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Efficient index structures for fast approximate nearest neighbor queries are required in many applications such as recommendation systems. In high-dimensional spaces, many conventional methods suffer from excessive usage of memory and slow…

We propose a parallel algorithm for local, on the fly, model checking of a fragment of CTL that is well-suited for modern, multi-core architectures. This model-checking algorithm takes bene t from a parallel state space construction…

The kernel method is a potential approach to analyzing structured data such as sequences, trees, and graphs; however, unordered trees have not been investigated extensively. Kimura et al. (2011) proposed a kernel function for unordered…

We present an algorithm for parallelising the TreePM code. We use both functional and domain decompositions. Functional decomposition is used to separate the computation of long range and short range forces, as well as the task of…

This paper presents \pandora, a novel parallel algorithm for efficiently constructing dendrograms for single-linkage hierarchical clustering, including \hdbscan. Traditional dendrogram construction methods from a minimum spanning tree…

Gaussian processes (GPs) produce good probabilistic models of functions, but most GP kernels require $O((n+m)n^2)$ time, where $n$ is the number of data points and $m$ the number of predictive locations. We present a new kernel that allows…

All-gather collective communication is one of the most important communication primitives in parallel and distributed computation, which plays an essential role in many HPC applications such as distributed Deep Learning (DL) with model and…

The suffix tree is a data structure for indexing strings. It is used in a variety of applications such as bioinformatics, time series analysis, clustering, text editing and data compression. However, when the string and the resulting suffix…

Computing an optimal classification tree that provably maximizes training performance within a given size limit, is NP-hard, and in practice, most state-of-the-art methods do not scale beyond computing optimal trees of depth three.…

Miller and Reif's FOCS'85 classic and fundamental tree contraction algorithm is a broadly applicable technique for the parallel solution of a large number of tree problems. Additionally it is also used as an algorithmic design technique for…

In this short paper, we explore a new way to refactor a simple but tricky-to-parallelize tree-traversal algorithm to harness multicore parallelism. Crucially, the refactoring draws from some classic techniques from programming-languages…

This Article presents two optimized multi-GPU algorithms for Fock matrix construction, building on the work of Ufimtsev et al. and Barca et al. The novel algorithms, opt-UM and opt-Brc, introduce significant enhancements, including improved…

The study of optimal decision trees has gained increasing attention in recent years; however, despite substantial progress, it still suffers from two major challenges: First, trees constructed by existing optimal decision tree (ODT)…

In this paper, we propose the distributed tree kernels (DTK) as a novel method to reduce time and space complexity of tree kernels. Using a linear complexity algorithm to compute vectors for trees, we embed feature spaces of tree fragments…

Large-scale parallel numerical simulations are essential for a wide range of engineering problems that involve complex, coupled physical processes interacting across a broad range of spatial and temporal scales. The data structures involved…

Graphics processing units have been extensively used to accelerate classical molecular dynamics simulations. However, there is much less progress on the acceleration of force evaluations for many-body potentials compared to pairwise ones.…

We present efficient algorithms to build data structures and the lists needed for fast multipole methods. The algorithms are capable of being efficiently implemented on both serial, data parallel GPU and on distributed architectures. With…

We present a deterministic algorithm for solving a wide range of dynamic programming problems in trees in $O(\log D)$ rounds in the massively parallel computation model (MPC), with $O(n^\delta)$ words of local memory per machine, for any…

Finding the exact close neighbors of each fluid element in mesh-free computational hydrodynamical methods, such as the Smoothed Particle Hydrodynamics (SPH), often becomes a main bottleneck for scaling their performance beyond a few million…

Data intensive applications on clusters often require requests quickly be sent to the node managing the desired data. In many applications, one must look through a sorted tree structure to determine the responsible node for accessing or…