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Bilevel optimization refers to scenarios whereby the optimal solution of a lower-level energy function serves as input features to an upper-level objective of interest. These optimal features typically depend on tunable parameters of the…
Phylogenetic networks are a generalization of evolutionary trees that are used by biologists to represent the evolution of organisms which have undergone reticulate evolution. Essentially, a phylogenetic network is a directed acyclic graph…
Finding a minimum spanning tree (MST) for $n$ points in an arbitrary metric space is a fundamental primitive for hierarchical clustering and many other ML tasks, but this takes $\Omega(n^2)$ time to even approximate. We introduce a…
Bidimensionality is the most common technique to design subexponential-time parameterized algorithms on special classes of graphs, particularly planar graphs. The core engine behind it is a combinatorial lemma of Robertson, Seymour and…
In a simple, undirected graph G, an edge 2-coloring is a coloring of the edges such that no vertex is incident to edges with more than 2 distinct colors. The problem maximum edge 2-coloring (ME2C) is to find an edge 2-coloring in a graph G…
We study the problem of learning a latent tree graphical model where samples are available only from a subset of variables. We propose two consistent and computationally efficient algorithms for learning minimal latent trees, that is, trees…
Bipartite graphs, representing two-mode networks, arise in many research fields. These networks have two disjoint node sets representing distinct entity types, for example persons and groups, with edges representing associations between the…
The Balanced Connected Subgraph problem (BCS) was recently introduced by Bhore et al. (CALDAM 2019). In this problem, we are given a graph $G$ whose vertices are colored by red or blue. The goal is to find a maximum connected subgraph of…
Finding the most parsimonious tree inside a phylogenetic network with respect to a given character is an NP-hard combinatorial optimization problem that for many network topologies is essentially inapproximable. In contrast, if the network…
Balanced minimum evolution is a distance-based criterion for the reconstruction of phylogenetic trees. Several algorithms exist to find the optimal tree with respect to this criterion. One approach is to minimize a certain linear functional…
Tree-based phylogenetic networks, which may be roughly defined as leaf-labeled networks built by adding arcs only between the original tree edges, have elegant properties for modeling evolutionary histories. We answer an open question of…
We analyse a maximum-likelihood approach for combining phylogenetic trees into a larger `supertree'. This is based on a simple exponential model of phylogenetic error, which ensures that ML supertrees have a simple combinatorial description…
Compatibility of unrooted phylogenetic trees is a well studied problem in phylogenetics. It asks to determine whether for a set of k input trees there exists a larger tree (called a supertree) that contains the topologies of all k input…
We investigate the tractability of a simple fusion of two fundamental structures on graphs, a spanning tree and a perfect matching. Specifically, we consider the following problem: given an edge-weighted graph, find a minimum-weight…
In the context of reconstructing phylogenetic networks from a collection of phylogenetic trees, several characterisations and subsequently algorithms have been established to reconstruct a phylogenetic network that collectively embeds all…
A maximum priority matching is a matching in an undirected graph that maximizes a priority score defined with respect to given vertex priorities. An earlier paper showed how to find maximum priority matchings in unweighted graphs. This…
A vertex of a plane digraph is bimodal if all its incoming edges (and hence all its outgoing edges) are consecutive in the cyclic order around it. A plane digraph is bimodal if all its vertices are bimodal. Bimodality is at the heart of…
An L(2,1)-labeling of a graph $G$ is an assignment $f$ from the vertex set $V(G)$ to the set of nonnegative integers such that $|f(x)-f(y)|\ge 2$ if $x$ and $y$ are adjacent and $|f(x)-f(y)|\ge 1$ if $x$ and $y$ are at distance 2, for all…
Two genes are xenologs in the sense of Fitch if they are separated by at least one horizontal gene transfer event. Horizonal gene transfer is asymmetric in the sense that the transferred copy is distinguished from the one that remains…
Given a connected undirected graph G = [V; E] where |E| =2(|V| -1), we present two algorithms to check if G can be decomposed into two edge disjoint spanning trees, and provide such a decomposition when it exists. Unlike previous algorithms…