相关论文: Heaviest Induced Ancestors and Longest Common Subs…
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…
We consider the NP-hard Tree Containment problem that has important applications in phylogenetics. The problem asks if a given leaf-labeled network contains a subdivision of a given leaf-labeled tree. We develop a fast algorithm for the…
Phylogenetic networks are often constructed by merging multiple conflicting phylogenetic signals into a directed acyclic graph. It is interesting to explore whether a network constructed in this way induces biologically-relevant…
Most of major algorithms for phylogenetic tree reconstruction assume that sequences in the analyzed set either do not have any offspring, or that parent sequences can maximally mutate into just two descendants. The graph resulting from such…
Genealogical networks, also known as family trees or population pedigrees, are commonly studied by genealogists wanting to know about their ancestry, but they also provide a valuable resource for disciplines such as digital demography,…
The suffix array, perhaps the most important data structure in modern string processing, is often augmented with the longest common prefix (LCP) array which stores the lengths of the LCPs for lexicographically adjacent suffixes of a string.…
Text indexing is a classical algorithmic problem that has been studied for over four decades: given a text $T$, pre-process it off-line so that, later, we can quickly count and locate the occurrences of any string (the query pattern) in $T$…
Word and graph embeddings are widely used in deep learning applications. We present a data structure that captures inherent hierarchical properties from an unordered flat embedding space, particularly a sense of direction between pairs of…
A pedigree is a directed graph in which each vertex (except the founder vertices) has two parents. The main result in this paper is a construction of an infinite family of counter examples to a reconstruction problem on pedigrees, thus…
We study a new variant of the string matching problem called cross-document string matching, which is the problem of indexing a collection of documents to support an efficient search for a pattern in a selected document, where the pattern…
This paper reveals the tree structure as an intermediate result of clustering by fast search and find of density peaks (DPCLUS), and explores the power of using this tree to perform hierarchical clustering. The array used to hold the index…
One strategy for reconstruction of phylogenetic networks is to solve the phylogenetic network problem, which involves inferring phylogenetic trees first and subsequently computing the smallest phylogenetic network that displays all the…
A metric phylogenetic tree relating a collection of taxa induces weighted rooted triples and weighted quartets for all subsets of three and four taxa, respectively. New intertaxon distances are defined that can be calculated from these…
Phylogenetic networks are a type of leaf-labelled, acyclic, directed graph used by biologists to represent the evolutionary history of species whose past includes reticulation events. A phylogenetic network is tree-child if each non-leaf…
A subtree can be induced in a natural way by a subset of leaves of a rooted tree. We study the number of nonisomorphic such subtrees induced by leaves (leaf-induced subtrees) of a rooted tree with no vertex of outdegree 1 (topological…
A widely used method for determining the similarity of two labeled trees is to compute a maximum agreement subtree of the two trees. Previous work on this similarity measure is only concerned with the comparison of labeled trees of two…
Let us call a sequence of numbers heapable if they can be sequentially inserted to form a binary tree with the heap property, where each insertion subsequent to the first occurs at a leaf of the tree, i.e. below a previously placed number.…
We consider the counting problem of the number of \textit{leaf-labeled increasing trees}, where internal nodes may have an arbitrary number of descendants. The set of all such trees is a discrete representation of the genealogies obtained…
Given two positions $i$ and $j$ in a string $T$ of length $N$, a longest common extension (LCE) query asks for the length of the longest common prefix between suffixes beginning at $i$ and $j$. A compressed LCE data structure is a data…
In the context of reconstructing phylogenetic networks from a collection of phylogenetic trees, several characterisations and subsequently algorithms have been established to reconstruct a phylogenetic network that collectively embeds all…