Related papers: A Simple Linear-Time Algorithm for the Common Refi…

Phylogenetic tree shapes capture fundamental signatures of evolution. We consider ``ranked'' tree shapes, which are equipped with a total order on the internal nodes compatible with the tree graph. Recent work has established an elegant…

In this paper, we investigate the computational complexity of subgraph reconfiguration problems in directed graphs. More specifically, we focus on the problem of reconfiguring arborescences in a digraph, where an arborescence is a directed…

There are many classical problems in P whose time complexities have not been improved over the past decades. Recent studies of "Hardness in P" have revealed that, for several of such problems, the current fastest algorithm is the best…

A kernel-independent treecode (KITC) is presented for fast summation of particle interactions. The method employs barycentric Lagrange interpolation at Chebyshev points to approximate well-separated particle-cluster interactions. The KITC…

We consider the phylogenetic tree reconstruction problem with insertions and deletions (indels). Phylogenetic algorithms proceed under a model where sequences evolve down the model tree, and given sequences at the leaves, the problem is to…

Combinatorial optimization lies at the core of many real-world problems. Especially since the rise of graph neural networks (GNNs), the deep learning community has been developing solvers that derive solutions to NP-hard problems by…

Label tree-based algorithms are widely used to tackle multi-class and multi-label problems with a large number of labels. We focus on a particular subclass of these algorithms that use probabilistic classifiers in the tree nodes. Examples…

In a previous work, we gave a metric on the class of semibinary tree-sibling time consistent phylogenetic networks that is computable in polynomial time; in particular, the problem of deciding if two networks of this kind are isomorphic is…

Dynamic programming over tree decompositions is a common technique in parameterized algorithms. In this paper, we study whether this technique can also be applied to compute Pareto sets of multiobjective optimization problems. We first…

Algorithms for partition refinement are actively studied for a variety of systems, often with the optimisation called Hopcroft's trick. However, the low-level description of those algorithms in the literature often obscures the essence of…

Phylogenetic networks are a generalization of phylogenetic trees to leaf-labeled directed acyclic graphs that represent ancestral relationships between species whose past includes non-tree-like events such as hybridization and horizontal…

Motivation: Millions of genes in the modern species belong to only thousands of `gene families'. A gene family includes instances of the same gene in different species (orthologs) and duplicate genes in the same species (paralogs). Genes…

Regression trees and their ensemble methods are popular methods for nonparametric regression: they combine strong predictive performance with interpretable estimators. To improve their utility for locally smooth response surfaces, we study…

Decision forests induce supervised similarities through the partition structure of their trees. Yet forest proximity computation is still often treated as a quadratic operation in the number of samples, which limits scalability and…

Tree-based models have proven to be an effective solution for web ranking as well as other problems in diverse domains. This paper focuses on optimizing the runtime performance of applying such models to make predictions, given an…

In this paper we propose and study a new complexity model for approximation algorithms. The main motivation are practical problems over large data sets that need to be solved many times for different scenarios, e.g., many multicast trees…

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…

Network redesign problems ask for modifications to the edges of a given graph to satisfy certain properties. In temporal graphs, where edges are only active at certain times, we are sometimes only allowed to modify when the edges are going…

This paper studies the "explanation problem" for tree- and linearly-ordered array data, a problem motivated by database applications and recently solved for the one-dimensional tree-ordered case. In this paper, one is given a matrix A whose…

Locally repairable codes (LRCs) are error correcting codes used in distributed data storage. A traditional approach is to look for codes which simultaneously maximize error tolerance and minimize storage space consumption. However, this…