Related papers: KATKA: A KRAKEN-like tool with $k$ given at query …

Cartesian tree matching is the problem of finding all substrings of a given text which have the same Cartesian trees as that of a given pattern. So far there is one linear-time solution for Cartesian tree matching, which is based on the KMP…

Transcription factors are short stretches of DNA (or $k$-mers) mainly located in promoters sequences that enhance or repress gene expression. With respect to an initial distribution of letters on the DNA alphabet, Behrens and Vingron…

Modern high throughput sequencing technologies like metagenomic sequencing generate millions of sequences which have to be classified based on their taxonomic rank. Modern approaches either apply local alignment and comparison to existing…

Trees or rooted trees have been generously studied in the literature. A forest is a set of trees or rooted trees. Here we give recurrence relations between the number of some kind of rooted forest with $k$ roots and that with $k+1$ roots on…

'Tree-based' phylogenetic networks proposed by Francis and Steel have attracted much attention of theoretical biologists in the last few years. At the heart of the definitions of tree-based phylogenetic networks is the notion of 'support…

Some parallel constructions of a SHAKE hash function using Sakura coding are introduced, whose basic operation is the Keccak's permutation. For each proposed tree-based algorithm, observations are made on both its parallel running time…

We introduce an improved version of RECKONER, an error corrector for Illumina whole genome sequencing data. By modifying its workflow we reduce the computation time even 10 times. We also propose a new method of determination of $k$-mer…

This paper proposes an efficient data structure, ikd-Tree, for dynamic space partition. The ikd-Tree incrementally updates a k-d tree with new coming points only, leading to much lower computation time than existing static k-d trees.…

KTA (KTH's timing analyzer) is a research tool for performing timing analysis of program code. The currently available toolchain can perform two different kinds of analyses: i) exhaustive fine-grained timing analysis, where timing…

Phylogenetic trees play a key role in the reconstruction of evolutionary relationships. Typically, they are derived from aligned sequence data (like DNA, RNA, or proteins) by using optimization criteria like, e.g., maximum parsimony (MP).…

The typical problem in Data Science is creating a structure that encodes the occurrence frequency of unique elements in rows and relations between different rows of a data frame. We present the probability tree abstract data structure, an…

Generating diverse responses from large language models (LLMs) is crucial for applications such as planning/search and synthetic data generation, where diversity provides distinct answers across generations. Prior approaches rely on…

This paper studies the performances of BERT combined with tree structure in short sentence ranking task. In retrieval-based question answering system, we retrieve the most similar question of the query question by ranking all the questions…

Genome assembly tools based on the de Bruijn graph framework rely on a parameter k, which represents a trade-off between several competing effects that are difficult to quantify. There is currently a lack of tools that would automatically…

Information retrieval based knowledge base question answering (KBQA) first retrieves a subgraph to reduce search space, then reasons on the subgraph to select answer entities. Existing approaches have three issues that impede the retrieval…

Phylogenetic networks allow modeling reticulate evolution, capturing events such as hybridization and horizontal gene transfer. A fundamental computational problem in this context is the Tree Containment problem, which asks whether a given…

We propose a new succinct representation of labeled trees which represents a tree T using |T|H_k(T) number of bits (plus some smaller order terms), where |T|H_k(T) denotes the k-th order (tree label) entropy, as defined by Ferragina at al.…

Suppose we are asked to index a text $T [0..n - 1]$ such that, given a pattern $P [0..m - 1]$, we can quickly report the maximal substrings of $P$ that each occur in $T$ at least $k$ times. We first show how we can add $O (r \log n)$ bits…

We introduce a new variant of the $k$-deck problem, which in its traditional formulation asks for determining the smallest $k$ that allows one to reconstruct any binary sequence of length $n$ from the multiset of its $k$-length…

The reconstruction of phylogenetic networks is an important but challenging problem in phylogenetics and genome evolution, as the space of phylogenetic networks is vast and cannot be sampled well. One approach to the problem is to solve the…