Tree-Independent Dual-Tree Algorithms

Dual-tree algorithms are a widely used class of branch-and-bound algorithms. Unfortunately, developing dual-tree algorithms for use with different trees and problems is often complex and burdensome. We introduce a four-part logical split: the tree, the traversal, the point-to-point base case, and the pruning rule. We provide a meta-algorithm which allows development of dual-tree algorithms in a tree-independent manner and easy extension to entirely new types of trees. Representations are provided for five common algorithms; for k-nearest neighbor search, this leads to a novel, tighter pruning bound. The meta-algorithm also allows straightforward extensions to massively parallel settings.Comment: accepted in ICML 201

JGraphT -- A Java library for graph data structures and algorithms

Mathematical software and graph-theoretical algorithmic packages to efficiently model, analyze and query graphs are crucial in an era where large-scale spatial, societal and economic network data are abundantly available. One such package is JGraphT, a programming library which contains very efficient and generic graph data-structures along with a large collection of state-of-the-art algorithms. The library is written in Java with stability, interoperability and performance in mind. A distinctive feature of this library is the ability to model vertices and edges as arbitrary objects, thereby permitting natural representations of many common networks including transportation, social and biological networks. Besides classic graph algorithms such as shortest-paths and spanning-tree algorithms, the library contains numerous advanced algorithms: graph and subgraph isomorphism; matching and flow problems; approximation algorithms for NP-hard problems such as independent set and TSP; and several more exotic algorithms such as Berge graph detection. Due to its versatility and generic design, JGraphT is currently used in large-scale commercial, non-commercial and academic research projects. In this work we describe in detail the design and underlying structure of the library, and discuss its most important features and algorithms. A computational study is conducted to evaluate the performance of JGraphT versus a number of similar libraries. Experiments on a large number of graphs over a variety of popular algorithms show that JGraphT is highly competitive with other established libraries such as NetworkX or the BGL.Comment: Major Revisio

Scaling Limits for Minimal and Random Spanning Trees in Two Dimensions

A general formulation is presented for continuum scaling limits of stochastic spanning trees. A spanning tree is expressed in this limit through a consistent collection of subtrees, which includes a tree for every finite set of endpoints in $\R^d$. Tightness of the distribution, as $\delta \to 0$, is established for the following two-dimensional examples: the uniformly random spanning tree on $\delta \Z^2$, the minimal spanning tree on $\delta \Z^2$ (with random edge lengths), and the Euclidean minimal spanning tree on a Poisson process of points in $\R^2$ with density $\delta^{-2}$. In each case, sample trees are proven to have the following properties, with probability one with respect to any of the limiting measures: i) there is a single route to infinity (as was known for $\delta > 0$), ii) the tree branches are given by curves which are regular in the sense of H\"older continuity, iii) the branches are also rough, in the sense that their Hausdorff dimension exceeds one, iv) there is a random dense subset of $\R^2$, of dimension strictly between one and two, on the complement of which (and only there) the spanning subtrees are unique with continuous dependence on the endpoints, v) branching occurs at countably many points in $\R^2$, and vi) the branching numbers are uniformly bounded. The results include tightness for the loop erased random walk (LERW) in two dimensions. The proofs proceed through the derivation of scale-invariant power bounds on the probabilities of repeated crossings of annuli.Comment: Revised; 54 pages, 6 figures (LaTex

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