Larry Bull

Michail-Antisthenis Tsompanas, Larry Bull, Andrew Adamatzky et al.

Evolutionary algorithms have long been used for optimization problems where the appropriate size of solutions is unclear a priori. The applicability of this methodology is here investigated on the problem of designing a nano-particle (NP) based drug delivery system targeting cancer tumours. Utilizing a treatment comprising of multiple types of NPs is expected to be more effective due to the higher complexity of the treatment. This paper begins by utilizing the well-known NK model to explore the effects of fitness landscape ruggedness upon the evolution of genome length and, hence, solution complexity. The size of a novel sequence and the absence or presence of sequence deletion are also considered. Results show that whilst landscape ruggedness can alter the dynamics of the process, it does not hinder the evolution of genome length. These findings are then explored within the aforementioned real-world problem. In the first known instance, treatments with multiple types of NPs are used simultaneously, via an agent-based open source physics-based cell simulator. The results suggest that utilizing multiple types of NPs is more efficient when the solution space is explored with the evolutionary techniques under a predefined computational budget.

Haixia Liu, Tim Brailsford, James Goulding et al.

This paper investigates how adjustments to deep learning architectures impact model performance in image classification. Small-scale experiments generate initial insights although the trends observed are not consistent with the entire dataset. Filtering operations in the image processing pipeline are crucial, with image filtering before pre-processing yielding better results. The choice and order of layers as well as filter placement significantly impact model performance. This study provides valuable insights into optimizing deep learning models, with potential avenues for future research including collaborative platforms.

Richard J. Preen, Larry Bull

This article presents the first results from using a learning classifier system capable of performing adaptive computation with deep neural networks. Individual classifiers within the population are composed of two neural networks. The first acts as a gating or guarding component, which enables the conditional computation of an associated deep neural network on a per instance basis. Self-adaptive mutation is applied upon reproduction and prediction networks are refined with stochastic gradient descent during lifetime learning. The use of fully-connected and convolutional layers are evaluated on handwritten digit recognition tasks where evolution adapts (i) the gradient descent learning rate applied to each layer (ii) the number of units within each layer, i.e., the number of fully-connected neurons and the number of convolutional kernel filters (iii) the connectivity of each layer, i.e., whether each weight is active (iv) the weight magnitudes, enabling escape from local optima. The system automatically reduces the number of weights and units while maintaining performance after achieving a maximum prediction error.

Larry Bull

Sexual selection is a fundamental aspect of evolution for all eukaryotic organisms with mating types. This paper suggests intersexual selection is best viewed as a mechanism to compensate for the unavoidable dynamics of coevolution between sexes that emerge with isogamy. Using the NK model of fitness landscapes, the conditions under which allosomes emerge are first explored. This extends previous work on the evolution of sex where the fitness landscape smoothing of a rudimentary form of the Baldwin effect is suggested as the underlying cause. The NKCS model of coevolution is then used to show how varying fitness landscape size, ruggedness, and connectedness can vary the conditions under which a very simple sexual selection mechanism proves beneficial. This is found to be the case whether one or both sexes exploit sexual selection.

Larry Bull

The significant role of dendritic processing within neuronal networks has become increasingly clear. This letter explores the effects of including a simple dendrite-inspired mechanism into neuroevolution. The phenomenon of separate dendrite activation thresholds on connections is allowed to emerge under an evolutionary process. It is shown how such processing can be positively selected for, particularly for connections between the hidden and output layer, and increases performance.

Larry Bull

The potentially beneficial interaction between learning and evolution, the Baldwin effect, has long been established. This paper considers their interaction within a coevolutionary scenario, ie, where the adaptations of one species typically affects the fitness of others. Using the NKCS model, which allows the systematic exploration of the effects of fitness landscape size, ruggedness, and degree of coupling, it is shown how the amount of learning and the relative rate of evolution can alter behaviour.

Larry Bull

The NK model has been used widely to explore aspects of natural evolution and complex systems. This paper introduces a modified form of the NK model for exploring distributed control in complex systems such as organisations, social networks, collective robotics, etc. Initial results show how varying the size and underlying functional structure of a given system affects the performance of different distributed control structures and decision making, including within dynamically formed structures and those with differing numbers of control nodes.

Michail-Antisthenis Tsompanas, Larry Bull, Andrew Adamatzky et al.

Conventional optimization methodologies may be hindered when the automated search is stuck into local optima because of a deceptive objective function landscape. Consequently, open ended search methodologies, such as novelty search, have been proposed to tackle this issue. Overlooking the objective, while putting pressure into discovering novel solutions may lead to better solutions in practical problems. Novelty search was employed here to optimize the simulated design of a targeted drug delivery system for tumor treatment under the PhysiCell simulator. A hybrid objective equation was used containing both the actual objective of an effective tumour treatment and the novelty measure of the possible solutions. Different weights of the two components of the hybrid equation were investigated to unveil the significance of each one.

Michail-Antisthenis Tsompanas, Larry Bull, Andrew Adamatzky et al.

Working towards the development of an evolvable cancer treatment simulator, the investigation of Differential Evolution was considered, motivated by the high efficiency of variations of this technique in real-valued problems. A basic DE algorithm, namely "DE/rand/1" was used to optimize the simulated design of a targeted drug delivery system for tumor treatment on PhysiCell simulator. The suggested approach proved to be more efficient than a standard genetic algorithm, which was not able to escape local minima after a predefined number of generations. The key attribute of DE that enables it to outperform standard EAs, is the fact that it keeps the diversity of the population high, throughout all the generations. This work will be incorporated with ongoing research in a more wide applicability platform that will design, develop and evaluate targeted drug delivery systems aiming cancer tumours.

Michail-Antisthenis Tsompanas, Larry Bull, Andrew Adamatzky et al.

This paper uses a recent explanation for the fundamental haploid-diploid lifecycle of eukaryotic organisms to present a new memetic algorithm that differs from all previous known work using diploid representations. A form of the Baldwin effect has been identified as inherent to the evolutionary mechanisms of eukaryotes and a simplified version is presented here which maintains such behaviour. Using a well-known abstract tuneable model, it is shown that varying fitness landscape ruggedness varies the benefit of haploid-diploid algorithms. Moreover, the methodology is applied to optimise the targeted delivery of a therapeutic compound utilizing nano-particles to cancerous tumour cells with the multicellular simulator PhysiCell.

Richard J. Preen, Stewart W. Wilson, Larry Bull

Autoencoders are data-specific compression algorithms learned automatically from examples. The predominant approach has been to construct single large global models that cover the domain. However, training and evaluating models of increasing size comes at the price of additional time and computational cost. Conditional computation, sparsity, and model pruning techniques can reduce these costs while maintaining performance. Learning classifier systems (LCS) are a framework for adaptively subdividing input spaces into an ensemble of simpler local approximations that together cover the domain. LCS perform conditional computation through the use of a population of individual gating/guarding components, each associated with a local approximation. This article explores the use of an LCS to adaptively decompose the input domain into a collection of small autoencoders where local solutions of different complexity may emerge. In addition to benefits in convergence time and computational cost, it is shown possible to reduce code size as well as the resulting decoder computational cost when compared with the global model equivalent.

Larry Bull

Autoencoders enable data dimensionality reduction and a key component of many (deep) learning systems. This short paper introduces a form of Holland's Learning Classifier System (LCS) to perform autoencoding building upon a previously presented form of LCS that utilises unsupervised learning for clustering. Initial results using a neural network representation suggest it is an effective approach to reduction.

Larry Bull

It has recently been suggested that evolution exploits a form of fitness landscape smoothing within eukaryotic sex due to the haploid-diploid cycle. This short paper presents a simple modification to the standard evolutionary computing algorithm to similarly benefit from the process. Using the well-known NK model of fitness landscapes it is shown that the benefit emerges as ruggedness is increased.

Larry Bull

It has been suggested that the fundamental haploid-diploid cycle of eukaryotic sex exploits a rudimentary form of the Baldwin effect. This paper uses the well-known NKCS model to explore the effects of coevolution upon the behaviour of eukaryotes. It is shown how varying fitness landscape size, ruggedness and connectedness can vary the conditions under which eukaryotic sex proves beneficial over asexual reproduction in haploids in a coevolutionary context. Moreover, eukaryotic sex is shown to be more sensitive to the relative rate of evolution exhibited by its partnering species than asexual haploids.

Richard J. Preen, Larry Bull, Andrew Adamatzky

The use of high-fidelity computational simulations promises to enable high-throughput hypothesis testing and optimisation of cancer therapies. However, increasing realism comes at the cost of increasing computational requirements. This article explores the use of surrogate-assisted evolutionary algorithms to optimise the targeted delivery of a therapeutic compound to cancerous tumour cells with the multicellular simulator, PhysiCell. The use of both Gaussian process models and multi-layer perceptron neural network surrogate models are investigated. We find that evolutionary algorithms are able to effectively explore the parameter space of biophysical properties within the agent-based simulations, minimising the resulting number of cancerous cells after a period of simulated treatment. Both model-assisted algorithms are found to outperform a standard evolutionary algorithm, demonstrating their ability to perform a more effective search within the very small evaluation budget. This represents the first use of efficient evolutionary algorithms within a high-throughput multicellular computing approach to find therapeutic design optima that maximise tumour regression.

Larry Bull, Neil Phillips

A new form of aerostat wind generation system which contains an array of interacting turbines is proposed. The design of the balloon turbine components is undertaken through the combination of artificial intelligence and rapid prototyping techniques such that the need for highly accurate models/simulations of the lift and wake dynamics is removed/reduced. Initial small-scale wind tunnel testing to determine design and algorithmic fundamentals will be presented.

Larry Bull

It has recently been suggested that the fundamental haploid-diploid cycle of eukaryotic sex exploits a rudimentary form of the Baldwin effect. Thereafter the other associated phenomena can be explained as evolution tuning the amount and frequency of learning experienced by an organism. Using the well-known NK model of fitness landscapes it is here shown that the emergence of dominance can also be explained under this view of eukaryotic evolution.

Larry Bull

It has recently been suggested that the fundamental haploid-diploid cycle of eukaryotic sex exploits a rudimentary form of the Baldwin effect. Thereafter the other associated phenomena can be explained as evolution tuning the amount and frequency of learning experienced by an organism. Using the well-known NK model of fitness landscapes it is here shown that the emergence of sex determination systems can also be explained under this view of eukaryotic evolution.

Richard J. Preen, Jiseon You, Larry Bull et al.

Microbial fuel cells (MFCs) perform wastewater treatment and electricity production through the conversion of organic matter using microorganisms. For practical applications, it has been suggested that greater efficiency can be achieved by arranging multiple MFC units into physical stacks in a cascade with feedstock flowing sequentially between units. In this paper, we investigate the use of computational intelligence to physically explore and optimise (potentially) heterogeneous MFC designs in a cascade, i.e. without simulation. Conductive structures are 3-D printed and inserted into the anodic chamber of each MFC unit, augmenting a carbon fibre veil anode and affecting the hydrodynamics, including the feedstock volume and hydraulic retention time, as well as providing unique habitats for microbial colonisation. We show that it is possible to use design mining to identify new conductive inserts that increase both the cascade power output and power density.

Larry Bull

This paper uses the recent idea that the fundamental haploid-diploid lifecycle of eukaryotic organisms implements a rudimentary form of learning within evolution. A general approach for evolutionary computation is here derived that differs from all previous known work using diploid representations. The primary role of recombination is also changed from that previously considered in both natural and artificial evolution under the new view. Using well-known abstract tuneable models it is shown that varying fitness landscape ruggedness varies the benefit of the new approach.

Larry Bull

This paper suggests that the fundamental haploid-diploid cycle of eukaryotic sex exploits a rudimentary form of the Baldwin effect. With this explanation for the basic cycle, the other associated phenomena can be explained as evolution tuning the amount and frequency of learning experienced by an organism. Using the well-known NK model of fitness landscapes it is shown that varying landscape ruggedness varies the benefit of the haploid-diploid cycle, whether based upon endomitosis or syngamy. The utility of pre-meiotic doubling and recombination during the cycle are also shown to vary with landscape ruggedness. This view is suggested as underpinning, rather than contradicting, many existing explanations for sex.

Larry Bull

The time taken for gene expression varies not least because proteins vary in length considerably. This paper uses an abstract, tuneable Boolean regulatory network model to explore gene expression time variation. In particular, it is shown how non-uniform expression times can emerge under certain conditions through simulated evolution. That is, gene expression time variance appears beneficial in the shaping of the dynamical behaviour of the regulatory network without explicit consideration of protein function.

David Howard, Larry Bull, Ben De Lacy Costello

Neuromorphic computing --- brainlike computing in hardware --- typically requires myriad CMOS spiking neurons interconnected by a dense mesh of nanoscale plastic synapses. Memristors are frequently citepd as strong synapse candidates due to their statefulness and potential for low-power implementations. To date, plentiful research has focused on the bipolar memristor synapse, which is capable of incremental weight alterations and can provide adaptive self-organisation under a Hebbian learning scheme. In this paper we consider the Unipolar memristor synapse --- a device capable of non-Hebbian switching between only two states (conductive and resistive) through application of a suitable input voltage --- and discuss its suitability for neuromorphic systems. A self-adaptive evolutionary process is used to autonomously find highly fit network configurations. Experimentation on a two robotics tasks shows that unipolar memristor networks evolve task-solving controllers faster than both bipolar memristor networks and networks containing constant nonplastic connections whilst performing at least comparably.

David Howard, Larry Bull, Pier-Luca Lanzi

Learning Classifier Systems (LCS) are population-based reinforcement learners that were originally designed to model various cognitive phenomena. This paper presents an explicitly cognitive LCS by using spiking neural networks as classifiers, providing each classifier with a measure of temporal dynamism. We employ a constructivist model of growth of both neurons and synaptic connections, which permits a Genetic Algorithm (GA) to automatically evolve sufficiently-complex neural structures. The spiking classifiers are coupled with a temporally-sensitive reinforcement learning algorithm, which allows the system to perform temporal state decomposition by appropriately rewarding "macro-actions," created by chaining together multiple atomic actions. The combination of temporal reinforcement learning and neural information processing is shown to outperform benchmark neural classifier systems, and successfully solve a robotic navigation task.

Richard J. Preen, Larry Bull

Design mining is the use of computational intelligence techniques to iteratively search and model the attribute space of physical objects evaluated directly through rapid prototyping to meet given objectives. It enables the exploitation of novel materials and processes without formal models or complex simulation. In this paper, we focus upon the coevolutionary nature of the design process when it is decomposed into concurrent sub-design threads due to the overall complexity of the task. Using an abstract, tuneable model of coevolution we consider strategies to sample sub-thread designs for whole system testing and how best to construct and use surrogate models within the coevolutionary scenario. Drawing on our findings, the paper then describes the effective design of an array of six heterogeneous vertical-axis wind turbines.

Gerard David Howard, Larry Bull, Ben de Lacy Costello et al.

Neuromorphic computing is a brainlike information processing paradigm that requires adaptive learning mechanisms. A spiking neuro-evolutionary system is used for this purpose; plastic resistive memories are implemented as synapses in spiking neural networks. The evolutionary design process exploits parameter self-adaptation and allows the topology and synaptic weights to be evolved for each network in an autonomous manner. Variable resistive memories are the focus of this research; each synapse has its own conductance profile which modifies the plastic behaviour of the device and may be altered during evolution. These variable resistive networks are evaluated on a noisy robotic dynamic-reward scenario against two static resistive memories and a system containing standard connections only. Results indicate that the extra behavioural degrees of freedom available to the networks incorporating variable resistive memories enable them to outperform the comparative synapse types.

Larry Bull

The editing of transcribed RNA by other molecules such that the form of the final product differs from that specified in the corresponding DNA sequence is ubiquitous. This paper uses an abstract, tunable Boolean genetic regulatory network model to explore aspects of RNA editing. In particular, it is shown how dynamically altering expressed sequences via a guide RNA-inspired mechanism can be selected for by simulated evolution under various single and multicellular scenarios.

Richard J. Preen, Larry Bull

An initial study of surrogate-assisted evolutionary algorithms used to design vertical-axis wind turbines wherein candidate prototypes are evaluated under fan generated wind conditions after being physically instantiated by a 3D printer has recently been presented. Unlike other approaches, such as computational fluid dynamics simulations, no mathematical formulations were used and no model assumptions were made. This paper extends that work by exploring alternative surrogate modelling and evolutionary techniques. The accuracy of various modelling algorithms used to estimate the fitness of evaluated individuals from the initial experiments is compared. The effect of temporally windowing surrogate model training samples is explored. A surrogate-assisted approach based on an enhanced local search is introduced; and alternative coevolution collaboration schemes are examined.

Larry Bull

Modern Learning Classifier Systems can be characterized by their use of rule accuracy as the utility metric for the search algorithm(s) discovering useful rules. Such searching typically takes place within the restricted space of co-active rules for efficiency. This paper gives an historical overview of the evolution of such systems up to XCS, and then some of the subsequent developments of XCS to different types of learning.

Larry Bull

Modern learning classifier systems typically exploit a niched genetic algorithm to facilitate rule discovery. When used for reinforcement learning, such rules represent generalisations over the state-action-reward space. Whilst encouraging maximal generality, the niching can potentially hinder the formation of generalisations in the state space which are symmetrical, or very similar, over different actions. This paper introduces the use of rules which contain multiple actions, maintaining accuracy and reward metrics for each action. It is shown that problem symmetries can be exploited, improving performance, whilst not degrading performance when symmetries are reduced.

Larry Bull

The computational modeling of genetic regulatory networks is now common place, either by fitting a system to experimental data or by exploring the behaviour of abstract systems with the aim of identifying underlying principles. This paper presents an approach to the latter, considering the response to environmental changes of a well-known model placed upon tunable fitness landscapes. The effects on genome size and gene connectivity are explored.

Richard J. Preen, Larry Bull

The production of renewable and sustainable energy is one of the most important challenges currently facing mankind. Wind has made an increasing contribution to the world's energy supply mix, but still remains a long way from reaching its full potential. In this paper, we investigate the use of artificial evolution to design vertical-axis wind turbine prototypes that are physically instantiated and evaluated under fan generated wind conditions. Initially a conventional evolutionary algorithm is used to explore the design space of a single wind turbine and later a cooperative coevolutionary algorithm is used to explore the design space of an array of wind turbines. Artificial neural networks are used throughout as surrogate models to assist learning and found to reduce the number of fabrications required to reach a higher aerodynamic efficiency. Unlike in other approaches, such as computational fluid dynamics simulations, no mathematical formulations are used and no model assumptions are made.

Larry Bull

The significant role of epigenetic mechanisms within natural systems has become increasingly clear. This paper uses a recently presented abstract, tunable Boolean genetic regulatory network model to explore aspects of epigenetics. It is shown how dynamically controlling transcription via a DNA methylation-inspired mechanism can be selected for by simulated evolution under various single and multiple cell scenarios. Further, it is shown that the effects of such control can be inherited without detriment to fitness.

Richard J. Preen, Larry Bull

A number of representation schemes have been presented for use within Learning Classifier Systems, ranging from binary encodings to Neural Networks, and more recently Dynamical Genetic Programming (DGP). This paper presents results from an investigation into using a fuzzy DGP representation within the XCSF Learning Classifier System. In particular, asynchronous Fuzzy Logic Networks are used to represent the traditional condition-action production system rules. It is shown possible to use self-adaptive, open-ended evolution to design an ensemble of such fuzzy dynamical systems within XCSF to solve several well-known continuous-valued test problems.

Richard J. Preen, Larry Bull

A number of representation schemes have been presented for use within Learning Classifier Systems, ranging from binary encodings to neural networks. This paper presents results from an investigation into using a discrete dynamical system representation within the XCS Learning Classifier System. In particular, asynchronous random Boolean networks are used to represent the traditional condition-action production system rules. It is shown possible to use self-adaptive, open-ended evolution to design an ensemble of such discrete dynamical systems within XCS to solve a number of well-known test problems.

Richard J. Preen, Larry Bull

We have recently presented an initial study of evolutionary algorithms used to design vertical-axis wind turbines (VAWTs) wherein candidate prototypes are evaluated under approximated wind tunnel conditions after being physically instantiated by a 3D printer. That is, unlike other approaches such as computational fluid dynamics simulations, no mathematical formulations are used and no model assumptions are made. However, the representation used significantly restricted the range of morphologies explored. In this paper, we present initial explorations into the use of a simple generative encoding, known as Gielis superformula, that produces a highly flexible 3D shape representation to design VAWT. First, the target-based evolution of 3D artefacts is investigated and subsequently initial design experiments are performed wherein each VAWT candidate is physically instantiated and evaluated under approximated wind tunnel conditions. It is shown possible to produce very closely matching designs of a number of 3D objects through the evolution of supershapes produced by Gielis superformula. Moreover, it is shown possible to use artificial physical evolution to identify novel and increasingly efficient supershape VAWT designs.

Richard J. Preen, Larry Bull

A number of representation schemes have been presented for use within learning classifier systems, ranging from binary encodings to neural networks. This paper presents results from an investigation into using discrete and fuzzy dynamical system representations within the XCSF learning classifier system. In particular, asynchronous random Boolean networks are used to represent the traditional condition-action production system rules in the discrete case and asynchronous fuzzy logic networks in the continuous-valued case. It is shown possible to use self-adaptive, open-ended evolution to design an ensemble of such dynamical systems within XCSF to solve a number of well-known test problems.

Larry Bull

This short paper introduces a new way by which to design production system rules. An indirect encoding scheme is presented which views such rules as protein complexes produced by the temporal behaviour of an artificial genetic regulatory network. This initial study begins by using a simple Boolean regulatory network to produce traditional ternary-encoded rules before moving to a fuzzy variant to produce real-valued rules. Competitive performance is shown with related genetic regulatory networks and rule-based systems on benchmark problems.

Gerard Howard, Larry Bull, Pier-Luca Lanzi

Learning Classifier Systems (LCS) are population-based reinforcement learners used in a wide variety of applications. This paper presents a LCS where each traditional rule is represented by a spiking neural network, a type of network with dynamic internal state. We employ a constructivist model of growth of both neurons and dendrites that realise flexible learning by evolving structures of sufficient complexity to solve a well-known problem involving continuous, real-valued inputs. Additionally, we extend the system to enable temporal state decomposition. By allowing our LCS to chain together sequences of heterogeneous actions into macro-actions, it is shown to perform optimally in a problem where traditional methods can fail to find a solution in a reasonable amount of time. Our final system is tested on a simulated robotics platform.