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

Index structures are a building block of query processing and computer science in general. Since the dawn of computer technology there have been index structures. And since then, a myriad of index structures are being invented and published…

We have developed a unified format for phylogenetic placements, that is, mappings of environmental sequence data (e.g. short reads) into a phylogenetic tree. We are motivated to do so by the growing number of tools for computing and…

Plastid genomes (plastomes) of angiosperms are of great interest among biologists. High-throughput sequencing is making many such genomes accessible, increasing the need for tools to perform rapid comparative analysis. This exploratory…

A phylogenetic tree shows the evolutionary relationships among species. Internal nodes of the tree represent speciation events and leaf nodes correspond to species. A goal of phylogenetics is to combine such trees into larger trees, called…

The recently proposed ToolkenGPT tool learning paradigm demonstrates promising performance but suffers from two major issues: first, it cannot benefit from tool documentation, and second, it often makes mistakes in whether to use a tool at…

Let $P$ be a set of $n$ points in ${\mathbb R}^{d}$. A point $p \in P$ is $k$\emph{-shallow} if it lies in a halfspace which contains at most $k$ points of $P$ (including $p$). We show that if all points of $P$ are $k$-shallow, then $P$ can…

A central task in string processing is text indexing, where the goal is to preprocess a text (a string of length $n$) into an efficient index (a data structure) supporting queries about the text. Cole, Gottlieb, and Lewenstein (STOC 2004)…

We introduce the Ants Nearby Treasure Search (ANTS) problem, which models natural cooperative foraging behavior such as that performed by ants around their nest. In this problem, k probabilistic agents, initially placed at a central…

In structural proof theory, designing and working on large calculi make it difficult to get intuitions about each rule individually and as part of a whole system. We introduce two novel tools to help working on calculi using the approach of…

In this paper, we consider a tree-structured data model used in many commercial databases like Dremel, F1, JSON stores. We define identity and referential constraints within each tree-structured record. The query language is a variant of…

Comparative analyses of phylogenetic trees typically require identical taxon sets, however, in practice, trees often include distinct but overlapping taxa. Pruning non-shared leaves discards phylogenetic signal, whereas tree completion can…

We introduce a new phylogenetic reconstruction algorithm which, unlike most previous rigorous inference techniques, does not rely on assumptions regarding the branch lengths or the depth of the tree. The algorithm returns a forest which is…

Modern software is constantly changing. Researchers and practitioners are increasingly aware that verification tools can be impactful if they embrace change through analyses that are compositional and span program versions. Reasoning about…

We describe a generating tree approach to the enumeration and exhaustive generation of k-nonnesting set partitions and permutations. Unlike previous work in the literature using the connections of these objects to Young tableaux and…

We consider a neutral dynamical model of biological diversity, where individuals live and reproduce independently. They have i.i.d. lifetime durations (which are not necessarily exponentially distributed) and give birth (singly) at constant…

A graph G is a k-leaf power, for an integer k >= 2, if there is a tree T with leaf set V(G) such that, for all vertices x, y in V(G), the edge xy exists in G if and only if the distance between x and y in T is at most k. Such a tree T is…

Tree Containment is a fundamental problem in phylogenetics useful for verifying a proposed phylogenetic network, representing the evolutionary history of certain species. Tree Containment asks whether the given phylogenetic tree (for…

Various specifiable combinatorial structures, with d extensive parameters, can be exactly sampled both by the recursive method, with linear arithmetic complexity if a heavy preprocessing is performed, or by the Boltzmann method, with…

We present an algorithm for phylogenetic reconstruction using quartets that returns the correct topology for $n$ taxa in $O(n \log n)$ time with high probability, in a probabilistic model where a quartet is not consistent with the true…

Given two rooted, ordered, and labeled trees $P$ and $T$ the tree inclusion problem is to determine if $P$ can be obtained from $T$ by deleting nodes in $T$. This problem has recently been recognized as an important query primitive in XML…