相关论文: KATKA: A KRAKEN-like tool with $k$ given at query …

The Cartesian tree of a sequence captures the relative order of the sequence's elements. In recent years, Cartesian tree matching has attracted considerable attention, particularly due to its applications in time series analysis. Consider a…

Phylogenetic networks provide a way to describe and visualize evolutionary histories that have undergone so-called reticulate evolutionary events such as recombination, hybridization or horizontal gene transfer. The level k of a network…

A $k$-ended tree is a tree with at most $k$ leaves. In this note, we give a simple proof for the following theorem. Let $G$ be a connected graph and $k$ be an integer ($k\geq 2$). Let $S$ be a vertex subset of $G$ such that $\alpha_{G}(S)…

Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently. However, it is well-known that the evolution of gene families…

The input to the agreement problem is a collection $P = \{T_1, T_2, \dots , T_k\}$ of phylogenetic trees, called input trees, over partially overlapping sets of taxa. The question is whether there exists a tree $T$, called an agreement…

Summary: TreeGrafter is a new software tool for annotating protein sequences using annotated phylogenetic trees. Cur-rently, the tool provides annotations to Gene Ontology terms, and PANTHER protein class, family and subfamily. The…

The analysis of biological sequencing data has been one of the biggest applications of string algorithms. The approaches used in many such applications are based on the analysis of k-mers, which are short fixed-length strings present in a…

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…

Cartesian tree pattern matching consists of finding all the factors of a text that have the same Cartesian tree than a given pattern. There already exist theoretical and practical solutions for the exact case. In this paper, we propose the…

One approach in phylogenomics to infer the tree of life is based on concatenated multiple sequence alignments from many genes. Unfortunately, the resulting so-called supermatrix is usually sparse, that is, not every gene sequence is…

Phylogenetic (i.e. leaf-labeled) trees play a fundamental role in evolutionary research. A typical problem is to reconstruct such trees from data like DNA alignments (whose columns are often referred to as characters), and a simple…

Learned top-K search is a promising approach for serving vector queries with both high accuracy and performance. However, current models trained for a specific K value fail to generalize to real-world multi-K queries: they suffer from…

k-means is a widely used clustering algorithm, but for $k$ clusters and a dataset size of $N$, each iteration of Lloyd's algorithm costs $O(kN)$ time. Although there are existing techniques to accelerate single Lloyd iterations, none of…

Phylogenetic trees are frequently used to model evolution. Such trees are typically reconstructed from data like DNA, RNA, or protein alignments using methods based on criteria like maximum parsimony (amongst others). Maximum parsimony has…

A phylogenetic network is a directed acyclic graph that visualises an evolutionary history containing so-called reticulations such as recombinations, hybridisations or lateral gene transfers. Here we consider the construction of a simplest…

In the small phylogeny problem we, are given a phylogenetic tree and gene orders of the extant species and our goal is to reconstruct all of the ancestral genomes so that the number of evolutionary operations is minimized. Algorithms for…

We consider the reconstruction of a phylogeny from multiple genes under the multispecies coalescent. We establish a connection with the sparse signal detection problem, where one seeks to distinguish between a distribution and a mixture of…

Cluster-based information retrieval is one of the Information retrieval(IR) tools that organize, extract features and categorize the web documents according to their similarity. Unlike traditional approaches, cluster-based IR is fast in…

Recent advances in retrieval models based on learned sparse representations generated by transformers have led us to, once again, consider score-at-a-time query evaluation techniques for the top-k retrieval problem. Previous studies…

A buffer k-d tree is a k-d tree variant for massively-parallel nearest neighbor search. While providing valuable speed-ups on modern many-core devices in case both a large number of reference and query points are given, buffer k-d trees are…