Related papers: A comparison between Fast Multipole Algorithm and …
Given two rooted phylogenetic trees on the same set of taxa X, the Maximum Agreement Forest problem (MAF) asks to find a forest that is, in a certain sense, common to both trees and has a minimum number of components. The Maximum Acyclic…
(Abridged) We have developed a numerical software library for collisionless N-body simulations named "Phantom-GRAPE" which highly accelerates force calculations among particles by use of a new SIMD instruction set extension to the x86…
We implement an adaptation of the COLA approach, a hybrid scheme that combines Lagrangian perturbation theory with an N-body approach, to model non-linear collapse in chameleon and symmetron modified gravity models. Gravitational screening…
An adaptation of the Particle-Particle/Particle-Mesh (P3M) code to the special purpose hardware GRAPE is presented. The short range force is calculated by a four chip GRAPE-3A board, while the rest of the calculation is performed on a Sun…
In this paper we study a scheduling problem arising from executing numerical simulations on HPC architectures. With a constant number of parallel machines, the objective is to minimize the makespan under memory constraints for the machines.…
The concept of gray-box optimization, in juxtaposition to black-box optimization, revolves about the idea of exploiting the problem structure to implement more efficient evolutionary algorithms (EAs). Work on factorized distribution…
We present a new algorithm to rapidly compute the two-point (2PCF), three-point (3PCF) and n-point (n-PCF) correlation functions in roughly O(N log N) time for N particles, instead of O(N^n) as required by brute force approaches. The…
We describe a new parallel N-body code for cosmological simulations. The code is based on a work- and data sharing scheme, and is implemented within the Cray Research Corporation's CRAFT programming environment. Different data distribution…
We call matrix algorithms superfast if they use much fewer flops and memory cells than the input matrix has entries. Using such algorithms is indispensable for Big Data Mining and Analysis, where the input matrices are so immense that one…
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.…
Cosmological simulations are useful tools for studying the evolution of galaxies, and it is critical to accurately identify galaxies and their halos from raw simulation data. The friends-of-friend (FoF) algorithm has been widely adopted for…
Decision trees and random forest remain highly competitive for classification on medium-sized, standard datasets due to their robustness, minimal preprocessing requirements, and interpretability. However, a single tree suffers from high…
We have developed a parallel Particle-Particle, Particle-Mesh (P3M) simulation code for the Cray T3E parallel supercomputer that is well suited to studying the time evolution of systems of particles interacting via gravity and gas forces in…
We consider the multivariate interlace polynomial introduced by Courcelle (2008), which generalizes several interlace polynomials defined by Arratia, Bollobas, and Sorkin (2004) and by Aigner and van der Holst (2004). We present an…
Efficient automatic protein classification is of central importance in genomic annotation. As an independent way to check the reliability of the classification, we propose a statistical approach to test if two sets of protein domain…
We study the robustness verification problem for tree-based models, including decision trees, random forests (RFs) and gradient boosted decision trees (GBDTs). Formal robustness verification of decision tree ensembles involves finding the…
In this paper, we present a numerical algorithm for the accurate and efficient computation of the convolution of the frequency domain layered media Green's function with a given density function. Instead of compressing the convolution…
The treedepth of a graph $G$ is the least possible depth of an elimination forest of $G$: a rooted forest on the same vertex set where every pair of vertices adjacent in $G$ is bound by the ancestor/descendant relation. We propose an…
Understanding how nonlinear dynamical systems (e.g., artificial neural networks and neural circuits) process information requires comparing their underlying dynamics at scale, across diverse architectures and large neural recordings. While…
In dislocation dynamics (DD) simulations, the most computationally intensive step is the evaluation of the elastic interaction forces among dislocation ensembles. Because the pair-wise interaction between dislocations is long-range, this…