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![Page 1: Leiden University. The university to discover. Leiden Institute of Advanced Computer Science LIACS Joost N. Kok, Wetenschappelijk Directeur.](https://reader035.fdocuments.us/reader035/viewer/2022062404/551b1b9c5503465e7d8b659b/html5/thumbnails/1.jpg)
Leiden University. The university to discover.
Leiden Institute of Advanced Computer Science
LIACS
Joost N. Kok, Wetenschappelijk Directeur
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Leiden University. The university to discover.
![Page 3: Leiden University. The university to discover. Leiden Institute of Advanced Computer Science LIACS Joost N. Kok, Wetenschappelijk Directeur.](https://reader035.fdocuments.us/reader035/viewer/2022062404/551b1b9c5503465e7d8b659b/html5/thumbnails/3.jpg)
Leiden University. The university to discover.
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Leiden University. The university to discover.
LIACS
- Het Informatica Instituut van de Universiteit Leiden
- Onderdeel Faculteit Wiskunde en Natuurwetenschappen
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Leiden University. The university to discover.
LIACS
- Management Team- Scientific Director- Director of Education- Managing Director
- Opleidingscommissie- Instituutsraad- Examencommissie- Raad van Toezicht
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Leiden University. The university to discover.
Onderzoeksclusters van LIACS
- Algorithms- Foundations of Software Technology- Computer Systems- Imagery and Media- Technology Innovation Management
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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 VerbeekTechnology Innovation Management – prof. dr.
Bernhard Katzy
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Leiden University. The university to discover.
Professors @ LIACS
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Leiden University. The university to discover.
LIACSFull ProfessorsAssociate ProfessorsAssistant ProfessorsPostdocsPhD studentsSupport staff
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Leiden University. The university to discover.
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Leiden University. The university to discover.
Taken
- 40% onderzoek – 40% onderwijs – 20% management
- 80% onderwijs – 20% onderzoek
- 1e, 2e en 3e geldstroom
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Leiden University. The university to discover.
Onderwijs
- Bachelor Informatica
- Master Computer Science- Master Media Technology- Master ICT in Businesss
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Leiden University. The university to discover.
Master Degrees Three Masters
Computer Science (including Bioinformatics Track)
Media Technology ICT in Business
Two years
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Leiden University. The university to discover.
PhD Education 60 PhD students @ LIACS
PromovendiBuiten Promovendi
Graduate SchoolOnderzoeksscholen
IPAACSISIKS
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Leiden University. The university to discover.Algorithms Cluster @ LIACS
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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.
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Leiden University. The university to discover.
Natural Computing
- Computers are to Computer Science as Comic Books to Literature
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Leiden University. The university to discover.
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Leiden University. The university to discover.
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.
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Leiden University. The university to discover.
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Leiden University. The university to discover.
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
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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
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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)
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Leiden University. The university to discover.
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Leiden University. The university to discover.
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
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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 databasetechnology solves suchquestions
Data mining technologycan sometimes solve suchquestions (computationsmay be (too) heavy)
Science fictionWhy is the virus to the left resistant to my drug, and the one to the right
not?
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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.
1
2
3
Class A Class B
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Leiden University. The university to discover.
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Leiden University. The university to discover.
Grand Challenges
- Lerende Auto’s
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Leiden University. The university to discover.
Robosail
- Website
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Leiden University. The university to discover.
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Leiden University. The university to discover.
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Leiden University. The university to discover.
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Leiden University. The university to discover.
Intelligent Bridge (InfraWatch)
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Leiden University. The university to discover.
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Leiden University. The university to discover.
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Leiden University. The university to discover.
Sensor network to monitor bridge behavior
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Leiden University. The university to discover.
145 sensors, 100Hz: 5GB/day
Vibration
Strain (longitudinal)
Strain (transverse)
Temperature
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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?
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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
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Leiden University. The university to discover.
Sensor Viewer
- We constructed a “mediaplayer” to view the data over time.
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Leiden University. The university to discover.
Graph Mining
Internet Map [lumeta.com]
Hyves
Protein Interactions [genomebiology.com]
Friendship Network [Moody]
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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
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Leiden University. The university to discover.
Visualisation
- Intelligent/Intelligible Data Analysis
- Intelligent = Methods- Intelligent = Human Interaction- Intelligible = Understandable
- First step:
- Visualisation of the data
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Leiden University. The university to discover.
DNA Visualisation
- Long patterns over small alphabets are hard to find …
- ababababababababababababababababababababababa . . .- (ab)
- abbbababaaababbabbbababaaababbabbbababaaababb . . .- (abbbababaaababb)
- abaaaababbbbabaaaababbbbabaaaababbbbabaaaabab . . .- (abaaaa · babbbb)
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Leiden University. The university to discover.
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Leiden University. The university to discover.
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
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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
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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.
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Leiden University. The university to discover.
DNA Visualisation
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Leiden University. The university to discover.
The first 160,000 nucleotides of the human Y-chromosome
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Leiden University. The university to discover.
The first 160,000 nucleotides of the human Y-chromosome
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Leiden University. The university to discover.
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Leiden University. The university to discover.
40,000–100,000 of the chromosome 1 (human)
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Leiden University. The university to discover.Algorithms Cluster @ LIACS
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Leiden University. The university to discover.