Related papers: Combinatorics of least squares trees
In the study of extensions of polytopes of combinatorial optimization problems, a notorious open question is that for the size of the smallest extended formulation of the Minimum Spanning Tree problem on a complete graph with $n$ nodes. The…
We define a search problem on trees that closely captures the backtracking behavior of all current practical graph isomorphism algorithms. Given two trees with colored leaves, the goal is to find two leaves of matching color, one in each of…
Polytrees are a subclass of Bayesian networks that seek to capture the conditional dependencies between a set of $n$ variables as a directed forest and are motivated by their more efficient inference and improved interpretability. Since the…
We consider linear error correcting codes associated to higher dimensional projective varieties defined over a finite field. The problem of determining the basic parameters of such codes often leads to some interesting and difficult…
The structure of an evolving network contains information about its past. Extracting this information efficiently, however, is, in general, a difficult challenge. We formulate a fast and efficient method to estimate the most likely history…
We study the problem of aggregating polygons by covering them with disjoint representative regions, thereby inducing a clustering of the polygons. Our objective is to minimize a weighted sum of the total area and the total perimeter of the…
We prove tight mixing time bounds for natural random walks on bases of matroids, determinantal distributions, and more generally distributions associated with log-concave polynomials. For a matroid of rank $k$ on a ground set of $n$…
We consider systems of recursively defined combinatorial structures. We give algorithms checking that these systems are well founded, computing generating series and providing numerical values. Our framework is an articulation of the…
The reconstruction of phylogenetic networks is an important but challenging problem in phylogenetics and genome evolution, as the space of phylogenetic networks is vast and cannot be sampled well. One approach to the problem is to solve the…
In 2007, Eickmeyer et al. showed that the tree topologies outputted by the Neighbor-Joining (NJ) algorithm and the balanced minimum evolution (BME) method for phylogenetic reconstruction are each determined by a polyhedral subdivision of…
We present new and improved fixed-parameter algorithms for computing maximum agreement forests (MAFs) of pairs of rooted binary phylogenetic trees. The size of such a forest for two trees corresponds to their subtree prune-and-regraft…
The problem of time series approximation by series of finite rank is considered from the viewpoint of signal extraction. For signal estimation, a weighted least-squares method is applied to the trajectory matrix of the considered time…
2-colored best match graphs (2-BMGs) form a subclass of sink-free bi-transitive graphs that appears in phylogenetic combinatorics. There, 2-BMGs describe evolutionarily most closely related genes between a pair of species. They are…
Low-rank approximation of a matrix by means of random sampling has been consistently efficient in its empirical studies by many scientists who applied it with various sparse and structured multipliers, but adequate formal support for this…
Maximum parsimony distance is a measure used to quantify the dissimilarity of two unrooted phylogenetic trees. It is NP-hard to compute, and very few positive algorithmic results are known due to its complex combinatorial structure. Here we…
A tree decomposition of a graph facilitates computations by grouping vertices into bags that are interconnected in an acyclic structure, hence their importance in a plethora of problems such as query evaluation over databases and inference…
We consider the problem of constructing an an optimal-weight tree from the 3*(n choose 4) weighted quartet topologies on n objects, where optimality means that the summed weight of the embedded quartet topologiesis optimal (so it can be the…
The probability that two randomly selected phylogenetic trees of the same size are isomorphic is found to be asymptotic to a decreasing exponential modulated by a polynomial factor. The number of symmetrical nodes in a random phylogenetic…
Motivation: The construction of statistics for summarizing posterior samples returned by a Bayesian phylogenetic study has so far been hindered by the poor geometric insights available into the space of phylogenetic trees, and ad hoc…
Fine-grained complexity theory is the area of theoretical computer science that proves conditional lower bounds based on the Strong Exponential Time Hypothesis and similar conjectures. This area has been thriving in the last decade, leading…