Related papers: An algorithm to represent inbreeding trees
We develop a time-optimal $O(mn^2)$-time algorithm to construct the subtree prune-regraft (SPR) graph on a collection of m phylogenetic trees with n leaves. This improves on the previous bound of $O(mn^3)$. Such graphs are used to better…
Hierarchical structure is ubiquitous in data across many domains. There are many hierarchical clustering methods, frequently used by domain experts, which strive to discover this structure. However, most of these methods limit discoverable…
The maximum common subtree isomorphism problem asks for the largest possible isomorphism between subtrees of two given input trees. This problem is a natural restriction of the maximum common subgraph problem, which is ${\sf NP}$-hard in…
Phylogenetic trees (i.e. evolutionary trees, additive trees or X-trees) play a key role in the processes of modeling and representing species evolution. Genome evolution of a given group of species is usually modeled by a species…
Family members' satisfaction with one another is central to creating healthy and supportive family environments. In this work, we propose and implement a novel computational technique aimed at exploring the possible relationship between the…
Online genealogy datasets contain extensive information about millions of people and their past and present family connections. This vast amount of data can assist in identifying various patterns in human population. In this study, we…
Phylogenetic trees are a central tool in understanding evolution. They are typically inferred from sequence data, and capture evolutionary relationships through time. It is essential to be able to compare trees from different data sources…
Trees are useful entities allowing to model data structures and hierarchical relationships in networked decision systems ubiquitously. An ordered tree is a rooted tree where the order of the subtrees (children) of a node is significant. In…
Generative models derived from large protein sequence alignments define complex fitness landscapes, but their utility for accurately modeling non-equilibrium evolutionary dynamics remains unclear. In this work, we perform a rigorous…
The class of self-nested trees presents remarkable compression properties because of the systematic repetition of subtrees in their structure. In this paper, we provide a better combinatorial characterization of this specific family of…
Phylogenetic networks are a generalization of phylogenetic trees that are used in biology to represent reticulate or non-treelike evolution. Recently, several algorithms have been developed which aim to construct phylogenetic networks from…
We define symmetric and asymmetric branching trees, a class of processes particularly suited for modeling genealogies of inhomogeneous populations where individuals may reproduce throughout life. In this framework, a broad class of…
The evolutionary relationships among organisms have traditionally been represented using rooted phylogenetic trees. However, due to reticulate processes such as hybridization or lateral gene transfer, evolution cannot always be adequately…
Population structure can be modelled by evolutionary graphs, which can have a substantial, but very subtle influence on the fate of the arising mutants. Individuals are located on the nodes of these graphs, competing with each other to…
Reconstructing the evolutionary past of a family of genes is an important aspect of many genomic studies. To help with this, simple operations on a set of sequences called orthology relations may be employed. In addition to being…
The statistical estimation of phylogenies is always associated with uncertainty, and accommodating this uncertainty is an important component of modern phylogenetic comparative analysis. The birth-death polytomy resolver is a method of…
Networks are ubiquitous in biology and computational approaches have been largely investigated for their inference. In particular, supervised machine learning methods can be used to complete a partially known network by integrating various…
This paper introduces a new combinatorial framework for modeling the growth of binary trees through a discrete evolution process that incorporates a growing rule and an extinction rule. Building upon the theory of increasingly labeled…
Not all nodes in a network are created equal. Differences and similarities exist at both individual node and group levels. Disentangling single node from group properties is crucial for network modeling and structural inference. Based on…
It is known that any chordal graph on $n$ vertices can be represented as the intersection of $n$ subtrees in a tree on $n$ nodes. This fact is recently used in [2] to generate random chordal graphs on $n$ vertices by generating $n$ subtrees…