Scalable Scientific Computing Algorithms Using MapReduce

Cloud computing systems, like MapReduce and Pregel, provide a scalable and fault tolerant environment for running computations at massive scale. However, these systems are designed primarily for data intensive computational tasks, while a large class of problems in scientific computing and business analytics are computationally intensive (i.e., they require a lot of CPU in addition to I/O). In this thesis, we investigate the use of cloud computing systems, in particular MapReduce, for computationally intensive problems, focusing on two classic problems that arise in scienti c computing and also in analytics: maximum clique and matrix inversion. The key contribution that enables us to e ectively use MapReduce to solve the maximum clique problem on dense graphs is a recursive partitioning method that partitions the graph into several subgraphs of similar size and running time complexity. After partitioning, the maximum cliques of the di erent partitions can be computed independently, and the computation is sped up using a branch and bound method. Our experiments show that our approach leads to good scalability, which is unachievable by other partitioning methods since they result in partitions of di erent sizes and hence lead to load imbalance. Our method is more scalable than an MPI algorithm, and is simpler and more fault tolerant. For the matrix inversion problem, we show that a recursive block LU decomposition allows us to e ectively compute in parallel both the lower triangular (L) and upper triangular (U) matrices using MapReduce. After computing the L and U matrices, their inverses are computed using MapReduce. The inverse of the original matrix, which is the product of the inverses of the L and U matrices, is also obtained using MapReduce. Our technique is the rst matrix inversion technique that uses MapReduce. We show experimentally that our technique has good scalability, and it is simpler and more fault tolerant than MPI implementations such as ScaLAPACK

High Performance Frequent Subgraph Mining on Transactional Datasets

Graph data mining has been a crucial as well as inevitable area of research. Large amounts of graph data are produced in many areas, such as Bioinformatics, Cheminformatics, Social Networks, and Web etc. Scalable graph data mining methods are getting increasingly popular and necessary due to increased graph complexities. Frequent subgraph mining is one such area where the task is to find overly recurring patterns/subgraphs. To tackle this problem, many main memory-based methods were proposed, which proved to be inefficient as the data size grew exponentially over time. In the past few years several research groups have attempted to handle the frequent subgraph mining (FSM) problem in multiple ways. Many authors have tried to achieve better performance using Graphic Processing Units (GPUs) which has multi-fold improvement over in-memory while dealing with large datasets. Later, Google\u27s MapReduce model with the Hadoop framework proved to be a major breakthrough in high performance large batch processing. Although MapReduce came with many benefits, its disk I/O and non-iterative style model could not help much for FSM domain since subgraph mining process is an iterative approach. In recent years, Spark has emerged to be the De Facto industry standard with its distributed in-memory computing capability. This is a right fit solution for iterative style of programming as well. In this work, we cover how high-performance computing has helped in improving the performance tremendously in the transactional directed and undirected aspect of graphs and performance comparisons of various FSM techniques are done based on experimental results

GraphR: Accelerating Graph Processing Using ReRAM

This paper presents GRAPHR, the first ReRAM-based graph processing accelerator. GRAPHR follows the principle of near-data processing and explores the opportunity of performing massive parallel analog operations with low hardware and energy cost. The analog computation is suit- able for graph processing because: 1) The algorithms are iterative and could inherently tolerate the imprecision; 2) Both probability calculation (e.g., PageRank and Collaborative Filtering) and typical graph algorithms involving integers (e.g., BFS/SSSP) are resilient to errors. The key insight of GRAPHR is that if a vertex program of a graph algorithm can be expressed in sparse matrix vector multiplication (SpMV), it can be efficiently performed by ReRAM crossbar. We show that this assumption is generally true for a large set of graph algorithms. GRAPHR is a novel accelerator architecture consisting of two components: memory ReRAM and graph engine (GE). The core graph computations are performed in sparse matrix format in GEs (ReRAM crossbars). The vector/matrix-based graph computation is not new, but ReRAM offers the unique opportunity to realize the massive parallelism with unprecedented energy efficiency and low hardware cost. With small subgraphs processed by GEs, the gain of performing parallel operations overshadows the wastes due to sparsity. The experiment results show that GRAPHR achieves a 16.01x (up to 132.67x) speedup and a 33.82x energy saving on geometric mean compared to a CPU baseline system. Com- pared to GPU, GRAPHR achieves 1.69x to 2.19x speedup and consumes 4.77x to 8.91x less energy. GRAPHR gains a speedup of 1.16x to 4.12x, and is 3.67x to 10.96x more energy efficiency compared to PIM-based architecture.Comment: Accepted to HPCA 201

Methods to Improve Applicability and Efficiency of Distributed Data-Centric Compute Frameworks

The success of modern applications depends on the insights they collect from their data repositories. Data repositories for such applications currently exceed exabytes and are rapidly increasing in size, as they collect data from varied sources - web applications, mobile phones, sensors and other connected devices. Distributed storage and data-centric compute frameworks have been invented to store and analyze these large datasets. This dissertation focuses on extending the applicability and improving the efficiency of distributed data-centric compute frameworks

Mining and Managing Large-Scale Temporal Graphs

Large-scale temporal graphs are everywhere in our daily life. From online social networks, mobile networks, brain networks to computer systems, entities in these large complex systems communicate with each other, and their interactions evolve over time. Unlike traditional graphs, temporal graphs are dynamic: both topologies and attributes on nodes/edges may change over time. On the one hand, the dynamics have inspired new applications that rely on mining and managing temporal graphs. On the other hand, the dynamics also raise new technical challenges. First, it is difficult to discover or retrieve knowledge from complex temporal graph data. Second, because of the extra time dimension, we also face new scalability problems. To address these new challenges, we need to develop new methods that model temporal information in graphs so that we can deliver useful knowledge, new queries with temporal and structural constraints where users can obtain the desired knowledge, and new algorithms that are cost-effective for both mining and management tasks.In this dissertation, we discuss our recent works on mining and managing large-scale temporal graphs.First, we investigate two mining problems, including node ranking and link prediction problems. In these works, temporal graphs are applied to model the data generated from computer systems and online social networks. We formulate data mining tasks that extract knowledge from temporal graphs. The discovered knowledge can help domain experts identify critical alerts in system monitoring applications and recover the complete traces for information propagation in online social networks. To address computation efficiency problems, we leverage the unique properties in temporal graphs to simplify mining processes. The resulting mining algorithms scale well with large-scale temporal graphs with millions of nodes and billions of edges. By experimental studies over real-life and synthetic data, we confirm the effectiveness and efficiency of our algorithms.Second, we focus on temporal graph management problems. In these study, temporal graphs are used to model datacenter networks, mobile networks, and subscription relationships between stream queries and data sources. We formulate graph queries to retrieve knowledge that supports applications in cloud service placement, information routing in mobile networks, and query assignment in stream processing system. We investigate three types of queries, including subgraph matching, temporal reachability, and graph partitioning. By utilizing the relatively stable components in these temporal graphs, we develop flexible data management techniques to enable fast query processing and handle graph dynamics. We evaluate the soundness of the proposed techniques by both real and synthetic data. Through these study, we have learned valuable lessons. For temporal graph mining, temporal dimension may not necessarily increase computation complexity; instead, it may reduce computation complexity if temporal information can be wisely utilized. For temporal graph management, temporal graphs may include relatively stable components in real applications, which can help us develop flexible data management techniques that enable fast query processing and handle dynamic changes in temporal graphs

DIAMIN: a software library for the distributed analysis of large-scale molecular interaction networks

Background Huge amounts of molecular interaction data are continuously produced and stored in public databases. Although many bioinformatics tools have been proposed in the literature for their analysis, based on their modeling through different types of biological networks, several problems still remain unsolved when the problem turns on a large scale. Results We propose DIAMIN, that is, a high-level software library to facilitate the development of applications for the efficient analysis of large-scale molecular interaction networks. DIAMIN relies on distributed computing, and it is implemented in Java upon the framework Apache Spark. It delivers a set of functionalities implementing different tasks on an abstract representation of very large graphs, providing a built-in support for methods and algorithms commonly used to analyze these networks. DIAMIN has been tested on data retrieved from two of the most used molecular interactions databases, resulting to be highly efficient and scalable. As shown by different provided examples, DIAMIN can be exploited by users without any distributed programming experience, in order to perform various types of data analysis, and to implement new algorithms based on its primitives. Conclusions The proposed DIAMIN has been proved to be successful in allowing users to solve specific biological problems that can be modeled relying on biological networks, by using its functionalities. The software is freely available and this will hopefully allow its rapid diffusion through the scientific community, to solve both specific data analysis and more complex tasks

Structure and topology of transcriptional regulatory networks and their applications in bio-inspired networking

Biological networks carry out vital functions necessary for sustenance despite environmental adversities. Transcriptional Regulatory Network (TRN) is one such biological network that is formed due to the interaction between proteins, called Transcription Factors (TFs), and segments of DNA, called genes. TRNs are known to exhibit functional robustness in the face of perturbation or mutation: a property that is proven to be a result of its underlying network topology. In this thesis, we first propose a three-tier topological characterization of TRN to analyze the interplay between the significant graph-theoretic properties of TRNs such as scale-free out-degree distribution, low graph density, small world property and the abundance of subgraphs called motifs. Specifically, we pinpoint the role of a certain three-node motif, called Feed Forward Loop (FFL) motif in topological robustness as well as information spread in TRNs. With the understanding of the TRN topology, we explore its potential use in design of fault-tolerant communication topologies. To this end, we first propose an edge rewiring mechanism that remedies the vulnerability of TRNs to the failure of well-connected nodes, called hubs, while preserving its other significant graph-theoretic properties. We apply the rewired TRN topologies in the design of wireless sensor networks that are less vulnerable to targeted node failure. Similarly, we apply the TRN topology to address the issues of robustness and energy-efficiency in the following networking paradigms: robust yet energy-efficient delay tolerant network for post disaster scenarios, energy-efficient data-collection framework for smart city applications and a data transfer framework deployed over a fog computing platform for collaborative sensing --Abstract, page iii

Graph set data mining

Graphs are among the most versatile abstract data types in computer science. With the variety comes great adoption in various application fields, such as chemistry, biology, social analysis, logistics, and computer science itself. With the growing capacities of digital storage, the collection of large amounts of data has become the norm in many application fields. Data mining, i.e., the automated extraction of non-trivial patterns from data, is a key step to extract knowledge from these datasets and generate value. This thesis is dedicated to concurrent scalable data mining algorithms beyond traditional notions of efficiency for large-scale datasets of small labeled graphs; more precisely, structural clustering and representative subgraph pattern mining. It is motivated by, but not limited to, the need to analyze molecular libraries of ever-increasing size in the drug discovery process. Structural clustering makes use of graph theoretical concepts, such as (common) subgraph isomorphisms and frequent subgraphs, to model cluster commonalities directly in the application domain. It is considered computationally demanding for non-restricted graph classes and with very few exceptions prior algorithms are only suitable for very small datasets. This thesis discusses the first truly scalable structural clustering algorithm StruClus with linear worst-case complexity. At the same time, StruClus embraces the inherent values of structural clustering algorithms, i.e., interpretable, consistent, and high-quality results. A novel two-fold sampling strategy with stochastic error bounds for frequent subgraph mining is presented. It enables fast extraction of cluster commonalities in the form of common subgraph representative sets. StruClus is the first structural clustering algorithm with a directed selection of structural cluster-representative patterns regarding homogeneity and separation aspects in the high-dimensional subgraph pattern space. Furthermore, a novel concept of cluster homogeneity balancing using dynamically-sized representatives is discussed. The second part of this thesis discusses the representative subgraph pattern mining problem in more general terms. A novel objective function maximizes the number of represented graphs for a cardinality-constrained representative set. It is shown that the problem is a special case of the maximum coverage problem and is NP-hard. Based on the greedy approximation of Nemhauser, Wolsey, and Fisher for submodular set function maximization a novel sampling approach is presented. It mines candidate sets that contain an optimal greedy solution with a probabilistic maximum error. This leads to a constant-time algorithm to generate the candidate sets given a fixed-size sample of the dataset. In combination with a cheap single-pass streaming evaluation of the candidate sets, this enables scalability to datasets with billions of molecules on a single machine. Ultimately, the sampling approach leads to the first distributed subgraph pattern mining algorithm that distributes the pattern space and the dataset graphs at the same time