Efficient Execution of Sequential Instructions Streams by Physical Machines

Any computational model which relies on a physical system is likely to be subject to the fact that information density and speed have intrinsic, ultimate limits. The RAM model, and in particular the underlying assumption that memory accesses can be carried out in time independent from memory size itself, is not physically implementable. This work has developed in the field of limiting technology machines, in which it is somewhat provocatively assumed that technology has achieved the physical limits. The ultimate goal for this is to tackle the problem of the intrinsic latencies of physical systems by encouraging scalable organizations for processors and memories. An algorithmic study is presented, which depicts the implementation of high concurrency programs for SP and SPE, sequential machine models able to compute direct-flow programs in optimal time. Then, a novel pieplined, hierarchical memory organization is presented, with optimal latency and bandwidth for a physical system. In order to both take full advantage of the memory capabilities and exploit the available instruction level parallelism of the code to be executed, a novel processor model is developed. Particular care is put in devising an efficient information flow within the processor itself. Both designs are extremely scalable, as they are based on fixed capacity and fixed size nodes, which are connected as a multidimensional array. Performance analysis on the resulting machine design has led to the discovery that latencies internal to the processor can be the dominating source of complexity in instruction flow execution, which adds to the effects of processor-memory interaction. A characterization of instruction flows is then developed, which is based on the topology induced by instruction dependences

Improving the accuracy and realism of Bayesian phylogenetic analyses

textCentral to the study of Life is knowledge both about the underlying relationships among living things and the processes that have molded them into their diverse forms. Phylogenetics provides a powerful toolkit for investigating both aspects. Bayesian phylogenetics has gained much popularity, due to its readily interpretable notion of probability. However, the posterior probability of a phylogeny, as well as any dependent biological inferences, is conditioned on the assumed model of evolution and its priors, necessitating care in model formulation. In Chapter 1, I outline the Bayesian perspective of phylogenetic inference and provide my view on its most outstanding questions. I then present results from three studies that aim to (i) improve the accuracy of Bayesian phylogenetic inference and (ii) assess when the model assumed in a Bayesian analysis is insufficient to produce an accurate phylogenetic estimate. As phylogenetic data sets increase in size, they must also accommodate a greater diversity of underlying evolutionary processes. Partitioned models represent one way of accounting for this heterogeneity. In Chapter 2, I describe a simulation study to investigate whether support for partitioning of empirical data sets represents a real signal of heterogeneity or whether it is merely a statistical artifact. The results suggest that empirical data are extremely heterogeneous. The incorporation of heterogeneity into inferential models is important for accurate phylogenetic inference. Bayesian phylogenetic estimates of branch lengths are often wildly unreasonable. However, branch lengths are important input for many other analyses. In Chapter 3, I study the occurrence of this phenomenon, identify the data sets most likely to be affected, demonstrate the causes of the bias, and suggest several solutions to avoid inaccurate inferences. Phylogeneticists rarely assess absolute fit between an assumed model of evolution and the data being analyzed. While an approach to assessing fit in a Bayesian framework has been proposed, it sometimes performs quite poorly in predicting a model’s phylogenetic utility. In Chapter 4, I propose and evaluate new test statistics for assessing phylogenetic model adequacy, which directly evaluate a model’s phylogenetic performance.Biological Sciences, School o

Channel routing: Efficient solutions using neural networks

Neural network architectures are effectively applied to solve the channel routing problem. Algorithms for both two-layer and multilayer channel-width minimization, and constrained via minimization are proposed and implemented. Experimental results show that the proposed channel-width minimization algorithms are much superior in all respects compared to existing algorithms. The optimal two-layer solutions to most of the benchmark problems, not previously obtained, are obtained for the first time, including an optimal solution to the famous Deutch\u27s difficult problem. The optimal solution in four-layers for one of the be lchmark problems, not previously obtained, is obtained for the first time. Both convergence rate and the speed with which the simulations are executed are outstanding. A neural network solution to the constrained via minimization problem is also presented. In addition, a fast and simple linear-time algorithm is presented, possibly for the first time, for coloring of vertices of an interval graph, provided the line intervals are given

Decision Support Algorithms for Sectorization of Water Distribution Networks

Many water utilities, especially ones in developing countries, continue to operate low efficient water distribution networks (WDNs) and are consequently faced with significant amount of water (e.g. leakage) and revenue losses (i.e. non-revenue water – NRW). First step in reducing the NRW is assessment of water balance in WDN aimed to establish the baseline level of water losses. Then, water utilities can plan NRW reduction activities according to this baseline. Sectorization of WDN into District Metered Areas (DMAs) is the most cost-effective strategy used for active leakage (i.e. water loss) control, achieved by monitoring the flow data on DMAs’ boundaries. Sectorization of WDN has to be designed carefully, as required network interventions can endanger network’s water supply and pressure distribution. In this thesis new methods and algorithms, aimed to support making more effective and objective decisions regarding the WDN sectorization procedure, are presented, tested and validated. Presented methods and algorithms are part of proposed decision support methodology compensating for disadvantages in available methods, valuable to practicing engineers commencing implementation of sectorization strategy in WDN. Main sectorization objective adopted in methodology presented in this thesis is to design layout of DMAs that will allow efficient tracking of water balance in the network. Least investment for field implementation and maintaining the same level of WDN’s operational efficiency are adopted as main design criteria. New sectorization algorithm, named DeNSE (Distribution Network SEctorization), is developed and presented, adopting above-named objective and design criteria. DeNSE algorithm utilizes newly developed uniformity index which drives the sectorization process and identifies clusters. New engineering heuristic is developed and used for placing the flow-meters and isolation valves on clusters’ boundary edges, making them DMAs. Post sectorization operational efficiency of WDN is evaluated using adopted performance indicators (PIs). Top-down approach to hierarchical sectorization of WDN, particulary convenient for water utilities constrained with limited funding and insufficient reliable input data, is also implemented in DeNSE algorithm. New method for hydraulic simulation, named TRIBAL-DQ is developed to address the issue of low computational efficiency, recognized in available sectorization methodologies employing optimization. TRIBAL-DQ is a loop-flow based method which combines the novel TRIangulation Based ALgorithm (TRIBAL) for loop identification with efficient implementation of the loop-flow hydraulic solver (DQ). TRIBAL-DQ method is tested on various networks of different complexities and topologies. This thesis reports only results of testing on literature benchmark networks, used to validate methods’ performance. TRIBAL-DQ method based hydraulic solver is compared to the node based solver implemented in EPANET, most prominent software for hydraulic calculation of WDN. New TRIBAL-DQ solver showed significant dominance in computational efficiency, with stable numerical performance and same level of prediction accuracy. DeNSE algorithm is benchmarked against other available sectorization methodologies on real-sized WDN. Obtained results demonstrate the ability of DeNSE algorithm to identify good set of feasible solutions, without worsening operational status of the WDN compared to its baseline condition. Reported computational efficiency of the algorithm is one of its strong points, as it allows generation of feasible solutions for large WDN in reasonable time. In this field, algorithm particularly outperforms methods employing multi-objective optimization (e.g. minutes compared to hours).Комунална предузећа која управљају водоводним системима, нарочита она у земљама у развоју, суочена су са проблемима дотрајале и лоше одржаване дистрибутивне мрже који за последицу имају значајне количине воде која се губи у дистрибуцији. Први корак ка смањењу губитака у водоводном систему је процена водног биланса у дистрибутивној мрежи како би се утврдило почетно стање система, а затим и приступило планирању и предузимању мера за смањење губитака како би се то стање поправило. Најисплативија, и опште прихваћена, стратегија за остваривање овог циља је подела дистрибутивне мреже, односно њена секторизација, на тзв. основне зоне билансирања (ОЗБ). ОЗБ се у мрежи успостављају јасним дефинисањем њихових граница, на којима се инсталирају изолациони затварачи и мерачи протока. Избор ОЗБ није једнозначан, и приликом њиховог дефинисања мора се водити рачуна о планираним интервенцијама у мрежи које могу имати негативан утицај на водоснабдевање потрошача и распоред притисака у мрежи. У овој дисератацији су приказане и тестиране нове методе и алгоритми намењени за подршку одлучивању приликом секторизације водоводне дистрибутивне мреже на ОЗБ. Презентоване методе и алгоритми надомешћују недостатке постојећих метода и могу бити од користи инжењерима који се у пракси баве задатком секторизације дистрибутивних мрежа. Основни циљ методологије за секторизацију приказане у овој дисертацији је дефинисање распореда ОЗБ који ће омогућити ефикасно праћење водног биланса у дистрибутивној мрежи. Основни критеријуми за вредновање и избор оптималног решења су минимална улагања у неопходне интервенције у мрежи и очување поузданости система. У дисертацији је приказан нови алгоритам за секторизацију водоводне мреже, назван DeNSE (Distribution Network SEctorization), заснован на претходно наведеном основном циљу и критеријумима. Секторизација применом DeNSE алгоритма је базирана на употреби новог индекса униформности мреже, који омогућава идентификацију зона у мрежи уједначених према потрошњи. За дефинисање ОЗБ, на границе претходно идентификованих зона потребно је поставити мераче протока и изолационе затвараче. За ове потребе развијена је и приказана методлогија засновна на практичним инжењерским принципима. За процену поузданости система након секторизације коришћени су усвојени индикатори перформанси (PIs – Performance Indicators). Предвиђена је и могућност за хијерархијску секторизацију дистрибутивне мреже, нарочито привлачна за комунална предузећа која располажу ограниченим финансијским средствима и имају потребу да процес секторизације изведу у неколико фаза. Услед проблема са значајним рачунарским временом који имају постојеће методе за секторизацију које користе оптимизацију, у оквиру истраживања је развијен и нови метод за хидраулички прорачун мрежа под притиском, назван TRIBAL-DQ. TRIBAL-DQ метод је заснован на примени новог алгоритма за идентификацију прстенова у мрежи базираног на триангулацији (TRIBAL – TRIangulation Based ALgorithm) и ефикасној имплементацији нумеричког модела хидрауличког прорачуна базираног на методи прстенова (DQ). TRIBAL-DQ метод је тестиран на бројним дистрибутивним мрежама различите сложености. У овој дисертацији су приказани само резултати добијени применом на тест-мрежама познатим из литературе, како би се потврдила њихова ваљаност. TRIBAL-DQ метод је упоређен са методом коју користи најпознатији софтвер за хидраулички прорачун мрежа под притиском – EPANET. Резултати приказују значајну предност новог метода у погледу рачунарске ефикаснонсти, уз очување нумеричке стабилности и тачности решења хидрауличког прорачуна. DeNSE алгоритам је упоређен са постојећим методама за секторизацију дистрибутивних мрежа. Резултати потврђују да је нови алгоритам у стању да идентификује скуп могућих решења, која не угрожавају поузданост система и снабдевање потрошача. Рачунарска ефикаснонст DeNSE алгоритма је једна од његових најзначајнијих предности јер омогућава идентификацију не једног, већ скупа могућих решења за реалне дистрибутивне мреже у релативно кратком рачунарском времену. Ова чињеница посебно долази до изражаја када се рачунарско време DeNSE алгоритма упореди са рачунарским временом метода које користе оптимизационе алгоритме (минути у поређењу са сатима).Belgrade: University of Belgrade-Faculty of Civil Engineerin

Scalable Schedule-Aware Bundle Routing

This thesis introduces approaches providing scalable delay-/disruption-tolerant routing capabilities in scheduled space topologies. The solution is developed for the requirements derived from use cases built according to predictions for future space topology, like the future Mars communications architecture report from the interagency operations advisory group. A novel routing algorithm is depicted to provide optimized networking performance that discards the scalability issues inherent to state-of-the-art approaches. This thesis also proposes a new recommendation to render volume management concerns generic and easily exchangeable, including a new simple management technique increasing volume awareness accuracy while being adaptable to more particular use cases. Additionally, this thesis introduces a more robust and scalable approach for internetworking between subnetworks to increase the throughput, reduce delays, and ease configuration thanks to its high flexibility.:1 Introduction 1.1 Motivation 1.2 Problem statement 1.3 Objectives 1.4 Outline 2 Requirements 2.1 Use cases 2.2 Requirements 2.2.1 Requirement analysis 2.2.2 Requirements relative to the routing algorithm 2.2.3 Requirements relative to the volume management 2.2.4 Requirements relative to interregional routing 3 Fundamentals 3.1 Delay-/disruption-tolerant networking 3.1.1 Architecture 3.1.2 Opportunistic and deterministic DTNs 3.1.3 DTN routing 3.1.4 Contact plans 3.1.5 Volume management 3.1.6 Regions 3.2 Contact graph routing 3.2.1 A non-replication routing scheme 3.2.2 Route construction 3.2.3 Route selection 3.2.4 Enhancements and main features 3.3 Graph theory and DTN routing 3.3.1 Mapping with DTN objects 3.3.2 Shortest path algorithm 3.3.3 Edge and vertex contraction 3.4 Algorithmic determinism and predictability 4 Preliminary analysis 4.1 Node and contact graphs 4.2 Scenario 4.3 Route construction in ION-CGR 4.4 Alternative route search 4.4.1 Yen’s algorithm scalability 4.4.2 Blocking issues with Yen 4.4.3 Limiting contact approaches 4.5 CGR-multicast and shortest-path tree search 4.6 Volume management 4.6.1 Volume obstruction 4.6.2 Contact sink 4.6.3 Ghost queue 4.6.4 Data rate variations 4.7 Hierarchical interregional routing 4.8 Other potential issues 5 State-of-the-art and related work 5.1 Taxonomy 5.2 Opportunistic and probabilistic approaches 5.2.1 Flooding approaches 5.2.2 PROPHET 5.2.3 MaxProp 5.2.4 Issues 5.3 Deterministic approaches 5.3.1 Movement-aware routing over interplanetary networks 5.3.2 Delay-tolerant link state routing 5.3.3 DTN routing for quasi-deterministic networks 5.3.4 Issues 5.4 CGR variants and enhancements 5.4.1 CGR alternative routing table computation 5.4.2 CGR-multicast 5.4.3 CGR extensions 5.4.4 RUCoP and CGR-hop 5.4.5 Issues 5.5 Interregional routing 5.5.1 Border gateway protocol 5.5.2 Hierarchical interregional routing 5.5.3 Issues 5.6 Further approaches 5.6.1 Machine learning approaches 5.6.2 Tropical geometry 6 Scalable schedule-aware bundle routing 6.1 Overview 6.2 Shortest-path tree routing for space networks 6.2.1 Structure 6.2.2 Tree construction 6.2.3 Tree management 6.2.4 Tree caching 6.3 Contact segmentation 6.3.1 Volume management interface 6.3.2 Simple volume manager 6.3.3 Enhanced volume manager 6.4 Contact passageways 6.4.1 Regional border definition 6.4.2 Virtual nodes 6.4.3 Pathfinding and administration 7 Evaluation 7.1 Methodology 7.1.1 Simulation tools 7.1.2 Simulator extensions 7.1.3 Algorithms and scenarios 7.2 Offline analysis 7.3 Eliminatory processing pressures 7.4 Networking performance 7.4.1 Intraregional unicast routing tests 7.4.2 Intraregional multicast tests 7.4.3 Interregional routing tests 7.4.4 Behavior with congestion 7.5 Requirement fulfillment 8 Summary and Outlook 8.1 Conclusion 8.2 Future works 8.2.1 Next development steps 8.2.2 Contact graph routin

Frustration in Biomolecules

Biomolecules are the prime information processing elements of living matter. Most of these inanimate systems are polymers that compute their structures and dynamics using as input seemingly random character strings of their sequence, following which they coalesce and perform integrated cellular functions. In large computational systems with a finite interaction-codes, the appearance of conflicting goals is inevitable. Simple conflicting forces can lead to quite complex structures and behaviors, leading to the concept of "frustration" in condensed matter. We present here some basic ideas about frustration in biomolecules and how the frustration concept leads to a better appreciation of many aspects of the architecture of biomolecules, and how structure connects to function. These ideas are simultaneously both seductively simple and perilously subtle to grasp completely. The energy landscape theory of protein folding provides a framework for quantifying frustration in large systems and has been implemented at many levels of description. We first review the notion of frustration from the areas of abstract logic and its uses in simple condensed matter systems. We discuss then how the frustration concept applies specifically to heteropolymers, testing folding landscape theory in computer simulations of protein models and in experimentally accessible systems. Studying the aspects of frustration averaged over many proteins provides ways to infer energy functions useful for reliable structure prediction. We discuss how frustration affects folding, how a large part of the biological functions of proteins are related to subtle local frustration effects and how frustration influences the appearance of metastable states, the nature of binding processes, catalysis and allosteric transitions. We hope to illustrate how Frustration is a fundamental concept in relating function to structural biology.Comment: 97 pages, 30 figure