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Different sources of information might tell different stories about the evolutionary history of a given set of species. This leads to (rooted) phylogenetic trees that "disagree" on triples of species, which we call "conflict triples". An…
The maximum agreement forest (MAF) problem in phylogenetics takes as input a set t >= 2 of binary phylogenetic trees T on the same set of taxa X. It asks for a partition of X into the smallest number of blocks such that the subtrees induced…
In mathematical phylogenetics, labeled histories describe the sequences by which sets of labeled lineages coalesce to a shared ancestral lineage. We study labeled histories for at-most-$r$-furcating trees. Consider a rooted leaf-labeled…
In phylogenetics, a central problem is to infer the evolutionary relationships between a set of species $X$; these relationships are often depicted via a phylogenetic tree -- a tree having its leaves univocally labeled by elements of $X$…
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…
Recent studies have demonstrated advantages of information fusion based on sparsity models for multimodal classification. Among several sparsity models, tree-structured sparsity provides a flexible framework for extraction of…
Extreme multi-label classification (XMLC) is a learning task of tagging instances with a small subset of relevant labels chosen from an extremely large pool of possible labels. Problems of this scale can be efficiently handled by organizing…
Full binary trees naturally represent commutative non-associative products. There are many important examples of these products: finite-precision floating-point addition and NAND gates, among others. Balance in such a tree is highly…
A widely used method for determining the similarity of two labeled trees is to compute a maximum agreement subtree of the two trees. Previous work on this similarity measure is only concerned with the comparison of labeled trees of two…
It is a known fact that, given two rooted binary phylogenetic trees, the concept of maximum acyclic agreement forests is sufficient to compute hybridization networks with minimum hybridization number. In this work, we demonstrate by first…
A classical problem in phylogenetic tree analysis is to decide whether there is a phylogenetic tree $T$ that contains all information of a given collection $\cP$ of phylogenetic trees. If the answer is "yes" we say that $\cP$ is compatible…
We introduce K-tree in an information retrieval context. It is an efficient approximation of the k-means clustering algorithm. Unlike k-means it forms a hierarchy of clusters. It has been extended to address issues with sparse…
A phylogenetic tree is a graphical representation of an evolutionary history of taxa in which the leaves correspond to the taxa and the non-leaves correspond to speciations. One of important problems in phylogenetic analysis is to assemble…
Merge trees, a type of topological descriptor, serve to identify and summarize the topological characteristics associated with scalar fields. They present a great potential for the analysis and visualization of time-varying data. First,…
Under any Multiclass Classification (MCC) setting defined by a collection of labeled point-cloud specified by a feature-set, we extract only stochastic partial orderings from all possible triplets of point-cloud without explicitly measuring…
Decision trees are one of the most popular methods for solving classification problems, mainly because of their good interpretability properties. Moreover, due to advances in recent years in mixed-integer optimization, several models have…
Deciding whether a collection of unrooted trees is compatible is a fundamental problem in phylogenetics. Two different graph-theoretic characterizations of tree compatibility have recently been proposed. In one of these, tree compatibility…
Trees with labelled leaves and with all other vertices of degree three play an important role in systematic biology and other areas of classification. A classical combinatorial result ensures that such trees can be uniquely reconstructed…
Manually labeling documents is tedious and expensive, but it is essential for training a traditional text classifier. In recent years, a few dataless text classification techniques have been proposed to address this problem. However,…
Tree alignment graphs (TAGs) provide an intuitive data structure for storing phylogenetic trees that exhibits the relationships of the individual input trees and can potentially account for nested taxonomic relationships. This paper…