Using Graph Properties to Speed-up GPU-based Graph Traversal: A Model-driven Approach

While it is well-known and acknowledged that the performance of graph algorithms is heavily dependent on the input data, there has been surprisingly little research to quantify and predict the impact the graph structure has on performance. Parallel graph algorithms, running on many-core systems such as GPUs, are no exception: most research has focused on how to efficiently implement and tune different graph operations on a specific GPU. However, the performance impact of the input graph has only been taken into account indirectly as a result of the graphs used to benchmark the system. In this work, we present a case study investigating how to use the properties of the input graph to improve the performance of the breadth-first search (BFS) graph traversal. To do so, we first study the performance variation of 15 different BFS implementations across 248 graphs. Using this performance data, we show that significant speed-up can be achieved by combining the best implementation for each level of the traversal. To make use of this data-dependent optimization, we must correctly predict the relative performance of algorithms per graph level, and enable dynamic switching to the optimal algorithm for each level at runtime. We use the collected performance data to train a binary decision tree, to enable high-accuracy predictions and fast switching. We demonstrate empirically that our decision tree is both fast enough to allow dynamic switching between implementations, without noticeable overhead, and accurate enough in its prediction to enable significant BFS speedup. We conclude that our model-driven approach (1) enables BFS to outperform state of the art GPU algorithms, and (2) can be adapted for other BFS variants, other algorithms, or more specific datasets

A Network Science perspective of Graph Convolutional Networks: A survey

The mining and exploitation of graph structural information have been the focal points in the study of complex networks. Traditional structural measures in Network Science focus on the analysis and modelling of complex networks from the perspective of network structure, such as the centrality measures, the clustering coefficient, and motifs and graphlets, and they have become basic tools for studying and understanding graphs. In comparison, graph neural networks, especially graph convolutional networks (GCNs), are particularly effective at integrating node features into graph structures via neighbourhood aggregation and message passing, and have been shown to significantly improve the performances in a variety of learning tasks. These two classes of methods are, however, typically treated separately with limited references to each other. In this work, aiming to establish relationships between them, we provide a network science perspective of GCNs. Our novel taxonomy classifies GCNs from three structural information angles, i.e., the layer-wise message aggregation scope, the message content, and the overall learning scope. Moreover, as a prerequisite for reviewing GCNs via a network science perspective, we also summarise traditional structural measures and propose a new taxonomy for them. Finally and most importantly, we draw connections between traditional structural approaches and graph convolutional networks, and discuss potential directions for future research

Benchmarking optimization algorithms for auto-tuning GPU kernels

Recent years have witnessed phenomenal growth in the application, and capabilities of Graphical Processing Units (GPUs) due to their high parallel computation power at relatively low cost. However, writing a computationally efficient GPU program (kernel) is challenging, and generally only certain specific kernel configurations lead to significant increases in performance. Auto-tuning is the process of automatically optimizing software for highly-efficient execution on a target hardware platform. Auto-tuning is particularly useful for GPU programming, as a single kernel requires re-tuning after code changes, for different input data, and for different architectures. However, the discrete, and non-convex nature of the search space creates a challenging optimization problem. In this work, we investigate which algorithm produces the fastest kernels if the time-budget for the tuning task is varied. We conduct a survey by performing experiments on 26 different kernel spaces, from 9 different GPUs, for 16 different evolutionary black-box optimization algorithms. We then analyze these results and introduce a novel metric based on the PageRank centrality concept as a tool for gaining insight into the difficulty of the optimization problem. We demonstrate that our metric correlates strongly with observed tuning performance.Comment: in IEEE Transactions on Evolutionary Computation, 202

Performance, memory efficiency and programmability: the ambitious triptych of combining vertex-centricity with HPC

The field of graph processing has grown significantly due to the flexibility and wide applicability of the graph data structure. In the meantime, so has interest from the community in developing new approaches to graph processing applications. In 2010, Google introduced the vertex-centric programming model through their framework Pregel. This consists of expressing computation from the perspective of a vertex, whilst inter-vertex communications are achieved via data exchanges along incoming and outgoing edges, using the message-passing abstraction provided. Pregel ’s high-level programming interface, designed around a set of simple functions, provides ease of programmability to the user. The aim is to enable the development of graph processing applications without requiring expertise in optimisation or parallel programming. Such challenges are instead abstracted from the user and offloaded to the underlying framework. However, fine-grained synchronisation, unpredictable memory access patterns and multiple sources of load imbalance make it difficult to implement the vertex centric model efficiently on high performance computing platforms without sacrificing programmability. This research focuses on combining vertex-centric and High-Performance Comput- ing (HPC), resulting in the development of a shared-memory framework, iPregel, which demonstrates that a performance and memory efficiency similar to that of non-vertex- centric approaches can be achieved while preserving the programmability benefits of vertex-centric. Non-volatile memory is then explored to extend single-node capabilities, during which multiple versions of iPregel are implemented to experiment with the various data movement strategies. Then, distributed memory parallelism is investigated to overcome the resource limitations of single node processing. A second framework named DiP, which ports applicable iPregel ’s optimisations to distributed memory, prioritises performance to high scalability. This research has resulted in a set of techniques and optimisations illustrated through a shared-memory framework iPregel and a distributed-memory framework DiP. The former closes a gap of several orders of magnitude in both performance and memory efficiency, even able to process a graph of 750 billion edges using non-volatile memory. The latter has proved that this competitiveness can also be scaled beyond a single node, enabling the processing of the largest graph generated in this research, comprising 1.6 trillion edges. Most importantly, both frameworks achieved these performance and capability gains whilst also preserving programmability, which is the cornerstone of the vertex-centric programming model. This research therefore demonstrates that by combining vertex-centricity and High-Performance Computing (HPC), it is possible to maintain performance, memory efficiency and programmability

Learning domain-specific sentiment lexicons with applications to recommender systems

Search is now going beyond looking for factual information, and people wish to search for the opinions of others to help them in their own decision-making. Sentiment expressions or opinion expressions are used by users to express their opinion and embody important pieces of information, particularly in online commerce. The main problem that the present dissertation addresses is how to model text to find meaningful words that express a sentiment. In this context, I investigate the viability of automatically generating a sentiment lexicon for opinion retrieval and sentiment classification applications. For this research objective we propose to capture sentiment words that are derived from online users’ reviews. In this approach, we tackle a major challenge in sentiment analysis which is the detection of words that express subjective preference and domain-specific sentiment words such as jargon. To this aim we present a fully generative method that automatically learns a domain-specific lexicon and is fully independent of external sources. Sentiment lexicons can be applied in a broad set of applications, however popular recommendation algorithms have somehow been disconnected from sentiment analysis. Therefore, we present a study that explores the viability of applying sentiment analysis techniques to infer ratings in a recommendation algorithm. Furthermore, entities’ reputation is intrinsically associated with sentiment words that have a positive or negative relation with those entities. Hence, is provided a study that observes the viability of using a domain-specific lexicon to compute entities reputation. Finally, a recommendation system algorithm is improved with the use of sentiment-based ratings and entities reputation

Similarity Search over Network Structure

With the advent of the Internet, graph-structured data are ubiquitous. An essential task for graph-structured data management is similarity search based on graph topology, with a wide spectrum of applications, e.g., web search, outlier detection, co-citation analysis, and collaborative filtering. These graph topology data arrive from multiple sources at an astounding velocity, volume and veracity. While the scale of network structured data is increasing, existing similarity search algorithms on large graphs are impractical due to their expensive costs in terms of computational time and memory space. Moreover, dynamic changes (e.g., noise and abnormality) exists in network data, and it arises from many factors, such as data loss in transfer, data incompleteness, and dirty reading. Thus, the dynamic changes have become the main barrier to gaining accurate results for efficient network analysis. In real Web applications, CoSimRank has been proposed as a robust measure of node-pair similarity based on graph topology. It follows a SimRank-like notion that “two nodes are considered as similar if their in-neighbours are similar”, but the similarity of each node with itself is not constantly 1, which is different from SimRank. However, existing work on CoSimRank is restricted to static graphs. Each node pair CoSimRank score is retrieved from the sum of dot products of two Personalised PageRank vectors. When the graph is updated with edges (nodes) addition and deletion over time, it is cost-inhibitive to recompute all CoSimRank scores from scratch, which is impractical. RoleSim is a popular graph-structural role similarity search measure with many applications (e.g., sociometry), it can get the automorphic equivalence of nodes pair similarity, which SimRank and CoSimRank lack. But the accuracy of RoleSim algorithm can be improved. In this study, (1) we propose fast dynamic scheme, D-CoSim and D-deCoSim, for accurate CoSimRank search over large-scale evolving graphs. (2) Based on D-CoSim, we also propose fast scheme, F-CoSim and Opt_F-CoSim, which greatly accelerates CoSimRank search over static graphs. Our theoretical analysis shows that D-CoSim, D-deCoSim F-CoSim and Opt_F-CoSim guarantee the exactness of CoSimRank scores. Experimental evaluations verify the superiority of D-CoSim and D-deCoSim over evolving graphs, and the fast speedupof F-CoSim and Opt_F-CoSim on large-scale static graphs against its competitors, without any loss of accuracy. (3) We propose a novel role similarity search algorithm FaRS, and a speedup algorithm Opt_FaRS, which guarantees the automorphic equivalence capture, and captures the information from the neighbour’s class. The experimental results of FaRS and Opt_FaRS show that our algorithms achieves higher accuracy than baseline algorithms

Exposition on over-squashing problem on GNNs: Current Methods, Benchmarks and Challenges

Graph-based message-passing neural networks (MPNNs) have achieved remarkable success in both node and graph-level learning tasks. However, several identified problems, including over-smoothing (OSM), limited expressive power, and over-squashing (OSQ), still limit the performance of MPNNs. In particular, OSQ serves as the latest identified problem, where MPNNs gradually lose their learning accuracy when long-range dependencies between graph nodes are required. In this work, we provide an exposition on the OSQ problem by summarizing different formulations of OSQ from current literature, as well as the three different categories of approaches for addressing the OSQ problem. In addition, we also discuss the alignment between OSQ and expressive power and the trade-off between OSQ and OSM. Furthermore, we summarize the empirical methods leveraged from existing works to verify the efficiency of OSQ mitigation approaches, with illustrations of their computational complexities. Lastly, we list some open questions that are of interest for further exploration of the OSQ problem along with potential directions from the best of our knowledge

Efficient Node Proximity and Node Significance Computations in Graphs

abstract: Node proximity measures are commonly used for quantifying how nearby or otherwise related to two or more nodes in a graph are. Node significance measures are mainly used to find how much nodes are important in a graph. The measures of node proximity/significance have been highly effective in many predictions and applications. Despite their effectiveness, however, there are various shortcomings. One such shortcoming is a scalability problem due to their high computation costs on large size graphs and another problem on the measures is low accuracy when the significance of node and its degree in the graph are not related. The other problem is that their effectiveness is less when information for a graph is uncertain. For an uncertain graph, they require exponential computation costs to calculate ranking scores with considering all possible worlds. In this thesis, I first introduce Locality-sensitive, Re-use promoting, approximate Personalized PageRank (LR-PPR) which is an approximate personalized PageRank calculating node rankings for the locality information for seeds without calculating the entire graph and reusing the precomputed locality information for different locality combinations. For the identification of locality information, I present Impact Neighborhood Indexing (INI) to find impact neighborhoods with nodes' fingerprints propagation on the network. For the accuracy challenge, I introduce Degree Decoupled PageRank (D2PR) technique to improve the effectiveness of PageRank based knowledge discovery, especially considering the significance of neighbors and degree of a given node. To tackle the uncertain challenge, I introduce Uncertain Personalized PageRank (UPPR) to approximately compute personalized PageRank values on uncertainties of edge existence and Interval Personalized PageRank with Integration (IPPR-I) and Interval Personalized PageRank with Mean (IPPR-M) to compute ranking scores for the case when uncertainty exists on edge weights as interval values.Dissertation/ThesisDoctoral Dissertation Computer Science 201