Corridor Location: Generating Competitive and Efficient Route Alternatives

The problem of transmission line corridor location can be considered, at best, a "wicked" public systems decision problem. It requires the consideration of numerous objectives while balancing the priorities of a variety of stakeholders, and designers should be prepared to develop diverse non-inferior route alternatives that must be defensible under the scrutiny of a public forum. Political elements aside, the underlying geographical computational problems that must be solved to provide a set of high quality alternatives are no less easy, as they require solving difficult spatial optimization problems on massive GIS terrain-based raster data sets.Transmission line siting methodologies have previously been developed to guide designers in this endeavor, but close scrutiny of these methodologies show that there are many shortcomings with their approaches. The main goal of this dissertation is to take a fresh look at the process of corridor location, and develop a set of algorithms that compute path alternatives using a foundation of solid geographical theory in order to offer designers better tools for developing quality alternatives that consider the entire spectrum of viable solutions. And just as importantly, as data sets become increasingly massive and present challenging computational elements, it is important that algorithms be efficient and able to take advantage of parallel computing resources.A common approach to simplify a problem with numerous objectives is to combine the cost layers into a composite a priori weighted single-objective raster grid. This dissertation examines new methods used for determining a spatially diverse set of near-optimal alternatives, and develops parallel computing techniques for brute-force near-optimal path enumeration, as well as more elegant methods that take advantage of the hierarchical structure of the underlying path-tree computation to select sets of spatially diverse near optimal paths.Another approach for corridor location is to simultaneously consider all objectives to determine the set of Pareto-optimal solutions between the objectives. This amounts to solving a discrete multi-objective shortest path problem, which is considered to be NP-Hard for computing the full set of non-inferior solutions. Given the difficulty of solving for the complete Pareto-optimal set, this dissertation develops an approximation heuristic to compute path sets that are nearly exact-optimal in a fraction of the time when compared to exact algorithms. This method is then applied as an upper bound to an exact enumerative approach, resulting in significant performance speedups. But as analytic computing continues to moved toward distributed clusters, it is important to optimize algorithms to take full advantage parallel computing. To that extent, this dissertation develops a scalable parallel framework that efficiently solves for the supported/convex solutions of a biobjective shortest path problem. This framework is equally applicable to other biobjective network optimization problems, providing a powerful tool for solving the next generation of location analysis and geographical optimization models

Graph Processing in Main-Memory Column Stores

Evermore, novel and traditional business applications leverage the advantages of a graph data model, such as the offered schema flexibility and an explicit representation of relationships between entities. As a consequence, companies are confronted with the challenge of storing, manipulating, and querying terabytes of graph data for enterprise-critical applications. Although these business applications operate on graph-structured data, they still require direct access to the relational data and typically rely on an RDBMS to keep a single source of truth and access. Existing solutions performing graph operations on business-critical data either use a combination of SQL and application logic or employ a graph data management system. For the first approach, relying solely on SQL results in poor execution performance caused by the functional mismatch between typical graph operations and the relational algebra. To the worse, graph algorithms expose a tremendous variety in structure and functionality caused by their often domain-specific implementations and therefore can be hardly integrated into a database management system other than with custom coding. Since the majority of these enterprise-critical applications exclusively run on relational DBMSs, employing a specialized system for storing and processing graph data is typically not sensible. Besides the maintenance overhead for keeping the systems in sync, combining graph and relational operations is hard to realize as it requires data transfer across system boundaries. A basic ingredient of graph queries and algorithms are traversal operations and are a fundamental component of any database management system that aims at storing, manipulating, and querying graph data. Well-established graph traversal algorithms are standalone implementations relying on optimized data structures. The integration of graph traversals as an operator into a database management system requires a tight integration into the existing database environment and a development of new components, such as a graph topology-aware optimizer and accompanying graph statistics, graph-specific secondary index structures to speedup traversals, and an accompanying graph query language. In this thesis, we introduce and describe GRAPHITE, a hybrid graph-relational data management system. GRAPHITE is a performance-oriented graph data management system as part of an RDBMS allowing to seamlessly combine processing of graph data with relational data in the same system. We propose a columnar storage representation for graph data to leverage the already existing and mature data management and query processing infrastructure of relational database management systems. At the core of GRAPHITE we propose an execution engine solely based on set operations and graph traversals. Our design is driven by the observation that different graph topologies expose different algorithmic requirements to the design of a graph traversal operator. We derive two graph traversal implementations targeting the most common graph topologies and demonstrate how graph-specific statistics can be leveraged to select the optimal physical traversal operator. To accelerate graph traversals, we devise a set of graph-specific, updateable secondary index structures to improve the performance of vertex neighborhood expansion. Finally, we introduce a domain-specific language with an intuitive programming model to extend graph traversals with custom application logic at runtime. We use the LLVM compiler framework to generate efficient code that tightly integrates the user-specified application logic with our highly optimized built-in graph traversal operators. Our experimental evaluation shows that GRAPHITE can outperform native graph management systems by several orders of magnitude while providing all the features of an RDBMS, such as transaction support, backup and recovery, security and user management, effectively providing a promising alternative to specialized graph management systems that lack many of these features and require expensive data replication and maintenance processes

Algorithmes auto-stabilisants pour la construction de structures couvrantes réparties

This thesis deals with the self-stabilizing construction of spanning structures over a distributed system. Self-stabilization is a paradigm for fault-tolerance in distributed algorithms. It guarantees that the system eventually satisfies its specification after transient faults hit the system. Our model of distributed system assumes locally shared memories for communicating, unique identifiers for symmetry-breaking, and distributed daemon for execution scheduling, that is, the weakest proper daemon. More generally, we aim for the weakest possible assumptions, such as arbitrary topologies, in order to propose the most versatile constructions of distributed spanning structures. We present four original self-stabilizing algorithms achieving k-clustering, (f,g)-alliance construction, and ranking. For every of these problems, we prove the correctness of our solutions. Moreover, we analyze their time and space complexity using formal proofs and simulations. Finally, for the (f,g)-alliance problem, we consider the notion of safe convergence in addition to self-stabilization. It enforces the system to first quickly satisfy a specification that guarantees a minimum of conditions, and then to converge to a more stringent specification.Cette thèse s'intéresse à la construction auto-stabilisante de structures couvrantes dans un système réparti. L'auto-stabilisation est un paradigme pour la tolérance aux fautes dans les algorithmes répartis. Plus précisément, elle garantit que le système retrouve un comportement correct en temps fini après avoir été perturbé par des fautes transitoires. Notre modèle de système réparti se base sur des mémoires localement partagées pour la communication, des identifiants uniques pour briser les symétries et un ordonnanceur inéquitable, c'est-à-dire le plus faible des ordonnanceurs. Dans la mesure du possible, nous nous imposons d'utiliser les plus faibles hypothèses, afin d'obtenir les constructions les plus générales de structures couvrantes réparties. Nous présentons quatre algorithmes auto-stabilisants originaux pour le k-partitionnement, la construction d'une (f,g)-alliance et l'indexation. Pour chacun de ces problèmes, nous prouvons la correction de nos solutions. De plus, nous analysons leur complexité en temps et en espace à l'aide de preuves formelles et de simulations. Enfin, pour le problème de (f,g)-alliance, nous prenons en compte la notion de convergence sûre qui vient s'ajouter à celle d'auto-stabilisation. Elle garantit d'abord que le comportement du système assure rapidement un minimum de conditions, puis qu'il continue de converger jusqu'à se conformer à une spécification plus exigeante

LIPIcs, Volume 274, ESA 2023, Complete Volume

LIPIcs, Volume 274, ESA 2023, Complete Volum

Algorithms for Analyzing and Mining Real-World Graphs

This thesis is about algorithms for analyzing large real-world graphs (or networks). Examples include (online) social networks, webgraphs, information networks, biological networks and scientific collaboration and citation networks. Although these graphs differ in terms of what kind of information the objects and relationships represent, it turns out that the structure of each these networks is surprisingly similar.For computer scientists, there is an obvious challenge to design efficient algorithms that allow large graphs to be processed and analyzed in a practical setting, facing the challenges of processing millions of nodes and billions of edges. Specifically, there is an opportunity to exploit the non-random structure of real-world graphs to efficiently compute or approximate various properties and measures that would be too hard to compute using traditional graph algorithms. Examples include computation of node-to-node distances and extreme distance measures such as the exact diameter and radius of a graph.NWOAlgorithms and the Foundations of Software technolog

Elixir: synthesis of parallel irregular algorithms

Algorithms in new application areas like machine learning and data analytics usually operate on unstructured sparse graphs. Writing efficient parallel code to implement these algorithms is very challenging for a number of reasons. First, there may be many algorithms to solve a problem and each algorithm may have many implementations. Second, synchronization, which is necessary for correct parallel execution, introduces potential problems such as data-races and deadlocks. These issues interact in subtle ways, making the best solution dependent both on the parallel platform and on properties of the input graph. Consequently, implementing and selecting the best parallel solution can be a daunting task for non-experts, since we have few performance models for predicting the performance of parallel sparse graph programs on parallel hardware. This dissertation presents a synthesis methodology and a system, Elixir, that addresses these problems by (i) allowing programmers to specify solutions at a high level of abstraction, and (ii) generating many parallel implementations automatically and using search to find the best one. An Elixir specification consists of a set of operators capturing the main algorithm logic and a schedule specifying how to efficiently apply the operators. Elixir employs sophisticated automated reasoning to merge these two components, and uses techniques based on automated planning to insert synchronization and synthesize efficient parallel code. Experimental evaluation of our approach demonstrates that the performance of the Elixir generated code is competitive to, and can even outperform, hand-optimized code written by expert programmers for many interesting graph benchmarks.Computer Science

FPGA-based Query Acceleration for Non-relational Databases

Database management systems are an integral part of today’s everyday life. Trends like smart applications, the internet of things, and business and social networks require applications to deal efficiently with data in various data models close to the underlying domain. Therefore, non-relational database systems provide a wide variety of database models, like graphs and documents. However, current non-relational database systems face performance challenges due to the end of Dennard scaling and therefore performance scaling of CPUs. In the meanwhile, FPGAs have gained traction as accelerators for data management. Our goal is to tackle the performance challenges of non-relational database systems with FPGA acceleration and, at the same time, address design challenges of FPGA acceleration itself. Therefore, we split this thesis up into two main lines of work: graph processing and flexible data processing. Because of the lacking benchmark practices for graph processing accelerators, we propose GraphSim. GraphSim is able to reproduce runtimes of these accelerators based on a memory access model of the approach. Through this simulation environment, we extract three performance-critical accelerator properties: asynchronous graph processing, compressed graph data structure, and multi-channel memory. Since these accelerator properties have not been combined in one system, we propose GraphScale. GraphScale is the first scalable, asynchronous graph processing accelerator working on a compressed graph and outperforms all state-of-the-art graph processing accelerators. Focusing on accelerator flexibility, we propose PipeJSON as the first FPGA-based JSON parser for arbitrary JSON documents. PipeJSON is able to achieve parsing at line-speed, outperforming the fastest, vectorized parsers for CPUs. Lastly, we propose the subgraph query processing accelerator GraphMatch which outperforms state-of-the-art CPU systems for subgraph query processing and is able to flexibly switch queries during runtime in a matter of clock cycles

Applications of Molecular Dynamics simulations for biomolecular systems and improvements to density-based clustering in the analysis

Molecular Dynamics simulations provide a powerful tool to study biomolecular systems with atomistic detail. The key to better understand the function and behaviour of these molecules can often be found in their structural variability. Simulations can help to expose this information that is otherwise experimentally hard or impossible to attain. This work covers two application examples for which a sampling and a characterisation of the conformational ensemble could reveal the structural basis to answer a topical research question. For the fungal toxin phalloidin—a small bicyclic peptide—observed product ratios in different cyclisation reactions could be rationalised by assessing the conformational pre-organisation of precursor fragments. For the C-type lectin receptor langerin, conformational changes induced by different side-chain protonations could deliver an explanation of the pH-dependency in the protein’s calcium-binding. The investigations were accompanied by the continued development of a density-based clustering protocol into a respective software package, which is generally well applicable for the use case of extracting conformational states from Molecular Dynamics data

Motion Planning for Manipulation With Heuristic Search

Heuristic searches such as A* search are a popular means of finding least-cost plans due to their generality, strong theoretical guarantees on completeness and optimality, simplicity in implementation, and consistent behavior. In planning for robotic manipulation, however, these techniques are commonly thought of as impractical due to the high-dimensionality of the planning problem. As part of this thesis work, we have developed a heuristic search-based approach to motion planning for manipulation that does deal effectively with the high-dimensionality of the problem. In this thesis, I will present the approach together with its theoretical properties and show how to apply it to single-arm and dual-arm motion planning with upright constraints on a PR2 robot operating in non-trivial cluttered spaces. Then I will explain how we extended our approach to manipulation planning for n-arms with regrasping. In this work, the planner itself makes all of the discrete decisions, including which arm to use for the pickup and putdown, whether handoffs are necessary and how the object should be grasped at each step along the way. An extensive experimental analysis in both simulation and on a physical PR2 shows that, in terms of runtime, our approach is on par with some of the most common sampling-based approaches. This includes benchmarking our planning framework on two domains that we constructed that are common to manufacturing: pick-and-place of fast moving objects and the autonomous assembly of small objects. Between these applications, the planner exhibited fast planning times and the ability to robustly plan paths into and out of tight working environments that are common to assembly. The closing work of this thesis includes an exhaustive study of the natural tradeoff that occurs between planning efficiency versus solution quality for different values of the heuristic inflation factor. A comparison of the solution quality of our planner to paths computed by an asymptotically optimal approach given a great deal of time for path optimization is included as well. Finally, a set of experimental results are included that show that due to our approach\u27s deterministic cost-minimization, similar input tends to lead to similarity in the output. This kind of local consistency is important to the predictability of the robot\u27s motions and contributes to human-robot safety