1. Leiden University. The university to discover. Leiden Institute of Advanced Computer Science LIACS Joost N. Kok, Wetenschappelijk Directeur

2. Leiden University. The university to discover.

4. LIACS -Het Informatica Instituut van de Universiteit Leiden -Onderdeel Faculteit Wiskunde en Natuurwetenschappen

5. Leiden University. The university to discover. LIACS -Management Team -Scientific Director -Director of Education -Managing Director -Opleidingscommissie -Instituutsraad -Examencommissie -Raad van Toezicht

6. Leiden University. The university to discover. Onderzoeksclusters van LIACS -Algorithms -Foundations of Software Technology -Computer Systems -Imagery and Media -Technology Innovation Management

7. Leiden University. The university to discover. LIACS Research Clusters  Algorithms - prof.dr. Thomas Bäck & prof.dr. Joost Kok  Computer Systems - prof.dr. Ed Deprettere & prof.dr. Harry Wijshoff  Foundation of Software Technology - prof.dr. Farhad Arbab & prof.dr. Joost Kok  Imaging - dr. Michael Lew & dr.ir. Fons Verbeek  Technology Innovation Management – prof. dr. Bernhard Katzy

8. Leiden University. The university to discover. Professors @ LIACS

9. Leiden University. The university to discover. LIACS  Full Professors  Associate Professors  Assistant Professors  Postdocs  PhD students  Support staff

10. Leiden University. The university to discover.

11. Taken -40% onderzoek – 40% onderwijs – 20% management -80% onderwijs – 20% onderzoek -1 e, 2 e en 3 e geldstroom

12. Leiden University. The university to discover. Onderwijs -Bachelor Informatica -Master Computer Science -Master Media Technology -Master ICT in Businesss

13. Leiden University. The university to discover. Master Degrees  Three Masters  Computer Science (including Bioinformatics Track)  Media Technology  ICT in Business  Two years

14. Leiden University. The university to discover. PhD Education  60 PhD students @ LIACS  Promovendi  Buiten Promovendi  Graduate School  Onderzoeksscholen  IPA  ACSI  SIKS

15. Leiden University. The university to discover. Algorithms Cluster @ LIACS

16. Leiden University. The university to discover. Natural computing -Natural computing focuses on computational methods gleaned from natural models, such as evolutionary computation, molecular computing, neural computing, cellular automata, and swarm intelligence.

17. Leiden University. The university to discover. Natural Computing -Computers are to Computer Science as Comic Books to Literature

18. Leiden University. The university to discover.

19. Evolutionary Algorithms for Multi-Parameter Physics -Evolutionary algorithms are applied to problems in multi-parameter physics, such as e.g. the control of femto-second lasers to impact molecules in a desired way.

20. Leiden University. The university to discover.

21. The Fourth Paradigm -Data-Intensive Scientific Discovery “One of the greatest challenges for 21st-century science is how we respond to this new era of data- intensive science. This is recognized as a new paradigm beyond experimental and theoretical research and computer simulations of natural phenomena—one that requires new tools, techniques, and ways of working.” — Douglas Kell, University of Manchester

22. Leiden University. The university to discover. Data Mining definitions -Secondary analysis of data -Induction of understandable useful models and patterns from data -Algorithms for large quantities of data

23. Leiden University. The university to discover. -Data Mining is the non-trivial process of identifying valid, novel, potentially useful, and ultimately understandable patterns in data useful novel, surprising comprehensible valid (accurate)

24. Leiden University. The university to discover.

25. Typical Data Mining Results -Forecasting what may happen in the future -Classifying people or things into groups by recognizing patterns -Clustering people or things into groups based on their attributes -Associating what events are likely to occur together -Sequencing what events are likely to lead to later events

26. Leiden University. The university to discover. From “Querying” to “Mining” Are there any occurrences of GAAT in this string? How many occurrences of AAT are there in this string? Which substrings of length 4 occur at least 2 times? Which substrings (of any length) occur significantly moreoften in the white string than in the black string? Standard database technology solves such questions Data mining technology can sometimes solve such questions (computations may be (too) heavy) Science fiction Why is the virus to the left resistant to my drug, and the one to the right not?

27. Leiden University. The university to discover. Subgroup Discovery -How to find comprehensible subgroups in large amounts of data? -As an example: subtypes in complex diseases. -Different types of input.

28. Leiden University. The university to discover.

29. Grand Challenges -Lerende Auto’sLerende Auto’s

30. Leiden University. The university to discover. Robosail -WebsiteWebsite

31. Leiden University. The university to discover.

34. Intelligent Bridge (InfraWatch)

35. Leiden University. The university to discover.

37. Sensor network to monitor bridge behavior

38. Leiden University. The university to discover. 145 sensors, 100Hz: 5GB/day Vibration Strain (longitudinal) Strain (transverse) Temperature

39. Leiden University. The university to discover. What are we looking for? Signs of decay (long) Effects of traffic, weather,... (medium) Individual ‘events’ (short) Relationships between different signals and why? Plan maintenance What kind of forces is bridge subjected to? How does bridge respond? How does one affect the other? What info do we really need? Fewer/different sensors?

40. Leiden University. The university to discover. The Challenge - Sensor network: 145 sensors: 5GB/day, 8TB/4years - Disk read @50MB/s takes 2 days - We would like 2 minutes/seconds

41. Leiden University. The university to discover. Sensor Viewer -We constructed a “mediaplayer” to view the data over time.

42. Leiden University. The university to discover. Graph Mining Internet Map [lumeta.com] Hyves Protein Interactions [genomebiology.com] Friendship Network [Moody]

43. Leiden University. The university to discover. Graph Mining Tasks -Object-Related -Link-Based Object Ranking -Link-Based Object Classification -Object Clustering (Subgroup Detection) -Object Identification (Entity Resolution) -Link-Related -Link Prediction -Graph-Related -Subgraph Discovery -Graph Classification -Generative Models for Graphs

44. Leiden University. The university to discover. Visualisation -Intelligent/Intelligible Data Analysis -Intelligent = Methods -Intelligent = Human Interaction -Intelligible = Understandable -First step: -Visualisation of the data

45. Leiden University. The university to discover. DNA Visualisation -Long patterns over small alphabets are hard to find … -ababababababababababababababababababababababa... -(ab)  -abbbababaaababbabbbababaaababbabbbababaaababb... -(abbbababaaababb)  -abaaaababbbbabaaaababbbbabaaaababbbbabaaaabab... -(abaaaa · babbbb) 

46. Leiden University. The university to discover.

47. DNA Visualisation -Associate each nucleotide A, C, T, G with a dimension -Four nucleotides => four dimensions -Build a structure in four dimensions -Project to three dimensions

48. Leiden University. The university to discover. DNA Visualisation -Expectation: -A non-predictable walk for information rich parts of the DNA -A true random walk for random parts -Lines (or approximate lines) for repeating parts of the DNA -Large identical substrings in the DNA can easily detected

49. Leiden University. The university to discover. DNA Visualisation -Select four three-dimensional vectors. -The vectors should be of comparable length -The four vectors should add up to 0 -Every subset of three vectors should be independent.

50. Leiden University. The university to discover. DNA Visualisation

51. Leiden University. The university to discover. The first 160,000 nucleotides of the human Y-chromosome

52. Leiden University. The university to discover. The first 160,000 nucleotides of the human Y-chromosome

53. Leiden University. The university to discover.

54. 40,000–100,000 of the chromosome 1 (human)

55. Leiden University. The university to discover. Algorithms Cluster @ LIACS

56. Leiden University. The university to discover.