相关论文: KATKA: A KRAKEN-like tool with $k$ given at query …
Inferring evolutionary histories (phylogenetic trees) has important applications in biology, criminology and public health. However, phylogenetic trees are complex mathematical objects that reside in a non-Euclidean space, which complicates…
When combining data from multiple sources, inconsistent data complicates the production of a coherent result. In this paper, we introduce a new type of constraints called edit rules under a partial key (EPKs). These constraints can model…
A major challenge in next-generation genome sequencing (NGS) is to assemble massive overlapping short reads that are randomly sampled from DNA fragments. To complete assembling, one needs to finish a fundamental task in many leading…
A new method for hierarchical clustering is presented. It combines treelets, a particular multiscale decomposition of data, with a projection on a reproducing kernel Hilbert space. The proposed approach, called kernel treelets (KT),…
Many problems in areas as diverse as recommendation systems, social network analysis, semantic search, and distributed root cause analysis can be modeled as pattern search on labeled graphs (also called "heterogeneous information networks"…
As large language models (LLMs) advance, their inability to autonomously execute tasks by directly interacting with external tools remains a critical limitation. Traditional methods rely on inputting tool descriptions as context, which is…
K-mer counting is a requisite process for DNA assembly because it speeds up its overall process. The frequency of K-mers is used for estimating the parameters of DNA assembly, error correction, etc. The process also provides a list of…
The boxicity of a graph G, denoted as box(G) is defined as the minimum integer t such that G is an intersection graph of axis-parallel t-dimensional boxes. A graph G is a k-leaf power if there exists a tree T such that the leaves of the…
Motivation: While the majority of gene histories found in a clade of organisms are expected to be generated by a common process (e.g. the coalescent process), it is well-known that numerous other coexisting processes (e.g. horizontal gene…
We present an algorithm for the Merkle tree traversal problem which combines the efficient space-time trade-off from the fractal Merkle tree [3] and the space efficiency from the improved log space-time Merkle trees traversal [8]. We give…
In collective tree exploration, a team of $k$ mobile agents is tasked to go through all edges of an unknown tree as fast as possible. An edge of the tree is revealed to the team when one agent becomes adjacent to that edge. The agents start…
An extension $K/k$ of analytic (i.e. real valued complete) fields is called small if it is topologically-algebraically generated by finitely many elements. We prove that this property is inherited by subextensions and hence topological…
In many modern applications, including analysis of gene expression and text documents, the data are noisy, high-dimensional, and unordered--with no particular meaning to the given order of the variables. Yet, successful learning is often…
k-mers (nucleotide strings of length k) form the basis of several algorithms in computational genomics. In particular, k-mer abundance information in sequence data is useful in read error correction, parameter estimation for genome…
We propose a model for evolution aiming to reproduce statistical features of fossil data, in particular the distributions of extinction events, the distribution of species per genus and the distribution of lifetimes, all of which are known…
We consider the well-studied pattern counting problem: given a permutation $\pi \in \mathbb{S}_n$ and an integer $k > 1$, count the number of order-isomorphic occurrences of every pattern $\tau \in \mathbb{S}_k$ in $\pi$. Our first result…
Phylogenetic trees describe the evolutionary history of a group of present-day species from a common ancestor. These trees are typically reconstructed from aligned DNA sequence data. In this paper we analytically address the following…
The recent advances in sequencing technologies enables the assembly of individual genomes to the reference quality. How to integrate multiple genomes from the same species and to make the integrated representation accessible to biologists…
A seed in a word is a relaxed version of a period in which the occurrences of the repeating subword may overlap. We show a linear-time algorithm computing a linear-size representation of all the seeds of a word (the number of seeds might be…
In the \emph{$k$-Diameter-Optimally Augmenting Tree Problem} we are given a tree $T$ of $n$ vertices as input. The tree is embedded in an unknown \emph{metric} space and we have unlimited access to an oracle that, given two distinct…