Metaheurísticas, optimización multiobjetivo y paralelismo para descubrir motifs en secuencias de ADN

La resolución de problemas complejos mediante técnicas evolutivas es uno de los aspectos más investigados en Informática. El objetivo principal de esta tesis doctoral es desarrollar nuevos algoritmos capaces de resolver estos problemas con el menor tiempo computacional posible, mejorando la calidad de los resultados obtenidos por los métodos ya existentes. Para ello, combinamos tres conceptos importantes: metaheurísticas, optimización multiobjetivo y paralelismo. Con este fin, primero buscamos un problema de optimización importante que aún no fuese resuelto de forma eficiente y encontramos el Problema del Descubrimiento de Motifs (PDM). El PDM tiene como objetivo descubrir pequeños patrones repetidos (motifs) en conjuntos de secuencias de ADN que puedan poseer cierto significado biológico. Para abordarlo, definimos una formulación multiobjetivo adecuada a los requerimientos del mundo real, implementamos un total de diez algoritmos de distinta naturaleza (población, trayectoria, inteligencia colectiva...), analizando aspectos como la capacidad de escalar y converger. Finalmente, diseñamos diversas técnicas paralelas, haciendo uso de entornos de programación como OpenMP y MPI, que tratan de combinar las propiedades de varias metaheurísticas en una única aplicación. Los resultados obtenidos son estudiados en detalle a través de la aplicación de numerosos test estadísticos, y las predicciones son comparadas con las descubiertas por un total de trece herramientas biológicas bien conocidas en la literatura. Las conclusiones obtenidas demuestran que la utilización de la optimización multiobjetivo en técnicas metaheurísticas favorece el descubrimiento de soluciones de calidad y que el paralelismo es útil para combinar las propiedades evolutivas de diferentes algoritmos.The resolution of complex problems by using evolutionary algorithms is one of the most researched issues in Computer Science. The main goal of this thesis is directly related with the development of new algorithms that can solve this kind of problems with the least possible computational time, improving the results achieved by the existing methods. To this end, we combine three important concepts: metaheuristics, multiobjective optimization, and parallelism. For doing this, we first look for a significant optimization problem that had not been solved in an efficient way and we find the Motif Discovery Problem (MDP). MDP aims to discover over-represented short patterns (motifs) in a set of DNA sequences that may have some biological significance. To address it, we defined a multiobjective formulation adjusted to the real-world biological requirements, we implemented a total of ten algorithms of different nature (population, trajectory, collective intelligence...), analyzing aspects such as the ability to scale and converge. Finally, we designed parallel techniques, by using parallel and distributed programming environments as OpenMP and MPI, which try to combine the properties of several metaheuristics in a single application. The obtained results are discussed in detail through numerous statistical tests, and the achieved predictions are compared with those discovered by a total of thirteen well-known biological tools. The drawn conclusions demonstrate that using multiobjective optimization in metaheuristic techniques favors the discovery of quality solutions, and that parallelism is useful for combining the properties of different evolutionary algorithms.Ministerio de Economía y Competitividad - FEDER (TIN2008-06491-C04-04; TIN2012-30685) Gobierno de Extremadura (GR10025-TIC015

LIPIcs, Volume 274, ESA 2023, Complete Volume

LIPIcs, Volume 274, ESA 2023, Complete Volum

Multi-level characterization and information extraction in directed and node-labeled functional brain networks

Current research in computational neuroscience puts great emphasis on the computation and analysis of the functional connectivity of the brain. The methodological developments presented in this work are concerned with a group-specific comprehensive analysis of networks that represent functional interaction patterns. Four application studies are presented, in which functional brain network samples of different clinical background were analyzed in different ways, using combinations of established approaches and own methodological developments. Study I is concerned with a sample-specific decomposition of the functional brain networks of depressed subjects and healthy controls into small functionally important and recurring subnetworks (motifs) using own developments. Study II investigates whether lithium treatment effects are reflected in the functional brain networks of HIV-positive subjects with diagnosed cognitive impairment. For it, microscopic and macroscopic structural properties were analyzed. Study III explores spatially highly resolved functional brain networks with regard to a functional segmentation given by identified module (community) structure. Also, ground truth networks with known module structure were generated using own methodological developments. They formed the basis of a comprehensive simulation study that quantified module structure quality and preservation in order to evaluate the effects of a novel approach for the identification of connectivity (lsGCI). Study IV tracks the time-evolution of module structure and introduces a newly developed own approach for the determination of edge weight thresholds based on multicriteria optimization. The methodological challenges that underly these different topological analyses, but also the various opportunities to gain an improved understanding of neural information processing among brain areas were highlighted by this work and the presented results

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

Statistical Analysis of Networks

This book is a general introduction to the statistical analysis of networks, and can serve both as a research monograph and as a textbook. Numerous fundamental tools and concepts needed for the analysis of networks are presented, such as network modeling, community detection, graph-based semi-supervised learning and sampling in networks. The description of these concepts is self-contained, with both theoretical justifications and applications provided for the presented algorithms. Researchers, including postgraduate students, working in the area of network science, complex network analysis, or social network analysis, will find up-to-date statistical methods relevant to their research tasks. This book can also serve as textbook material for courses related to the statistical approach to the analysis of complex networks. In general, the chapters are fairly independent and self-supporting, and the book could be used for course composition “à la carte”. Nevertheless, Chapter 2 is needed to a certain degree for all parts of the book. It is also recommended to read Chapter 4 before reading Chapters 5 and 6, but this is not absolutely necessary. Reading Chapter 3 can also be helpful before reading Chapters 5 and 7. As prerequisites for reading this book, a basic knowledge in probability, linear algebra and elementary notions of graph theory is advised. Appendices describing required notions from the above mentioned disciplines have been added to help readers gain further understanding

Artificial Superintelligence: Coordination & Strategy

Attention in the AI safety community has increasingly started to include strategic considerations of coordination between relevant actors in the field of AI and AI safety, in addition to the steadily growing work on the technical considerations of building safe AI systems. This shift has several reasons: Multiplier effects, pragmatism, and urgency. Given the benefits of coordination between those working towards safe superintelligence, this book surveys promising research in this emerging field regarding AI safety. On a meta-level, the hope is that this book can serve as a map to inform those working in the field of AI coordination about other promising efforts. While this book focuses on AI safety coordination, coordination is important to most other known existential risks (e.g., biotechnology risks), and future, human-made existential risks. Thus, while most coordination strategies in this book are specific to superintelligence, we hope that some insights yield “collateral benefits” for the reduction of other existential risks, by creating an overall civilizational framework that increases robustness, resiliency, and antifragility

Incentive-driven QoS in peer-to-peer overlays

A well known problem in peer-to-peer overlays is that no single entity has control over the software, hardware and configuration of peers. Thus, each peer can selfishly adapt its behaviour to maximise its benefit from the overlay. This thesis is concerned with the modelling and design of incentive mechanisms for QoS-overlays: resource allocation protocols that provide strategic peers with participation incentives, while at the same time optimising the performance of the peer-to-peer distribution overlay. The contributions of this thesis are as follows. First, we present PledgeRoute, a novel contribution accounting system that can be used, along with a set of reciprocity policies, as an incentive mechanism to encourage peers to contribute resources even when users are not actively consuming overlay services. This mechanism uses a decentralised credit network, is resilient to sybil attacks, and allows peers to achieve time and space deferred contribution reciprocity. Then, we present a novel, QoS-aware resource allocation model based on Vickrey auctions that uses PledgeRoute as a substrate. It acts as an incentive mechanism by providing efficient overlay construction, while at the same time allocating increasing service quality to those peers that contribute more to the network. The model is then applied to lagsensitive chunk swarming, and some of its properties are explored for different peer delay distributions. When considering QoS overlays deployed over the best-effort Internet, the quality received by a client cannot be adjudicated completely to either its serving peer or the intervening network between them. By drawing parallels between this situation and well-known hidden action situations in microeconomics, we propose a novel scheme to ensure adherence to advertised QoS levels. We then apply it to delay-sensitive chunk distribution overlays and present the optimal contract payments required, along with a method for QoS contract enforcement through reciprocative strategies. We also present a probabilistic model for application-layer delay as a function of the prevailing network conditions. Finally, we address the incentives of managed overlays, and the prediction of their behaviour. We propose two novel models of multihoming managed overlay incentives in which overlays can freely allocate their traffic flows between different ISPs. One is obtained by optimising an overlay utility function with desired properties, while the other is designed for data-driven least-squares fitting of the cross elasticity of demand. This last model is then used to solve for ISP profit maximisation

Talk Derby to Me: Intellectual Property Norms Governing Roller Derby Pseudonyms

Some groups use endemic social norms rather than formal law to regulate their intellectual property (IP). This qualitative empirical study extends and critiques existing work on this topic by examining how roller derby skaters guarantee exclusive use of the pseudonyms under which they compete. Roller derby names are a central part of this countercultural, all-girl sport, adding to its distinctive combination of punk and camp. Skaters have developed an elaborate rule structure, registration system, and governance regime to protect the uniqueness of their pseudonyms. The development of this extralegal governance scheme despite the ready availability of IP theories (e.g., trademark, right of publicity) to protect derby names shows that IP norms emerge independently of law's substantive (un)availability, so long as the relevant group is close-knit and the norms are welfare enhancing. These groups are especially likely to craft formal regulation and registration schemes to buttress informal norms where the relevant community is identity constitutive and where the intangible goods arise from nonmarket production. This study also suggests another way of thinking about the problem of supplying property systems, casts (further) doubt on the coherence of the prevailing neoclassical economic assumptions underlying IP law, and reflects on what it means for rules to be law

Statistical Analysis of Networks

This book is a general introduction to the statistical analysis of networks, and can serve both as a research monograph and as a textbook. Numerous fundamental tools and concepts needed for the analysis of networks are presented, such as network modeling, community detection, graph-based semi-supervised learning and sampling in networks. The description of these concepts is self-contained, with both theoretical justifications and applications provided for the presented algorithms. Researchers, including postgraduate students, working in the area of network science, complex network analysis, or social network analysis, will find up-to-date statistical methods relevant to their research tasks. This book can also serve as textbook material for courses related to the statistical approach to the analysis of complex networks. In general, the chapters are fairly independent and self-supporting, and the book could be used for course composition “à la carte”. Nevertheless, Chapter 2 is needed to a certain degree for all parts of the book. It is also recommended to read Chapter 4 before reading Chapters 5 and 6, but this is not absolutely necessary. Reading Chapter 3 can also be helpful before reading Chapters 5 and 7. As prerequisites for reading this book, a basic knowledge in probability, linear algebra and elementary notions of graph theory is advised. Appendices describing required notions from the above mentioned disciplines have been added to help readers gain further understanding

1992-1993 Catalog

This catalog lists available courses for the 1992-1993 term. The College Catalog is a document of record issued in September 1992. The Catalog contains current information regarding the College calendar, admissions, degree requirements, fees, regulations and course offerings.https://crossworks.holycross.edu/course_catalog/1107/thumbnail.jp