Related papers: Relative Suffix Trees
Single-nucleotide polymorphisms (SNPs) account for most variations between human genomes. We show how, if the genomes in a database differ only by a reasonable number of SNPs and the substrings between those SNPs are unique, then we can…
The well-known dictionary-based algorithms of the Lempel-Ziv (LZ) 77 family are the basis of several universal lossless compression techniques. These algorithms are asymmetric regarding encoding/decoding time and memory requirements, with…
We solve the problem of finding interspersed maximal repeats using a suffix array construction. As it is well known, all the functionality of suffix trees can be handled by suffix arrays, gaining practicality. Our solution improves the…
It is commonly accepted in the practice of on-line analytical processing of databases that the multidimensional database organization is less scalable than the relational one. It is easy to see that the size of the multidimensional…
We present several results about position heaps, a relatively new alternative to suffix trees and suffix arrays. First, we show that, if we limit the maximum length of patterns to be sought, then we can also limit the height of the heap and…
Big data, encompassing extensive datasets, has seen rapid expansion, notably with a considerable portion being textual data, including strings and texts. Simple compression methods and standard data structures prove inadequate for…
The problem of string reconstruction from substring information has found many applications due to its relevance in DNA- and polymer-based data storage. One practically important and challenging paradigm requires reconstructing mixtures of…
The quadratic complexity of self-attention constrains Large Language Models (LLMs) in processing long contexts, a capability essential for many advanced applications. Context compression aims to alleviate this computational bottleneck while…
Technology progress in DNA sequencing boosts the genomic database growth at faster and faster rate. Compression, accompanied with random access capabilities, is the key to maintain those huge amounts of data. In this paper we present an…
A suffix tree is able to efficiently locate a pattern in an indexed string, but not in general the most recent copy of the pattern in an online stream, which is desirable in some applications. We study the most general version of the…
Suffixient sets are a novel prefix array (PA) compression technique based on subsampling PA (rather than compressing the entire array like previous techniques used to do): by storing very few entries of PA (in fact, a compressed number of…
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…
A Supertree synthesizes the topologies of a set of phylogenetic trees carrying overlapping taxa set. In process, conflicts in the tree topologies are aimed to be resolved with the consensus clades. Such a problem is proved to be NP-hard.…
A central challenge in scaling up explicit state-space search for large tasks is compactly representing the set of generated states. Tree databases, a data structure from model checking, require constant space per generated state in the…
Can we do arithmetic in a completely different way, with a radically different data structure? Could this approach provide practical benefits, like operations on giant numbers while having an average performance similar to traditional…
Large-alphabet strings are common in scenarios such as information retrieval and natural-language processing. The efficient storage and processing of such strings usually introduces several challenges that are not witnessed in…
We study a suffix tree built from a sequence generated by a Markovian source. Such sources are more realistic probabilistic models for text generation, data compression, molecular applications, and so forth. We prove that the average size…
Document clustering as an unsupervised approach extensively used to navigate, filter, summarize and manage large collection of document repositories like the World Wide Web (WWW). Recently, focuses in this domain shifted from traditional…
Natural language text corpora are often available as sets of syntactically parsed trees. A wide range of expressive tree queries are possible over such parsed trees that open a new avenue in searching over natural language text. They not…
Rank and select queries are basic operations on sequences, with applications in compressed text indexes and other space-efficient data structures. One of the standard data structures supporting these queries is the wavelet tree. In this…