Related papers: Extending the Burrows-Wheeler Transform for Cartes…
The need for Knowledge and Data Discovery Management Systems (KDDMS) that support ad hoc data mining queries has been long recognized. A significant amount of research has gone into building tightly coupled systems that integrate…
We consider the design of adaptive data structures for searching elements of a tree-structured space. We use a natural generalization of the rotation-based online binary search tree model in which the underlying search space is the set of…
In this paper, we revisit the problem of indexing multi-dimensional data in memory for the efficient support of multi-dimensional range queries and nearest neighbor queries. This is a classic problem in main-memory databases, where there is…
The issue of internal fragmentation in data structures is a fundamental challenge in database design. A seminal result of Yao in this field shows that evenly splitting the leaves of a B-tree against a workload of uniformly random insertions…
Compact and I/O-efficient data representations play an important role in efficient algorithm design, as memory bandwidth and latency can present a significant performance bottleneck, slowing the computation by orders of magnitude. While…
Motivation: Burrows-Wheeler Transform (BWT) is a common component in full-text indices. Initially developed for data compression, it is particularly powerful for encoding redundant sequences such as pangenome data. However, BWT construction…
The widespread use of GPS-enabled devices generates voluminous and continuous amounts of traffic data but analyzing such data for interpretable and actionable insights poses challenges. A hierarchical clustering of the trips has many uses…
In recent years, non-parametric methods utilizing random walks on graphs have been used to solve a wide range of machine learning problems, but in their simplest form they do not scale well due to the quadratic complexity. In this paper, a…
Traditional indexing techniques commonly employed in da\-ta\-ba\-se systems perform poorly on multidimensional array scientific data. Bitmap indices are widely used in commercial databases for processing complex queries, due to their…
We propose a novel framework for fast integral operations by uncovering hidden geometries in the row and column structures of the underlying operators. This is accomplished through the \texttt{Questionnaire} algorithm, an iterative…
In this paper, we present a new data structure called the packed compact trie (packed c-trie) which stores a set $S$ of $k$ strings of total length $n$ in $n \log\sigma + O(k \log n)$ bits of space and supports fast pattern matching queries…
A basic problem in metagenomics is to assign a sequenced read to the correct species in the reference collection. In typical applications in genomic epidemiology and viral metagenomics the reference collection consists of set of species…
Constructing the Burrows-Wheeler transform (BWT) for long strings poses significant challenges regarding construction time and memory usage. We use a prefix of the suffix array to partition a long string into shorter substrings, thereby…
We introduce the lazy search tree data structure. The lazy search tree is a comparison-based data structure on the pointer machine that supports order-based operations such as rank, select, membership, predecessor, successor, minimum, and…
One of the challenges for optimizing compilers is to predict whether applying an optimization will improve its execution speed. Programmers may override the compiler's profitability heuristic using optimization directives such as pragmas in…
Creating or modifying a primary index is a time-consuming process, as the index typically needs to be rebuilt from scratch. In this paper, we explore a more graceful "just-in-time" approach to index reorganization, where small changes are…
We develop an efficient algorithm to implement the recently introduced binary tree state (BTS) ansatz on a classical computer. BTS allows a simple approximation to permanents arising from the computationally intractable antisymmetric…
There now exist compact indexes that can efficiently list all the occurrences of a pattern in a dataset consisting of thousands of genomes, or even all the occurrences of all the pattern's maximal exact matches (MEMs) with respect to the…
It is known that the exact form of the Burrows-Wheeler-Transform (BWT) of a string collection depends, in most implementations, on the input order of the strings in the collection. Reordering strings of an input collection affects the…
Spatiotemporal vector retrieval has emerged as a critical paradigm in modern information retrieval, enabling efficient access to massive, heterogeneous data that evolve over both time and space. However, existing spatiotemporal retrieval…