Related papers: A Simple Linear-Time Algorithm for the Common Refi…
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…
Approximating the roots of a holomorphic function in an input box is a fundamental problem in many domains. Most algorithms in the literature for solving this problem are conditional, i.e., they make some simplifying assumptions, such as,…
In this work, we answer an open problem in the study of phylogenetic networks. Phylogenetic trees are rooted binary trees in which all edges are directed away from the root, whereas phylogenetic networks are rooted acyclic digraphs. For the…
Tree kernels are fundamental tools that have been leveraged in many applications, particularly those based on machine learning for Natural Language Processing tasks. In this paper, we devise a parallel implementation of the sequential…
Data augmentation is widely used for training a neural network given little labeled data. A common practice of augmentation training is applying a composition of multiple transformations sequentially to the data. Existing augmentation…
Levin Tree Search (LTS) (Orseau et al., 2018) is a search algorithm for deterministic environments that uses a user-specified policy to guide the search. It comes with a formal guarantee on the number of search steps (node visits) for…
Graph Isomorphism (GI) is a fundamental algorithmic problem. Amongst graph classes for which the computational complexity of GI has been resolved, trees are arguably the most fundamental. Tree Isomorphism is complete for deterministic…
A numerical method is developed to solve linear semi-infinite programming problem (LSIP) in which the iterates produced by the algorithm are feasible for the original problem. This is achieved by constructing a sequence of standard linear…
Suffix trees are key and efficient data structure for solving string problems. A suffix tree is a compressed trie containing all the suffixes of a given text of length $n$ with a linear construction cost. In this work, we introduce an…
Rooted phylogenetic networks provide an explicit representation of the evolutionary history of a set $X$ of sampled species. In contrast to phylogenetic trees which show only speciation events, networks can also accommodate reticulate…
In the laminar-constrained spanning tree problem, the goal is to find a minimum-cost spanning tree which respects upper bounds on the number of times each cut in a given laminar family is crossed. This generalizes the well-studied…
Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently. However, it is well-known that the evolution of gene families…
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.…
We give practical, efficient algorithms that automatically determine the asymptotic distributed round complexity of a given locally checkable graph problem in the $[\Theta(\log n), \Theta(n)]$ region, in two settings. We present one…
In this work, we develop the low-space Massively Parallel Computation (MPC) complexity landscape for a family of fundamental graph problems on trees. We present a general method that solves most locally checkable labeling (LCL) problems…
The way to infer well-supported phylogenetic trees that precisely reflect the evolutionary process is a challenging task that completely depends on the way the related core genes have been found. In previous computational biology studies,…
Recently much attention has been devoted to the construction of phylogenetic networks which generalize phylogenetic trees in order to accommodate complex evolutionary processes. Here we present an efficient, practical algorithm for…
We develop a time-optimal $O(mn^2)$-time algorithm to construct the subtree prune-regraft (SPR) graph on a collection of m phylogenetic trees with n leaves. This improves on the previous bound of $O(mn^3)$. Such graphs are used to better…
Given two strings $T$ and $S$ and a set of strings $P$, for each string $p \in P$, consider the unique substrings of $T$ that have $p$ as their prefix and $S$ as their suffix. Two problems then come to mind; the first problem being the…
Given two rooted, ordered, and labeled trees $P$ and $T$ the tree inclusion problem is to determine if $P$ can be obtained from $T$ by deleting nodes in $T$. This problem has recently been recognized as an important query primitive in XML…