Related papers: Reduction rules for the maximum parsimony distance…
The supertree construction problem is about combining several phylogenetic trees with possibly conflicting information into a single tree that has all the leaves of the source trees as its leaves and the relationships between the leaves are…
In this study, we investigate the problem of comparing gene trees reconciled with the same species tree using a novel semi-metric, called the Path-Label Reconciliation (PLR) dissimilarity measure. This approach not only quantifies…
We consider the phylogenetic tree reconstruction problem with insertions and deletions (indels). Phylogenetic algorithms proceed under a model where sequences evolve down the model tree, and given sequences at the leaves, the problem is to…
We study the Monotone Sliding Reconfiguration (MSR) problem, in which $\textit{labeled}$ pairwise interior-disjoint objects in a planar workspace need to be brought $\textit{one by one}$ from their initial positions to given target…
The problem of computing topological distance between two scalar fields based on Reeb graphs or contour trees has been studied and applied successfully to various problems in topological shape matching, data analysis, and visualization.…
Tuffley and Steel (1997) proved that Maximum Likelihood and Maximum Parsimony methods in phylogenetics are equivalent for sequences of characters under a simple symmetric model of substitution with no common mechanism. This result has been…
Rearrangement operations transform a phylogenetic tree into another one and hence induce a metric on the space of phylogenetic trees. Popular operations for unrooted phylogenetic trees are NNI (nearest neighbour interchange), SPR (subtree…
Phylogenetic trees summarize evolutionary relationships between organisms, and tools to analyze collections of phylogenetic trees enable contrasts between different genes' ancestry. The BHV metric space has enabled the analysis of…
A conjecture of Bandelt and Dress states that the maximum quartet distance between any two phylogenetic trees on $n$ leaves is at most $(\frac 23 +o(1))\binom{n}{4}$. Using the machinery of flag algebras we improve the currently known…
In evolutionary biology, genetic sequences carry with them a trace of the underlying tree that describes their evolution from a common ancestral sequence. The question of how many sequence sites are required to recover this evolutionary…
This paper studies Minimum Spanning Trees under incomplete information for its vertices. We assume that no information is available on the precise placement of vertices so that it is only known that vertices belong to some neighborhoods…
Phylogenetic trees play a key role in the reconstruction of evolutionary relationships. Typically, they are derived from aligned sequence data (like DNA, RNA, or proteins) by using optimization criteria like, e.g., maximum parsimony (MP).…
Temporal sequences of terrains arise in various application areas. To analyze them efficiently, one generally needs a suitable abstraction of the data as well as a method to compare and match them over time. In this paper we consider merge…
Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of non-treelike evolutionary events, like recombination, hybridization, or lateral gene transfer. In this paper, we present and study a new…
Tree projections provide a unifying framework to deal with most structural decomposition methods of constraint satisfaction problems (CSPs). Within this framework, a CSP instance is decomposed into a number of sub-problems, called views,…
We study linear codes that maximize minimum distance subject to arbitrary support constraints on the parity-check matrix. Such constraints arise naturally in the design of LDPC codes, locally repairable codes, and hardware-constrained…
It is an open question whether there exists a polynomial-time algorithm for computing the rotation distances between pairs of extended ordered binary trees. The problem of computing the rotation distance between an arbitrary pair of trees,…
The Maximum Agreement Forest problem has been extensively studied in phylogenetics. Most previous work is on two binary phylogenetic trees. In this paper, we study a generalized version of the problem: the Maximum Agreement Forest problem…
Metric learning has the aim to improve classification accuracy by learning a distance measure which brings data points from the same class closer together and pushes data points from different classes further apart. Recent research has…
Building trees to represent or to fit distances is a critical component of phylogenetic analysis, metric embeddings, approximation algorithms, geometric graph neural nets, and the analysis of hierarchical data. Much of the previous…