Related papers: Bigger Buffer k-d Trees on Multi-Many-Core Systems

Background: Short sequence substrings of a fixed length k, called k-mers, are a ubiquitous computational primitive in bioinformatics, used across sequence indexing, read mapping, genome assembly, metagenomic classification, and comparative…

Embedded devices collect and process significant amounts of data in a variety of applications including environmental monitoring, industrial automation and control, and other Internet of Things (IoT) applications. Storing data efficiently…

The whole computer hardware industry embraced multicores. For these machines, the extreme optimisation of sequential algorithms is no longer sufficient to squeeze the real machine power, which can be only exploited via thread-level…

Between the leaves and the nodes of a complete binary tree, a separate parent-child-sister hierarchy is employed independent of the parent-child-sister hierarchy used for the rest of the tree. Two different versions of such a local…

A recent work shows how we can optimize a tree based mode of operation for a rate 1 hash function. In particular, an algorithm and a theorem are presented for selecting a good tree topology in order to optimize both the running time and the…

In this paper, we present a probabilistic self-balancing dictionary data structure for massive data sets, and prove expected amortized I/O-optimal bounds on the dictionary operations. We show how to use the structure as an I/O-optimal…

There is a large discrepancy in our understanding of uncapacitated and capacitated versions of network location problems. This is perhaps best illustrated by the classical k-center problem: there is a simple tight 2-approximation algorithm…

Cartesian tree matching is the problem of finding all substrings of a given text which have the same Cartesian trees as that of a given pattern. So far there is one linear-time solution for Cartesian tree matching, which is based on the KMP…

The original description of the k-d tree recognized that rebalancing techniques, such as are used to build an AVL tree or a red-black tree, are not applicable to a k-d tree. Hence, in order to build a balanced k-d tree, it is necessary to…

In optimization or machine learning problems we are given a set of items, usually points in some metric space, and the goal is to minimize or maximize an objective function over some space of candidate solutions. For example, in clustering…

In this paper, we study the parallel query complexity of reconstructing biological and digital phylogenetic trees from simple queries involving their nodes. This is motivated from computational biology, data protection, and computer…

Graphs have been widely used in many applications such as social networks, collaboration networks, and biological networks. One important graph analytics is to explore cohesive subgraphs in a large graph. Among several cohesive subgraphs…

K-means is a popular clustering method used in data mining area. To work with large datasets, researchers propose PKMeans, which is a parallel k-means on MapReduce. However, the existing k-means parallelization methods including PKMeans…

Accurate and consistent methods for counting trees based on remote sensing data are needed to support sustainable forest management, assess climate change mitigation strategies, and build trust in tree carbon credits. Two-dimensional remote…

The kd-tree is a fundamental tool in computer science. Among others, an application of the kd-tree search (oct-tree method) to fast evaluation of particle interactions and neighbor search is highly important since computational complexity…

Tree boosting is a highly effective and widely used machine learning method. In this paper, we describe a scalable end-to-end tree boosting system called XGBoost, which is used widely by data scientists to achieve state-of-the-art results…

Establishing the correspondences between newly acquired points and historically accumulated data (i.e., map) through nearest neighbors search is crucial in numerous robotic applications. However, static tree data structures are inadequate…

Despite the growing popularity of explainable and interpretable machine learning, there is still surprisingly limited work on inherently interpretable clustering methods. Recently, there has been a surge of interest in explaining the…

Database Management Systems and K/V-Stores operate on updatable datasets -- massively exceeding the size of available main memory. Tree-based K/V storage management structures became particularly popular in storage engines. B+ Trees allow…

The Block Tree (BT) is a novel compact data structure designed to compress sequence collections. It obtains compression ratios close to Lempel-Ziv and supports efficient direct access to any substring. The BT divides the text recursively…