Martyn Amos

Martyn Amos
Northumbria University · Department of Computer Information and Data Sciences

About

134
Publications
15,543
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1,512
Citations
Citations since 2016
37 Research Items
731 Citations
2016201720182019202020212022020406080100120140
2016201720182019202020212022020406080100120140
2016201720182019202020212022020406080100120140
2016201720182019202020212022020406080100120140

Publications

Publications (134)
Article
Crowd simulations are used extensively to study the dynamics of human collectives. Such studies are underpinned by specific movement models, which encode rules and assumptions about how people navigate a space and handle interactions with others. These models often give rise to macroscopic simulated crowd behaviours that are statistically valid, bu...
Article
The Virtual Machine Placement (VMP) problem is a challenging optimization task that involves the assignment of virtual machines to physical machines in a cloud computing environment. The placement of virtual machines can significantly affect the use of resources in a cluster, with a subsequent impact on operational costs and the environment. In thi...
Article
Japanese puzzle games such as Sudoku and Futoshiki are familiar recreational pursuits, but they also present an interesting computational challenge. A number of algorithms exist for the automated solution of such puzzles, but, until now, these have not been compared in a unified way. Here, we present an integrated framework for the study of com...
Article
Planned egress drills are required by building codes around the world, and are commonly used to both train occupants and assess evacuation procedures. However, capturing the idea of a “successful” drill is often difficult. Data from both drills and unplanned evacuations are often incomplete and unreliable, which raises a key question: How well-matc...
Article
Full-text available
Evacuation drills are generally the main mechanism for improving or measuring occupant performance in emergency situations, but their effectiveness is often hard to measure, and there is limited evidence for sustained training benefits. However, innovations in technology (e.g., augmented/virtual reality, novel sensors and wearable tech) offer (when...
Article
Full-text available
The accuracy and believability of crowd simulations underpins computational studies of human collective behaviour, with implications for urban design, policing, security and many other areas. Accuracy concerns the closeness of the fit between a simulation and observed data, and believability concerns the human perception of plausibility. In this pa...
Article
Full-text available
Synthetic biology uses living cells as the substrate for performing human-defined computations. Many current implementations of cellular computing are based on the “genetic circuit” metaphor, an approximation of the operation of silicon-based computers. Although this conceptual mapping has been relatively successful, we argue that it fundamentally...
Preprint
Full-text available
The realism and believability of crowd simulations underpins computational studies of human collective behaviour, with implications for urban design, policing, security and many other areas. Realism concerns the closeness of the fit between a simulation and observed data, and believability concerns the human perception of plausibility. In this pape...
Article
Full-text available
In this paper we present a new algorithm for the well-known and computationally-challenging Sudoku puzzle game. Our Ant Colony Optimization-based method significantly out-performs the state-of-the-art algorithm on the hardest, large instances of Sudoku. We provide evidence that – compared to traditional backtracking methods – our algorithm offers a...
Conference Paper
We present the first nature-inspired algorithm for the NP-complete Nurikabe pencil puzzle. Our method, based on Ant Colony Optimization (ACO), offers competitive performance with a direct logic-based solver, with improved run-time performance on smaller instances, but poorer performance on large instances. Importantly, our algorithm is "problem agn...
Preprint
Full-text available
We present the first nature-inspired algorithm for the NP-complete Nurikabe pencil puzzle. Our method, based on Ant Colony Optimization (ACO), offers competitive performance with a direct logic-based solver, with improved run-time performance on smaller instances, but poorer performance on large instances. Importantly, our algorithm is "problem agn...
Article
Full-text available
This article presents a glossary of terms that are frequently used in research on human crowds. This topic is inherently multidisciplinary as it includes work in and across computer science, engineering, mathematics, physics, psychology and social science, for example. We do not view the glossary presented here as a collection of finalised and form...
Article
Full-text available
We present a scheme for implementing a version of task switching in engineered bacteria, based on the manipulation of plasmid copy numbers. Our method allows for the embedding of multiple computations in a cellular population, whilst minimising resource usage inefficiency. We describe the results of computational simulations of our model, and discu...
Preprint
Full-text available
We present a scheme for implementing a version of task switching in engineered bacteria, based on the manipulation of plasmid copy numbers. Our method allows for the embedding of multiple computations in a cellular population, whilst minimising resource usage inefficiency. We describe the results of computational simulations of our model, and discu...
Chapter
All computing is physical, requiring a substrate in which to perform the computation. Conventional computation (CCOMP), based on the Church-Turing thesis and the von Neumann architecture, is built upon logical states that are engineered into the substrate. By contrast, in materio computation does not impose a computational model upon the substrate,...
Chapter
Synthetic biology is an emerging, rapidly growing research field in which engineering principles are applied to natural, living systems. A major goal of synthetic biology is to harness the inherent “biological nanotechnology” of living cells for a number of applications, including computation, production, and diagnosis. In its infancy, synthetic bi...
Article
Vaccination coverage in the United Kingdom is below the level recommended by the World Health Organisation, and when vaccination coverage is not sufficient, outbreaks of infectious diseases can occur. In 2015, coverage of the first dose of the Measles-Mumps-Rubella vaccine declined in the United Kingdom for the first time since 2008, indicating a n...
Preprint
In this paper we present a new Ant Colony Optimisation-based algorithm for Sudoku, which out-performs existing methods on large instances. Our method includes a novel anti-stagnation operator, which we call Best Value Evaporation.
Article
Full-text available
Background Current immunisation levels in England currently fall slightly below the threshold recommended by the World Health Organization, and the three-year trend for vaccination uptake is downwards. Attitudes towards vaccination can affect future decisions on whether or not to vaccinate, and this can have significant public health implications....
Data
PowerPoint presentation used with Group B. (PPTX)
Data
Attitudinal scores dataset. (DOCX)
Data
Initial scoping interview schedule. (DOCX)
Data
Worksheet used with intervention groups. (DOCX)
Data
Information needs/personal choice dataset. (DOCX)
Conference Paper
Full-text available
The increased availability of high-performance parallel architectures such as the Graphics Processing Unit (GPU) has led to significant interest in modified versions of metaheuristics that take advantage of their capabilities. Parallel Ant Colony Optimization (ACO) algorithms are now widely-used, but these often present a challenge in terms of maxi...
Article
Full-text available
Shape optimization techniques are becoming increasingly important in design and engineering. This growing significance reflects the need to exploit advances in digital fabrication technologies, and the desire to create new types of surface designs for various engineering applications. Evolutionary algorithms offer several key advantages for shape o...
Article
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As synthetic biology moves away from trial and error and embraces more formal processes, workflows have emerged that cover the roadmap from conceptualization of a genetic device to its construction and measurement. This latter aspect (i.e., characterization and measurement of synthetic genetic constructs) has received relatively little attention to...
Article
Full-text available
Ant colony optimisation (ACO) is a nature-inspired, population-based metaheuristic that has been used to solve a wide variety of computationally hard problems. In order to take full advantage of the inherently stochastic and distributed nature of the method, we describe a parallelization strategy that leverages these features on heterogeneous and l...
Chapter
This chapter considers the application of evolutionary algorithms and regulatory networks to problems in architectural design. Computer technologies have transformed architectural design. The proliferation of computer-aided design (CAD) software has significantly enhanced the control and analysis of three-dimensional designs, while computer-aided m...
Book
This book constitutes the refereed proceedings of the 15th International Conference on Unconventional Computation and Natural Computation, UCNC 2016, held in Manchester, UK, in July 2016. The 15 revised full papers presented together with 5 invited papers were carefully reviewed and selected from 30 submissions. The papers cover a wide range of top...
Conference Paper
In bacterial populations, cells are able to cooperate in order to yield complex collective functionalities. Interest in population-level cellular behaviour is increasing, due to both our expanding knowledge of the underlying biological principles, and the growing range of possible applications for engineered microbial consortia. The ability of cell...
Article
Full-text available
We describe strategies for the construction of bacterial computing platforms by describing a number of results from the recently completed bacterial computing with engineered populations project. In general, the implementation of such systems requires a framework containing various components such as intracellular circuits, single cell input/output...
Article
Synthetic biology is an emerging research field, in which engineering principles are applied to natural, living systems. A major goal of synthetic biology is to harness the inherent “biological nanotechnology” of living cells for the purposes of computation, production or diagnosis. As the field evolves, it is gradually developing from a single-cel...
Article
Full-text available
The rapidly growing field of nature-inspired computing concerns the development and application of algorithms and methods based on biological or physical principles. This approach is particularly compelling for practitioners in high-performance computing, as natural algorithms are often inherently parallel in nature (for example, they may be based...
Article
Full-text available
In many types of network, the relationship between structure and function is of great significance. We are particularly interested in community structures, which arise in a wide variety of domains. We apply a simple oscillator model to networks with community structures and show that waves of regular oscillation are caused by synchronised clusters...
Article
Full-text available
Recent efforts in synthetic biology have focussed on the implementation of logical functions within living cells. One aim is to facilitate both internal "re-programming" and external control of cells, with potential applications in a wide range of domains. However, fundamental limitations on the degree to which single cells may be re-engineered hav...
Data
Comparison of stochastic and deterministic behaviour in plasmid concentration. Twelve different simulations of Figure 1B (case 1-1) over 150 min. Only and are monitored. Copy number equals 1 (six graphs on the left) and 20 (six graphs on the right). Rate equals 2E-5 (top row), 2E-6 (middle row) and 2E-3 (bottom row). The unrealistic transitions of...
Data
Simulation results of NOR_2 during its logic 1-0 case. This case means that molecules are present (logic “1” = 1000 molecules at the start; = 500 molecules min−1) and the plasmids coming from donors (NOR_1) are all in configuration . In this scenario, we would expect a logic “0” in the output (no GFP). However, we can observe an initial GFP express...
Data
Validation of DiSCUS. Left (figures A–C): validation of conjugation dynamics using real data. A. Figure extracted from [60] where a colony of Pseudomonas putida is divided into dark red donor cells (DsRed), yellow recipient cells (YFP) and transconjugants, expressing both yellow and green light (YFP and GFP). The upper row shows the transconjugant...
Data
Python code for the intra-cell circuits. Equations 1 to 13, that explain the deterministic behaviour of the first 2-strain NOR population are coded in the file NORdet.py while the rates are simulated stochastically (Gillespie) in the file NOTsto.py. Regarding the XOR example, the NOR_1 strain is simulated deterministically in XOR(NOR1)det.py (ODEs...
Data
Alternative spatial simulations to Figure 3 with greater conjugation frequency. Red outline cells: donors (senders). Blue outline cells: recipients (receivers). Green colour intensity proportional to GFP concentration level (output). A. Logic 0-0 case. B. Logic 1-1 case. Bars in bar graphs proportional to plasmid numbers in the whole population (ex...
Data
Perturbation analysis of model reaction rates. In each graph (A–D), the results of 50 simulations are shown, 45 of which use a perturbed set of reaction rates, and 5 of which use the original rates (control set, above dashed horizontal lines in graphs). In each experiment, we perturb every rate by adding Gaussian noise to the original value (starda...
Data
Molecular deterministic relations in the simulation of Figure 1B. Using the same simulation of Figure 2 (case 1-1), these graphs show the behavioural changes in the relation between different molecules when the rate (Cre deletion rate) is changed. All graphs show information at time = 200 min. A. Cre proteins and altered plasmids (copy number = 1)....
Data
Alternative spatial simulation for case 0-0 in Figure 6 with lower conjugation frequency. Snapshot of an XOR population after 32 h when no inputs are present (right) and bar graph showing the average number of plasmids (per configuration) in receivers (left) at the same instant (y axis in logarithmic scale). By setting up the conjugation frequency...
Data
Effects of manual mixing on conjugation frequency. A. Recipient-trapping behaviour ofa population wth donors (red), transconjugants (green) and recipients (yellow). Two snapshots depict clearly-observed clusters. B. Population arfter random mixing, where the clusters are automatically dissolved. C. Graph showing conjugation frequencies (Y = T/(R+T)...
Data
The 2-strain NOR population (0-0). Spatial simulation of the 0-0 logic case from where images in Figure 3 are taken. 24-hour video where the community is shuffled randomly every 400 min as stated in the text. (MOV)
Data
The 2-strain NOR population (1-1). Spatial simulation of the 1-1 logic case from where images in Figure 3 are taken. 24-hour video where the community is shuffled randomly every 400 min as stated in the text. (MOV)
Data
Full-text available
Reactions and rates used in the simulations. This text contains the chemical reactions and the rate values used in all simulations of the paper. (PDF)
Article
Full-text available
The problem of parameterization is often central to the effective deployment of nature-inspired algorithms. However, finding the optimal set of parameter values for a combination of problem instance and solution method is highly challenging, and few concrete guidelines exist on how and when such tuning may be performed. Previous work tends to eithe...
Article
Full-text available
The aim of this learning exercise was to harness current interest in zombies in order to educate audiences about the epidemiology of infectious disease. Participants in the activity were provided with an outbreak scenario, which they then used as the basis of play-based activities. By considering the mode and speed of transmission, size of outbreak...
Article
We present GPU implementations of two different nature-inspired optimization methods for well-known optimization problems. Ant Colony Optimization (ACO) is a two-stage population-based method modelled on the foraging behaviour of ants, while P systems provide a high-level computational modelling framework that combines the structure and dynamic asp...
Article
A significant amount of high-impact contemporary scientific research occurs where biology, computer science, engineering and chemistry converge. Although programmes have been put in place to support such work, the complex dynamics of interdisciplinarity are still poorly understood. In this paper we highlight potential barriers to effective research...
Article
In bacterial populations, cells are able to cooperate in order to yield complex collective functionalities. Interest in population-level cellular behaviour is increasing, due to both our expanding knowledge of the underlying biological principles, and the growing range of possible applications for engineered microbial consortia. Researchers in the...
Chapter
Glossary Definition of the Subject Introduction The DNA Molecule The First DNA Computation Models of DNA Computation Subsequent Work Assessment Future Directions Bibliography
Conference Paper
Full-text available
A significant challenge in nature-inspired algorithmics is the identification of specific characteristics of problems that make them harder (or easier) to solve using specific methods. The hope is that, by identifying these characteristics, we may more easily predict which algorithms are best-suited to problems sharing certain features. Here, we ap...
Article
Full-text available
Background Engineering genetic Boolean logic circuits is a major research theme of synthetic biology. By altering or introducing connections between genetic components, novel regulatory networks are built in order to mimic the behaviour of electronic devices such as logic gates. While electronics is a highly standardized science, genetic logic is s...
Article
Full-text available
In this paper we present a novel genetic algorithm (GA) solution to a simple yet challenging commercial puzzle game known as Zen Puzzle Garden (ZPG). We describe the game in detail, before presenting a suitable encoding scheme and fitness function for candidate solutions. By constructing a simulator for the game, we compare the performance of the G...
Article
Full-text available
We present a developmental genotype-phenotype growth process, or embryogeny, which is used to evolve, in silico, efficient three-dimensional structures that exhibit real-world architectural performance. The embryogeny defines a sequential assembly of architectural components within a three-dimensional volume, and indirectly establishes a regulatory...
Article
In this paper we consider the problem of representation and measurement in genetic circuits, and investigate how they can affect the reliability of engineered systems. We propose a design scheme, based on the notion of continuous computation, which addresses these issues. We illustrate the methodology by showing how a concept from computer architec...
Article
Unconventional computation (UCOMP) is an important and emerging area of scientifc research, which explores new ways of computing that go beyond the traditional model, as well as quantum- and brain inspired com- puting. Such alternatives may encompass novel substrates (e.g., DNA, liv- ing cells, or mixtures of the two) as well as new paradigms which...
Chapter
Motivated by questions in biology and distributed computing, the authors investigate the behaviour of particular cellular automata, modelled as one-dimensional arrays of identical finite automata. They investigate what kinds of self-stabilising cooperative behaviour may be induced in terms of waves of cellular state changes along a filament of cell...
Article
Full-text available
Biological and chemical information technologies (bio/chem IT) have the potential to reshape the scientific and technological landscape. In this paper we briefly review the main challenges and opportunities in the field, before presenting several case studies based on ongoing FP7 research projects.
Conference Paper
In this paper we describe a general method for the conversion of an equation-based model to an agent-based simulation. We illustrate the process by converting a well-known recent case-study in epidemiology (zombie infection), and show how we may obtain qualitatively similar results, whilst gaining access to the many benefits of an agent-based imple...