NDLI: P system model optimisation by means of evolutionary based search algorithms

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Particle swarm optimization with triggered mutation and its implementation based on GPU

Honey-bee dancing-inspired architecture for fault tolerance in wireless sensor networks

Cooperative self-organization in a heterogeneous swarm robotic system

Morphological evolution of freeform robots

Protein structure prediction on a lattice model via multimodal optimization techniques

Efficient protein-ligand docking using sustainable evolutionary algorithm

An efficient algorithm for generalized minimum spanning tree problem

Optimum design of grillage systems under code provisions using particle swarm optimization

Spurious dependencies and EDA scalability

A new DSM clustering algorithm for linkage groups identification

On the analysis of self-adaptive evolution strategies on elliptic model: first results

Biogeography-based optimization with blended migration for constrained optimization problems

A sphere-dominance based preference immune-inspired algorithm for dynamic multi-objective optimization

Multiobjective evolutionary community detection for dynamic networks

Transfer learning through indirect encoding

Morphological scaffolding: how evolution and development improve robot behavior generation

Approaches to multidimensional scaling for adaptive landscape visualization

The K-bit-swap: a new genetic algorithm operator

Efficiently evolving programs through the search for novelty

Population restarting: a study case of feature extraction from remotely sensed imagery using textural information

A first assessment of the use of extended relational alphabets in accuracy classifier systems

A clonal selection clustering algorithm using pointed symmetry-based distance measure

Parallel FPGA-based implementation of scatter search

Fast parallelization of differential evolution algorithm using MapReduce

A method of association rule analysis for incomplete database using genetic network programming

Shorter, more reliable and valid tests by means of a genetic algorithm

Approximate backbone based multilevel algorithm for next release problem

Multiobjective evolutionary algorithm for software project portfolio optimization

Ant colony optimization and the minimum cut problem

Definition of a crossover based distance for genetic algorithms

Time series forecasting using a perturbative intelligent system

Particle swarm optimizer with self-adjusting neighborhoods

An parallel particle swarm optimization approach for multiobjective optimization problems

Evolution of vision capabilities in embodied virtual creatures

Neuronal replicators solve the stability-plasticity dilemma

On the use of genetic programming for the prediction of survival in cancer

Solving the DNA fragment assembly problem efficiently using iterative optimization with evolved hypermutations

Consultant-guided search: a new metaheuristic for combinatorial optimization problems

Beating exhaustive search at its own game: revisiting evolutionary mastermind

Multivariate multi-model approach for globally multimodal problems

Fitting multi-planet transit models to photometric time-data series by evolution strategies

Pruning association rules using statistics and genetic relation algoritm

Deterministic helper-objective sequences applied to job-shop scheduling

A multi-objective meta-model assisted memetic algorithm with non gradient-based local search

The baldwin effect in developing neural networks

NEATfields: evolution of neural fields

Breaking ties with secondary fitness in a genetic algorithm for the bin packing problem

EvoBassComposer: a multi-objective genetic algorithm for 4-voice compositions

AUC analysis of the pareto-front using multi-objective GP for classification with unbalanced data

Confidence intervals of success rates in evolutionary computation

Coevolution in a large search space using resource-limited nash memory

Learning classifier system using both labeled and unlabeled data

Selection pressure and takeover time of distributed evolutionary algorithms

A neuro-evolutionary approach to micro aerial vehicle control

Optimization of an image set by genetic feature selection for real-time photomosaics

On the use of genetic programming for automated refactoring and the introduction of design patterns

Coevolutionary automated software correction

Theoretical analysis of evolutionary computation on continuously differentiable functions

Optimization speed and fair sets of functions

An empirical comparison of parallel and distributed particle swarm optimization methods

Particle swarm optimisation for outlier detection

Revising the evolutionary computation abstraction: minimal criteria novelty search

Challenges rising from learning motif evaluation functions using genetic programming

Fast genome-wide epistasis analysis using ant colony optimization for multifactor dimensionality reduction analysis on graphics processing units

A hierarchical cooperative evolutionary algorithm

A framework for accelerating metaheuristics via pattern reduction

A robust estimation of distribution algorithm for power electronic circuits design

Active covariance matrix adaptation for the (1+1)-CMA-ES

Forced optimal covariance adaptive learning: modified CMA-ES for efficient hessian determination

Evolving agent behavior in multiobjective domains using fitness-based shaping

Exploring evolutionary detected fuzzy equilibria: a link between normative theory and real life

Evolving the placement and density of neurons in the hyperneat substrate

A developmental algorithm for multi-agent swarms with scalable hierarchies

NK landscapes, problem difficulty, and hybrid evolutionary algorithms

Adaptive genetic algorithm using harmony search

Symbiosis, complexification and simplicity under GP

Improved forecasting of time series data of real system using genetic programming

Genetic rule extraction optimizing brier score

On the problems of using learning classifier systems for fraud detection

GPU-based island model for evolutionary algorithms

Robust neuro-control for a micro quadrotor

Adaptive probabilistic task allocation in large-scale multi-agent systems and its evaluation

Search-based test data generation from stateflow statecharts

Elementary landscapes of frequency assignment problems

An ant-colony-system-based activity scheduling method for the lifetime maximization of heterogeneous wireless sensor networks

Pseudo-hierarchical ant-based clustering using a heterogeneous agent hierarchy and automatic boundary formation

Guarding against premature convergence while accelerating evolutionary search

Selecting predictive features for recognition of hypersensitive sites of regulatory genomic sequences with an evolutionary algorithm

On the generality of parameter tuning in evolutionary planning

Effective heuristic methods for finding non-optimal solutions of interest in constrained optimization models

Effective structure learning for EDA via L1-regularizedbayesian networks

Exponential natural evolution strategies

Finding multiple solutions for multimodal optimization problems using a multi-objective evolutionary approach

Enhanced hospital resource management using anticipatory policies in online dynamic multi-objective optimization

Evolving heterochrony for cellular differentiation using vector field embryogeny

Complex energy landscape mapping by histogram assisted genetic algorithm

Hybrid evolutionary algorithm of planning VLSI

The estimation of hölderian regularity using genetic programming

A novel genetic programming based morphological image analysis algorithm

Adaption of XCS to multi-learner predator/prey scenarios

An estimation of distribution algorithm for the automatic generation of clustering algorithms

Shared memory genetic algorithms in a multi-agent context

Interday foreign exchange trading using linear genetic programming

A double-deck elevator systems controller with idle cage assignment algorithm using genetic network programming

Today/future importance analysis

Necessary and sufficient conditions for success of the metropolis algorithm for optimization

Pheromone-distribution-based adaptive ant colony system

Crossing the reality gap in evolutionary robotics by promoting transferable controllers

P system model optimisation by means of evolutionary based search algorithms

Efficient stochastic local search algorithm for solving the shortest common supersequence problem

Problem-state representations in a hyper-heuristic approach for the 2D irregular BPP

Entropy-based substructural local search for the bayesian optimization algorithm

Tuning optimization algorithms for real-world problems by means of surrogate modeling

Integrating decision space diversity into hypervolume-based multiobjective search

Age-fitness pareto optimization

Self modifying cartesian genetic programming: finding algorithms that calculate pi and e to arbitrary precision

Analysis of the effects of lifetime learning on population fitness using vose model

Using a Meta-GA for parametric optimization of simple gas in the computational chemistry domain

Semantics based crossover for boolean problems

Incremental evolution of local search heuristics

How XCS deals with rarities in domains with continuous attributes

Context-sensitive refinements for stochasticoptimization algorithms in inductive logic programming

The benefit of migration in parallel evolutionary algorithms

Optimization of the hölder image descriptor using a genetic algorithm

A covariance matrix adaptation based evolutionary methodology for phase adjustment in financial time series forecasting

Factors affecting the use of genetic algorithms in test suite augmentation

Elementary landscape decomposition of the quadratic assignment problem

Self-adaptive differential evolution based on PSO learning strategy

Coevolution of heterogeneous multi-robot teams

The application of michigan-style learning classifiersystems to address genetic heterogeneity and epistasisin association studies

Towards improved dispatching rules for complex shop floor scenarios: a genetic programming approach

An evaluation of off-line calibration techniques for evolutionary algorithms

Entropy measurement-based estimation model for bayesian optimization algorithm

Adaptive strategy selection in differential evolution

A grid-based fitness strategy for evolutionary many-objective optimization

Moving away from error-based learning in multi-objective estimation of distribution algorithms

Importing the computational neuroscience toolbox into neuro-evolution-application to basal ganglia

Investigating EA solutions for approximate KKT conditions in smooth problems

Mixed-coded evolutionary algorithm for Gaussian mixture maximum likelihood clustering with model selection

Measuring bloat, overfitting and functional complexity in genetic programming

When does Cartesian genetic programming minimize the phenotype size implicitly?

Multi-task evolutionary shaping without pre-specified representations

Emergence of competitive and cooperative behavior using coevolution

Evolutionary algorithms in large-scale open pit mine scheduling

Integrated pre-design step methodology based onmulti-objective evolutionary optimization

Empirically studying the role of selection operators duringsearch-based test suite prioritization

Can quantum search accelerate evolutionary algorithms?

Stigmergic landmark routing: a routing algorithm for wireless mobile ad-hoc networks

Evolution of division of labor in genetically homogenous groups

Initialization parameter sweep in ATHENA: optimizing neural networks for detecting gene-gene interactions in the presence of small main effects

Discrete versus continuous parametrization of bank credit rating systems optimization using differential evolution

Solving OCST problems with problem-specific guided local search

The anticipated mean shift and cluster registration in mixture-based EDAs for multi-objective optimization

A mono surrogate for multiobjective optimization

Image compression of natural images using artificial gene regulatory networks

Co-evolution of cooperative strategies under egoism

Evolutionary detection of aumann equilibrium

New crossover operators in linear genetic programming for multiclass object classification

Model selection in genetic programming

Speeding up the evaluation of evolutionary learning systems using GPGPUs

Constructing numerically stable real number codes using evolutionary computation

Psychological preference-based optimization framework on the nurse scheduling problem

Superstate identification for state machines using search-based clustering

Black-box search by unbiased variation

Development of efficient particle swarm optimizers by using concepts from evolutionary algorithms

Resource abundance promotes the evolution of public goods cooperation

Heuristics for sampling repetitions in noisy landscapes with fitness caching

D-vine EDA: a new estimation of distribution algorithm based on regular vines

An archived-based stochastic ranking evolutionary algorithm (asrea) for multi-objective optimization

Neuroevolution of mobile ad hoc networks

Aging beyond restarts

Genetic evolution of fuzzy finite state machines to control bots in a first-person shooter game

Abstract functions and lifetime learning in genetic programming for symbolic regression

Constant versus variable arity operators in genetic programming

Negative selection algorithms without generating detectors

Evolutionary-based conflict-free scheduling of collective communications on spidergon NoCs

Proposal of a multi-core processor architecture for effective evolutionary computation

Multiplicative drift analysis

A few ants are enough: ACO with iteration-best update

An ant colony optimization approach to the multiple-choice multidimensional knapsack problem

Improved step size adaptation for the MO-CMA-ES

Sustaining behavioral diversity in NEAT

Network crossover performance on NK landscapes and deceptive problems

Why recombination should be adaptive

Towards an understanding of locality in genetic programming

GGGP-based method for modeling time series: operator selection, parameter optimization and expert evaluation

In search of targeted-complexity problems

Multiobjective evolutionary algorithms for dynamic social network clustering

Multi-objective optimization of process parameters in friction stir welding

Quasirandom evolutionary algorithms

The impact of design choices of multiobjective antcolony optimization algorithms on performance: an experimental study on the biobjective TSP

Set-based multi-objective optimization, indicators, and deteriorative cycles

Evolving neural networks in compressed weight space

Optimizing genetic operator rates using a markov chain model of genetic algorithms

Noise pressure: systematic overestimation of population fitness in genetic algorithms with noisy fitness functions

Grammar guided genetic programming for multiple instance learning: an experimental study

Mixed-integer evolution strategy using multiobjective selection applied to warehouse design optimization

Mitigation strategies in epidemics: evolutionary optimization using a hierarchy of objective functions

Ant colony optimization for stochastic shortest path problems

DBSCAN-based multi-objective niching to approximate equivalent pareto-subsets

Evolving CPPNs to grow three-dimensional physical structures

A heuristic-based hybrid genetic algorithm for heterogeneous multiprocessor scheduling

Amount and type of information: a GA-hardness taxonomy

Robust symbolic regression with affine arithmetic

Evolving viral marketing strategies

Configuration of a genetic algorithm for multi-objective optimisation of solar gain to buildings

The maximum hypervolume set yields near-optimal approximation

Investigating whether hyperNEAT produces modular neural networks

Solving multiobjective flexible job-shop scheduling using an adaptive representation

A probabilistic functional crossover operator for genetic programming

Selection mechanisms in memory consideration for examination timetabling with harmony search

Towards drift correction in chemical sensors using an evolutionary strategy

Simultaneous use of different scalarizing functions in MOEA/D

A hybrid genetic algorithm for automatic graph drawing based on the topology-shape-metric approach.

Coevolutionary multi-population genetic programming for data classification

Malware detection based on dependency graph using hybrid genetic algorithm

Performance evaluation of evolutionary algorithms for road detection

Indicator-based evolutionary algorithm with hypervolume approximation by achievement scalarizing functions

Probabilistic performance profiles for the experimental evaluation of stochastic algorithms

Knowledge mining with genetic programming methods for variable selection in flavor design

A new modular genetic programming for finding attractive technical patterns in stock markets

Edge-based representation beats vertex-based representation in shortest path problems

Predicting solution rank to improve performance

Improving reliability of embedded systems through dynamic memory manager optimization using grammatical evolution

Toward comparison-based adaptive operator selection

Object-level recombination of commodity applications

Biogeography-based optimization of neuro-fuzzy system parameters for diagnosis of cardiac disease

Generalized crowding for genetic algorithms

Designing better fitness functions for automated program repair

Multi-objective optimization of doping profile in semiconductor design

Coevolving influence maps for spatial team tactics in a RTS game

Evolving robust controller parameters using covariance matrix adaptation

Phenotype feedback genetic algorithm operators for heuristic encoding of snakes within hypercubes

Evolutionary multi-objective optimization and decision making for selective laser sintering

Applying the triple parameter hypothesis to maintenance scheduling

Multiprocessor systems-on-chip synthesis using multi-objective evolutionary computation

An exploration into dynamic population sizing

ConBreO: a music performance rendering system using hybrid approach of IEC and automated evolution

On heuristics for two-sided matching: revisiting the stable marriage problem as a multiobjective problem

Evolutionary optimization of flavors

Using feature construction to avoid large feature spaces in text classification

P system model optimisation by means of evolutionary based search algorithms

Content Provider	ACM Digital Library
Author	Twycross, Jamie Lima, Claudio Lozano, Manuel García-Martínez, Carlos Krasnogor, Natalio
Abstract	Executable Biology, also called Algorithmic Systems Biology, uses rigorous concepts from computer science and mathematics to build computational models of biological entities. P systems are emerging as one of the key modelling frameworks within Executable Biology. In this paper, we address the continuous backward problem: given a P system model structure and a target phenotype (i.e. an intended biological behaviour), one is tasked with finding the (near) optimal parameters for the model that would make the P system model produce the target behaviour as closely as possible. We test several real-valued parameter optimisation algorithms on this problem. More specifically, using four different test cases of increasing complexity, we perform experiments with four evolutionary algorithms, and one variable neighbourhood search method combining three other evolutionary algorithms. The results show that, when there are few parameters to optimise, a genetic and two differential evolution based algorithms are robust optimisers attaining the best results. However, when the number of parameters increases, the variable neighbourhood search approach performs better.
Starting Page	187
Ending Page	194
Page Count	8
File Format	PDF
ISBN	9781450300728
DOI	10.1145/1830483.1830517
Language	English
Publisher	Association for Computing Machinery (ACM)
Publisher Date	2010-07-07
Publisher Place	New York
Access Restriction	Subscribed
Subject Keyword	Real-valued parameter optimisation Executable biology Evolutionary algorithms P systems
Content Type	Text
Resource Type	Article

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