Discovering Functional Communities in Dynamical Networks

Many networks are important because they are substrates for dynamical systems, and their pattern of functional connectivity can itself be dynamic -- they can functionally reorganize, even if their underlying anatomical structure remains fixed. However, the recent rapid progress in discovering the community structure of networks has overwhelmingly focused on that constant anatomical connectivity. In this paper, we lay out the problem of discovering_functional communities_, and describe an approach to doing so. This method combines recent work on measuring information sharing across stochastic networks with an existing and successful community-discovery algorithm for weighted networks. We illustrate it with an application to a large biophysical model of the transition from beta to gamma rhythms in the hippocampus.Comment: 18 pages, 4 figures, Springer "Lecture Notes in Computer Science" style. Forthcoming in the proceedings of the workshop "Statistical Network Analysis: Models, Issues and New Directions", at ICML 2006. Version 2: small clarifications, typo corrections, added referenc

A modular modelling framework for hypotheses testing in the simulation of urbanisation

In this paper, we present a modelling experiment developed to study systems of cities and processes of urbanisation in large territories over long time spans. Building on geographical theories of urban evolution, we rely on agent-based models to 1/ formalise complementary and alternative hypotheses of urbanisation and 2/ explore their ability to simulate observed patterns in a virtual laboratory. The paper is therefore divided into two sections : an overview of the mechanisms implemented to represent competing hypotheses used to simulate urban evolution; and an evaluation of the resulting model structures in their ability to simulate - efficiently and parsimoniously - a system of cities (the Former Soviet Union) over several periods of time (before and after the crash of the USSR). We do so using a modular framework of model-building and evolutionary algorithms for the calibration of several model structures. This project aims at tackling equifinality in systems dynamics by confronting different mechanisms with similar evaluation criteria. It enables the identification of the best-performing models with respect to the chosen criteria by scanning automatically the parameter along with the space of model structures (as combinations of modelled dynamics).Comment: 21 pages, 3 figures, working pape

A Semantic Consistency Model to Reduce Coordination in Replicated Systems

Large-scale distributed applications need to be available and responsive to satisfy millions of users, which can be achieved by having data geo-replicated in multiple replicas. However, a partitioned system cannot sustain availability and consistency at fully. The usage of weak consistency models might lead to data integrity violations, triggered by problematic concurrent updates, such as selling twice the last ticket on a flight company service. To overcome possible conflicts, programmers might opt to apply strong consistency, which guarantees a total order between operations, while preserving data integrity. Nevertheless, the illusion of being a non-replicated system affects its availability. In contrast, weaker notions might be used, such as eventual consistency, that boosts responsiveness, as operations are executed directly at the source replica and their effects are propagated to remote replicas in the background. However, this approach might put data integrity at risk. Current protocols that preserve invariants rely on, at least, causal consistency, a consistency model that maintains causal dependencies between operations. In this dissertation, we propose a protocol that includes a semantic consistency model. This consistency model stands between eventual consistency and causal consistency. We guarantee better performance comparing with causal consistency, and ensure data integrity. Through semantic analysis, relying on the static analysis tool CISE3, we manage to limit the maximum number of dependencies that each operation will have. To support the protocol, we developed a communication algorithm in a cluster. Additionally, we present an architecture that uses Akka, an actor-based middleware in which actors communicate by exchanging messages. This architecture adopts the publish/subscribe pattern and includes data persistence. We also consider the stability of operations, as well as a dynamic cluster environment, ensuring the convergence of the replicated state. Finally, we perform an experimental evaluation regarding the performance of the algorithm using standard case studies. The evaluation confirms that by relying on semantic analysis, the system requires less coordination between the replicas than causal consistency, ensuring data integrity.Aplicações distribuídas em larga escala necessitam de estar disponíveis e de serem responsivas para satisfazer milhões de utilizadores, o que pode ser alcançado através da geo-replicação dos dados em múltiplas réplicas. No entanto, um sistema particionado não consegue garantir disponibilidade e consistência na sua totalidade. O uso de modelos de consistência fraca pode levar a violações da integridade dos dados, originadas por escritas concorrentes problemáticas. Para superar possíveis conflitos, os programadores podem optar por aplicar modelos de consistência forte, originando uma ordem total das operações, assegurando a integridade dos dados. Em contrapartida, podem ser utilizadas noções mais fracas, como a consistência eventual, que aumenta a capacidade de resposta, uma vez que as operações são executadas diretamente na réplica de origem e os seus efeitos são propagados para réplicas remotas. No entanto, esta abordagem pode colocar em risco a integridade dos dados. Os protocolos existentes que preservam as invariantes dependem, pelo menos, da consistência causal, um modelo de consistência que mantém as dependências causais entre operações. Nesta dissertação propomos um protocolo que inclui um modelo de consistência semântica. Este modelo situa-se entre a consistência eventual e a consistência causal. Garantimos um melhor desempenho em comparação com a consistência causal, e asseguramos a integridade dos dados. Através de uma análise semântica, obtida através da ferramenta de análise estática CISE3, conseguimos limitar o número de dependências de cada operação. Para suportar o protocolo, desenvolvemos um algoritmo de comunicação entre um aglomerado de réplicas. Adicionalmente, apresentamos uma arquitetura que utiliza Akka, um middleware baseado em atores que trocam mensagens entre si. Esta arquitetura utiliza o padrão publish/subscribe e inclui a persistência dos dados. Consideramos também a estabilidade das operações, bem como um ambiente dinâmico de réplicas, assegurando a convergência do estado. Por último, apresentamos a avaliação do desempenho do algoritmo desenvolvido, que confirma que a análise semântica das operações requer menos coordenação entre as réplicas que a consistência causal

CATS: linearizability and partition tolerance in scalable and self-organizing key-value stores

Distributed key-value stores provide scalable, fault-tolerant, and self-organizing storage services, but fall short of guaranteeing linearizable consistency in partially synchronous, lossy, partitionable, and dynamic networks, when data is distributed and replicated automatically by the principle of consistent hashing. This paper introduces consistent quorums as a solution for achieving atomic consistency. We present the design and implementation of CATS, a distributed key-value store which uses consistent quorums to guarantee linearizability and partition tolerance in such adverse and dynamic network conditions. CATS is scalable, elastic, and self-organizing; key properties for modern cloud storage middleware. Our system shows that consistency can be achieved with practical performance and modest throughput overhead (5%) for read-intensive workloads

Khazana: a flexible wide area data store

technical reportKhazana is a peer-to-peer data service that supports efficient sharing and aggressive caching of mutable data across the wide area while giving clients significant control over replica divergence. Previous work on wide-area replicated services focussed on at most two of the following three properties: aggressive replication, customizable consistency, and generality. In contrast, Khazana provides scalable support for large numbers of replicas while giving applications considerable flexibility in trading off consistency for availability and performance. Its flexibility enables applications to effectively exploit inherent data locality while meeting consistency needs. Khazana exports a file system-like interface with a small set of consistency controls which can be combined to yield a broad spectrum of consistency flavors ranging from strong consistency to best-effort eventual consistency. Khazana servers form failure-resilient dynamic replica hierarchies to manage replicas across variable quality network links. In this report, we outline Khazana?s design and show how its flexibility enables three diverse network services built on top of it to meet their individual consistency and performance needs: (i) a wide-area replicated file system that supports serializable writes as well as traditional file sharing across wide area, (ii) an enterprise data service that exploits locality by caching enterprise data closer to end-users while ensuring strong consistency for data integrity, and (iii) a replicated database that reaps order of magnitude gains in throughput by relaxing consistency

Creativity and the Brain

Neurocognitive approach to higher cognitive functions that bridges the gap between psychological and neural level of description is introduced. Relevant facts about the brain, working memory and representation of symbols in the brain are summarized. Putative brain processes responsible for problem solving, intuition, skill learning and automatization are described. The role of non-dominant brain hemisphere in solving problems requiring insight is conjectured. Two factors seem to be essential for creativity: imagination constrained by experience, and filtering that selects most interesting solutions. Experiments with paired words association are analyzed in details and evidence for stochastic resonance effects is found. Brain activity in the process of invention of novel words is proposed as the simplest way to understand creativity using experimental and computational means. Perspectives on computational models of creativity are discussed

Feedback Control as a Framework for Understanding Tradeoffs in Biology

Control theory arose from a need to control synthetic systems. From regulating steam engines to tuning radios to devices capable of autonomous movement, it provided a formal mathematical basis for understanding the role of feedback in the stability (or change) of dynamical systems. It provides a framework for understanding any system with feedback regulation, including biological ones such as regulatory gene networks, cellular metabolic systems, sensorimotor dynamics of moving animals, and even ecological or evolutionary dynamics of organisms and populations. Here we focus on four case studies of the sensorimotor dynamics of animals, each of which involves the application of principles from control theory to probe stability and feedback in an organism's response to perturbations. We use examples from aquatic (electric fish station keeping and jamming avoidance), terrestrial (cockroach wall following) and aerial environments (flight control in moths) to highlight how one can use control theory to understand how feedback mechanisms interact with the physical dynamics of animals to determine their stability and response to sensory inputs and perturbations. Each case study is cast as a control problem with sensory input, neural processing, and motor dynamics, the output of which feeds back to the sensory inputs. Collectively, the interaction of these systems in a closed loop determines the behavior of the entire system.Comment: Submitted to Integr Comp Bio