Related papers: Representing Partitions on Trees
Phylogenetic analysis of DNA or other data commonly gives rise to a collection or sample of inferred evolutionary trees. Principal Components Analysis (PCA) cannot be applied directly to collections of trees since the space of evolutionary…
A "tree-partition" of a graph $G$ is a partition of $V(G)$ such that identifying the vertices in each part gives a tree. It is known that every graph with treewidth $k$ and maximum degree $\Delta$ has a tree-partition with parts of size…
We present a bijective algorithm with which an arbitrary permutation decomposes canonically into elementary blocks which we call families, which are sets with a specified number of ascents and descents. We show that families, arranged in an…
The statistical analysis of the structure of bipartite ecological networks has increased in importance in recent years. Yet, both algorithms and software packages for the analysis of network structure focus on properties of unipartite…
An evolutionary tree (phylogenetic tree) is a binary, rooted, unordered tree that models the evolutionary history of currently living species in which leaves are labeled by species. In this paper, we investigate the problem of finding the…
Staged trees are probabilistic graphical models capable of representing any class of non-symmetric independence via a coloring of its vertices. Several structural learning routines have been defined and implemented to learn staged trees…
Trigraph list homomorphism problems (also known as list matrix partition problems) have generated recent interest, partly because there are concrete problems that are not known to be polynomial time solvable or NP-complete. Thus while…
Rooted phylogenetic networks are often used to represent conflicting phylogenetic signals. Given a set of clusters, a network is said to represent these clusters in the "softwired" sense if, for each cluster in the input set, at least one…
Given a set of colored points in the plane, we ask if there exists a crossing-free straight-line drawing of a spanning forest, such that every tree in the forest contains exactly the points of one color class. We show that the problem is…
The decision tree recursively partitions the input space into regions and derives axis-aligned decision boundaries from data. Despite its simplicity and interpretability, decision trees lack parameterized representation, which makes it…
We consider three bivariate polynomial invariants $P$, $A$, and $S$ for rooted trees, as well as a trivariate polynomial invariant $M$. These invariants are motivated by random destruction processes such as the random cutting model or site…
Maximum bipartite matching is a fundamental algorithmic problem which can be solved in polynomial time. We consider a natural variant in which there is a separation constraint: the vertices on one side lie on a path or a grid, and two…
In this thesis, Minimal Partitioning (MP) algorithm, an innovative algorithm for enumerating all the spanning trees in an undirected graph is presented. While MP algorithm uses a computational tree graph to traverse all possible spanning…
We introduce a problem class we call Polynomial Constraint Satisfaction Problems, or PCSP. Where the usual CSPs from computer science and optimization have real-valued score functions, and partition functions from physics have monomials,…
The ongoing explosion of genome sequence data is transforming how we reconstruct and understand the histories of biological systems. Across biological scales, from individual cells to populations and species, trees-based models provide a…
P.L. Erdos and L.A. Szekely [Adv. Appl. Math. 10(1989), 488-496] gave a bijection between rooted semilabeled trees and set partitions. L.H. Harper's results [Ann. Math. Stat. 38(1967), 410-414] on the asymptotic normality of the Stirling…
Graph packing and partitioning problems have been studied in many contexts, including from the algorithmic complexity perspective. Consider the packing problem of determining whether a graph contains a spanning tree and a cycle that do not…
We prove that deciding whether the edge set of a graph can be partitionned into two spanning trees with orientation constraints is NP-complete. If P $\neq$ NP then this disproves a conjecture of Recski.
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…
Bipartition cover probabilities quantify whether a collection of gene trees contains every bipartition of the underlying species tree, a condition that underlies finite-sample guarantees for summary methods such as ASTRAL. We study this…