Adventures in Time and Space: What Shapes Behavioural Decisions in Drosophila melanogaster?

Variation in behaviour can be observed both between individuals, based on their condition and experience as well as between populations due to sources of heterogeneity in the environment. These behavioural differences have evolved as a result of natural and sexual selection where different strategies may be favoured depending on the costs and benefits associated with those behaviours. In this thesis I examine two sources of heterogeneity within the environment and their behavioural consequences: how spatial complexity mediates sexual selection over time, and how inter and intraspecific signals and individual condition influence social oviposition behaviour. By increasing spatial complexity, we were able to manipulate male-female interaction rate which in turn influenced courtship behaviour and male-induced harm, the consequence of this was an increase in female fecundity especially in the later days of the assay and no change in offspring fitness. These results supported the idea that spatial complexity is able to mediate sexual selection through decreased harm to females. Oviposition decisions are of high consequence to an individual’s fitness and can be shaped by many environmental conditions. Instead of expending energy to evaluate all their different costs and benefits of the conditions of potential oviposition sites females can chose to rely on the signals left by others, in this case it would be beneficial for females to identify signals most like themselves. While we found females oviposited with individuals of the same species and diet, when given the option they showed more interest in and laid more eggs on media that previously held virgin males, bringing into question many assumptions of copying behaviour. In Drosophila melanogaster the only control females have over their offspring is who they mate with and where they oviposit their eggs, thus, these two factors can have a long-lasting impact on individual fitness for future generations. It is also important to consider how the standard lab environment may be shaping these behaviours, and the consequences this has for the evolutionary trajectory of lab populations

Partitioning workflow applications over federated clouds to meet non-functional requirements

PhD ThesisWith cloud computing, users can acquire computer resources when they need them on a pay-as-you-go business model. Because of this, many applications are now being deployed in the cloud, and there are many di erent cloud providers worldwide. Importantly, all these various infrastructure providers o er services with di erent levels of quality. For example, cloud data centres are governed by the privacy and security policies of the country where the centre is located, while many organisations have created their own internal \private cloud" to meet security needs. With all this varieties and uncertainties, application developers who decide to host their system in the cloud face the issue of which cloud to choose to get the best operational conditions in terms of price, reliability and security. And the decision becomes even more complicated if their application consists of a number of distributed components, each with slightly di erent requirements. Rather than trying to identify the single best cloud for an application, this thesis considers an alternative approach, that is, combining di erent clouds to meet users' non-functional requirements. Cloud federation o ers the ability to distribute a single application across two or more clouds, so that the application can bene t from the advantages of each one of them. The key challenge for this approach is how to nd the distribution (or deployment) of application components, which can yield the greatest bene ts. In this thesis, we tackle this problem and propose a set of algorithms, and a framework, to partition a work ow-based application over federated clouds in order to exploit the strengths of each cloud. The speci c goal is to split a distributed application structured as a work ow such that the security and reliability requirements of each component are met, whilst the overall cost of execution is minimised. To achieve this, we propose and evaluate a cloud broker for partitioning a work ow application over federated clouds. The broker integrates with the e-Science Central cloud platform to automatically deploy a work ow over public and private clouds. We developed a deployment planning algorithm to partition a large work ow appli- - i - cation across federated clouds so as to meet security requirements and minimise the monetary cost. A more generic framework is then proposed to model, quantify and guide the partitioning and deployment of work ows over federated clouds. This framework considers the situation where changes in cloud availability (including cloud failure) arise during work ow execution

FIN: Practical Signature-Free Asynchronous Common Subset in Constant Time

Asynchronous common subset (ACS) is a powerful paradigm enabling applications such as Byzantine fault-tolerance (BFT) and multi-party computation (MPC). The most efficient ACS framework in the information-theoretic setting is due to Ben-Or, Kelmer, and Rabin (BKR, 1994). The BKR ACS protocol has been both theoretically and practically impactful. However, the BKR protocol has an $O(\log n)$ running time (where $n$ is the number of replicas) due to the usage of $n$ parallel asynchronous binary agreement (ABA) instances, impacting both performance and scalability. Indeed, for a network of 16~64 replicas, the parallel ABA phase occupies about 95%~97% of the total runtime in BKR. A long-standing open problem is whether we can build an ACS framework with $O(1)$ time while not increasing the message or communication complexity of the BKR protocol. In this paper, we resolve the open problem, presenting the first constant-time ACS protocol with $O(n^3)$ messages in the information-theoretic and signature-free settings. Moreover, as a key ingredient of our new ACS framework and an interesting primitive in its own right, we provide the first information-theoretic multivalued validated Byzantine agreement (MVBA) protocol with $O(1)$ time and $O(n^3)$ messages. Both results can improve---asymptotically and concretely---various applications using ACS and MVBA in the information-theoretic, quantum-safe, or signature-free settings. As an example, we implement FIN, a BFT protocol instantiated using our framework. Via a 121-server deployment on Amazon EC2, we show FIN is significantly more efficient than PACE (CCS 2022), the state-of-the-art asynchronous BFT protocol of the same type. In particular, FIN reduces the overhead of the ABA phase to as low as 1.23% of the total runtime, and FIN achieves up to 3.41x the throughput of PACE. We also show that FIN outperforms other BFT protocols with the standard liveness property such as Dumbo and Speeding Dumbo

PACE: Fully Parallelizable BFT from Reproposable Byzantine Agreement

The classic asynchronous Byzantine fault tolerance (BFT) framework of Ben-Or, Kemler, and Rabin (BKR) and its descendants rely on reliable broadcast (RBC) and asynchronous binary agreement (ABA). However, BKR does not allow all ABA instances to run in parallel, a well-known performance bottleneck. We propose PACE, a generic framework that removes the bottleneck, allowing fully parallelizable ABA instances. PACE is built on RBC and reproposable ABA (RABA). Different from the conventional ABA, RABA allows a replica to change its mind and vote twice. We show how to efficiently build RABA protocols from existing ABA protocols and a new ABA protocol that we introduce. We implement six new BFT protocols: three in the BKR framework, and three in the PACE framework. Via a deployment using 91 replicas on Amazon EC2 across five continents, we show that all PACE instantiations, in both failure-free and failure scenarios, significantly outperform their BKR counterparts, and prior BFT protocols such as BEAT and Dumbo, in terms of latency, throughput, latency vs. throughput, and scalability

Byzantine fault-tolerant agreement protocols for wireless Ad hoc networks

Tese de doutoramento, Informática (Ciências da Computação), Universidade de Lisboa, Faculdade de Ciências, 2010.The thesis investigates the problem of fault- and intrusion-tolerant consensus in resource-constrained wireless ad hoc networks. This is a fundamental problem in distributed computing because it abstracts the need to coordinate activities among various nodes. It has been shown to be a building block for several other important distributed computing problems like state-machine replication and atomic broadcast. The thesis begins by making a thorough performance assessment of existing intrusion-tolerant consensus protocols, which shows that the performance bottlenecks of current solutions are in part related to their system modeling assumptions. Based on these results, the communication failure model is identified as a model that simultaneously captures the reality of wireless ad hoc networks and allows the design of efficient protocols. Unfortunately, the model is subject to an impossibility result stating that there is no deterministic algorithm that allows n nodes to reach agreement if more than n2 omission transmission failures can occur in a communication step. This result is valid even under strict timing assumptions (i.e., a synchronous system). The thesis applies randomization techniques in increasingly weaker variants of this model, until an efficient intrusion-tolerant consensus protocol is achieved. The first variant simplifies the problem by restricting the number of nodes that may be at the source of a transmission failure at each communication step. An algorithm is designed that tolerates f dynamic nodes at the source of faulty transmissions in a system with a total of n 3f + 1 nodes. The second variant imposes no restrictions on the pattern of transmission failures. The proposed algorithm effectively circumvents the Santoro- Widmayer impossibility result for the first time. It allows k out of n nodes to decide despite dn 2 e(nk)+k2 omission failures per communication step. This algorithm also has the interesting property of guaranteeing safety during arbitrary periods of unrestricted message loss. The final variant shares the same properties of the previous one, but relaxes the model in the sense that the system is asynchronous and that a static subset of nodes may be malicious. The obtained algorithm, called Turquois, admits f < n 3 malicious nodes, and ensures progress in communication steps where dnf 2 e(n k f) + k 2. The algorithm is subject to a comparative performance evaluation against other intrusiontolerant protocols. The results show that, as the system scales, Turquois outperforms the other protocols by more than an order of magnitude.Esta tese investiga o problema do consenso tolerante a faltas acidentais e maliciosas em redes ad hoc sem fios. Trata-se de um problema fundamental que captura a essência da coordenação em actividades envolvendo vários nós de um sistema, sendo um bloco construtor de outros importantes problemas dos sistemas distribuídos como a replicação de máquina de estados ou a difusão atómica. A tese começa por efectuar uma avaliação de desempenho a protocolos tolerantes a intrusões já existentes na literatura. Os resultados mostram que as limitações de desempenho das soluções existentes estão em parte relacionadas com o seu modelo de sistema. Baseado nestes resultados, é identificado o modelo de falhas de comunicação como um modelo que simultaneamente permite capturar o ambiente das redes ad hoc sem fios e projectar protocolos eficientes. Todavia, o modelo é restrito por um resultado de impossibilidade que afirma não existir algoritmo algum que permita a n nós chegaram a acordo num sistema que admita mais do que n2 transmissões omissas num dado passo de comunicação. Este resultado é válido mesmo sob fortes hipóteses temporais (i.e., em sistemas síncronos) A tese aplica técnicas de aleatoriedade em variantes progressivamente mais fracas do modelo até ser alcançado um protocolo eficiente e tolerante a intrusões. A primeira variante do modelo, de forma a simplificar o problema, restringe o número de nós que estão na origem de transmissões faltosas. É apresentado um algoritmo que tolera f nós dinâmicos na origem de transmissões faltosas em sistemas com um total de n 3f + 1 nós. A segunda variante do modelo não impõe quaisquer restrições no padrão de transmissões faltosas. É apresentado um algoritmo que contorna efectivamente o resultado de impossibilidade Santoro-Widmayer pela primeira vez e que permite a k de n nós efectuarem progresso nos passos de comunicação em que o número de transmissões omissas seja dn 2 e(n k) + k 2. O algoritmo possui ainda a interessante propriedade de tolerar períodos arbitrários em que o número de transmissões omissas seja superior a . A última variante do modelo partilha das mesmas características da variante anterior, mas com pressupostos mais fracos sobre o sistema. Em particular, assume-se que o sistema é assíncrono e que um subconjunto estático dos nós pode ser malicioso. O algoritmo apresentado, denominado Turquois, admite f < n 3 nós maliciosos e assegura progresso nos passos de comunicação em que dnf 2 e(n k f) + k 2. O algoritmo é sujeito a uma análise de desempenho comparativa com outros protocolos na literatura. Os resultados demonstram que, à medida que o número de nós no sistema aumenta, o desempenho do protocolo Turquois ultrapassa os restantes em mais do que uma ordem de magnitude.FC

Stochastic Network Design: Models and Scalable Algorithms

Many natural and social phenomena occur in networks. Examples include the spread of information, ideas, and opinions through a social network, the propagation of an infectious disease among people, and the spread of species within an interconnected habitat network. The ability to modify a phenomenon towards some desired outcomes has widely recognized benefits to our society and the economy. The outcome of a phenomenon is largely determined by the topology or properties of its underlying network. A decision maker can take management actions to modify a network and, therefore, change the outcome of the phenomenon. A management action is an activity that changes the topology or other properties of a network. For example, species that live in a small area may expand their population and gradually spread into an interconnected habitat network. However, human development of various structures such as highways and factories may destroy natural habitats or block paths connecting different habitat patches, which results in a population decline. To facilitate the dispersal of species and help the population recover, artificial corridors (e.g., a wildlife highway crossing) can be built to restore connectivity of isolated habitats, and conservation areas can be established to restore historical habitats of species, both of which are examples of management actions. The set of management actions that can be taken is restricted by a budget, so we must find cost-effective allocations of limited funding resources. In the thesis, the problem of finding the (nearly) optimal set of management actions is formulated as a discrete and stochastic optimization problem. Specifically, a general decision-making framework called stochastic network design is defined to model a broad range of similar real-world problems. The framework is defined upon a stochastic network, in which edges are either present or absent with certain probabilities. It defines several metrics to measure the outcome of the underlying phenomenon and a set of management actions that modify the network or its parameters in specific ways. The goal is to select a subset of management actions, subject to a budget constraint, to maximize a specified metric. The major contribution of the thesis is to develop scalable algorithms to find high- quality solutions for different problems within the framework. In general, these problems are NP-hard, and their objective functions are neither submodular nor super-modular. Existing algorithms, such as greedy algorithms and heuristic search algorithms, either lack theoretical guarantees or have limited scalability. In the thesis, fast approximate algorithms are developed under three different settings that are gradually more general. The most restricted setting is when a network is tree-structured. For this case, fully polynomial-time approximation schemes (FPTAS) are developed using dynamic programming algorithms and rounding techniques. A more general setting is when networks are general directed graphs. We use a sampling technique to convert the original stochastic optimization problem into a deterministic optimization problem and develop a primal-dual algorithm to solve it efficiently. In the previous two problem settings, the goal is to maximize connectivity of networks. In the most general setting, the goal is to maximize the number of nodes being connected and minimize the distance between these connected nodes. For example, we do not only want the species to reach a large number of habitat areas but also want them to be able to get there within a reasonable amount of time. The scalable algorithms for this setting combine a fast primal-dual algorithm and a sampling procedure. Three real-world problems from the areas of computational sustainability and emergency response are used to evaluate these algorithms. They are the barrier removal problem aimed to determine which instream barriers to remove to help fish access their historical habitats in a river network, the spatial conservation planning problem to determine which habitat units to set as conservation areas to encourage the dispersal of endangered species in a landscape, and the pre-disaster preparation problem aimed to minimize the disruption of emergency medical services by natural disasters. In these three problems, the developed algorithms are much more scalable than the existing state-of-the-arts and produce high-quality solutions

Human mobility: Models and applications

This is the author accepted manuscript. The final version is available from the publisher via the DOI in this recordRecent years have witnessed an explosion of extensive geolocated datasets related to human movement, enabling scientists to quantitatively study individual and collective mobility patterns, and to generate models that can capture and reproduce the spatiotemporal structures and regularities in human trajectories. The study of human mobility is especially important for applications such as estimating migratory flows, traffic forecasting, urban planning, and epidemic modeling. In this survey, we review the approaches developed to reproduce various mobility patterns, with the main focus on recent developments. This review can be used both as an introduction to the fundamental modeling principles of human mobility, and as a collection of technical methods applicable to specific mobility-related problems. The review organizes the subject by differentiating between individual and population mobility and also between short-range and long-range mobility. Throughout the text the description of the theory is intertwined with real-world applications.US Army Research Offic

Human mobility:Models and applications

Recent years have witnessed an explosion of extensive geolocated datasets related to human movement, enabling scientists to quantitatively study individual and collective mobility patterns, and to generate models that can capture and reproduce the spatiotemporal structures and regularities in human trajectories. The study of human mobility is especially important for applications such as estimating migratory flows, traffic forecasting, urban planning, and epidemic modeling. In this survey, we review the approaches developed to reproduce various mobility patterns, with the main focus on recent developments. This review can be used both as an introduction to the fundamental modeling principles of human mobility, and as a collection of technical methods applicable to specific mobility-related problems. The review organizes the subject by differentiating between individual and population mobility and also between short-range and long-range mobility. Throughout the text the description of the theory is intertwined with real-world applications.Comment: 126 pages, 45+ figure