Andrew Adamatzky

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.

Yukio-Pegio Gunji, Andrew Adamatzky, Panagiotis Mougkogiannis et al.

By uncovering the contrast between Artificial Intelligence and Natural-born Intelligence as a computational process, we define closed computing and open computing, and implement open computing within chemical reactions. This involves forming a mixture and invalidation of the computational process and the execution environment, which are logically distinct, and coalescing both to create a system that adjusts fluctuations. We model chemical reactions by considering the computation as the chemical reaction and the execution environment as the degree of aggregation of molecules that interact with the reactive environment. This results in a chemical reaction that progresses while repeatedly clustering and de-clustering, where concentration no longer holds significant meaning. Open computing is segmented into Token computing, which focuses on the individual behavior of chemical molecules, and Type computing, which focuses on normative behavior. Ultimately, both are constructed as an interplay between the two. In this system, Token computing demonstrates self-organizing critical phenomena, while Type computing exhibits quantum logic. Through their interplay, the recruitment of fluctuations is realized, giving rise to interactions between quantum logical subspaces corresponding to quantum coherence across different Hilbert spaces. As a result, spike waves are formed, enabling signal transmission. This occurrence may be termed quantum-like coherence, implying the source of enzymes responsible for controlling spike waves and biochemical rhythms.

Genaro J. Martinez, Andrew Adamatzky, Ricardo Q. Figueroa et al.

Propagating patterns are used to transfer and process information in chemical and physical prototypes of unconventional computing devices. Logical values are represented by fronts of traveling diffusive, trigger or phase waves. We apply this concept of pattern based computation to develop experimental prototypes of computing circuits implemented in small modular robots. In the experimental prototypes the modular robots Cubelets are concatenated into channels and junction. The structures developed by Cubelets propagate signals in parallel and asynchronously. The approach is illustrated with a working circuit of a one-bit full adder. Complementarily a formalization of these constructions are developed across Sleptsov nets. Finally, a perspective to swarm dynamics is discussed.

Namid Stillman, Igor Balaz, Antisthenis Tsompanas et al.

We present the EVONANO platform for the evolution of nanomedicines with application to anti-cancer treatments. EVONANO includes a simulator to grow tumours, extract representative scenarios, and then simulate nanoparticle transport through these scenarios to predict nanoparticle distribution. The nanoparticle designs are optimised using machine learning to efficiently find the most effective anti-cancer treatments. We demonstrate our platform with two examples optimising the properties of nanoparticles and treatment to selectively kill cancer cells over a range of tumour environments.

Karolos-Alexandros Tsakalos, Georgios Ch. Sirakoulis, Andrew Adamatzky et al.

Nowadays we witness a miniaturisation trend in the semiconductor industry backed up by groundbreaking discoveries and designs in nanoscale characterisation and fabrication. To facilitate the trend and produce ever smaller, faster and cheaper computing devices, the size of nanoelectronic devices is now reaching the scale of atoms or molecules - a technical goal undoubtedly demanding for novel devices. Following the trend, we explore an unconventional route of implementing a reservoir computing on a single protein molecule and introduce neuromorphic connectivity with a small-world networking property. We have chosen Izhikevich spiking neurons as elementary processors, corresponding to the atoms of verotoxin protein, and its molecule as a 'hardware' architecture of the communication networks connecting the processors. We apply on a single readout layer various training methods in a supervised fashion to investigate whether the molecular structured Reservoir Computing (RC) system is capable to deal with machine learning benchmarks. We start with the Remote Supervised Method, based on Spike-Timing-Dependent-Plasticity, and carry on with linear regression and scaled conjugate gradient back-propagation training methods. The RC network is evaluated as a proof-of-concept on the handwritten digit images from the MNIST dataset and demonstrates acceptable classification accuracy in comparison with other similar approaches.

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.

Alexander E. Beasley, Mohammed-Salah Abdelouahab, René Lozi et al.

Memristors close the loop for I-V characteristics of the traditional, passive, semi-conductor devices. Originally proposed in 1971, the hunt for the memristor has been going ever since. The key feature of a memristor is that its current resitance is a function of its previous resistance. As such, the behaviour of the device is influenced by changing the way in which potential is applied across it. Ultimately, information can be encoded on memristors. Biological substrates have already been shown to exhibit some memristive properties. However, many memristive devices are yet to be found. Here we show that the fruit bodies of grey oyster fungi Pleurotus ostreatus exhibit memristive behaviours. This paper presents the I-V characteristics of the mushrooms. By examination of the conducted current for a given voltage applied as a function of the previous voltage, it is shown that the mushroom is a memristor. Our results demonstrate that nature continues to provide specimens that hold these unique and valuable electrical characteristics and which have the potential to advance the field of hybrid electronic systems.

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.

Michail-Antisthenis Tsompanas, Claire Fullarton, Andrew Adamatzky

We show how to control the movement of a wheeled robot using on-board liquid marbles made of Belousov-Zhabotinsky solution droplets coated with polyethylene powder. Two stainless steel, iridium coated electrodes were inserted in a marble and the electrical potential recorded was used to control the robot's motor. We stimulated the marble with a laser beam. It responded to the stimulation by pronounced changes in the electrical potential output. The electrical output was detected by robot. The robot was changing its trajectory in response to the stimulation. The results open new horizons for applications for oscillatory chemical reactions in robotics.

Mohammad Mahdi Dehshibi, Jitka Cejkova, Dominik Svara et al.

Decanol droplets in a thin layer of sodium decanoate with sodium chloride exhibit bifurcation branching growth due to interplay between osmotic pressure, diffusion and surface tension. We aimed to evaluate if morphology of the branching droplets changes when the droplets are subject to electrical potential difference. We analysed graph-theoretic structure of the droplets and applied several complexity measures. We found that, in overall, the current increases complexity of the branching droplets in terms of number of connected components and nodes in their graph presentations, morphological complexity and compressibility.

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.

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.

Xiaoge Zhang, Andrew Adamatzky, Xin-She Yang et al.

A supply chain is a system which moves products from a supplier to customers. The supply chains are ubiquitous. They play a key role in all economic activities. Inspired by biological principles of nutrients' distribution in protoplasmic networks of slime mould Physarum polycephalum we propose a novel algorithm for a supply chain design. The algorithm handles the supply networks where capacity investments and product flows are variables. The networks are constrained by a need to satisfy product demands. Two features of the slime mould are adopted in our algorithm. The first is the continuity of a flux during the iterative process, which is used in real-time update of the costs associated with the supply links. The second feature is adaptivity. The supply chain can converge to an equilibrium state when costs are changed. Practicality and flexibility of our algorithm is illustrated on numerical examples.

Ella Gale, Ben de Lacy Costello, Andrew Adamatzky

Memristors have been suggested as a novel route to neuromorphic computing based on the similarity between neurons (synapses and ion pumps) and memristors. The D.C. action of the memristor is a current spike, which we think will be fruitful for building memristor computers. In this paper, we introduce 4 different logical assignations to implement sequential logic in the memristor and introduce the physical rules, summation, `bounce-back', directionality and `diminishing returns', elucidated from our investigations. We then demonstrate how memristor sequential logic works by instantiating a NOT gate, an AND gate and a Full Adder with a single memristor. The Full Adder makes use of the memristor's memory to add three binary values together and outputs the value, the carry digit and even the order they were input in.

Ella Gale, Ben de Lacy Costello, Andrew Adamatzky

Time perception is essential for task switching, and in the mammalian brain appears alongside other processes. Memristors are electronic components used as synapses and as models for neurons. The d.c. response of memristors can be considered as a type of short-term memory. Interactions of the memristor d.c. response within networks of memristors leads to the emergence of oscillatory dynamics and intermittent spike trains, which are similar to neural dynamics. Based on this data, the structure of a memristor network control for a robot as it undergoes task switching is discussed and it is suggested that these emergent network dynamics could improve the performance of role switching and learning in an artificial intelligence and perhaps create artificial time perception.

Ella Gale, Ben de Lacy Costello, Andrew Adamatzky

It is not always possible for a robot to process all the information from its sensors in a timely manner and thus quick and yet valid approximations of the robot's situation are needed. Here we design hybrid control for a robot within this limit using algorithms inspired by ant worker placement behaviour and based on memristor-based non-linearity.

Ella Gale, Ben de Lacy Costello, Andrew Adamatzky

Memristors are used to compare three gathering techniques in an already-mapped environment where resource locations are known. The All Site model, which apportions gatherers based on the modeled memristance of that path, proves to be good at increasing overall efficiency and decreasing time to fully deplete an environment, however it only works well when the resources are of similar quality. The Leaf Cutter method, based on Leaf Cutter Ant behaviour, assigns all gatherers first to the best resource, and once depleted, uses the All Site model to spread them out amongst the rest. The Leaf Cutter model is better at increasing resource influx in the short-term and vastly out-performs the All Site model in a more varied environments. It is demonstrated that memristor based abstractions of gatherer models provide potential methods for both the comparison and implementation of agent controls.

Ella Gale, Oliver Matthews, Ben de Lacy Costello et al.

We undertook a study of the use of a memristor network for music generation, making use of the memristor's memory to go beyond the Markov hypothesis. Seed transition matrices are created and populated using memristor equations, and which are shown to generate musical melodies and change in style over time as a result of feedback into the transition matrix. The spiking properties of simple memristor networks are demonstrated and discussed with reference to applications of music making. The limitations of simulating composing memristor networks in von Neumann hardware is discussed and a hardware solution based on physical memristor properties is presented.

William M. Stevens, Andrew Adamatzky, Ishrat Jahan et al.

We demonstrate an improved technique for implementing logic circuits in light-sensitive chemical excitable media. The technique makes use of the constant-speed propagation of waves along defined channels in an excitable medium based on the Belousov-Zhabotinsky reaction, along with the mutual annihilation of colliding waves. What distinguishes this work from previous work in this area is that regions where channels meet at a junction can periodically alternate between permitting the propagation of waves and blocking them. These valve-like areas are used to select waves based on the length of time that it takes waves to propagate from one valve to another. In an experimental implementation, the channels which make up the circuit layout are projected by a digital projector connected to a computer. Excitable channels are projected as dark areas, unexcitable regions as light areas. Valves alternate between dark and light: every valve has the same period and phase, with a 50% duty cycle. This scheme can be used to make logic gates based on combinations of OR and AND-NOT operations, with few geometrical constraints. Because there are few geometrical constraints, compact circuits can be implemented. Experimental results from an implementation of a 4-bit input, 2-bit output integer square root circuit are given. This is the most complex logic circuit that has been implemented in BZ excitable media to date.