the story beyond artificial immune systems zhou ji, ph.d. center for computational biology and...
TRANSCRIPT
NATURAL COMPUTINGThe story beyond Artificial
Immune Systems
Zhou Ji, Ph.D.Center for Computational Biology and BioinformaticsColumbia UniversityWuhan, China 2009
… maybe this is a better title
Alan Turing
1912-1954
Artificial Immune SystemsSwarm Intelligence
Fractal GeometryMolecular Computing
Genetics Algorithm
Artificial Neural Network
Bioinformatics
Computational Biology
Evolutionary Algorithms
Artificial Life
DNA Computing
Artificial Immune SystemsSwarm Intelligence
Fractal GeometryMolecular Computing
Genetics Algorithm
Artificial Neural Network
Bioinformatics
Computational Biology
Evolutionary Algorithms
Artificial Life
DNA Computing
Three examples
Genetic algorithm – a well established algorithm
Artificial Immune Systems – a new area that are diverse and to be defined
Bioinformatics – what is both biology and computer science at the same time
Multiple levels of biological study
cellular
molecular
organ
population
Tissue
Genetic algorithm
1. Chromosomes change between generations• crossover• Mutation
2. Survival of the fittest
How does evolution happen?
Genetic algorithm
Typical problem handled with GA optimization
What is search space? – all possible parameters It is UNKNOWN in general
GA’s basic idea and procedure Start a population Evaluate fitness New population
Selection, crossover, mutation, accepting Replace Test (absolute or relative criterion) and loop
Artificial immune systems
Any computing methods inspired by immune system and computational effort for immunology motivation Clonal selection Immune network model Negative selection algorithms Danger theory and other new directions
components of the immune system
Immune network model• Typical application: clustering• Network of “B-cells” to represent the types of antibody• Develop based on Interaction between nodes and between node and training data (‘antibody’)
Negative selection algorithms
an illustration of detector set
Danger theory
Bioinformatics
FEAST OF THREE
BiologistsStatisticiansComputer
Scientists
Protein’s hierarchical structure
secondary structurea helix and b sheet
Life’s secret:how DNA encodes protein
Each of the four letters takes 2 bits to store. One byte thus can store four letters.
Human genome include about 3 billion nucleotides: 3 X 10^9 /4 = 8 X 10^8 = 800,000,000 800 MB - that takes about one regular CD to store.
DNA is strings A, T(U), C, G.
Summary
Natural computing bridges between biology and computer science Bio-inspired computing Emulated life Computing with natural materials
Biology is very interesting from the computer science point of view.
Questions or comments?