Related papers: Order-Dependent Dissimilarity Measures on Phylogen…
A chief problem in phylogenetics and database theory is the computation of a maximum consistent tree from a set of rooted or unrooted trees. A standard input are triplets, rooted binary trees on three leaves, or quartets, unrooted binary…
The Neighbor-Joining algorithm is a popular distance-based phylogenetic method that computes a tree metric from a dissimilarity map arising from biological data. Realizing dissimilarity maps as points in Euclidean space, the algorithm…
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…
Image ordinal estimation is to predict the ordinal label of a given image, which can be categorized as an ordinal regression problem. Recent methods formulate an ordinal regression problem as a series of binary classification problems. Such…
Statistically consistent estimation of phylogenetic trees or gene trees is possible if pairwise sequence dissimilarities can be converted to a set of distances that are proportional to the true evolutionary distances. Susko et al. (2004)…
Tree edit distance is a well-studied measure of dissimilarity between rooted trees with node labels. It can be computed in $O(n^3)$ time [Demaine, Mozes, Rossman, and Weimann, ICALP 2007], and fine-grained hardness results suggest that the…
Phylogenetic networks are used to represent the evolutionary history of species. Recently, the new class of orchard networks was introduced, which were later shown to be interpretable as trees with additional horizontal arcs. This makes the…
Pairwise ordered tree alignment are combinatorial objects that appear in RNA secondary structure comparison. However, the usual representation of tree alignments as supertrees is ambiguous, i.e. two distinct supertrees may induce identical…
Neighborhood algorithms may take a considerable percentage of computer time in discrete element methods (DEM). While the sort-and-sweep algorithm is ideal in some ways, as it only deal with particles whose relative positions change in one…
Understanding the mutational history of tumor cells is a critical endeavor in unraveling the mechanisms underlying cancer. Since the modeling of tumor cell evolution employs labeled trees, researchers are motivated to develop different…
Rotation distance between rooted binary trees measures the number of simple operations it takes to transform one tree into another. There are no known polynomial-time algorithms for computing rotation distance. We give an efficient,…
Phylogenetic comparative methods are well established tools for using inter-species variation to analyse phenotypic evolution and adaptation. They are generally hampered, however, by predominantly univariate approaches and failure to…
Frequency-limited model order reduction aims to approximate a high-order model with a reduced-order model that maintains high fidelity within a specific frequency range. Beyond this range, a decrease in accuracy is acceptable due to the…
Determining the interaction partners among protein/domain families poses hard computational problems, in particular in the presence of paralogous proteins. Available approaches aim to identify interaction partners among protein/domain…
We prove that there is a randomized polynomial-time algorithm that given an edge-weighted graph $G$ excluding a fixed-minor $Q$ on $n$ vertices and an accuracy parameter $\varepsilon>0$, constructs an edge-weighted graph~$H$ and an…
A geophylogeny is a phylogenetic tree (or dendrogram) where each leaf (e.g. biological taxon) has an associated geographic location (site). To clearly visualize a geophylogeny, the tree is typically represented as a crossing-free drawing…
We present both $hp$-a priori and $hp$-a posteriori error analysis of a mixed-order hybrid high-order (HHO) method to approximate second-order elliptic problems on simplicial meshes. Our main result on the $hp$-a priori error analysis is a…
We present an algorithm for computing a maximum agreement subtree of two unrooted evolutionary trees. It takes O(n^{1.5} log n) time for trees with unbounded degrees, matching the best known time complexity for the rooted case. Our…
Given two rooted, labeled trees $P$ and $T$ the tree path subsequence problem is to determine which paths in $P$ are subsequences of which paths in $T$. Here a path begins at the root and ends at a leaf. In this paper we propose this…
Our input is a directed, rooted graph $G = (V \cup \{r\},E)$ where each vertex in $V$ has a partial order preference over its incoming edges. The preferences of a vertex extend naturally to preferences over arborescences rooted at $r$. We…