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In a population with haploid reproduction any individual has a single parent in the previous generation. If all genealogical distances among pairs of individuals (generations from the closest common ancestor) are known it is possible to…
We study the problem of learning a Bayesian network (BN) of a set of variables when structural side information about the system is available. It is well known that learning the structure of a general BN is both computationally and…
Let $G=(V,E)$ be a simple, unweighted, connected graph. Let $d(u,v)$ denote the distance between vertices $u,v$. A resolving set of $G$ is a subset $S$ of $V$ such that knowing the distance from a vertex $v$ to every vertex in $S$ uniquely…
It is an open question whether there exists a polynomial-time algorithm for computing the rotation distances between pairs of extended ordered binary trees. The problem of computing the rotation distance between an arbitrary pair of trees,…
Tree-structured neural networks encode a particular tree geometry for a sentence in the network design. However, these models have at best only slightly outperformed simpler sequence-based models. We hypothesize that neural sequence models…
We consider here the problem of chaining seeds in ordered trees. Seeds are mappings between two trees Q and T and a chain is a subset of non overlapping seeds that is consistent with respect to postfix order and ancestrality. This problem…
Motivated by applications in polymer-based data storage, we study the problem of reconstructing a string from part of its composition multiset. We give a full description of the structure of the strings that cannot be uniquely reconstructed…
We investigate the tractability of a simple fusion of two fundamental structures on graphs, a spanning tree and a perfect matching. Specifically, we consider the following problem: given an edge-weighted graph, find a minimum-weight…
Many algorithms have been developed for NP-hard problems on graphs with small treewidth $k$. For example, all problems that are expressable in linear extended monadic second order can be solved in linear time on graphs of bounded treewidth.…
A graph is rectilinear planar if it admits a planar orthogonal drawing without bends. While testing rectilinear planarity is NP-hard in general (Garg and Tamassia, 2001), it is a long-standing open problem to establish a tight upper bound…
We study compact straight-line embeddings of trees. We show that perfect binary trees can be embedded optimally: a tree with $n$ nodes can be drawn on a $\sqrt n$ by $\sqrt n$ grid. We also show that testing whether a given binary tree has…
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…
This paper investigates the impact of query topology on the difficulty of answering conjunctive queries in the presence of OWL 2 QL ontologies. Our first contribution is to clarify the worst-case size of positive existential (PE),…
The tree-depth problem can be seen as finding an elimination tree of minimum height for a given input graph $G$. We introduce a bicriteria generalization in which additionally the width of the elimination tree needs to be bounded by some…
The last decade brought a significant increase in the amount of data and a variety of new inference methods for reconstructing the detailed evolutionary history of various cancers. This brings the need of designing efficient procedures for…
Generalizing the decomposition of a connected planar graph into a tree and a dual tree, we prove a combinatorial analog of the classic Helmholz-Hodge decomposition of a smooth vector field. Specifically, we show that for every polyhedral…
In this article, we study the complexity of the upgrading version of the maximal covering location problem with edge length modifications on networks. This problem is NP-hard on general networks. However, in some particular cases, we prove…
Trigraph list homomorphism problems (also known as list matrix partition problems) have generated recent interest, partly because there are concrete problems that are not known to be polynomial time solvable or NP-complete. Thus while…
We prove that the complexity of the uniform first-order theory of ground tree rewrite graphs is in ATIME(2^{2^{poly(n)}},O(n)). Providing a matching lower bound, we show that there is some fixed ground tree rewrite graph whose first-order…
A suffix tree is a data structure used mainly for pattern matching. It is known that the space complexity of simple suffix trees is quadratic in the length of the string. By a slight modification of the simple suffix trees one gets the…