相关论文: KATKA: A KRAKEN-like tool with $k$ given at query …
Efficient methods for storing and querying are critical for scaling high-order n-gram language models to large corpora. We propose a language model based on compressed suffix trees, a representation that is highly compact and can be easily…
In phylogenetics, phylogenetic trees are rooted binary trees, whereas phylogenetic networks are rooted arbitrary acyclic digraphs. Edges are directed away from the root and leaves are uniquely labeled with taxa in phylogenetic networks. For…
Initial knowledge regarding group size can be crucial for collective performance. We study this relation in the context of the {\em Ants Nearby Treasure Search (ANTS)} problem \cite{FKLS}, which models natural cooperative foraging behavior…
Rational Tracer (Ratracer) is a tool to simplify complicated arithmetic expressions using modular arithmetics and rational function reconstruction, with the main idea of separating the construction of expressions (via tracing, i.e.…
Although retrieval-augmented generation(RAG) significantly improves generation quality by retrieving external knowledge bases and integrating generated content, it faces computational efficiency bottlenecks, particularly in knowledge…
The $k^2$-tree is a compact data structure designed to efficiently store sparse binary matrices by leveraging both sparsity and clustering of nonzero elements. This representation supports efficiently navigational operations and complex…
A $k$-universal permutation, or $k$-superpermutation, is a permutation that contains all permutations of length $k$ as patterns. The problem of finding the minimum length of a $k$-superpermutation has recently received significant attention…
We propose a novel method for automatic program synthesis. P-Tree Programming represents the program search space through a single probabilistic prototype tree. From this prototype tree we form program instances which we evaluate on a given…
In this paper we present a CAT generation algorithm for Dyck paths with a fixed length n. It is the formalization of a method for the exhaustive generation of this kind of paths which can be described by means of two equivalent strategies.…
In this paper, we address the problem of enumerating all induced subtrees in an input k-degenerate graph, where an induced subtree is an acyclic and connected induced subgraph. A graph G = (V, E) is a k-degenerate graph if for any its…
In this note we discuss trees similar to the Calkin-Wilf tree, a binary tree that enumerates all positive rational numbers in a simple way. The original construction of Calkin and Wilf is reformulated in a more algebraic language, and an…
When Requirements Engineering(RE) models are unreasonably complex, they cannot support efficient decision making. SHORT is a tool to simplify that reasoning by exploiting the "key" decisions within RE models. These "keys" have the property…
We study a generalization of the recently introduced order-preserving pattern matching, where instead of looking for an exact copy of the pattern, we only require that the relative order between the elements is the same. In our variant, we…
Motivation: Recent advances in single-cell analysis have introduced new computational challenges. Researchers often need to use multiple analysis tools written in different programming languages while managing version conflicts between…
In the literature on Kleene algebra (KA), a number of variants have been proposed such as Kleene algebra with tests, commutative KA, bi-KA, and concurrent KA. The equational theories of some of these structures have then been studied in the…
A graph $G$ is a $k$-leaf power if there exists a tree $T$ whose leaf set is $V(G)$, and such that $uv \in E(G)$ if and only if the distance between $u$ and $v$ in $T$ is at most $k$. The graph classes of $k$-leaf powers have several…
A variant of Turing machines is introduced where the tape is replaced by a single tree which can be manipulated in a style akin to purely functional programming. This yields two benefits: first, the extra structure on the tape can be…
The concept of $k$-compatibility measures how many phylogenetic trees it would take to display all splits in a given set. A set of trees that display every single possible split is termed a \textit{universal tree set}. In this note, we find…
We present TreeClone, a latent feature allocation model to reconstruct tumor subclones subject to phylogenetic evolution that mimics tumor evolution. Similar to most current methods, we consider data from next-generation sequencing of tumor…
Quantum computing is a popular topic in computer science, which has recently attracted many studies in various areas such as machine learning and network. However, the topic of quantum data structures seems neglected. There is an open…