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This paper investigates the execution of tree-shaped task graphs using multiple processors. Each edge of such a tree represents some large data. A task can only be executed if all input and output data fit into memory, and a data can only…
Comparing and aligning large datasets is a pervasive problem occurring across many different knowledge domains. We introduce and study MREC, a recursive decomposition algorithm for computing matchings between data sets. The basic idea is to…
We give an overview of the theoretical results for matrix block-recursive algorithms in commutative domains and present the results of experiments that we conducted with new parallel programs based on these algorithms on a supercomputer…
Trees or rooted trees have been generously studied in the literature. A forest is a set of trees or rooted trees. Here we give recurrence relations between the number of some kind of rooted forest with $k$ roots and that with $k+1$ roots on…
This paper presents a new algorithm for the fast, shared memory, multi-core computation of augmented contour trees on triangulations. In contrast to most existing parallel algorithms our technique computes augmented trees, enabling the full…
Determining the interaction partners among protein/domain families poses hard computational problems, in particular in the presence of paralogous proteins. Available approaches aim to identify interaction partners among protein/domain…
Most of major algorithms for phylogenetic tree reconstruction assume that sequences in the analyzed set either do not have any offspring, or that parent sequences can maximally mutate into just two descendants. The graph resulting from such…
This study presents constructions of the space-time Conservation Element and Solution Element (CESE) methods to accommodate adaptive unstructured quadrilateral meshes. Subsequently, a novel algorithm is devised to effectively manage the…
In this paper, we present a distributed algorithm to compute various parameters of a tree such as the process number, the edge search number or the node search number and so the pathwidth. This algorithm requires n steps, an overall…
We present here the result of continuation work, performed to further fulfill the vision we outlined in [Harel,Lekien,P\'eba\"y-2017] for the visualization and analysis of tree-based adaptive mesh refinement (AMR) simulations, using the…
Neural Networks and Decision Trees: two popular techniques for supervised learning that are seemingly disconnected in their formulation and optimization method, have recently been combined in a single construct. The connection pivots on…
Reverse search is a convenient method for enumerating structured objects, that can be used both to address theoretical issues and to solve data mining problems. This method has already been successfully developed to handle unordered trees.…
Balanced search trees are widely used in computer science to efficiently maintain dynamic ordered data. To support efficient set operations (e.g., union, intersection, difference) using trees, the join-based framework is widely studied.…
This paper presents an octree construction method, called Cornerstone, that facilitates global domain decomposition and interactions between particles in mesh-free numerical simulations. Our method is based on algorithms developed for 3D…
We describe an OctTree algorithm for the MPI-parallel, adaptive mesh-refinement code {\sc FLASH}, which can be used to calculate the gas self-gravity, and also the angle-averaged local optical depth, for treating ambient diffuse radiation.…
Deep research agents, which synthesize information across diverse sources, are significantly constrained by the sequential nature of reasoning. This bottleneck results in high latency, poor runtime adaptability, and inefficient resource…
Existing parallel algorithms for wavelet tree construction have a work complexity of $O(n\log\sigma)$. This paper presents parallel algorithms for the problem with improved work complexity. Our first algorithm is based on parallel integer…
Neighborhood algorithms may take a considerable percentage of computer time in discrete element methods (DEM). While the sort-and-sweep algorithm is ideal in some ways, as it only deal with particles whose relative positions change in one…
This work introduces a novel, fully robust and highly-scalable, $h$-adaptive aggregated unfitted finite element method for large-scale interface elliptic problems. The new method is based on a recent distributed-memory implementation of the…
Algorithms based on spatial tree traversal are widely regarded as among the most efficient and flexible approaches for many problems in CPU-based high-performance computing (HPC). However, directly transferring these algorithms to GPU…