For a long time engineering design has relied on human engineers manually crafting and refining designs using their expertise and experience. In Bio-inspired Evolutionary Development (EvoDevo), generative algorithms are employed to investigate a broader design space that may go beyond what human engineers have considered. Previous literature has demonstrated the use of quality and diversity (QD) algorithms in evolutionary approaches to drive the process to better quality solutions. This paper provides a study to understand the effects of using QD algorithms in EvoDevo processes for engineering design. This paper also analyses the impact of using different behavioural characterisations (BC) in the performance of the quality of the solutions found. The results demonstrate that quality and diversity algorithms can find better solutions than other EAs for engineering design problems. It was also found that the characterisation of the BC is important to get the best results.

In recent years, the evolutionary developmental (Evo- Devo) concept has gained traction in the field of engineering design. This paper presents a new biologically inspired approach rooted in Evo- Devo principles to iteratively develop car chassis designs based on a specified design brief. The proposed method draws inspiration from biological cell growth and differentiation behaviors to generate intricate engineering designs. Employing evolutionary algorithms, the paper aims to evolve gene regulatory networks that govern the growth of a minimal viable design. The primary goal is to achieve an optimal design capable of withstanding sudden crash impacts within safety limits. Comprehensive simulation results demonstrate that the proposed approach, using genetic algorithms, evolves gene regulatory networks that generate a spectrum of viable designs. Furthermore, the best-evolved solution exhibits generalizability and adaptability across different simulation parameters.

Engineering design optimization poses a significant challenge, usually requiring human expertise to discover superior solutions. Although various search techniques have been employed to generate diverse designs, their effectiveness is often limited by problem-specific parameter tuning, making them less generalizable and scalable. This article introduces a framework inspired by evolutionary and developmental (evo-devo) concepts, aiming to automate the evolution of structural engineering designs. In biological systems, evo-devo governs the growth of single-cell organisms into multicellular organisms through the use of gene regulatory networks (GRNs). GRNs are inherently complex and highly nonlinear, and this article explores the use of neural networks and genetic programming as artificial representations of GRNs to emulate such behaviors. To evolve a wide range of Pareto fronts for artificial GRNs, this article introduces a new technique, a real value-encoded neuroevolutionary method termed real-encoded NEAT (RNEAT). The performance of RNEAT is compared with that of two well-known evolutionary search techniques across different 2-D and 3-D problems. The experimental results demonstrate two key findings. First, the proposed framework effectively generates a population of GRNs that can produce diverse structures for both 2-D and 3-D problems. Second, the proposed RNEAT algorithm outperforms its competitors on more than 50% of the problems examined. These results validate the proof of concept underlying the proposed evo-devo-based engineering design evolution.

We argue that attempting to quantify open-endedness misses the point: The nature of open-endedness is such that an open-ended system will eventually move outside its current model of behavior, and hence outside any measure based on that model. This presents a challenge for analyzing Artificial Life systems, leading us to conclude that the focus should be on understanding the mechanisms underlying open-endedness, not simply on attempting to quantify it. To demonstrate this, we apply several measures to eight long experimental runs of the spatial version of the Stringmol automata chemistry. These experiments were originally designed to examine the hypothesis that spatial structure provides a defense against parasites. The runs successfully show this defense, but also show a range of innovative, and possibly open-ended, behaviors involved in countering a parasitic arms race. Commencing with system-generic measures, we develop and use a variety of measures dedicated to analyzing some of these innovations. We argue that a process of analysis, starting with system-generic measures but going on to system-specific measures, will be needed wherever the phenomenon of open-endedness is involved.

In nature, the exploration of a design space is achieved by evolution. However, using artificial evolution to evolve physical shapes has been challenging because both the mapping from the genotype to phenotype and the means of measuring the resulting shape to estimate fitness are not straightforward. This contribution brings together recent advances in generative design with novelty search, an evolutionary method that replaces the fitness function with reward based purely on novelty. Bringing these techniques together yields a new methodology for exploring the power of shape descriptors. Novelty search with and without an archive is used to explore the range of shapes that are reachable from a hand-designed genotype, and compared with random walk mutations. Results indicate that the novelty search technique without an archive evolves a wider range of shapes than when an archive is used, but both are better than random walk.

MOTIVATION: Classification of archaeological animal samples is commonly achieved via manual examination of matrix-assisted laser desorption/ionization time-of-flight (MALDI-ToF) spectra. This is a time-consuming process which requires significant training and which does not produce a measure of confidence in the classification. We present a new, automated method for arriving at a classification of a MALDI-ToF sample, provided the collagen sequences for each candidate species are available. The approach derives a set of peptide masses from the sequence data for comparison with the sample data, which is carried out by cross-correlation. A novel way of combining evidence from multiple marker peptides is used to interpret the raw alignments and arrive at a classification with an associated confidence measure. RESULTS: To illustrate the efficacy of the approach, we tested the new method with a previously published classification of parchment folia from a copy of the Gospel of Luke, produced around 1120 C.E. by scribes at St Augustine's Abbey in Canterbury, UK. In total, 80 of the 81 samples were given identical classifications by both methods. In addition, the new method gives a quantifiable level of confidence in each classification. AVAILABILITY AND IMPLEMENTATION: The software can be found at https://github.com/bioarch-sjh/bacollite, and can be installed in R using devtools. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Computational reflection uses software architectures that are capable of self- modification at runtime. These systems have implementations between two extremes: procedural reflection, in which unlimited self-modification is available at the expense of infinite recursion; and declarative reflection, which uses pre-defined metrics to drive the self-modification and is hence limited in scope. Biological processes also exploit the concept of reflection, where natural selection drives the process of modification. The concept of a program in computing has an analogy with an individual member of a species. The process of life is discretised into a series of autonomous systems, each of which creates modified versions of itself as offspring. This paper unifies the concept of computational reflection with biological systems via a new analysis of von Neumanns Universal Constructor. The result is a bio-reflective architecture that is capable of unconstrained self-modification without the problems of infinite recursion that exist in the computational counterparts. The new architecture is a blueprint for applications in Artificial Life studies, Evolutionary Algorithms, and Artificial Intelligence.

Automata chemistries are good vehicles for experimentation in open-ended evolution, but they are by necessity complex systems whose low-level properties require careful design. To aid the process of designing automata chemistries, we develop an abstract model that classifies the features of a chemistry from a physical (bottom up) perspective and from a biological (top down) perspective. There are two levels: things that can evolve, and things that cannot. We equate the evolving level with biology and the non-evolving level with physics. We design our initial organisms in the biology, so they can evolve. We design the physics to facilitate evolvable biologies. This architecture leads to a set of design principles that should be observed when creating an instantiation of the architecture. These principles are Everything Evolves, Everything's Soft, and Everything Dies. To evaluate these ideas, we present experiments in the recently developed Stringmol automata chemistry. We examine the properties of Stringmol with respect to the principles, and so demonstrate the usefulness of the principles in designing automata chemistries.

We present a survey of the first 21 years of web-based artificial life (WebAL) research and applications, broadly construed to include the many different ways in which artificial life and web technologies might intersect. Our survey covers the period from 1994-when the first WebAL work appeared-up to the present day, together with a brief discussion of relevant precursors. We examine recent projects, from 2010-2015, in greater detail in order to highlight the current state of the art. We follow the survey with a discussion of common themes and methodologies that can be observed in recent work and identify a number of likely directions for future work in this exciting area.

We describe the content and outcomes of the First Workshop on Open-Ended Evolution: Recent Progress and Future Milestones (OEE1), held during the ECAL 2015 conference at the University of York, UK, in July 2015. We briefly summarize the content of the workshop's talks, and identify the main themes that emerged from the open discussions. Two important conclusions from the discussions are: (1) the idea of pluralism about OEE-it seems clear that there is more than one interesting and important kind of OEE; and (2) the importance of distinguishing observable behavioral hallmarks of systems undergoing OEE from hypothesized underlying mechanisms that explain why a system exhibits those hallmarks. We summarize the different hallmarks and mechanisms discussed during the workshop, and list the specific systems that were highlighted with respect to particular hallmarks and mechanisms. We conclude by identifying some of the most important open research questions about OEE that are apparent in light of the discussions. The York workshop provides a foundation for a follow-up OEE2 workshop taking place at the ALIFE XV conference in Cancún, Mexico, in July 2016. Additional materials from the York workshop, including talk abstracts, presentation slides, and videos of each talk, are available at http://alife.org/ws/oee1 .

Open-ended evolutionary systems offer us the tantalising prospect of creating artificial life from simple precursors. One of the issues in designing open ended systems is that there exist few metrics for measuring their evolutionary activity. Current measures of evolutionary activity are only applicable to systems in which the fitness of a single component is defined by an explicit fitness function. However, this is not guaranteed in systems where a significant part of the fitness is intrinsic (for example caused by interactions between components). In this paper, we evaluate a new approach to the problem of measuring evolutionary activity that is applicable to systems exhibiting both explicit and intrinsic fitness pressures. To evaluate this measure, we ran 22,000 grid-based simulations of two automata chemistries, Tierra and Stringmol. Both of these systems have strong intrinsic fitness pressures. We examine the effect of varying the mutation rate in both systems, and demonstrate that the new measure identifies an optimal mutation rate.

We report a study of networks constructed from mutation patterns observed in biology. These networks form evolutionary trajectories, which allow for both frequent substitution of closely related structures, and a small evolutionary distance between any two structures. These two properties define the small-world phenomenon. The mutation behavior between tokens in an evolvable artificial chemistry determines its ability to explore evolutionary space. This concept is underrepresented in previous work on string-based chemistries. We argue that small-world mutation networks will confer better exploration of the evolutionary space than either random or fully regular mutation strategies. We calculate network statistics from two data sets: amino acid substitution matrices, and codon-level single point mutations. The first class are observed data from protein alignments; while the second class is defined by the standard genetic code that is used to translate RNA into amino acids. We report a methodology for creating small-world mutation networks for artificial chemistries with arbitrary node count and connectivity. We argue that ALife systems would benefit from this approach, as it delivers a more viable exploration of evolutionary space.

The bacterial genome is well understood by biologists. Although its efficiency and adaptability should make it a good model for evolutionary algorithms, the bacterial genome is tightly coupled with the components of the bacterial metabolism, referred to here as the metabolome. This paper explores an approach to modelling an artificial bacterial metabolome in an efficient and modular manner, so that analogues of bacterial genome organisation and gene regulation can be implemented in evolutionary algorithms. We propose a particulate model of bacterial metabolic pathways in which the constituents drift in a fixed, limited space and obey a limited set of biologically plausible reaction rules. The potential of this model is demonstrated by creating a network that is capable of appropriate behavioural switching that can be observed in bacteria.

The problem of object recognition may be cast into a spatial grammar framework. The system comprises three novel elements: a spatial organisation of line features, an efficient two dimensional parsing engine, and a genetic algorithm learning routine that induces spatial grammars. Labelling the spatial organisation of feature pairs allows the terminal symbols of the spatial grammar to be defined, and constrains the search space of the feature parser. A genetic algorithm approach is then used to induce appropriate grammars using a supervised learning routine. Early results show that similar foreground and background features can be discriminated using this approach.

An integrated map of all utility services in a locale would facilitate better management of the road infrastructure and the utilities themselves. To meet this goal, there exists a need to integrate raster scans of paper maps into GIS by capturing the semantic relationships between the objects in the drawings. In this context, commercially available vectorisation algorithms do not produce a sufficiently rich object representation. We present a structural object recognition system that successfully isolates sectional sub- diagrams in maps of underground utilities. This is built upon a vectorisation system based on a constrained Delau-nay triangulation of pen strokes.

The structural health of airframes is often monitored by analysis of the frequency of occurrence matrix (FOOM) produced after each flight. Each cell in the matrix records a stress event of a particular severity. These matrices are used to determine how much of the aircraft's life has been used up in each flight. Unfortunately the sensors that produce this data are subject to degradation themselves, resulting in corruption of FOOMs. The paper reports a method of automating detection of sensor faults. It is the only known method that is capable of detecting such faults. The method is in essence a dimensionality reduction algorithm coupled to a novelty detection algorithm that produces measures of unusual counts of stress elements at the level of the individual cell and unusual distributions of counts over the entire FOOM. Cell-level error is detected using a probability threshold and a sum of standard deviations. FOOM-level error is detected using a novel application of the eigenface algorithm. Novelty is measured using a mixture of Gaussian model of the data, fitted using the expectation-maximisation algorithm.

The structural health of airframes is often monitored by analysis of the frequency of occurrence matrix (FOOM) produced after each flight. Each cell in the matrix records a stress event of a particular severity. These matrices are used to determine how much of the aircraft's life has been used up in each flight. Unfortunately, the sensors that produce this data are subject to degradation themselves, resulting in corruption of FOOMs. The paper reports a method of automating detection of sensor faults. It is the only known method that is capable of detecting such faults. The method is in essence a dimensionality reduction algorithm coupled to a novelty detection algorithm that produce measures of unusual counts of stress events at the level of the individual cell and unusual distributions of counts over the entire FOOM. Cell-level error is detected using a probability threshold and a sum of standard deviations. FOOM-level error is detected using a novel application of the eigenface algorithm. Novelty is measured using a Gaussian basis function neural network fitted using the expectation-maximisation algorithm.

This paper describes a statistical framework for the unsupervised learning of linear filter combinations for feature characterisation. The learning strategy is two step. In the first instance, the EM algorithm is used to learn the foreground probability distribution. This is an abductive process, since we have a detailed model of the background process based on the known noise-response characteristics of the filter-bank. The second phase uses the a posteriori foreground and background probabilities to compute a weighted between-class covariance matrix. We use the principal components analysis to locate the linear filter combinations that maximise the between class covariance matrix. The new feature characterisation method is illustrated for the problem of extracting linear features from complex millimetre radar images. The method proves to be effective in learning a mixture of sine and cosine phase Gabor functions necessary to capture shadowed line structures.

This paper describes a novel technique for segmenting frequency modulated line-textures. Textures of this sort abound in nature and are typified by growth patterns in which the deposition rate varies over time. The basic idea underpinning the technique is to use the S-Gabor kernel as a frequency modulated channel response function. According to this channel model, the central frequency changes exponentially with distance from the centre of the kernel. In order to segment the resulting texture response, we use fuzzy clustering to locate peaks in the Fourier power spectrum. In this way we estimate both the centre-frequency and the modulation parameters of the filter bank. We illustrate the effectiveness of our technique on the segmentation of growth patterns on fish scales.