Bio-inspired Computing and Smart Mobility

Por último, se aborda la predicción de plazas libres de aparcamiento utilizando técnicas de aprendizaje automático, tales como series temporales, agrupamiento, etc., incluyendo un prototipo de aplicación web. La tercera parte de esta tesis doctoral se enfoca en el diseño y evaluación de un nuevo algoritmo inspirado en la epigénesis, el Algoritmo Epigenético. Luego de la descripción del modelo en el que se basa y de sus partes, se utiliza este nuevo algoritmo para la resolución del problema de la mochila multidimensional y se comparan sus resultados con los de otros algoritmos del estado de arte. Por último se emplea también el Algoritmo Epigenético para la optimización de la arquitectura Yellow Swarm, un problema de movilidad inteligente resuelto por un nuevo algoritmo bioinspirado. A lo largo de esta tesis doctoral se han descrito los problemas de movilidad inteligente y propuesto nuevas herramientas para su optimización. A partir de los experimentos realizados se concluye que estas herramientas, basadas en algoritmos bioinspirados, son eficientes para abordar estos problemas, obteniendo resultados competitivos comparados con los del estado del arte, los cuales han sido validados estadísticamente. Esto representa un aporte científico pero también una serie de mejoras para la sociedad toda, tanto en su salud como en el aprovechamiento de su tiempo libre. Fecha de lectura de Tesis: 01 octubre 2018.Esta tesis doctoral propone soluciones a problemas de movilidad inteligente, concretamente la reducción de los tiempos de viajes en las vías urbanas, las emisiones de gases de efecto invernadero y el consumo de combustible, mediante el diseño y uso de nuevos algoritmos bioinspirados. Estos algoritmos se utilizan para la optimización de escenarios realistas, cuyo trazado urbano se obtiene desde OpenStreetMap, y que son luego evaluados en el microsimulador SUMO. Primero se describen las bases científicas y tecnológicas, incluyendo la definición y estado del arte de los problemas a abordar, las metaheurísticas que se utilizarán durante el desarrollo de los experimentos, así como las correspondientes validaciones estadísticas. A continuación se describen los simuladores de movilidad como principal herramienta para construir y evaluar los escenarios urbanos. Por último se presenta una propuesta para generar tráfico vehicular realista a partir de datos de sensores que cuentan el número de vehículos en la ciudad, utilizando herramientas incluidas en SUMO combinadas con algoritmos evolutivos. En la segunda parte se modelan y resuelven problemas de movilidad inteligente utilizando las nuevas arquitecturas Red Swarm y Green Swarm para sugerir nuevas rutas a los vehículos utilizando nodos con conectividad Wi-Fi. Red Swarm se centra en la reducción de tiempos de viajes evitando la congestión de las calles, mientras que Green Swarm está enfocado en la reducción de emisiones y consumo de combustible. Luego se propone la arquitectura Yellow Swarm que utiliza una serie de paneles LED para indicar desvíos que los vehículos pueden seguir en lugar de nodos Wi-Fi haciendo esta propuesta más accesible. Además se propone un método para genera rutas alternativas para los navegadores GPS de modo que se aprovechen mejor las calles secundarias de las ciudades, reduciendo los atascos

Using MapReduce Streaming for Distributed Life Simulation on the Cloud

Distributed software simulations are indispensable in the study of large-scale life models but often require the use of technically complex lower-level distributed computing frameworks, such as MPI. We propose to overcome the complexity challenge by applying the emerging MapReduce (MR) model to distributed life simulations and by running such simulations on the cloud. Technically, we design optimized MR streaming algorithms for discrete and continuous versions of Conway’s life according to a general MR streaming pattern. We chose life because it is simple enough as a testbed for MR’s applicability to a-life simulations and general enough to make our results applicable to various lattice-based a-life models. We implement and empirically evaluate our algorithms’ performance on Amazon’s Elastic MR cloud. Our experiments demonstrate that a single MR optimization technique called strip partitioning can reduce the execution time of continuous life simulations by 64%. To the best of our knowledge, we are the first to propose and evaluate MR streaming algorithms for lattice-based simulations. Our algorithms can serve as prototypes in the development of novel MR simulation algorithms for large-scale lattice-based a-life models.https://digitalcommons.chapman.edu/scs_books/1014/thumbnail.jp

Simulations and Modelling for Biological Invasions

Biological invasions are characterized by the movement of organisms from their native geographic region to new, distinct regions in which they may have significant impacts. Biological invasions pose one of the most serious threats to global biodiversity, and hence significant resources are invested in predicting, preventing, and managing them. Biological systems and processes are typically large, complex, and inherently difficult to study naturally because of their immense scale and complexity. Hence, computational modelling and simulation approaches can be taken to study them. In this dissertation, I applied computer simulations to address two important problems in invasion biology. First, in invasion biology, the impact of genetic diversity of introduced populations on their establishment success is unknown. We took an individual-based modelling approach to explore this, leveraging an ecosystem simulation called EcoSim to simulate biological invasions. We conducted reciprocal transplants of prey individuals across two simulated environments, over a gradient of genetic diversity. Our simulation results demonstrated that a harsh environment with low and spatially-varying resource abundance mediated a relationship between genetic diversity and short-term establishment success of introduced populations rather than the degree of difference between native and introduced ranges. We also found that reducing Allee effects by maintaining compactness, a measure of spatial density, was key to the establishment success of prey individuals in EcoSim, which were sexually reproducing. Further, we found evidence of a more complex relationship between genetic diversity and long-term establishment success, assuming multiple introductions were occurring. Low-diversity populations seemed to benefit more strongly from multiple introductions than high-diversity populations. Our results also corroborated the evolutionary imbalance hypothesis: the environment that yielded greater diversity produced better invaders and itself was less invasible. Finally, our study corroborated a mechanical explanation for the evolutionary imbalance hypothesis – the populations evolved in a more intense competitive environment produced better invaders. Secondly, an important advancement in invasion biology is the use of genetic barcoding or metabarcoding, in conjunction with next-generation sequencing, as a potential means of early detection of aquatic introduced species. Barcoding and metabarcoding invariably requires some amount of computational DNA sequence processing. Unfortunately, optimal processing parameters are not known in advance and the consequences of suboptimal parameter selection are poorly understood. We aimed to determine the optimal parameterization of a common sequence processing pipeline for both early detection of aquatic nonindigenous species and conducting species richness assessments. We then aimed to determine the performance of optimized pipelines in a simulated inoculation of sequences into community samples. We found that early detection requires relatively lenient processing parameters. Further, optimality depended on the research goal – what was optimal for early detection was suboptimal for estimating species richness and vice-versa. Finally, with optimal parameter selection, fewer than 11 target sequences were required in order to detect 90% of nonindigenous species

Visual navigation in ants

Les remarquables capacités de navigation des insectes nous prouvent à quel point ces " mini-cerveaux " peuvent produire des comportements admirablement robustes et efficaces dans des environnements complexes. En effet, être capable de naviguer de façon efficace et autonome dans un environnement parfois hostile (désert, forêt tropicale) sollicite l'intervention de nombreux processus cognitifs impliquant l'extraction, la mémorisation et le traitement de l'information spatiale préalables à une prise de décision locomotrice orientée dans l'espace. Lors de leurs excursions hors du nid, les insectes tels que les abeilles, guêpes ou fourmis, se fient à un processus d'intégration du trajet, mais également à des indices visuels qui leur permettent de mémoriser des routes et de retrouver certains sites alimentaires familiers et leur nid. L'étude des mécanismes d'intégration du trajet a fait l'objet de nombreux travaux, par contre, nos connaissances à propos de l'utilisation d'indices visuels sont beaucoup plus limitées et proviennent principalement d'études menées dans des environnements artificiellement simplifiés, dont les conclusions sont parfois difficilement transposables aux conditions naturelles. Cette thèse propose une approche intégrative, combinant 1- des études de terrains et de laboratoire conduites sur deux espèces de fourmis spécialistes de la navigation visuelle (Melophorus bagoti et Gigantiops destructor) et 2- des analyses de photos panoramiques prisent aux endroits où les fourmis naviguent qui permettent de quantifier objectivement l'information visuelle accessible à l'insecte. Les résultats convergents obtenus sur le terrain et au laboratoire permettent de montrer que, chez ces deux espèces, les fourmis ne fragmentent pas leur monde visuel en multiples objets indépendants, et donc ne mémorisent pas de 'repères visuels' ou de balises particuliers comme le ferait un être humain. En fait, l'efficacité de leur navigation émergerait de l'utilisation de paramètres visuels étendus sur l'ensemble de leur champ visuel panoramique, incluant repères proximaux comme distaux, sans les individualiser. Contre-intuitivement, de telles images panoramiques, même à basse résolution, fournissent une information spatiale précise et non ambiguë dans les environnements naturels. Plutôt qu'une focalisation sur des repères isolés, l'utilisation de vues dans leur globalité semble être plus efficace pour représenter la complexité des scènes naturelles et être mieux adaptée à la basse résolution du système visuel des insectes. Les photos panoramiques enregistrées peuvent également servir à l'élaboration de modèles navigationnels. Les prédictions de ces modèles sont ici directement comparées au comportement des fourmis, permettant ainsi de tester et d'améliorer les différentes hypothèses envisagées. Cette approche m'a conduit à la conclusion selon laquelle les fourmis utilisent leurs vues panoramiques de façons différentes suivant qu'elles se déplacent en terrain familier ou non. Par exemple, aligner son corps de manière à ce que la vue perçue reproduise au mieux l'information mémorisée est une stratégie très efficace pour naviguer le long d'une route bien connue ; mais n'est d'aucune efficacité si l'insecte se retrouve en territoire nouveau, écarté du chemin familier. Dans ces cas critiques, les fourmis semblent recourir à une seconde stratégie qui consiste à se déplacer vers les régions présentant une ligne d'horizon plus basse que celle mémorisée, ce qui généralement conduit vers le terrain familier. Afin de choisir parmi ces deux différentes stratégies, les fourmis semblent tout simplement se fier au degré de familiarisation avec le panorama perçu. Cette thèse soulève aussi la question de la nature de l'information visuelle mémorisée par les insectes. Le modèle du " snapshot " qui prédomine dans la littérature suppose que les fourmis mémorisent une séquence d'instantanés photographiques placés à différents points le long de leurs routes. A l'inverse, les résultats obtenus dans le présent travail montrent que l'information visuelle mémorisée au bout d'une route (15 mètres) modifie l'information mémorisée à l'autre extrémité de cette même route, ce qui suggère que la connaissance visuelle de l'ensemble de la route soit compactée en une seule et même représentation mémorisée. Cette hypothèse s'accorde aussi avec d'autres de nos résultats montrant que la mémoire visuelle ne s'acquiert pas instantanément, mais se développe et s'affine avec l'expérience répétée. Lorsqu'une fourmi navigue le long de sa route, ses récepteurs visuels sont stimulés de façon continue par une scène évoluant doucement et régulièrement au fur et à mesure du déplacement. Mémoriser un pattern général de stimulations, plutôt qu'une série de " snapshots " indépendants et très ressemblants les uns aux autres, constitue une hypothèse parcimonieuse. Cette hypothèse s'applique en outre particulièrement bien aux modèles en réseaux de neurones, suggérant sa pertinence biologique. Dans l'ensemble, cette thèse s'intéresse à la nature des perceptions et de la mémoire visuelle des fourmis, ainsi qu'à la manière dont elles sont intégrées et traitées afin de produire une réponse navigationnelle appropriée. Nos résultats sont aussi discutés dans le cadre de la cognition comparée. Insectes comme vertébrés ont résolu le même problème qui consiste à naviguer de façon efficace sur terre. A la lumière de la théorie de l'évolution de Darwin, il n'y a 'a priori' aucune raison de penser qu'il existe une forme de transition brutale entre les mécanismes cognitifs des différentes espèces animales. Le fossé marqué entre insectes et vertébrés au sein des sciences cognitives pourrait bien être dû à des approches différentes plutôt qu'à de vraies différences ontologiques. Historiquement, l'étude de la navigation de l'insecte a suivi une approche de type 'bottom-up' qui recherche comment des comportements apparemment complexes peuvent découler de mécanismes simples. Ces solutions parcimonieuses, comme celles explorées dans cette thèse, peuvent fournir de remarquables hypothèses de base pour expliquer la navigation chez d'autres espèces animales aux cerveaux et comportements apparemment plus complexes, contribuant ainsi à une véritable cognition comparée.Navigating efficiently in the outside world requires many cognitive abilities like extracting, memorising, and processing information. The remarkable navigational abilities of insects are an existence proof of how small brains can produce exquisitely efficient, robust behaviour in complex environments. During their foraging trips, insects, like ants or bees, are known to rely on both path integration and learnt visual cues to recapitulate a route or reach familiar places like the nest. The strategy of path integration is well understood, but much less is known about how insects acquire and use visual information. Field studies give good descriptions of visually guided routes, but our understanding of the underlying mechanisms comes mainly from simplified laboratory conditions using artificial, geometrically simple landmarks. My thesis proposes an integrative approach that combines 1- field and lab experiments on two visually guided ant species (Melophorus bagoti and Gigantiops destructor) and 2- an analysis of panoramic pictures recorded along the animal's route. The use of panoramic pictures allows an objective quantification of the visual information available to the animal. Results from both species, in the lab and the field, converged, showing that ants do not segregate their visual world into objects, such as landmarks or discrete features, as a human observers might assume. Instead, efficient navigation seems to arise from the use of cues widespread on the ants' panoramic visual field, encompassing both proximal and distal objects together. Such relatively unprocessed panoramic views, even at low resolution, provide remarkably unambiguous spatial information in natural environment. Using such a simple but efficient panoramic visual input, rather than focusing on isolated landmarks, seems an appropriate strategy to cope with the complexity of natural scenes and the poor resolution of insects' eyes. Also, panoramic pictures can serve as a basis for running analytical models of navigation. The predictions of these models can be directly compared with the actual behaviour of real ants, allowing the iterative tuning and testing of different hypotheses. This integrative approach led me to the conclusion that ants do not rely on a single navigational technique, but might switch between strategies according to whether they are on or off their familiar terrain. For example, ants can recapitulate robustly a familiar route by simply aligning their body in a way that the current view matches best their memory. However, this strategy becomes ineffective when displaced away from the familiar route. In such a case, ants appear to head instead towards the regions where the skyline appears lower than the height recorded in their memory, which generally leads them closer to a familiar location. How ants choose between strategies at a given time might be simply based on the degree of familiarity of the panoramic scene currently perceived. Finally, this thesis raises questions about the nature of ant memories. Past studies proposed that ants memorise a succession of discrete 2D 'snapshots' of their surroundings. Contrastingly, results obtained here show that knowledge from the end of a foraging route (15 m) impacts strongly on the behaviour at the beginning of the route, suggesting that the visual knowledge of a whole foraging route may be compacted into a single holistic memory. Accordingly, repetitive training on the exact same route clearly affects the ants' behaviour, suggesting that the memorised information is processed and not 'obtained at once'. While navigating along their familiar route, ants' visual system is continually stimulated by a slowly evolving scene, and learning a general pattern of stimulation rather than storing independent but very similar snapshots appears a reasonable hypothesis to explain navigation on a natural scale; such learning works remarkably well with neural networks. Nonetheless, what the precise nature of ants' visual memories is and how elaborated they are remain wide open question. Overall, my thesis tackles the nature of ants' perception and memory as well as how both are processed together to output an appropriate navigational response. These results are discussed in the light of comparative cognition. Both vertebrates and insects have resolved the same problem of navigating efficiently in the world. In light of Darwin's theory of evolution, there is no a priori reason to think that there is a clear division between cognitive mechanisms of different species. The actual gap between insect and vertebrate cognitive sciences may result more from different approaches rather than real differences. Research on insect navigation has been approached with a bottom-up philosophy, one that examines how simple mechanisms can produce seemingly complex behaviour. Such parsimonious solutions, like the ones explored in the present thesis, can provide useful baseline hypotheses for navigation in other larger-brained animals, and thus contribute to a more truly comparative cognition

On a wildlife tracking and telemetry system : a wireless network approach

Includes abstract.Includes bibliographical references (p. 239-261).Motivated by the diversity of animals, a hybrid wildlife tracking system, EcoLocate, is proposed, with lightweight VHF-like tags and high performance GPS enabled tags, bound by a common wireless network design. Tags transfer information amongst one another in a multi-hop store-and-forward fashion, and can also monitor the presence of one another, enabling social behaviour studies to be conducted. Information can be gathered from any sensor variable of interest (such as temperature, water level, activity and so on) and forwarded through the network, thus leading to more effective game reserve monitoring. Six classes of tracking tags are presented, varying in weight and functionality, but derived from a common set of code, which facilitates modular tag design and deployment. The link between the tags means that tags can dynamically choose their class based on their remaining energy, prolonging lifetime in the network at the cost of a reduction in function. Lightweight, low functionality tags (that can be placed on small animals) use the capabilities of heavier, high functionality devices (placed on larger animals) to transfer their information. EcoLocate is a modular approach to animal tracking and sensing and it is shown how the same common technology can be used for diverse studies, from simple VHF-like activity research to full social and behavioural research using wireless networks to relay data to the end user. The network is not restricted to only tracking animals – environmental variables, people and vehicles can all be monitored, allowing for rich wildlife tracking studies

Task Allocation in Foraging Robot Swarms:The Role of Information Sharing

Autonomous task allocation is a desirable feature of robot swarms that collect and deliver items in scenarios where congestion, caused by accumulated items or robots, can temporarily interfere with swarm behaviour. In such settings, self-regulation of workforce can prevent unnecessary energy consumption. We explore two types of self-regulation: non-social, where robots become idle upon experiencing congestion, and social, where robots broadcast information about congestion to their team mates in order to socially inhibit foraging. We show that while both types of self-regulation can lead to improved energy efficiency and increase the amount of resource collected, the speed with which information about congestion flows through a swarm affects the scalability of these algorithms

Facultative bacterial symbionts from European Orius species: Evidence for an ancestral symbiotic association

Pest control in agriculture employs diverse strategies, among which the use of predatory insects has steadily increased. The use of several species within the genus Orius in pest control is widely spread, particularly in Mediterranean Europe. The use of predatory insects in pest control in agriculture has spread worldwide and increased significantly, especially in the use of various Orius species. Currently, most studies about Orius species have been focused on the diet manipulation or selective breeding methods to reduce the rearing costs and improve the efficiency, only a few studies were associated to their Wolbachia symbionts. The characterisation and contribution of microbial symbionts to Orius sp. fitness, behaviour, and potential impact on human health has been neglected. Therefore, there is a lack of knowledge regarding Orius’ symbionts such as their taxonomic characterisation, the functions of the symbionts and potential influences on human health. This project was focused on the first comparative genomics report of genome sequences level description of the predominant culturable facultative bacterial symbionts associated with the analyses of draft genomes of facultative symbionts using Next Generation Sequencing (NGS) technique related to five Orius species (Orius laevigatus, Orius niger, Orius pallidicornis, Orius majusculus and Orius albidipennis) and collected from various European countries (Greece, Italy, and Spain). Initially, coxl (COI) based taxonomic classification of the Orius species used was performed, followed by the isolation of culturable bacteria from live insects. The whole genome sequences of the bacterial isolates were generated and assembled into draft genomes using NGS. The isolates of two predominant bacteria belong to Serratia and Leucobacter genera, the third predominant bacteria are most likely to be a new genus within the Erwiniaceae. Orius sp. Serratia isolates genomes are more similar to Serratia sp. SCBI. Pan-genome analysis of Serratia sp. Orius isolates evidenced an open pan-genome, and 279 accessory genes were related to the insect symbiosis trait. Additionally, pan-genome analyses of the Serratia sp. isolates offered clues linking Type VI secretion system effector–immunity proteins from the Tai4 sub-family to the symbiotic lifestyle. These symbionts were found to colonise all the insect specimens tested, which evidenced an ancestral symbiotic association between these bacteria and the genus Orius. Additionally, plasmid sequence analyses suggest sequence exchanges between Serratia sp. Orius isolates and pathogenic Serratia species, which may have implications for food safety and human health