Related papers: Size-constrained Weighted Ancestors with Applicati…
In this paper we consider the problem of connected edge searching of weighted trees. It is shown that there exists a polynomial-time algorithm for finding optimal connected search strategy for bounded degree trees with arbitrary weights on…
Sequence partition problems arise in many fields, such as sequential data analysis, information transmission, and parallel computing. In this paper, we study the following partition problem variant: given a sequence of $n$ items…
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…
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 solve the dynamic Predecessor Problem with high probability (whp) in constant time, using only $n^{1+\delta}$ bits of memory, for any constant $\delta > 0$. The input keys are random wrt a wider class of the well studied and practically…
Given an edge-weighted tree $T$ with $n$ leaves, sample the leaves uniformly at random without replacement and let $W_k$, $2 \le k \le n$, be the length of the subtree spanned by the first $k$ leaves. We consider the question, "Can $T$ be…
Motivated by an application in computational topology, we consider a novel variant of the problem of efficiently maintaining dynamic rooted trees. This variant requires merging two paths in a single operation. In contrast to the standard…
We calculate the probability distribution of repetitions of ancestors in a genealogical tree for simple neutral models of a closed population with sexual reproduction and non-overlapping generations. Each ancestor at generation g in the…
An ancestry labeling scheme assigns labels (bit strings) to the nodes of rooted trees such that ancestry queries between any two nodes in a tree can be answered merely by looking at their corresponding labels. The quality of an ancestry…
We consider an index data structure for similar strings. The generalized suffix tree can be a solution for this. The generalized suffix tree of two strings $A$ and $B$ is a compacted trie representing all suffixes in $A$ and $B$. It has…
We initiate the theoretical study of Ext-TSP, a problem that originates in the area of profile-guided binary optimization. Given a graph $G=(V, E)$ with positive edge weights $w: E \rightarrow R^+$, and a non-increasing discount function…
We show that the compressed suffix array and the compressed suffix tree for a string of length $n$ over an integer alphabet of size $\sigma\leq n$ can both be built in $O(n)$ (randomized) time using only $O(n\log\sigma)$ bits of working…
Levin Tree Search (LTS) (Orseau et al., 2018) is a search algorithm for deterministic environments that uses a user-specified policy to guide the search. It comes with a formal guarantee on the number of search steps (node visits) for…
Burrows-Wheeler transform (BWT) is an invertible text transformation that, given a text $T$ of length $n$, permutes its symbols according to the lexicographic order of suffixes of $T$. BWT is one of the most heavily studied algorithms in…
Information extraction from textual data, where the query is represented by a finite transducer and the task is to enumerate all results without repetition, and its extension to the weighted case, where each output element has a weight and…
We study the inference of network archaeology in growing random geometric graphs. We consider the root finding problem for a random nearest neighbor tree in dimension $d \in \mathbb{N}$, generated by sequentially embedding vertices…
Path partition problems on trees have found various applications. In this paper, we present an $O(n \log n)$ time algorithm for solving the following variant of path partition problem: given a rooted tree of $n$ nodes $1, \ldots, n$, where…
In the field of algorithmic analysis, one of the more well-known exercises is the subset sum problem. That is, given a set of integers, determine whether one or more integers in the set can sum to a target value. Aside from the brute-force…
A labeling scheme for nearest common ancestors assigns a distinct binary string, called the label, to every node of a tree, so that given the labels of two nodes (and no further information about the topology of the tree) we can compute the…
The string indexing problem is a fundamental computational problem with numerous applications, including information retrieval and bioinformatics. It aims to efficiently solve the pattern matching problem: given a text T of length n for…