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Natural Computing

Natural Computing. The story beyond Artificial Immune Systems. Zhou Ji, Ph.D. Center for Computational Biology and Bioinformatics Columbia University Wuhan, China 2009. … maybe this is a better title. The Romance between. Biology & Computer Science. Alan Turing. 1912-1954.

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Natural Computing

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  1. Natural Computing The story beyond Artificial Immune Systems Zhou Ji, Ph.D. Center for Computational Biology and Bioinformatics Columbia University Wuhan, China 2009

  2. … maybe this is a better title The Romance between Biology & Computer Science

  3. Alan Turing 1912-1954

  4. Evolutionary Algorithms Artificial Neural Network Bioinformatics Artificial Life Artificial Immune Systems Swarm Intelligence Fractal Geometry Molecular Computing DNA Computing Genetics Algorithm Computational Biology

  5. Evolutionary Algorithms Artificial Neural Network Bioinformatics Artificial Life Artificial Immune Systems Swarm Intelligence Fractal Geometry Molecular Computing DNA Computing Genetics Algorithm Computational Biology

  6. 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

  7. Multiple levels of biological study cellular Tissue molecular organ population

  8. Genetic algorithm How does evolution happen? • Chromosomes change between generations • crossover • Mutation • Survival of the fittest

  9. 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

  10. 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

  11. components of the immune system

  12. 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’)

  13. Negative selection algorithms

  14. an illustration of detector set

  15. Danger theory

  16. Bioinformatics Biologists Statisticians Computer Scientists Feast of threE

  17. Protein’s hierarchical structure

  18. secondary structurea helix and b sheet

  19. 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.

  20. 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.

  21. Questions or comments?

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