Related papers: A note on efficient computation of hybridization n…

We introduce a hybrid metaphor for the visualization of the reconciliations of co-phylogenetic trees, that are mappings among the nodes of two trees. The typical application is the visualization of the co-evolution of hosts and parasites in…

We propose a novel dependency-based hybrid tree model for semantic parsing, which converts natural language utterance into machine interpretable meaning representations. Unlike previous state-of-the-art models, the semantic information is…

Fixed parameter tractable algorithms for bounded treewidth are known to exist for a wide class of graph optimization problems. While most research in this area has been focused on exact algorithms, it is hard to find decompositions of…

Identifying a subset of taxa that maximizes Phylogenetic Diversity (PD) is a cornerstone of quantitative conservation planning. Traditionally, PD is defined over a phylogenetic tree in which leaves resemble present-day taxa and the branch…

Treewidth and hypertree width have proven to be highly successful structural parameters in the context of the Constraint Satisfaction Problem (CSP). When either of these parameters is bounded by a constant, then CSP becomes solvable in…

Solving (mixed) integer linear programs, (M)ILPs for short, is a fundamental optimization task. While hard in general, recent years have brought about vast progress for solving structurally restricted, (non-mixed) ILPs: $n$-fold, tree-fold,…

Hybridization events complicate the accurate reconstruction of phylogenies, as they lead to patterns of genetic heritability that are unexpected under traditional, bifurcating models of species trees. This has led to the development of…

While almost all existing works which optimally solve just-in-time scheduling problems propose dedicated algorithmic approaches, we propose in this work mixed integer formulations. We consider a single machine scheduling problem that aims…

This paper tackles the problem of the existence of solutions for recursive systems of Horn clauses with second-order variables interpreted as integer relations, and harnessed by quantifier-free difference bounds arithmetic. We start by…

The phylogenetic tree space introduced by Billera, Holmes, and Vogtmann (BHV tree space) is a CAT(0) continuous space that represents trees with edge weights with an intrinsic geodesic distance measure. The geodesic distance measure unique…

We propose a new methodology to develop heuristic algorithms using tree decompositions. Traditionally, such algorithms construct an optimal solution of the given problem instance through a dynamic programming approach. We modify this…

When modeling an application of practical relevance as an instance of a combinatorial problem X, we are often interested not merely in finding one optimal solution for that instance, but in finding a sufficiently diverse collection of good…

A phylogenetic tree shows the evolutionary relationships among species. Internal nodes of the tree represent speciation events and leaf nodes correspond to species. A goal of phylogenetics is to combine such trees into larger trees, called…

We propose an algorithm named best-scored random forest for binary classification problems. The terminology "best-scored" means to select the one with the best empirical performance out of a certain number of purely random tree candidates…

Combining a set of phylogenetic trees into a single phylogenetic network that explains all of them is a fundamental challenge in evolutionary studies. Existing methods are computationally expensive and can either handle only small numbers…

This paper studies the unification problem with associative, commutative, and associative-commutative functions mainly from a viewpoint of the parameterized complexity on the number of variables. It is shown that both associative and…

We study the problem of minimizing a multivariate polynomial function over the unit hypercube. By representing the polynomial through a hypergraph and exploiting its sparsity structure, we establish a new sufficient condition under which…

Random Forest (RFs) are among the most widely used Machine Learning (ML) classifiers. Even though RFs are not interpretable, there are no dedicated non-heuristic approaches for computing explanations of RFs. Moreover, there is recent work…

Attempting to recognize a tree inside a phylogenetic network is a fundamental undertaking in evolutionary analysis. In the last few years, therefore, tree-based phylogenetic networks, which are defined by a spanning tree called a…

This article presents two novel algorithms for generating random increasing trees. The first algorithm efficiently generates strictly increasing binary trees using an ad hoc method. The second algorithm improves the recursive method for…