High performance graph analysis on parallel architectures

PhD ThesisOver the last decade pharmacology has been developing computational methods to enhance drug development and testing. A computational method called network pharmacology uses graph analysis tools to determine protein target sets that can lead on better targeted drugs for diseases as Cancer. One promising area of network-based pharmacology is the detection of protein groups that can produce better e ects if they are targeted together by drugs. However, the e cient prediction of such protein combinations is still a bottleneck in the area of computational biology. The computational burden of the algorithms used by such protein prediction strategies to characterise the importance of such proteins consists an additional challenge for the eld of network pharmacology. Such computationally expensive graph algorithms as the all pairs shortest path (APSP) computation can a ect the overall drug discovery process as needed network analysis results cannot be given on time. An ideal solution for these highly intensive computations could be the use of super-computing. However, graph algorithms have datadriven computation dictated by the structure of the graph and this can lead to low compute capacity utilisation with execution times dominated by memory latency. Therefore, this thesis seeks optimised solutions for the real-world graph problems of critical node detection and e ectiveness characterisation emerged from the collaboration with a pioneer company in the eld of network pharmacology as part of a Knowledge Transfer Partnership (KTP) / Secondment (KTS). In particular, we examine how genetic algorithms could bene t the prediction of protein complexes where their removal could produce a more e ective 'druggable' impact. Furthermore, we investigate how the problem of all pairs shortest path (APSP) computation can be bene ted by the use of emerging parallel hardware architectures as GPU- and FPGA- desktop-based accelerators. In particular, we address the problem of critical node detection with the development of a heuristic search method. It is based on a genetic algorithm that computes optimised node combinations where their removal causes greater impact than common impact analysis strategies. Furthermore, we design a general pattern for parallel network analysis on multi-core architectures that considers graph's embedded properties. It is a divide and conquer approach that decomposes a graph into smaller subgraphs based on its strongly connected components and computes the all pairs shortest paths concurrently on GPU. Furthermore, we use linear algebra to design an APSP approach based on the BFS algorithm. We use algebraic expressions to transform the problem of path computation to multiple independent matrix-vector multiplications that are executed concurrently on FPGA. Finally, we analyse how the optimised solutions of perturbation analysis and parallel graph processing provided in this thesis will impact the drug discovery process.This research was part of a Knowledge Transfer Partnership (KTP) and Knowledge Transfer Secondment (KTS) between e-therapeutics PLC and Newcastle University. It was supported as a collaborative project by e-therapeutics PLC and Technology Strategy boar

GraphBLAST: A High-Performance Linear Algebra-based Graph Framework on the GPU

High-performance implementations of graph algorithms are challenging to implement on new parallel hardware such as GPUs because of three challenges: (1) the difficulty of coming up with graph building blocks, (2) load imbalance on parallel hardware, and (3) graph problems having low arithmetic intensity. To address some of these challenges, GraphBLAS is an innovative, on-going effort by the graph analytics community to propose building blocks based on sparse linear algebra, which will allow graph algorithms to be expressed in a performant, succinct, composable and portable manner. In this paper, we examine the performance challenges of a linear-algebra-based approach to building graph frameworks and describe new design principles for overcoming these bottlenecks. Among the new design principles is exploiting input sparsity, which allows users to write graph algorithms without specifying push and pull direction. Exploiting output sparsity allows users to tell the backend which values of the output in a single vectorized computation they do not want computed. Load-balancing is an important feature for balancing work amongst parallel workers. We describe the important load-balancing features for handling graphs with different characteristics. The design principles described in this paper have been implemented in "GraphBLAST", the first high-performance linear algebra-based graph framework on NVIDIA GPUs that is open-source. The results show that on a single GPU, GraphBLAST has on average at least an order of magnitude speedup over previous GraphBLAS implementations SuiteSparse and GBTL, comparable performance to the fastest GPU hardwired primitives and shared-memory graph frameworks Ligra and Gunrock, and better performance than any other GPU graph framework, while offering a simpler and more concise programming model.Comment: 50 pages, 14 figures, 14 table

Heuristics for Sparsest Cut Approximations in Network Flow Applications

The Maximum Concurrent Flow Problem (MCFP) is a polynomially bounded problem that has been used over the years in a variety of applications. Sometimes it is used to attempt to find the Sparsest Cut, an NP-hard problem, and other times to find communities in Social Network Analysis (SNA) in its hierarchical formulation, the HMCFP. Though it is polynomially bounded, the MCFP quickly grows in space utilization, rendering it useful on only small problems. When it was defined, only a few hundred nodes could be solved, where a few decades later, graphs of one to two thousand nodes can still be too much for modern commodity hardware to handle. This dissertation covers three approaches to heuristics to the MCFP that run significantly faster in practice than the LP formulation with far less memory utilization. The first two approaches are based on the Maximum Adjacency Search (MAS) and apply to both the MCFP and the HMCFP used for community detection. We compare the three approaches to the LP performance in terms of accuracy, runtime, and memory utilization on several classes of synthetic graphs representing potential real-world applications. We find that the heuristics are often correct, and run using orders of magnitude less memory and time

Scalability considerations for multivariate graph visualization

Real-world, multivariate datasets are frequently too large to show in their entirety on a visual display. Still, there are many techniques we can employ to show useful partial views-sufficient to support incremental exploration of large graph datasets. In this chapter, we first explore the cognitive and architectural limitations which restrict the amount of visual bandwidth available to multivariate graph visualization approaches. These limitations afford several design approaches, which we systematically explore. Finally, we survey systems and studies that exhibit these design strategies to mitigate these perceptual and architectural limitations

Structured Prediction Problem Archive

Structured prediction problems are one of the fundamental tools in machinelearning. In order to facilitate algorithm development for their numericalsolution, we collect in one place a large number of datasets in easy to readformats for a diverse set of problem classes. We provide archival links todatasets, description of the considered problems and problem formats, and ashort summary of problem characteristics including size, number of instancesetc. For reference we also give a non-exhaustive selection of algorithmsproposed in the literature for their solution. We hope that this centralrepository will make benchmarking and comparison to established works easier.We welcome submission of interesting new datasets and algorithms for inclusionin our archive.<br

Algorithm Engineering for fundamental Sorting and Graph Problems

Fundamental Algorithms build a basis knowledge for every computer science undergraduate or a professional programmer. It is a set of basic techniques one can find in any (good) coursebook on algorithms and data structures. In this thesis we try to close the gap between theoretically worst-case optimal classical algorithms and the real-world circumstances one face under the assumptions imposed by the data size, limited main memory or available parallelism

Robot Navigation in Human Environments

For the near future, we envision service robots that will help us with everyday chores in home, office, and urban environments. These robots need to work in environments that were designed for humans and they have to collaborate with humans to fulfill their tasks. In this thesis, we propose new methods for communicating, transferring knowledge, and collaborating between humans and robots in four different navigation tasks. In the first application, we investigate how automated services for giving wayfinding directions can be improved to better address the needs of the human recipients. We propose a novel method based on inverse reinforcement learning that learns from a corpus of human-written route descriptions what amount and type of information a route description should contain. By imitating the human teachers' description style, our algorithm produces new route descriptions that sound similarly natural and convey similar information content, as we show in a user study. In the second application, we investigate how robots can leverage background information provided by humans for exploring an unknown environment more efficiently. We propose an algorithm for exploiting user-provided information such as sketches or floor plans by combining a global exploration strategy based on the solution of a traveling salesman problem with a local nearest-frontier-first exploration scheme. Our experiments show that the exploration tours are significantly shorter and that our system allows the user to effectively select the areas that the robot should explore. In the second part of this thesis, we focus on humanoid robots in home and office environments. The human-like body plan allows humanoid robots to navigate in environments and operate tools that were designed for humans, making humanoid robots suitable for a wide range of applications. As localization and mapping are prerequisites for all navigation tasks, we first introduce a novel feature descriptor for RGB-D sensor data and integrate this building block into an appearance-based simultaneous localization and mapping system that we adapt and optimize for the usage on humanoid robots. Our optimized system is able to track a real Nao humanoid robot more accurately and more robustly than existing approaches. As the third application, we investigate how humanoid robots can cover known environments efficiently with their camera, for example for inspection or search tasks. We extend an existing next-best-view approach by integrating inverse reachability maps, allowing us to efficiently sample and check collision-free full-body poses. Our approach enables the robot to inspect as much of the environment as possible. In our fourth application, we extend the coverage scenario to environments that also include articulated objects that the robot has to actively manipulate to uncover obstructed regions. We introduce algorithms for navigation subtasks that run highly parallelized on graphics processing units for embedded devices. Together with a novel heuristic for estimating utility maps, our system allows to find high-utility camera poses for efficiently covering environments with articulated objects. All techniques presented in this thesis were implemented in software and thoroughly evaluated in user studies, simulations, and experiments in both artificial and real-world environments. Our approaches advance the state of the art towards universally usable robots in everyday environments.Roboternavigation in menschlichen Umgebungen In naher Zukunft erwarten wir Serviceroboter, die uns im Haushalt, im Büro und in der Stadt alltägliche Arbeiten abnehmen. Diese Roboter müssen in für Menschen gebauten Umgebungen zurechtkommen und sie müssen mit Menschen zusammenarbeiten um ihre Aufgaben zu erledigen. In dieser Arbeit schlagen wir neue Methoden für die Kommunikation, Wissenstransfer und Zusammenarbeit zwischen Menschen und Robotern bei Navigationsaufgaben in vier Anwendungen vor. In der ersten Anwendung untersuchen wir, wie automatisierte Dienste zur Generierung von Wegbeschreibungen verbessert werden können, um die Beschreibungen besser an die Bedürfnisse der Empfänger anzupassen. Wir schlagen eine neue Methode vor, die inverses bestärkendes Lernen nutzt, um aus einem Korpus von von Menschen geschriebenen Wegbeschreibungen zu lernen, wie viel und welche Art von Information eine Wegbeschreibung enthalten sollte. Indem unser Algorithmus den Stil der Wegbeschreibungen der menschlichen Lehrer imitiert, kann der Algorithmus neue Wegbeschreibungen erzeugen, die sich ähnlich natürlich anhören und einen ähnlichen Informationsgehalt vermitteln, was wir in einer Benutzerstudie zeigen. In der zweiten Anwendung untersuchen wir, wie Roboter von Menschen bereitgestellte Hintergrundinformationen nutzen können, um eine bisher unbekannte Umgebung schneller zu erkunden. Wir schlagen einen Algorithmus vor, der Hintergrundinformationen wie Gebäudegrundrisse oder Skizzen nutzt, indem er eine globale Explorationsstrategie basierend auf der Lösung eines Problems des Handlungsreisenden kombiniert mit einer lokalen Explorationsstrategie. Unsere Experimente zeigen, dass die Erkundungstouren signifikant kürzer werden und dass der Benutzer mit unserem System effektiv die zu erkundenden Regionen spezifizieren kann. Der zweite Teil dieser Arbeit konzentriert sich auf humanoide Roboter in Umgebungen zu Hause und im Büro. Der menschenähnliche Körperbau ermöglicht es humanoiden Robotern, in Umgebungen zu navigieren und Werkzeuge zu benutzen, die für Menschen gebaut wurden, wodurch humanoide Roboter für vielfältige Aufgaben einsetzbar sind. Da Lokalisierung und Kartierung Grundvoraussetzungen für alle Navigationsaufgaben sind, führen wir zunächst einen neuen Merkmalsdeskriptor für RGB-D-Sensordaten ein und integrieren diesen Baustein in ein erscheinungsbasiertes simultanes Lokalisierungs- und Kartierungsverfahren, das wir an die Besonderheiten von humanoiden Robotern anpassen und optimieren. Unser System kann die Position eines realen humanoiden Roboters genauer und robuster verfolgen, als es mit existierenden Ansätzen möglich ist. Als dritte Anwendung untersuchen wir, wie humanoide Roboter bekannte Umgebungen effizient mit ihrer Kamera abdecken können, beispielsweise zu Inspektionszwecken oder zum Suchen eines Gegenstands. Wir erweitern ein bestehendes Verfahren, das die nächstbeste Beobachtungsposition berechnet, durch inverse Erreichbarkeitskarten, wodurch wir kollisionsfreie Ganzkörperposen effizient generieren und prüfen können. Unser Ansatz ermöglicht es dem Roboter, so viel wie möglich von der Umgebung zu untersuchen. In unserer vierten Anwendung erweitern wir dieses Szenario um Umgebungen, die auch bewegbare Gegenstände enthalten, die der Roboter aktiv bewegen muss um verdeckte Regionen zu sehen. Wir führen Algorithmen für Teilprobleme ein, die hoch parallelisiert auf Grafikkarten von eingebetteten Systemen ausgeführt werden. Zusammen mit einer neuen Heuristik zur Schätzung von Nutzenkarten ermöglicht dies unserem System Beobachtungspunkte mit hohem Nutzen zu finden, um Umgebungen mit bewegbaren Objekten effizient zu inspizieren. Alle vorgestellten Techniken wurden in Software implementiert und sorgfältig evaluiert in Benutzerstudien, Simulationen und Experimenten in künstlichen und realen Umgebungen. Unsere Verfahren bringen den Stand der Forschung voran in Richtung universell einsetzbarer Roboter in alltäglichen Umgebungen