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?