Related papers: FMtree: A fast locating algorithm of FM-indexes fo…
Summary: We present a new method to incrementally construct the FM-index for both short and long sequence reads, up to the size of a genome. It is the first algorithm that can build the index while implicitly sorting the sequences in the…
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…
We propose BS-tree, an in-memory implementation of the B+-tree that adopts the structure of the disk-based index (i.e., a balanced, multiway tree), setting the node size to a memory block that can be processed fast and in parallel using…
In this paper we present a novel probabilistic sampling-based motion planning algorithm called the Fast Marching Tree algorithm (FMT*). The algorithm is specifically aimed at solving complex motion planning problems in high-dimensional…
LRM-Trees are an elegant way to partition a sequence of values into sorted consecutive blocks, and to express the relative position of the first element of each block within a previous block. They were used to encode ordinal trees and to…
We propose a new linear-size data structure which provides a fast access to all palindromic substrings of a string or a set of strings. This structure inherits some ideas from the construction of both the suffix trie and suffix tree. Using…
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 texts…
The FM-index is a well-known compressed full-text index, based on the Burrows-Wheeler transform (BWT). During a pattern search, the BWT sequence is accessed at "random" locations, which is cache-unfriendly. In this paper, we are interested…
The recent introduction of learned indexes has shaken the foundations of the decades-old field of indexing data structures. Combining, or even replacing, classic design elements such as B-tree nodes with machine learning models has proven…
Text indexing is a classical algorithmic problem that has been studied for over four decades: given a text $T$, pre-process it off-line so that, later, we can quickly count and locate the occurrences of any string (the query pattern) in $T$…
Inducing latent tree structures from sequential data is an emerging trend in the NLP research landscape today, largely popularized by recent methods such as Gumbel LSTM and Ordered Neurons (ON-LSTM). This paper proposes FASTTREES, a new…
Searching for all occurrences of a pattern in a text is a fundamental problem in computer science with applications in many other fields, like natural language processing, information retrieval and computational biology. In the last two…
In this paper, we describe a new type of match between a pattern and a text that aren't necessarily maximal in the query, but still contain useful matching information: locally maximal exact matches (LEMs). There are usually a large amount…
The suffix array is an efficient data structure for in-memory pattern search. Suffix arrays can also be used for external-memory pattern search, via two-level structures that use an internal index to identify the correct block of suffix…
We consider the task of optimizing the B-tree data structure, used extensively in operating systems and databases, for sustainable usage on multi-level flash memory. Empirical evidence shows that this new flash memory tree, or FM Tree,…
Next Generation Sequencing (NGS) platforms and, more generally, high-throughput technologies are giving rise to an exponential growth in the size of nucleotide sequence databases. Moreover, many emerging applications of nucleotide datasets…
An indexed sequence of strings is a data structure for storing a string sequence that supports random access, searching, range counting and analytics operations, both for exact matches and prefix search. String sequences lie at the core of…
Efficiently word storing and searching is an important task in computer science. An application space complexity, time complexity, and overall performance depend on this string data. Many word searching data structures and algorithms exist…
We address the problem of summarizing embedded tree patterns extracted from large data trees. We do so by defining and mining closed and maximal embedded unordered tree patterns from a single large data tree. We design an embedded frequent…
Text retrieval using learned sparse representations of queries and documents has, over the years, evolved into a highly effective approach to search. It is thanks to recent advances in approximate nearest neighbor search-with the emergence…