A Partition-centric Distributed Algorithm for Identifying Euler Circuits in Large Graphs

Finding the Eulerian circuit in graphs is a classic problem, but inadequately explored for parallel computation. With such cycles finding use in neuroscience and Internet of Things for large graphs, designing a distributed algorithm for finding the Euler circuit is important. Existing parallel algorithms are impractical for commodity clusters and Clouds. We propose a novel partition-centric algorithm to find the Euler circuit, over large graphs partitioned across distributed machines and executed iteratively using a Bulk Synchronous Parallel (BSP) model. The algorithm finds partial paths and cycles within each partition, and refines these into longer paths by recursively merging the partitions. We describe the algorithm, analyze its complexity, validate it on Apache Spark for large graphs, and offer experimental results. We also identify memory bottlenecks in the algorithm and propose an enhanced design to address it.Comment: To appear in Proceedings of 5th IEEE International Workshop on High-Performance Big Data, Deep Learning, and Cloud Computing, In conjunction with The 33rd IEEE International Parallel and Distributed Processing Symposium (IPDPS 2019), Rio de Janeiro, Brazil, May 20th, 201

Online Social Networks: Measurements, Analysis and Solutions for Mining Challenges

In the last decade, online social networks showed enormous growth. With the rise of these networks and the consequent availability of wealth social network data, Social Network Analysis (SNA) led researchers to get the opportunity to access, analyse and mine the social behaviour of millions of people, explore the way they communicate and exchange information. Despite the growing interest in analysing social networks, there are some challenges and implications accompanying the analysis and mining of these networks. For example, dealing with large-scale and evolving networks is not yet an easy task and still requires a new mining solution. In addition, finding communities within these networks is a challenging task and could open opportunities to see how people behave in groups on a large scale. Also, the challenge of validating and optimizing communities without knowing in advance the structure of the network due to the lack of ground truth is yet another challenging barrier for validating the meaningfulness of the resulting communities. In this thesis, we started by providing an overview of the necessary background and key concepts required in the area of social networks analysis. Our main focus is to provide solutions to tackle the key challenges in this area. For doing so, first, we introduce a predictive technique to help in the prediction of the execution time of the analysis tasks for evolving networks through employing predictive modeling techniques to the problem of evolving and large-scale networks. Second, we study the performance of existing community detection approaches to derive high quality community structure using a real email network through analysing the exchange of emails and exploring community dynamics. The aim is to study the community behavioral patterns and evaluate their quality within an actual network. Finally, we propose an ensemble technique for deriving communities using a rich internal enterprise real network in IBM that reflects real collaborations and communications between employees. The technique aims to improve the community detection process through the fusion of different algorithms

Domain-specific Architectures for Data-intensive Applications

Graphs' versatile ability to represent diverse relationships, make them effective for a wide range of applications. For instance, search engines use graph-based applications to provide high-quality search results. Medical centers use them to aid in patient diagnosis. Most recently, graphs are also being employed to support the management of viral pandemics. Looking forward, they are showing promise of being critical in unlocking several other opportunities, including combating the spread of fake content in social networks, detecting and preventing fraudulent online transactions in a timely fashion, and in ensuring collision avoidance in autonomous vehicle navigation, to name a few. Unfortunately, all these applications require more computational power than what can be provided by conventional computing systems. The key reason is that graph applications present large working sets that fail to fit in the small on-chip storage of existing computing systems, while at the same time they access data in seemingly unpredictable patterns, thus cannot draw benefit from traditional on-chip storage. In this dissertation, we set out to address the performance limitations of existing computing systems so to enable emerging graph applications like those described above. To achieve this, we identified three key strategies: 1) specializing memory architecture, 2) processing data near its storage, and 3) message coalescing in the network. Based on these strategies, this dissertation develops several solutions: OMEGA, which employs specialized on-chip storage units, with co-located specialized compute engines to accelerate the computation; MessageFusion, which coalesces messages in the interconnect; and Centaur, providing an architecture that optimizes the processing of infrequently-accessed data. Overall, these solutions provide 2x in performance improvements, with negligible hardware overheads, across a wide range of applications. Finally, we demonstrate the applicability of our strategies to other data-intensive domains, by exploring an acceleration solution for MapReduce applications, which achieves a 4x performance speedup, also with negligible area and power overheads.PHDComputer Science & EngineeringUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/163186/1/abrahad_1.pd

AN EDGE-CENTRIC PERSPECTIVE FOR BRAIN NETWORK COMMUNITIES

Thesis (Ph.D.) - Indiana University, Department of Psychological and Brain Sciences and Program in Neuroscience, 2021The brain is a complex system organized on multiple scales and operating in both a local and distributed manner. Individual neurons and brain regions participate in specific functions, while at the same time existing in the context of a larger network, supporting a range of different functionalities. Building brain networks comprised of distinct neural elements (nodes) and their interrelationships (edges), allows us to model the brain from both local and global perspectives, and to deploy a wide array of computational network tools. A popular network analysis approach is community detection, which aims to subdivide a network’s nodes into clusters that can used to represent and evaluate network organization. Prevailing community detection approaches applied to brain networks are designed to find densely interconnected sets of nodes, leading to the notion that the brain is organized in an exclusively modular manner. Furthermore, many brain network analyses tend to focus on the nodes, evidenced by the search for modular groupings of neural elements that might serve a common function. In this thesis, we describe the application of community detection algorithms that are sensitive to alternative cluster configurations, enhancing our understanding of brain network organization. We apply a framework called the stochastic block model, which we use to uncover evidence of non-modular organization in human anatomical brain networks across the life span, and in the informatically-collated rat cerebral cortex. We also propose a framework to cluster functional brain network edges in human data, which naturally results in an overlapping organization at the level of nodes that bridges canonical functional systems. These alternative methods utilize the connection patterns of brain network edges in ways that prevailing approaches do not. Thus, we motivate an alternative outlook which focuses on the importance of information provided by the brain’s interconnections, or edges. We call this an edge-centric perspective. The edge-centric approaches developed here offer new ways to characterize distributed brain organization and contribute to a fundamental change in perspective in our thinking about the brain

SPICE²: A Spatial, Parallel Architecture for Accelerating the Spice Circuit Simulator

Spatial processing of sparse, irregular floating-point computation using a single FPGA enables up to an order of magnitude speedup (mean 2.8X speedup) over a conventional microprocessor for the SPICE circuit simulator. We deliver this speedup using a hybrid parallel architecture that spatially implements the heterogeneous forms of parallelism available in SPICE. We decompose SPICE into its three constituent phases: Model-Evaluation, Sparse Matrix-Solve, and Iteration Control and parallelize each phase independently. We exploit data-parallel device evaluations in the Model-Evaluation phase, sparse dataflow parallelism in the Sparse Matrix-Solve phase and compose the complete design in streaming fashion. We name our parallel architecture SPICE²: Spatial Processors Interconnected for Concurrent Execution for accelerating the SPICE circuit simulator. We program the parallel architecture with a high-level, domain-specific framework that identifies, exposes and exploits parallelism available in the SPICE circuit simulator. This design is optimized with an auto-tuner that can scale the design to use larger FPGA capacities without expert intervention and can even target other parallel architectures with the assistance of automated code-generation. This FPGA architecture is able to outperform conventional processors due to a combination of factors including high utilization of statically-scheduled resources, low-overhead dataflow scheduling of fine-grained tasks, and overlapped processing of the control algorithms. We demonstrate that we can independently accelerate Model-Evaluation by a mean factor of 6.5X(1.4--23X) across a range of non-linear device models and Matrix-Solve by 2.4X(0.6--13X) across various benchmark matrices while delivering a mean combined speedup of 2.8X(0.2--11X) for the two together when comparing a Xilinx Virtex-6 LX760 (40nm) with an Intel Core i7 965 (45nm). With our high-level framework, we can also accelerate Single-Precision Model-Evaluation on NVIDIA GPUs, ATI GPUs, IBM Cell, and Sun Niagara 2 architectures. We expect approaches based on exploiting spatial parallelism to become important as frequency scaling slows down and modern processing architectures turn to parallelism (\eg multi-core, GPUs) due to constraints of power consumption. This thesis shows how to express, exploit and optimize spatial parallelism for an important class of problems that are challenging to parallelize.</p

Modelling and measurement in synthetic biology

Synthetic biology applies engineering principles to make progress in the study of complex biological phenomena. The aim is to develop understanding through the praxis of construction and design. The computational branch of this endeavour explicitly brings the tools of abstraction and modularity to bear. This thesis pursues two distinct lines of inquiry concerning the application of computational tools in the setting of synthetic biology. One thread traces a narrative through multi-paradigm computational simulations, interpretation of results, and quantification of biological order. The other develops computational infrastructure for describing, simulating and discovering, synthetic genetic circuits. The emergence of structure in biological organisms, morphogenesis, is critically important for understanding both normal and pathological development of tissues. Here, we focus on epithelial tissues because models of two dimensional cellular monolayers are computationally tractable. We use a vertex model that consists of a potential energy minimisation process interwoven with topological changes in the graph structure of the tissue. To make this interweaving precise, we define a language for propagators from which an unambiguous description of the simulation methodology can be constructed. The vertex model is then used to reproduce laboratory results of patterning in engineered mammalian cells. The assertion that the claim of reproduction is justified is based on a novel measure of structure on coloured graphs which we call path entropy. This measure is then extended to the setting of continuous regions and used to quantify the development of structure in house mouse (Mus musculus) embryos using three dimensional segmented anatomical models. While it is recognised that DNA can be considered a powerful computational environment, it is far from obvious how to program with nucleic acids. Using rule-based modelling of modular biological parts, we develop a method for discovering synthetic genetic programs that meet a specification provided by the user. This method rests on the concept of annotation as applied to rule-based programs. We begin with annotating rules and proceed to generating entire rule-based programs from annotations themselves. Building on those tools we describe an evolutionary algorithm for discovering genetic circuits from specifications provided in terms of probability distributions. This strategy provides a dual benefit: using stochastic simulation captures circuit behaviour at low copy numbers as well as complex properties such as oscillations, and using standard biological parts produces results that are implementable in the laboratory

An input centric paradigm for program dynamic optimizations and lifetime evolvement

Accurately predicting program behaviors (e.g., memory locality, method calling frequency) is fundamental for program optimizations and runtime adaptations. Despite decades of remarkable progress, prior studies have not systematically exploited the use of program inputs, a deciding factor of program behaviors, to help in program dynamic optimizations. Triggered by the strong and predictive correlations between program inputs and program behaviors that recent studies have uncovered, the dissertation work aims to bring program inputs into the focus of program behavior analysis and program dynamic optimization, cultivating a new paradigm named input-centric program behavior analysis and dynamic optimization.;The new optimization paradigm consists of three components, forming a three-layer pyramid. at the base is program input characterization, a component for resolving the complexity in program raw inputs and extracting important features. In the middle is input-behavior modeling, a component for recognizing and modeling the correlations between characterized input features and program behaviors. These two components constitute input-centric program behavior analysis, which (ideally) is able to predict the large-scope behaviors of a program\u27s execution as soon as the execution starts. The top layer is input-centric adaptation, which capitalizes on the novel opportunities created by the first two components to facilitate proactive adaptation for program optimizations.;This dissertation aims to develop this paradigm in two stages. In the first stage, we concentrate on exploring the implications of program inputs for program behaviors and dynamic optimization. We construct the basic input-centric optimization framework based on of line training to realize the basic functionalities of the three major components of the paradigm. For the second stage, we focus on making the paradigm practical by addressing multi-facet issues in handling input complexities, transparent training data collection, predictive model evolvement across production runs. The techniques proposed in this stage together cultivate a lifelong continuous optimization scheme with cross-input adaptivity.;Fundamentally the new optimization paradigm provides a brand new solution for program dynamic optimization. The techniques proposed in the dissertation together resolve the adaptivity-proactivity dilemma that has been limiting the effectiveness of existing optimization techniques. its benefits are demonstrated through proactive dynamic optimizations in Jikes RVM and version selection using IBM XL C Compiler, yielding significant performance improvement on a set of Java and C/C++ programs. It may open new opportunities for a broad range of runtime optimizations and adaptations. The evaluation results on both Java and C/C++ applications demonstrate the new paradigm is promising in advancing the current state of program optimizations