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

This paper proposes an efficient and novel method to address range search on multidimensional points in $\theta(t)$ time, where $t$ is the number of points reported in $\Re^k$ space. This is accomplished by introducing a new data structure,…

To tackle the challenge of producing tractable phylogenetic trees in contexts where complete information is available, we introduce APOGeT: an online, pluggable, clustering algorithm for a stream of genomes. It is designed to run alongside…

Given a reference set $R$ of $n$ points and a query set $Q$ of $m$ points in a metric space, this paper studies an important problem of finding $k$-nearest neighbors of every point $q \in Q$ in the set $R$ in a near-linear time. In the…

Knowing the reasoning chains from knowledge to the predicted answers can help construct an explainable question answering (QA) system. Advances on QA explanation propose to explain the answers with entailment trees composed of multiple…

Given an undirected graph $G$ and a parameter $k$, the $k$-Leaf Spanning Tree ($k$-LST) problem asks if $G$ contains a spanning tree with at least $k$ leaves. This problem has been extensively studied over the past three decades. In 2000,…

Phylogenetic networks generalize phylogenetic trees, and have been introduced in order to describe evolution in the case of transfer of genetic material between coexisting species. There are many classes of phylogenetic networks, which can…

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…

Counting the frequencies of k-mers in read libraries is often a first step in the analysis of high-throughput sequencing experiments. Infrequent k-mers are assumed to be a result of sequencing errors. The frequent k-mers constitute a…

Given a set $P$ of $n$ points in $\mathbb{R}^2$ and an input line $\gamma$ in $\mathbb{R}^2$, we present an algorithm that runs in optimal $\Theta(n\log n)$ time and $\Theta(n)$ space to solve a restricted version of the $1$-Steiner tree…

The linear matter power spectrum $P(k,z)$ connects theory with large scale structure observations in cosmology. Its scale dependence is entirely encoded in the matter transfer function $T(k)$, which can be computed numerically by Boltzmann…

Given a finite set $X$, a collection $\mathcal{T}$ of rooted phylogenetic trees on $X$ and an integer $k$, the Hybridization Number problem asks if there exists a phylogenetic network on $X$ that displays all trees from $\mathcal{T}$ and…

For a given set $\mathcal{L}$ of species and a set $\mathcal{T}$ of triplets on $\mathcal{L}$, one wants to construct a phylogenetic network which is consistent with $\mathcal{T}$, i.e which represents all triplets of $\mathcal{T}$. The…

K-mer abundance analysis is widely used for many purposes in nucleotide sequence analysis, including data preprocessing for de novo assembly, repeat detection, and sequencing coverage estimation. We present the khmer software package for…

We introduce the software tool NTRFinder to find the complex repetitive structure in DNA we call a nested tandem repeat (NTR). An NTR is a recurrence of two or more distinct tandem motifs interspersed with each other. We propose that nested…

Motivation: Many inference tools use the Perfect Phylogeny Model (PPM) to learn trees from noisy variant allele frequency (VAF) data. Learning in this setting is hard, and existing tools use approximate or heuristic algorithms. An…

Distances between sequences based on their $k$-mer frequency counts can be used to reconstruct phylogenies without first computing a sequence alignment. Past work has shown that effective use of k-mer methods depends on 1) model-based…

We propose a data structure that stores, in a compressed way, object trajectories, which at the same time, allow to efficiently response queries without the need to decompress the data. We use a data structure, called $k^{2}$-tree, to store…

Frequent itemset mining has emerged as a fundamental problem in data mining and plays an important role in many data mining tasks, such as association analysis, classification, etc. In the framework of frequent itemset mining, the results…

Large language models have achieved high performance on various question answering (QA) benchmarks, but the explainability of their output remains elusive. Structured explanations, called entailment trees, were recently suggested as a way…

The kTree problem is a special case of Subgraph Isomorphism where the pattern graph is a tree, that is, the input is an $n$-node graph $G$ and a $k$-node tree $T$, and the goal is to determine whether $G$ has a subgraph isomorphic to $T$.…