The document discusses research into automated design and optimization of complex systems using artificial intelligence and machine learning techniques. It describes challenges in analytically designing large physical, chemical, and biological systems. The research aims to develop sophisticated algorithms beyond exhaustive search to automatically design and optimize models of complex systems. The goal is to enable "dialing in" desired patterns and behaviors in different types of complex systems through automated design and optimization methods.
Influencing policy (training slides from Fast Track Impact)
Interdisciplinary Optimisation Laboratory Research
1. ASAP - Interdisciplinary Optimisation
Laboratory
Natalio Krasnogor
ASAP - Interdisciplinary Optimisation Laboratory
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
Ben-Gurion University of the Negev - June 23rd to July 5th 2009 - Distinguished Scientist Visitor Program - Beer Sheva, Israel 1 /41
Wednesday, 24 June 2009
2. Research Themes
• The IOL mission is the development of cutting-edge decision
support, optimisation and search methodologies for problems arising
in the natural sciences.
• Research activities lie at the interface of Computer Science and the
Natural Sciences, e.g. Biology, Physics, Chemistry.
• In particular, we focus on developing innovative and competitive
search methodologies and intelligent decision support systems with
an emphasis on transdisciplinary optimisation, modeling of complex
systems and very-large datasets processing.
• We have applied our expertise in Bioinformatics, Systems Biology,
Synthetic Biology, Nanoscience and Chemistry.
Ben-Gurion University of the Negev - June 23rd to July 5th 2009 - Distinguished Scientist Visitor Program - Beer Sheva, Israel 2 /41
Wednesday, 24 June 2009
3. Acknowledgements
(in no particular order) (in no particular order)
Peter Siepmann
School of Physics and Astronomy
Contributors to the talks I will give at BGU
Pawel Widera
School of Chemistry
James Smaldon School of Pharmacy
Azhar Ali Shah School of Biosciences
Jack Chaplin School of Mathematics
Enrico Glaab School of Computer Science
German Terrazas Centre for Biomolecular Sciences
all the above at UoN
Hongqing Cao
Jamie Twycross Funding From:
Jonathan Blake BBSRC, EPSRC, EU, ESF, UoN
Francisco Romero-Campero
Thanks also go to:
Maria Franco
Adam Sweetman Ben Gurion University of the Negev’s
Linda Fiaschi Distinguished Scientists Visitor Program
Open PhD Vacancy
Professor Dr. Moshe Sipper
Open PostDoc Vacancy
Ben-Gurion University of the Negev - June 23rd to July 5th 2009 - Distinguished Scientist Visitor Program - Beer Sheva, Israel 3 /41
Wednesday, 24 June 2009
4. Motivation
• Automated design and optimisation of complex
systems’ target behaviour
• cellular automata/ ODEs/ P-systems models
• physically/chemically/biologically implemented
• Present a methodology to tackle this problem
• Supported by experimental demonstration
Ben-Gurion University of the Negev - June 23rd to July 5th 2009 - Distinguished Scientist Visitor Program - Beer Sheva, Israel 4 /41
Wednesday, 24 June 2009
5. Major advances in the 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 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
Ben-Gurion University of the Negev - June 23rd to July 5th 2009 - Distinguished Scientist Visitor Program - Beer Sheva, Israel 5 /41
Wednesday, 24 June 2009
6. Major advances in the analytical design of large and
complex systems have been reported in the literature
This has happened before in other research
and more disciplines,e.g: automated design and
and industrial recently the
optimisation of these systems by modern AI and
•VLSI design
Optimisationdesign/optimisation been introduced.
tools have
•Space antennae design
•Transport Network
•Personnel Rostering
•Scheduling and timetabling
It is unrealistic to expect every large & complex physical,
chemical or biological system to be amenable to 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
Ben-Gurion University of the Negev - June 23rd to July 5th 2009 - Distinguished Scientist Visitor Program - Beer Sheva, Israel 5 /41
Wednesday, 24 June 2009
7. Major advances in the analytical design of large and
complex systems have been reported in the literature
This has happened before in other research
and more disciplines,e.g: automatedcomplex systems are plagued with
and industrial recently the
That is, design and
optimisation of these systems by modern AI and
•VLSI design NP-Hardness, non-approximability,
uncertainty, undecidability, etc results
Optimisationdesign/optimisation been introduced.
tools have
•Space antennae design
•Transport Network
•Personnel Rostering
•Scheduling and timetabling
It is unrealistic to expect every large & complex physical,
chemical or biological system to be amenable to 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
Ben-Gurion University of the Negev - June 23rd to July 5th 2009 - Distinguished Scientist Visitor Program - Beer Sheva, Israel 5 /41
Wednesday, 24 June 2009
8. Major advances in the analytical design of large and
complex systems have been reported in the literature
This has happened before in other research
and more disciplines,e.g: automatedcomplex systems are plagued with
and industrial recently the
That is, design and
optimisation of these systems by modern AI and
•VLSI design NP-Hardness, non-approximability,
uncertainty, undecidability, etc results
Optimisationdesign/optimisation been introduced.
tools have
•Space antennae design
•Transport Network
•Personnel Rostering
•Scheduling and timetabling
It is unrealistic to expect every large & complex physical,
chemical or biological system to be amenable to 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
Yet, they are routinely solved by
sophisticated optimisation and design
design and optimisation based like evolutionary
techniques,
on sophisticated AI &
machine learning algorithms, machine learning, etc
Ben-Gurion University of the Negev - June 23rd to July 5th 2009 - Distinguished Scientist Visitor Program - Beer Sheva, Israel 5 /41
Wednesday, 24 June 2009
9. 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)
Space of all possible designs/optimisations
Automated
Analytical
Design
Design
(e.g. evolutionary)
A distinct view of the space of possible designs could
enhance the understanding of underlying system
Ben-Gurion University of the Negev - June 23rd to July 5th 2009 - Distinguished Scientist Visitor Program - Beer Sheva, Israel 6 /41
Wednesday, 24 June 2009
10. 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.
To develop adequate data mining and interpretation techniques
working on both the resulting designs/optimisation and the process
itself.
Ben-Gurion University of the Negev - June 23rd to July 5th 2009 - Distinguished Scientist Visitor Program - Beer Sheva, Israel 7 /41
Wednesday, 24 June 2009
11. Towards “Dial a Pattern” in Complex Systems
Ben-Gurion University of the Negev - June 23rd to July 5th 2009 - Distinguished Scientist Visitor Program - Beer Sheva, Israel 8 /41
Wednesday, 24 June 2009
12. Towards “Dial a Pattern” in Complex Systems
s e
ctur
Stru
ical S
Lex
.
teC
cre
rete
Dis
d
Disc
ute
st rib
Di
Continuous (simulated) CS
How do we program?
Disc
rete
/Con
tin. (
phys
ical)
CS
Dis
cre
te/C
ont
inu
os
(Bi
olo
gic
al)
Ben-Gurion University of the Negev - June 23rd to July 5th 2009 - Distinguished Scientist Visitor Program - Beer Sheva, Israel 8 /41
Wednesday, 24 June 2009
13. Methodological Overview
Dial a Pattern requires:
Parameter Learning/Evolution Technology
Structural Learning/Evolution Technology
Integrated Parameter/Structural Learning/Evolution Tech.
“Plastic” algorithms to continuously self-improve (without
which scalability is an issue)
Ben-Gurion University of the Negev - June 23rd to July 5th 2009 - Distinguished Scientist Visitor Program - Beer Sheva, Israel 9 /41
Wednesday, 24 June 2009
14. Datamining, Classification and Clustering
For the last five years we have been working on the
application of LCS/GBML methods to large-scale
datasets
Tumor Grade Classification for Microarrays Breast
Cancer Samples
Pre-normalised data (log-scale, min:4.9, max: 13.3)
128 samples and ~47000 genes
3 tumour grades
1(33),2(52),3(43)
majority
class classification = 40.6 accuracy
random classification (avg): 34.4% accuracy
Ben-Gurion University of the Negev - June 23rd to July 5th 2009 - Distinguished Scientist Visitor Program - Beer Sheva, Israel 10/41
Wednesday, 24 June 2009
15. Goal = Dimensionality Reduction
remove irrelevant genes, reduce complexity.
2 basic approaches:
Foldchange/variance filtering
Gene Set Analysis
Samples Clustering
PCA, ICA
Supervised Learning
Ben-Gurion University of the Negev - June 23rd to July 5th 2009 - Distinguished Scientist Visitor Program - Beer Sheva, Israel 11 /41
Wednesday, 24 June 2009
16. Protein Structure
Varying: size, shape, structure
“Natures Robots”
Structure determines their biological activity
Understanding protein structure is key to
understanding function and dysfunction
Ben-Gurion University of the Negev - June 23rd to July 5th 2009 - Distinguished Scientist Visitor Program - Beer Sheva, Israel 12/41
Wednesday, 24 June 2009
17. Protein Structure Prediction (PSP) aims to predict the
3D structure of a protein based on its primary
sequence
Primary Sequence 3D Structure
Ben-Gurion University of the Negev - June 23rd to July 5th 2009 - Distinguished Scientist Visitor Program - Beer Sheva, Israel /41
Wednesday, 24 June 2009
18. Evolving Energy Potentials for
PSP
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Wednesday, 24 June 2009
19. Prediction Scheme
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20. Ben-Gurion University of the Negev - June 23rd to July 5th 2009 - Distinguished Scientist Visitor Program - Beer Sheva, Israel 16/41
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21. Ben-Gurion University of the Negev - June 23rd to July 5th 2009 - Distinguished Scientist Visitor Program - Beer Sheva, Israel 17/41
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22. Ben-Gurion University of the Negev - June 23rd to July 5th 2009 - Distinguished Scientist Visitor Program - Beer Sheva, Israel 18/41
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23. Beside the overall 3D PSP, we can predict several
structural aspects of protein residues
•Coordination number
•Solvent accessibility
•Secondary structure
•Disulfide bonding
Accurate prediction of these features can help PSP in
many ways by:
•Constraining the conformation space
•Identifying better homolog proteins
These predictions can help research in other areas,
beside the main PSP problem
•Surface prediction
•Functional prediction
Ben-Gurion University of the Negev - June 23rd to July 5th 2009 - Distinguished Scientist Visitor Program - Beer Sheva, Israel /41
Wednesday, 24 June 2009
24. Coordination Number
Two residues of a chain are said to be in contact if their
distance is less than a certain threshold
Primary Contact Native State
Sequence
CN of a residue : count of contacts of a residue
CN gives us a simplified profile of the density of packing
of the protein
Ben-Gurion University of the Negev - June 23rd to July 5th 2009 - Distinguished Scientist Visitor Program - Beer Sheva, Israel /41
Wednesday, 24 June 2009
25. Recursive Convex Hull
•Structural feature that we have
proposed recently [Stout, Bacardit,
Hirst & Krasnogor, Bioinformatics
2008 24(7):916-923;]
•We model a protein as an onion,
assigning each residue to a different
layer of the onion, i.e., its convex
hull
•The convex hull of a point set is a
metric easy and fast to compute
•Recursive Convex Hull is computed
by iteratively identifying the layers
(hulls) of a protein
Ben-Gurion University of the Negev - June 23rd to July 5th 2009 - Distinguished Scientist Visitor Program - Beer Sheva, Israel /41
Wednesday, 24 June 2009
26. How to predict these features?
Two dimensions to decide
Inputs: What input information (derived from the
protein primary sequence) is used?
Outputs: How are we modelling the feature that we
are predicting?
Predicting the actual (continuous) feature
Predicting, for instance, buried or exposed
Discretization is applied to the original feature,
dividing it into 2, 3 or 5 states
Ben-Gurion University of the Negev - June 23rd to July 5th 2009 - Distinguished Scientist Visitor Program - Beer Sheva, Israel /41
Wednesday, 24 June 2009
27. Input information
Two types of input information
Local information: From the target residue and its
closest neighbours in the chain
Ri-5 Ri-4 Ri-3 Ri-2 Ri-1 Ri Ri+1 Ri+2 Ri+3 Ri+4 Ri+5
CNi-5 CNi-4 CNi-3 CNi-2 CNi-1 CNi CNi+1 CNi+2 CNi+3 CNi+4 CNi+5
Ri-1,Ri,Ri+1 CNi
Ri,Ri+1,Ri+2 CNi+1
Ri+1,Ri+2,Ri+3 CNi+2
Global information: From the whole chain we are
predicting
Ben-Gurion University of the Negev - June 23rd to July 5th 2009 - Distinguished Scientist Visitor Program - Beer Sheva, Israel /41
Wednesday, 24 June 2009
28. Size of the problem
Dataset characteristics:
•1050 protein chains
•~260000 instances
•In the most simple representation we may have
just 10-20 discrete attributes, but with high
cardinality (20 Amino Acids)
•Depending on the representation, hundreds of
continuous attributes
Ben-Gurion University of the Negev - June 23rd to July 5th 2009 - Distinguished Scientist Visitor Program - Beer Sheva, Israel /41
Wednesday, 24 June 2009
29. Protein Structure Comparison (PSC)
Similar or not?
How? Where
similar?
Knowing the similarity helps to:
1. Infer functional information
2. Organise (classify) all proteins
3. Design new proteins with specific function
Ben-Gurion University of the Negev - June 23rd to July 5th 2009 - Distinguished Scientist Visitor Program - Beer Sheva, Israel 25/41
Wednesday, 24 June 2009
30. Protein Structure Comparison (PSC)
Similar or not?
How? Where
similar?
Methods:
Knowing the similarity helps to: • USM
1. Infer functional information • MaxCMO
• DaliLite
2. Organise (classify) all proteins • CE
3. Design new proteins with specific function • FAST
• TM-Align
• …
Ben-Gurion University of the Negev - June 23rd to July 5th 2009 - Distinguished Scientist Visitor Program - Beer Sheva, Israel 25/41
Wednesday, 24 June 2009
31. PSC: Computation time per single pair
Method Algorithm/technique Measure Time
/metric [sec]
DaliLite Distance matrices, Combinatorial, simulated AL,Z, RMSD 3.33
annealing
MaxCMO Variable neighbourhood search (VNS) AL, OL 3.32
CE Heuristics, dynamic programming AL,Z, RMSD 1.27
USM Kolmogorov complexity USM-distance 0.34
TM-Align Rotation matrix, dynamic programming AL, RMSD,TMS 0.21
Fast Heuristics, dynamic programming RMSD, AL, SN 0.07
per pair of comparison
Ben-Gurion University of the Negev - June 23rd to July 5th 2009 - Distinguished Scientist Visitor Program - Beer Sheva, Israel 26/41
Wednesday, 24 June 2009
32. PDB Current Holdings Breakdown (May 12, 2009)
Protein/
Protein
Exp. Method Nucleic Acids NA Other Total
s
Complexes
X-ray 46071 1142 2118 17 49348
NMR 6844 850 144 7 7845
Electron Microscopy 163 16 59 0 238
Other 110 4 4 9 127
Total 53188 2012 2325 33 57558
Source: http://www.rcsb.org
Ben-Gurion University of the Negev - June 23rd to July 5th 2009 - Distinguished Scientist Visitor Program - Beer Sheva, Israel 27/41
Wednesday, 24 June 2009
33. PSC- Challenges
Lack of single gold standard methods
Need for Consensus Based Results
Growth of structural data
Currentholdings of PDB >53,000
~5000 new structures per year
High-throughput requirements
Need of more scalable techniques based on
distributed/grid computing architecture
Ben-Gurion University of the Negev - June 23rd to July 5th 2009 - Distinguished Scientist Visitor Program - Beer Sheva, Israel 28/41
Wednesday, 24 June 2009
34. Distribution: Problem space
All-against-all comparison of a dataset of P protein structures using m different
similarity comparison methods can be represented as 3D cube.
o ds
h
et
M
Heterogeneity:
1) Each structure has different length i.e
number of residues
2) Each method has different execution time
Structures
even for same pair of structures
3) Back-end computational nodes may have
different speeds etc
4) Each method has different measures
and metrics
Structures
Ben-Gurion University of the Negev - June 23rd to July 5th 2009 - Distinguished Scientist Visitor Program - Beer Sheva, Israel 29/41
Wednesday, 24 June 2009
35. Distribution: Problem space
All-against-all comparison of a dataset of P protein structures using m different
similarity comparison methods can be represented as 3D cube.
Intelligent load balancing
strategies
o ds
h
et
M
Heterogeneity:
1) Each structure has different length i.e
number of residues
2) Each method has different execution time
Structures
even for same pair of structures
3) Back-end computational nodes may have
different speeds etc
4) Each method has different measures
and metrics
Structures
Ben-Gurion University of the Negev - June 23rd to July 5th 2009 - Distinguished Scientist Visitor Program - Beer Sheva, Israel 29/41
Wednesday, 24 June 2009
36. Distribution: Problem space
All-against-all comparison of a dataset of P protein structures using m different
similarity comparison methods can be represented as 3D cube.
Intelligent load balancing
strategies
o ds
h
et
M
Heterogeneity:
1) Each structure has different length i.e
number of residues
2) Each method has different execution time
Structures
even for same pair of structures
3) Back-end computational nodes may have
different speeds etc
4) Each method has different measures
and metrics
Data standardization and
Structures normalization techniques
Ben-Gurion University of the Negev - June 23rd to July 5th 2009 - Distinguished Scientist Visitor Program - Beer Sheva, Israel 29/41
Wednesday, 24 June 2009
37. Distribution: Nomenclature
P Number of proteins
n Number of nodes (processors)
m Number of methods (e.g. FAST, USM, …)
Average size of proteins
Average time of all methods per single pair of comparison
Row_protx Number of row proteins present on node x
Col_protx Number of column proteins present on node x
Average execution time of all methods over all pairs of proteins stored on
node x
Ben-Gurion University of the Negev - June 23rd to July 5th 2009 - Distinguished Scientist Visitor Program - Beer Sheva, Israel 30/41
Wednesday, 24 June 2009
38. MC-PSC: Problem Complexity
Job complexity:
Where, P =number of proteins and m = number of methods
Space Complexity (number of data items in the output
matrix):
Where, Sc= space complexity, P= number of proteins, Nmt= total number of
measures/metrics and 2 makes home for two protein IDs for each pair.
Ben-Gurion University of the Negev - June 23rd to July 5th 2009 - Distinguished Scientist Visitor Program - Beer Sheva, Israel 31/41
Wednesday, 24 June 2009
39. MC-PSC: Problem Complexity
Time complexity:
Given a single P4 (1.86GHz) workstation and a set of
6 methods:
Target-against-all mode:
i.ecomparison of all structures against one designated target
structure
All-against-all mode:
i.e comparison of all structures against all structures
Ben-Gurion University of the Negev - June 23rd to July 5th 2009 - Distinguished Scientist Visitor Program - Beer Sheva, Israel 32/41
Wednesday, 24 June 2009
40. Distribution: PCAM technique
Source: Designing and Building Parallel Programs, by Ian Foster
Ben-Gurion University of the Negev - June 23rd to July 5th 2009 - Distinguished Scientist Visitor Program - Beer Sheva, Israel 33/41
Wednesday, 24 June 2009
41. Synthetic Biology
• Aims at designing, constructing and developing artificial biological systems
•Offers new routes to ‘genetically modified’ organisms, synthetic living
entities, smart drugs and hybrid computational-biological devices.
• Potentially enormous societal impact, e.g., healthcare, environmental
protection and remediation, etc
• Synthetic Biology's basic assumption:
• Methods commonly used to build non-biological systems could also
be use to specify, design, implement, verify, test and deploy novel
synthetic biosystems.
• These method come from computer science, engineering and maths.
• Modelling and optimisation run through all of the above.
Ben-Gurion University of the Negev - June 23rd to July 5th 2009 - Distinguished Scientist Visitor Program - Beer Sheva, Israel 34/41
Wednesday, 24 June 2009
42. InfoBiotics
www.infobiotic.net
•The utilisation of cutting-edge information
processing techniques for biological modelling and
synthesis
•The understanding of life itself as multi-scale
(Spatial/Temporal) information processing systems
•Composed of 3 key components:
•Executable Biology (or other modeling techniques)
•Automated Model and Parameter Estimation
•Model Checking (and other formal analysis)
Ben-Gurion University of the Negev - June 23rd to July 5th 2009 - Distinguished Scientist Visitor Program - Beer Sheva, Israel 35/41
Wednesday, 24 June 2009
43. Automated Model Synthesis and Optimisation
Modeling is an intrinsically difficult process
It involves “feature selection” and disambiguation
Model Synthesis requires
design the topology or structure of the system in
terms of molecular interactions
estimate the kinetic parameters associated with
each molecular interaction
All the above iterated
Ben-Gurion University of the Negev - June 23rd to July 5th 2009 - Distinguished Scientist Visitor Program - Beer Sheva, Israel 36/41
Wednesday, 24 June 2009
44. Once a model has been prototyped,
whether derived from existing literature or
“ab initio” ➡ Use some optimisation
method to fine tune parameters/model
structure
adopts an incremental methodology,
namely starting from very simple P system
modules (BioBricks) specifying basic
molecular interactions, more complicated
modules are produced to model more
complex molecular systems.
Ben-Gurion University of the Negev - June 23rd to July 5th 2009 - Distinguished Scientist Visitor Program - Beer Sheva, Israel 37/41
Wednesday, 24 June 2009
45. Large Literature on Model Synthesis
• Mason et al. use a random Local Search (LS) as the mutation to evolve
electronic networks with desired dynamics
• Chickarmane et al. use a standard GA to optimize the kinetic parameters of
a population of ODE-based reaction networks having the desired topology.
• Spieth et al. propose a Memetic Algorithm to find gene regulatory networks
from experimental DNA microarray data where the network structure is
optimized with a GA and the parameters are optimized with an Evolution
Strategy (ES).
• Jaramillo et al. use Simulated Annealing as the main search strategy for
model inference based on (O)DEs
Ben-Gurion University of the Negev - June 23rd to July 5th 2009 - Distinguished Scientist Visitor Program - Beer Sheva, Israel 38/41
Wednesday, 24 June 2009
46. Evolutionary Algorithms for Automated
Model Synthesis and Optimisation
EA are potentially very useful for AMSO
There’s a substantial amount of work on:
using GP-like systems to evolve executable
structures
using EAs for continuous/discrete optimisation
An EA population represents alternative models
(could lead to different experimental setups)
EAs have the potential to capture, rather than avoid,
evolvability of models
Ben-Gurion University of the Negev - June 23rd to July 5th 2009 - Distinguished Scientist Visitor Program - Beer Sheva, Israel 39/41
Wednesday, 24 June 2009
47. Methods
Evolutionary Algorithm
GAs
GP
Learning Classifier Systems
Memetic Algorithms
Ben-Gurion University of the Negev - June 23rd to July 5th 2009 - Distinguished Scientist Visitor Program - Beer Sheva, Israel 40/41
Wednesday, 24 June 2009
48. Related Papers
F. J. Romero-Campero, J. Twycross, M. Camara, M. Bennett, M. Gheorghe, and N. Krasnogor.
Modular assembly of cell systems biology models using p systems. International Journal of
Foundations of Computer Science, 2009
J.Bacardit, M.Stout, J.D. Hirst, A.Valencia, R.E.Smith, and N.Krasnogor. Automated alphabet
reduction for protein datasets. BMC Bioinformatics, 10(6), 2009
M.T. Oakley, D. Barthel, Y. Bykov, J.M. Garibaldi, E.K. Burke, N. Krasnogor, and J.D. Hirst. Search
strategies in structural bioinformatics. Current Protein and Peptide Science (Bentham Science
Publishers), 9(3):260-274, 2008
M. Stout, J. Bacardit, J.D. Hirst, and N. Krasnogor. Prediction of recursive convex hull class
assignment for protein residues. Bioinformatics, 24(7):916-923, 2008
M. Stout, J. Bacardit, J.D. Hirst, R.E Smith, and N. Krasnogor. Prediction of topological contacts in
proteins using learning classifier systems. Journal Soft Computing - A Fusion of Foundations,
Methodologies and Applications, 13(3):245-258, 2008.
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
G. Terrazas, P. Siepman, G. Kendal, and N. Krasnogor. An evolutionary methodology for the
automated design of cellular automaton-based complex systems. Journal of Cellular Automata,
2(1):77-102, 2007
N. Krasnogor and J.E. Smith. A tutorial for competent memetic algorithms: model, taxonomy and
design issues. IEEE Transactions on Evolutionary Computation, 9(5):474- 488, 2005.
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Wednesday, 24 June 2009