Related papers: A Simple Linear-Time Algorithm for the Common Refi…
We define a search problem on trees that closely captures the backtracking behavior of all current practical graph isomorphism algorithms. Given two trees with colored leaves, the goal is to find two leaves of matching color, one in each of…
We systematically study the computational complexity of a broad class of computational problems in phylogenetic reconstruction. The class contains for example the rooted triple consistency problem, forbidden subtree problems, the quartet…
This paper presents the novel `uniqueness tree' algorithm, as one possible method for determining whether two finite, undirected graphs are isomorphic. We prove that the algorithm has polynomial time complexity in the worst case, and that…
A fundamental problem in the study of phylogenetic networks is to determine whether or not a given phylogenetic network contains a given phylogenetic tree. We develop a quadratic-time algorithm for this problem for binary nearly-stable…
We introduce a simple algorithm for reconstructing phylogenies from multiple gene trees in the presence of incomplete lineage sorting, that is, when the topology of the gene trees may differ from that of the species tree. We show that our…
Causal representation learning (CRL) has garnered increasing interest from the causal inference and artificial intelligence communities due to its potential to disentangle complex data-generating mechanism into causally interpretable latent…
A simple greedy refinement procedure for the generation of data-adapted triangulations is proposed and studied. Given a function of two variables, the algorithm produces a hierarchy of triangulations and piecewise polynomial approximations…
We consider the Steiner tree problem on graphs where we are given a set of nodes and the goal is to find a tree sub-graph of minimum weight that contains all nodes in the given set, potentially including additional nodes. This is a…
In this work we introduce a new linear time compression algorithm, called "Re-pair for Trees", which compresses ranked ordered trees using linear straight-line context-free tree grammars. Such grammars generalize straight-line context-free…
In this study, we investigate the problem of comparing gene trees reconciled with the same species tree using a novel semi-metric, called the Path-Label Reconciliation (PLR) dissimilarity measure. This approach not only quantifies…
A recently proposed exact algorithm for the maximum independent set problem is analyzed. The typical running time is improved exponentially in some parameter regions compared to simple binary search. The algorithm also overcomes the core…
An anytime decoding algorithm for tree codes using Monte-Carlo tree search is proposed. The meaning of anytime decoding here is twofold: 1) the decoding algorithm is an anytime algorithm, whose decoding performance improves as more…
Identifying optimal basic feasible solutions to linear programming problems is a critical task for mixed integer programming and other applications. The crossover method, which aims at deriving an optimal extreme point from a suboptimal…
The reformulation-linearization technique (RLT) is a prominent approach to constructing tight linear relaxations of non-convex continuous and mixed-integer optimization problems. The goal of this paper is to extend the applicability and…
In real practice, questions are typically complex and knowledge-intensive, requiring Large Language Models (LLMs) to recognize the multifaceted nature of the question and reason across multiple information sources. Iterative and adaptive…
We present a general framework for balancing expressions (terms) in form of so called tree straight-line programs. The latter can be seen as circuits over the free term algebra extended by contexts (terms with a hole) and the operations…
We revisit the classic combinatorial pattern matching problem of finding a longest common subsequence (LCS). For strings $x$ and $y$ of length $n$, a textbook algorithm solves LCS in time $O(n^2)$, but although much effort has been spent,…
Clique tree conversion solves large-scale semidefinite programs by splitting an $n\times n$ matrix variable into up to $n$ smaller matrix variables, each representing a principal submatrix of up to $\omega\times\omega$. Its fundamental…
The Aho, Hopcroft and Ullman (AHU) algorithm has been the state of the art since the 1970s for determining in linear time whether two unordered rooted trees are isomorphic or not. However, it has been criticized (by Campbell and Radford)…
We consider the problem of embedding the Steiner points of a Steiner tree with given topology into the rectilinear plane. Thereby, the length of the path between a distinguished terminal and each other terminal must not exceed given length…