Related papers: A third strike against perfect phylogeny
We introduce a population dynamics model, where individual genomes are represented by bit-strings. Selection is described by death probabilities which depend on these genomes, and new individuals continuously replace the ones that die,…
Dirac's theorem determines the sharp minimum degree threshold for graphs to contain perfect matchings and Hamiltonian cycles. There have been various attempts to generalize this theorem to hypergraphs with larger uniformity by considering…
Given $n$ men, $n$ women, and $n$ dogs, each man has an incomplete preference list of women, each woman does an incomplete preference list of dogs, and each dog does an incomplete preference list of men. We understand a family as a triple…
Rooted phylogenetic networks provide a more complete representation of the ancestral relationship between species than phylogenetic trees when reticulate evolutionary processes are at play. One way to reconstruct a phylogenetic network is…
In this paper, we study the complexity of two types of digraph packing problems: perfect out-forests problem and Steiner cycle packing problem. For the perfect out-forest problem, we prove that it is NP-hard to decide whether a given strong…
If $G$ is a bridgeless cubic graph, Fulkerson conjectured that we can find 6 perfect matchings (a{\em Fulkerson covering}) with the property that every edge of $G$ is contained in exactly two of them. A consequence of the Fulkerson…
In phylogenetic studies, the evolution of molecular sequences is assumed to have taken place along the phylogeny traced by the ancestors of extant species. In the presence of lateral gene transfer (LGT), however, this may not be the case,…
In recent years, significant progress has been made on algorithms for learning optimal decision trees, primarily in the context of binary features. Extending these methods to continuous features remains substantially more challenging due to…
A well-known result of Verstra\"ete \cite{V00} shows that for each integer $k\geq 2$ every graph $G$ with average degree at least $8k$ contains cycles of $k$ consecutive even lengths, the shortest of which is at most twice the radius of…
Phylogenetic trees are simple models of evolutionary processes. They describe conditionally independent divergent evolution of taxa from common ancestors. Phylogenetic trees commonly do not have enough flexibility to adequately model all…
Phylogenetic networks are a generalization of phylogenetic trees to leaf-labeled directed acyclic graphs that represent ancestral relationships between species whose past includes non-tree-like events such as hybridization and horizontal…
The maximum agreement forest (MAF) problem in phylogenetics takes as input a set t >= 2 of binary phylogenetic trees T on the same set of taxa X. It asks for a partition of X into the smallest number of blocks such that the subtrees induced…
The reconstruction of a central tendency `species tree' from a large number of conflicting gene trees is a central problem in systematic biology. Moreover, it becomes particularly problematic when taxon coverage is patchy, so that not all…
The reliability of a phylogenetic inference method from genomic sequence data is ensured by its statistical consistency. Bayesian inference methods produce a sample of phylogenetic trees from the posterior distribution given sequence data.…
A \emph{binary tanglegram} is a drawing of a pair of rooted binary trees whose leaf sets are in one-to-one correspondence; matching leaves are connected by inter-tree edges. For applications, for example, in phylogenetics, it is essential…
In any given machine learning problem, there may be many models that could explain the data almost equally well. However, most learning algorithms return only one of these models, leaving practitioners with no practical way to explore…
In evolutionary biology, networks are becoming increasingly used to represent evolutionary histories for species that have undergone non-treelike or reticulate evolution. Such networks are essentially directed acyclic graphs with a leaf set…
Let $X$ be a set of $n$ points in the plane, not all on a line. According to the Gallai-Sylvester theorem, $X$ always spans an \emph{ordinary line}, i.e., one that passes through precisely 2 elements of $X$. Given an integer $c\ge 2,$ a…
The Stochastic Context Tree (SCOT) is a useful tool for studying infinite random sequences generated by an m-Markov Chain (m-MC). It captures the phenomenon that the probability distribution of the next state sometimes depends on less than…
We show that it is decidable, given an automatic sequence $\bf s$ and a constant $c$, whether all prefixes of $\bf s$ have a string attractor of size $\leq c$. Using a decision procedure based on this result, we show that all prefixes of…