Related papers: Linear-Time Tree Containment in Phylogenetic Netwo…
We consider the problem of learning underlying tree structure from noisy, mixed data obtained from a linear model. To achieve this, we use the expectation maximization algorithm combined with Chow-Liu minimum spanning tree algorithm. This…
Arising from structural graph theory, treewidth has become a focus of study in fixed-parameter tractable algorithms in various communities including combinatorics, integer-linear programming, and numerical analysis. Many NP-hard problems…
Most of major algorithms for phylogenetic tree reconstruction assume that sequences in the analyzed set either do not have any offspring, or that parent sequences can maximally mutate into just two descendants. The graph resulting from such…
We study the problem of finding a temporal hybridization network for a set of phylogenetic trees that minimizes the number of reticulations. First, we introduce an FPT algorithm for this problem on an arbitrary set of $m$ binary trees with…
Many modern multiclass and multilabel problems are characterized by increasingly large output spaces. For these problems, label embeddings have been shown to be a useful primitive that can improve computational and statistical efficiency.…
There are several tools available to infer phylogenetic trees, which depict the evolutionary relationships among biological entities such as viral and bacterial strains in infectious outbreaks, or cancerous cells in tumor progression trees.…
Given a dense triplet set $\mathcal{T}$, there arise two interesting questions: Does there exists any phylogenetic network consistent with $\mathcal{T}$? And if so, can we find an effective algorithm to construct one? For cases of networks…
Automatic detection and segmentation of overlapping leaves in dense foliage can be a difficult task, particularly for leaves with strong textures and high occlusions. We present Dense-Leaves, an image dataset with ground truth segmentation…
Comparative analyses of phylogenetic trees typically require identical taxon sets, however, in practice, trees often include distinct but overlapping taxa. Pruning non-shared leaves discards phylogenetic signal, whereas tree completion can…
An SPQR-tree is a data structure that efficiently represents all planar embeddings of a biconnected planar graph. It is a key tool in a number of constrained planarity testing algorithms, which seek a planar embedding of a graph subject to…
This technical note extends recent results on the computational complexity of globally minimizing the error of piecewise-affine models to the related problem of minimizing the error of switching linear regression models. In particular, we…
Driven by the need for better models that allow one to shed light into the question how life's diversity has evolved, phylogenetic networks have now joined phylogenetic trees in the center of phylogenetics research. Like phylogenetic trees,…
Structural information of phylogenetic tree topologies plays an important role in phylogenetic inference. However, finding appropriate topological structures for specific phylogenetic inference tasks often requires significant design effort…
Rank of divisor on graph was introduced in 2007 and it quickly attracts many attentions. Recently, in 2015 the problem for computing this quantity was proved to be NP-hard. In this paper, we describe a linear time algorithm for this problem…
Tree-based networks are a class of phylogenetic networks that attempt to formally capture what is meant by "tree-like" evolution. A given non-tree-based phylogenetic network, however, might appear to be very close to being tree-based, or…
In many real-world networks, nodes have class labels, attributes, or variables that affect the network's topology. If the topology of the network is known but the labels of the nodes are hidden, we would like to select a small subset of…
Phylogenetic networks are an extension of phylogenetic trees that allow for the representation of reticulate evolution events. One of the classes of networks that has gained the attention of the scientific community over the last years is…
Several computational problems in phylogenetic reconstruction can be formulated as restrictions of the following general problem: given a formula in conjunctive normal form where the literals are rooted triples, is there a rooted binary…
The sorting problem is one of the most relevant problems in computer science. Within the scope of modern computer science it has been studied for more than 70 years. In spite of these facts, new sorting algorithms have been developed in…
Trees with many leaves have applications on broadcasting, which is a method in networks for transferring a message to all recipients simultaneously. Internal nodes of a broadcasting tree require more expensive technology, because they have…