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Tensors are a natural way to express correlations among many physical variables, but storing tensors in a computer naively requires memory which scales exponentially in the rank of the tensor. This is not optimal, as the required memory is…
As an entry for the 2012 Gordon-Bell performance prize, we report performance results of astrophysical N-body simulations of one trillion particles performed on the full system of K computer. This is the first gravitational trillion-body…
We develop the Blooming Tree Algorithm, a new technique that uses spectroscopic redshift data alone to identify the substructures and the surrounding groups of galaxy clusters, along with their member galaxies. Based on the estimated…
Fast multipole methods have O(N) complexity, are compute bound, and require very little synchronization, which makes them a favorable algorithm on next-generation supercomputers. Their most common application is to accelerate N-body…
Finding a maximum clique in a given graph is one of the fundamental NP-hard problems. We compare two multi-core thread-parallel adaptations of a state-of-the-art branch and bound algorithm for the maximum clique problem, and provide a novel…
The rigid gang task model is based on the idea of executing multiple threads simultaneously on a fixed number of processors to increase efficiency and performance. Although there is extensive literature on global rigid gang scheduling,…
Supertree construction is the process by which a set of phylogenetic trees, each on a subset of the overall set X of species, is combined into a tree on the full set S. The traditional use of supertree methods is the assembly of a large…
The understanding of the mechanisms driving vascular development is still limited. Techniques to generate vascular trees synthetically have been developed to tackle this problem. However, most algorithms are limited to single trees inside…
Machine learning has an emerging critical role in high-performance computing to modulate simulations, extract knowledge from massive data, and replace numerical models with efficient approximations. Decision forests are a critical tool…
In this paper, we present a new algorithm for parallel Monte Carlo tree search (MCTS). It is based on the pipeline pattern and allows flexible management of the control flow of the operations in parallel MCTS. The pipeline pattern provides…
Optimal power flow (OPF) is an important problem for power generation and it is in general non-convex. With the employment of renewable energy, it will be desirable if OPF can be solved very efficiently so its solution can be used in real…
We study the problem of finding a temporal hybridization network for a set of phylogenetic trees that minimizes the number of reticulations. First, we introduce an FPT algorithm for this problem on an arbitrary set of $m$ binary trees with…
Algorithms for finding minimum or bounded vertex covers in graphs use a branch-and-reduce strategy, which involves exploring a highly imbalanced search tree. Prior GPU solutions assign different thread blocks to different sub-trees, while…
Despite its groundbreaking success in Go and computer games, Monte Carlo Tree Search (MCTS) is computationally expensive as it requires a substantial number of rollouts to construct the search tree, which calls for effective…
The arboricity $\Gamma$ of a graph is the minimum number of forests its edge set can be partitioned into. Previous approximation schemes were nonconstructive, i.e., they only approximated the arboricity as a value without computing a…
Dynamic regression trees are an attractive option for automatic regression and classification with complicated response surfaces in on-line application settings. We create a sequential tree model whose state changes in time with the…
Training and inference in Gaussian processes (GPs) require solving linear systems with $n\times n$ kernel matrices. To address the prohibitive $\mathcal{O}(n^3)$ time complexity, recent work has employed fast iterative methods, like…
We present linear-time algorithms for partitioning a path or a tree with weights on the vertices by removing $k$ edges to maximize the minimum-weight component. We also use the same framework to partition a path with weight on the vertices,…
Depth first search (DFS) tree is one of the most well-known data structures for designing efficient graph algorithms. Given an undirected graph $G=(V,E)$ with $n$ vertices and $m$ edges, the textbook algorithm takes $O(n+m)$ time to…
We continue our presentation of VINE. We begin with a description of relevant architectural properties of the serial and shared memory parallel computers on which VINE is intended to run, and describe their influences on the design of the…