network robustness and fragility: percolation on random graphs)
• The groups should have about three students. If you have preferences about the group you want to be in, send those to Leena Salmela (Leena.Salmela@cs.helsinki.fi) before Thu 19.1. I will then assign you to groups and assign one paper to each group.

Exercises

• 20% of the grade
• completed at home, returned in writing to Hongyu Su (Hongyu.Su@cs.helsinki.fi) prior to the session (don't return late if you want exercise points!), reviewed in the exercise sessions
• Four exercise sessions:
  • Monday 30.1. Exercise Set 1    and    Solution1
  • Monday 06.2. Exercise Set 2    and    Solution2
  • Monday 13.2. Exercise Set 3    and    Solution3 updated!
  • Monday 20.2. Exercise Set 4    and    Solution4 updated!

Course exam

70% of the grade

Grading

The course will be graded in the scale 1-5. 50% of the maximum points will give the grade of 1/5, 90% of the maximum will give the grade of 5/5.