www.cs.nott.ac.uk/~nxk Faculty of Mathematics and Physics Charles University - December 2008 /59 An Evolutionary Algorithm Approach to Guiding the Evolution of Self-Organised Nanostructured Systems 1 Natalio Krasnogor Interdisciplinary Optimisation Laboratory Automated Scheduling, Optimisation & Planning Research Group School of Computer Science Centre for Integrative Systems Biology School of Biology Centre for Healthcare Associated Infections Institute of Infection, Immunity & Inflammation University of Nottingham
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Evolutionary Algorithms and Self-Organised Systems
This talk presents the results from one of our papers on the use of an evolutionary algorithm for an "inverse problem" on self-organised nano particles.
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www.cs.nott.ac.uk/~nxkFaculty of Mathematics and PhysicsCharles University - December 2008 /59
An Evolutionary Algorithm Approach to Guiding the Evolution of
Self-Organised Nanostructured Systems
1
Natalio KrasnogorInterdisciplinary Optimisation LaboratoryAutomated Scheduling, Optimisation & Planning Research GroupSchool of Computer Science
Centre for Integrative Systems BiologySchool of Biology
Centre for Healthcare Associated InfectionsInstitute of Infection, Immunity & Inflammation
www.cs.nott.ac.uk/~nxkFaculty of Mathematics and PhysicsCharles University - December 2008 /59
This work was done in collaboration with Prof. P. Moriarty and his group at the School of Physics and Astronomy at the University of Nottingham
Based on the paper:
P.Siepmann, C.P. Martin, I. Vancea, P.J. Moriarty, and N. Krasnogor. A genetic algorithm approach to probing the evolution of self-organised nanostructured systems. Nano Letters, 7(7):1985-1990, 2007.
www.cs.nott.ac.uk/~nxkFaculty of Mathematics and PhysicsCharles University - December 2008 /59
Major advances in the rational/analytical design of large and complex systems have been reported in the literature and more recently the automated design and optimisation of these systems by modern AI and Optimisation tools have been introduced.
It is unrealistic to expect every large & complex physical, chemical or biological system to be amenable to hand-made fully analytical designs/optimisations.
We anticipate that as the number of research challenges and applications in these domains (and their complexity) increase we will need to rely even more on automated design and optimisation based on sophisticated AI & machine learning
www.cs.nott.ac.uk/~nxkFaculty of Mathematics and PhysicsCharles University - December 2008 /59
Major advances in the rational/analytical design of large and complex systems have been reported in the literature and more recently the automated design and optimisation of these systems by modern AI and Optimisation tools have been introduced.
It is unrealistic to expect every large & complex physical, chemical or biological system to be amenable to hand-made fully analytical designs/optimisations.
We anticipate that as the number of research challenges and applications in these domains (and their complexity) increase we will need to rely even more on automated design and optimisation based on sophisticated AI & machine learning
This has happened before in other research and industrial disciplines,e.g:
•VLSI design•Space antennae design•Transport Network design/optimisation•Personnel Rostering•Scheduling and timetabling
www.cs.nott.ac.uk/~nxkFaculty of Mathematics and PhysicsCharles University - December 2008 /59
Major advances in the rational/analytical design of large and complex systems have been reported in the literature and more recently the automated design and optimisation of these systems by modern AI and Optimisation tools have been introduced.
It is unrealistic to expect every large & complex physical, chemical or biological system to be amenable to hand-made fully analytical designs/optimisations.
We anticipate that as the number of research challenges and applications in these domains (and their complexity) increase we will need to rely even more on automated design and optimisation based on sophisticated AI & machine learning
This has happened before in other research and industrial disciplines,e.g:
•VLSI design•Space antennae design•Transport Network design/optimisation•Personnel Rostering•Scheduling and timetabling
That is, complex systems are plagued with NP-Hardness, non-approximability, uncertainty, undecidability, etc results
www.cs.nott.ac.uk/~nxkFaculty of Mathematics and PhysicsCharles University - December 2008 /59
Major advances in the rational/analytical design of large and complex systems have been reported in the literature and more recently the automated design and optimisation of these systems by modern AI and Optimisation tools have been introduced.
It is unrealistic to expect every large & complex physical, chemical or biological system to be amenable to hand-made fully analytical designs/optimisations.
We anticipate that as the number of research challenges and applications in these domains (and their complexity) increase we will need to rely even more on automated design and optimisation based on sophisticated AI & machine learning
This has happened before in other research and industrial disciplines,e.g:
•VLSI design•Space antennae design•Transport Network design/optimisation•Personnel Rostering•Scheduling and timetabling
That is, complex systems are plagued with NP-Hardness, non-approximability, uncertainty, undecidability, etc results
Yet, they are routinely solved by sophisticated optimisation and design techniques, like evolutionary algorithms, machine learning, etc
www.cs.nott.ac.uk/~nxkFaculty of Mathematics and PhysicsCharles University - December 2008 /59
Automated Design/Optimisation is not only good because it can solve larger problems but also because this approach gives access to different regions of the space of possible designs (examples of this abound in the literature)
AnalyticalDesign
AutomatedDesign
(e.g. evolutionary)
Space of all possible designs/optimisations
A distinct view of the space of possible designs couldenhance the understanding of underlying system
www.cs.nott.ac.uk/~nxkFaculty of Mathematics and PhysicsCharles University - December 2008 /59
The research challenge :
For the Engineer, Chemist, Physicist, Biologist :
To come up with a relevant (MODEL) SYSTEM M*
For the Computer Scientist:
To develop adequate sophisticated algorithms -beyond exhaustive search- to automatically design or optimise existing designs on M* regardless of computationally (worst-case) unfavourable results of exact algorithms.
www.cs.nott.ac.uk/~nxkFaculty of Mathematics and PhysicsCharles University - December 2008 /59
- infinite, regular grid of cells- each cell in one of a finite number of states- at a given time, t, the state of a cell is a function of the states of its neighbourhood at time t-1.
Example- infinite sheet of graph paper - each square is either black or white- in this case, neighbours of a cell are the eight squares touching it- for each of the 28 possible patterns, a rules table would state whether the center cell will be black or white on the next time step.
?
- Self-organising processes
- Modelled using cellular automata, gass latice, ODEs, etc
www.cs.nott.ac.uk/~nxkFaculty of Mathematics and PhysicsCharles University - December 2008 /59
The Evolutionary Engine“we will implement an object-oriented, platform-independent, evolutionary engine (EE). The EE will have a user-friendly interface that will allow the various platform users to specify the platform with which the EE will interact”
Evolvable CHELLware grant application
generic GA resultsspecialisedGA
XML
web-based configuration
module
Java servlet
web-based executionmodule
- no data types- no evaluation module- no parameters
- data types and bounds - evaluation module (‘plug in’) - GA parameters
www.cs.nott.ac.uk/~nxkFaculty of Mathematics and PhysicsCharles University - December 2008 /59
• The simulation proceeds by the Metropolis algorithm:
– Each solvent cell is examined and an attempt is made to convert from liquid to vapour (or vice-versa) with an acceptance probability pacc = min[1, exp(-ΔH/kBT)]
– Similarly, the particles perform a random walk on wet areas of the substrate, but cannot move into dry areas.
– The Hamiltonian from which ΔH is obtained is as follows:
P.Siepmann, C.P. Martin, I. Vancea, P.J. Moriarty, and N. Krasnogor. A Genetic Algorithm for Evolving Patterns in Nanostructured systems.Nano Letters (to appear)
The analysis of the designability of specific patterns is important as some patterns are more evolvable (multiple solutions) than others and
www.cs.nott.ac.uk/~nxkFaculty of Mathematics and PhysicsCharles University - December 2008 /59
• We can evolve target simulated behaviour using a GA with the USM but the USM is not enough
•For evolving target experimental designs we used Minkowsky functionals (e.g. Area, Perimeter, Euler Characteristics)
• Using Fitness Distance Correlation and Clustering, we can show whether a given fitness function is/isn’t an appropriate objective function for a given domain.
• Can we generate a target spatio-temporal behaviour in a CA/Real system? YES - GA generates very convincing designoid patterns
www.cs.nott.ac.uk/~nxkFaculty of Mathematics and PhysicsCharles University - December 2008 /59
Applications (in design and manufacture) and further work
- Many, many systems can be modelled using CAs/Monte Carlos
-Many complex physical/chemical systems need to be programmed
- Research into chemical ‘design’
and self-organising nanostructured systems
e.g. designoid patterns in the BZ reaction
We are actively working towards these practical goals in the context of the EPSRC grant CHELLnet (EP/D023343/1), which comprises Evolvable CHELLware (EP/D021847/1), vesiCHELL (EP/D022304/1), brainCHELL (EP/D023645/1) and wellCHELL (EP/D023807/1).