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

Phylogenetically decisive collections of taxon sets have the property that if trees are chosen for each of their elements, as long as these trees are compatible, the resulting supertree is unique. This means that as long as the trees…

A sparse Merkle tree is a Merkle tree with fixed height and indexed leaves given by a map from indices to leaf values. It allows for both efficient membership and non-membership proofs. It has been widely used as an authenticated data…

The Fenwick tree is a classical implicit data structure that stores an array in such a way that modifying an element, accessing an element, computing a prefix sum and performing a predecessor search on prefix sums all take logarithmic time.…

We propose a statistical method to test whether two phylogenetic trees with given alignments are significantly incongruent. Our method compares the two distributions of phylogenetic trees given by the input alignments, instead of comparing…

Billey et al. [arXiv:1507.04976] have recently discovered a surprisingly simple formula for the number $a_n(\sigma)$ of leaf-labelled rooted non-embedded binary trees (also known as phylogenetic trees) with $n\geq 1$ leaves, fixed (for the…

In a complete graph $K_n$ with edge weights drawn independently from a uniform distribution $U(0,1)$ (or alternatively an exponential distribution $\operatorname{Exp}(1)$), let $T_1$ be the MST (the spanning tree of minimum weight) and let…

There are several ways to formally represent families of data, such as lambda terms, in a type theory such as the dependent type theory of Coq. Mathematical representations are very compact ones and usually rely on the use of dependent…

Recently, the minimum number of reticulation events that is required to simultaneously embed a collection P of rooted binary phylogenetic trees into a so-called temporal network has been characterized in terms of cherry-picking sequences.…

The $k$d-tree is one of the most widely used data structures to manage multi-dimensional data. Due to the ever-growing data volume, it is imperative to consider parallelism in $k$d-trees. However, we observed challenges in existing parallel…

We propose a lightweight data structure for indexing and querying collections of NGS reads data in main memory. The data structure supports the interface proposed in the pioneering work by Philippe et al. for counting and locating $k$-mers…

We show that a finite set of integers $A \subseteq \mathbb{Z}$ with $|A+A| \le K |A|$ contains a large piece $X \subseteq A$ with Fre\u{i}man dimension $O(\log K)$, where large means $|A|/|X| \ll \exp(O(\log^2 K))$. This can be thought of…

We consider a general class of branching processes in discrete time, where particles have types belonging to a Polish space and reproduce independently according to their type. If the process is critical and the mean distribution of types…

The simulation of genealogical trees backwards in time, from observations up to the most recent common ancestor (MRCA), is hindered by the fact that, while approaching the root of the tree, coalescent events become rarer, with a…

Knowledge Base Question Answering (KBQA) aims to answer natural language questions over large-scale knowledge bases (KBs), which can be summarized into two crucial steps: knowledge retrieval and semantic parsing. However, three core…

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…

Large Transformer networks are increasingly used in settings where low inference latency can improve the end-user experience and enable new applications. However, autoregressive inference is resource intensive and requires parallelism for…

In computational phylogenetics, the problem of constructing a supertree of a given set of rooted input trees can be formalized in different ways, to cope with contradictory information in the input. We consider the Minimum Flip Supertree…

Nearest-neighbor search dominates the asymptotic complexity of sampling-based motion planning algorithms and is often addressed with k-d tree data structures. While it is generally believed that the expected complexity of nearest-neighbor…

We study the problem of finding a temporal hybridization network for a set of phylogenetic trees that minimizes the number of reticulations. First, we introduce an FPT algorithm for this problem on an arbitrary set of $m$ binary trees with…

"There and Back Again" (TABA) is a programming pattern where the recursive calls traverse one data structure and the subsequent returns traverse another. This article presents new TABA examples, refines existing ones, and formalizes both…