Related papers: FMtree: A fast locating algorithm of FM-indexes fo…
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…
Traditional decision tree algorithms are explainable but struggle with non-linear, high-dimensional data, limiting its applicability in complex decision-making. Neural networks excel at capturing complex patterns but sacrifice…
Data mining has been widely recognized as a powerful tool to explore added value from large-scale databases. Finding frequent item sets in databases is a crucial in data mining process of extracting association rules. Many algorithms were…
Recent studies have shown that Dense Retrieval (DR) techniques can significantly improve the performance of first-stage retrieval in IR systems. Despite its empirical effectiveness, the application of DR is still limited. In contrast to…
Substructure search in chemical compound databases is a fundamental task in cheminformatics with critical implications for fields such as drug discovery, materials science, and toxicology. However, the increasing size and complexity of…
String matching is the problem of finding all the substrings of a text which match a given pattern. It is one of the most investigated problems in computer science, mainly due to its very diverse applications in several fields. Recently,…
In applications such as biological, social, and transportation networks, interactions between objects span multiple aspects. For accurately modeling such applications, multilayer networks have been proposed. Community search allows for…
Small devices collecting data for agricultural, environmental, and industrial monitoring enable Internet of Things (IoT) applications. Given their critical role in data collection, there is a need for optimizations to improve on-device data…
In order to speed-up classification models when facing a large number of categories, one usual approach consists in organizing the categories in a particular structure, this structure being then used as a way to speed-up the prediction…
Bi-directional search is a widely used strategy to increase the success and convergence rates of sampling-based motion planning algorithms. Yet, few results are available that merge both bi-directional search and asymptotic optimality into…
Collapse Lineage Tree (CLTree) is a software tool that annotates, roots, and evaluates phylogenetic trees by using lineages. A recursive algorithm was designed to annotate the branches by the common taxonomic lineage of its descendants in a…
High order structures (cavities and cliques) of the gene network of influenza A virus reveal tight associations among viruses during evolution and are key signals that indicate viral cross-species infection and cause pandemics. As…
Supervised hashing aims to map the original features to compact binary codes that are able to preserve label based similarity in the Hamming space. Non-linear hash functions have demonstrated the advantage over linear ones due to their…
Full-text search engines are important tools for information retrieval. In a proximity full-text search, a document is relevant if it contains query terms near each other, especially if the query terms are frequently occurring words. For…
Cartesian tree matching is a form of generalized pattern matching where a substring of the text matches with the pattern if they share the same Cartesian tree. This form of matching finds application for time series of stock prices and can…
The run-length compressed Burrows-Wheeler transform (RLBWT) used in conjunction with the backward search introduced in the FM index is the centerpiece of most compressed indexes working on highly-repetitive data sets like biological…
In this paper, we consider the problem of compressing a trie while supporting the powerful \emph{locate} queries: to return the pre-order identifiers of all nodes reached by a path labeled with a given query pattern. Our result builds on…
Many data-based statistical algorithms require that one find \textit{near or nearest neighbors} to a given vector among a set of points in that vector space, usually with Euclidean topology. The k-d data structure and search algorithms are…
The supertree problem asking for a tree displaying a set of consistent input trees has been largely considered for the reconstruction of species trees. Here, we rather explore this framework for the sake of reconstructing a gene tree from a…
Recently, a compressed index for similar strings, called the FM-index of alignment (FMA), has been proposed with the functionalities of pattern search and random access. The FMA is quite efficient in space requirement and pattern search…