Related papers: A Self-Index on Block Trees
Containment-based trees encompass various handy structures such as B+-trees, R-trees and M-trees. They are widely used to build data indexes, range-queryable overlays, publish/subscribe systems both in centralized and distributed contexts.…
Log-Structured Merge (LSM) Trees provide a tiered data storage and retrieval paradigm that is attractive for write-optimized data systems. Maintaining an efficient buffer in memory and deferring updates past their initial write-time, the…
Large Language Models (LLMs) show promise in code generation tasks. However, their code-writing abilities are often limited in scope: while they can successfully implement simple functions, they struggle with more complex tasks. A…
Tree-structured neural networks encode a particular tree geometry for a sentence in the network design. However, these models have at best only slightly outperformed simpler sequence-based models. We hypothesize that neural sequence models…
The class of self-nested trees presents remarkable compression properties because of the systematic repetition of subtrees in their structure. In this paper, we provide a better combinatorial characterization of this specific family of…
We define an algorithm that parses multidimensional arrays sequentially into mainly unrepeated but nested multidimensional sub-arrays of increasing size, and show that the resulting sub-block pointer encoder compresses almost every…
Shannon's entropy is a clear lower bound for statistical compression. The situation is not so well understood for dictionary-based compression. A plausible lower bound is $b$, the least number of phrases of a general bidirectional parse of…
We present the first worst-case linear-time algorithm to compute the Lempel-Ziv 78 factorization of a given string over an integer alphabet. Our algorithm is based on nearest marked ancestor queries on the suffix tree of the given string.…
A common approach to implementing similarity search applications is the usage of distance functions, where small distances indicate high similarity. In the case of metric distance functions, metric index structures can be used to accelerate…
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…
Recent advancements in large language models have significantly improved their context windows, yet challenges in effective long-term memory management remain. We introduce MemTree, an algorithm that leverages a dynamic, tree-structured…
In this paper we describe compressed indexes that support pattern matching queries for strings with wildcards. For a constant size alphabet our data structure uses $O(n\log^{\varepsilon}n)$ bits for any $\varepsilon>0$ and reports all…
We show how, given a straight-line program with $g$ rules for a binary string $B$ of length $n$, in $O(g^{2 / 3} n^{4 / 3})$ time we can build a linear-space index such that, given $m$ and $c$, in O(1) time we can determine whether there is…
Indexing highly repetitive texts --- such as genomic databases, software repositories and versioned text collections --- has become an important problem since the turn of the millennium. A relevant compressibility measure for repetitive…
We show how a few modifications to the red-black trees allow for $O(1)$ worst-case update time (once the position of the inserted or deleted element is known). The resulting structure is based on relaxing some of the properties of the…
The order preserving pattern matching (OPPM) problem is, given a pattern string $p$ and a text string $t$, find all substrings of $t$ which have the same relative orders as $p$. In this paper, we consider two variants of the OPPM problem…
The wavelet tree (Grossi et al. [SODA, 2003]) and wavelet matrix (Claude et al. [Inf. Syst., 47:15--32, 2015]) are compact indices for texts over an alphabet $[0,\sigma)$ that support rank, select and access queries in $O(\lg \sigma)$ time.…
A recent work shows how we can optimize a tree based mode of operation for a hash function where the sizes of input message blocks and digest are the same, subject to the constraint that the involved tree structure has all its leaves at the…
As an emerging field, MS-based proteomics still requires software tools for efficiently storing and accessing experimental data. In this work, we focus on the management of LC-MS data, which are typically made available in standard…
We introduce top trees as a design of a new simpler interface for data structures maintaining information in a fully-dynamic forest. We demonstrate how easy and versatile they are to use on a host of different applications. For example, we…