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We consider the problem of finding a subgraph of a given graph which minimizes the sum of given functions at vertices evaluated at their subgraph degrees. While the problem is NP-hard already when all functions are the same, we show that it…
We prove that, in all dimensions d>=4, every simple open polygonal chain and every tree may be straightened, and every simple closed polygonal chain may be convexified. These reconfigurations can be achieved by algorithms that use…
In this paper, we study the parallel query complexity of reconstructing biological and digital phylogenetic trees from simple queries involving their nodes. This is motivated from computational biology, data protection, and computer…
We introduce a new model of indeterminacy in graphs: instead of specifying all the edges of the graph, the input contains all triples of vertices that form a connected subgraph. In general, different (labelled) graphs may have the same set…
Pairwise ordered tree alignment are combinatorial objects that appear in RNA secondary structure comparison. However, the usual representation of tree alignments as supertrees is ambiguous, i.e. two distinct supertrees may induce identical…
In the \emph{trace reconstruction problem}, an unknown source string $x \in \{0,1\}^n$ is transmitted through a probabilistic \emph{deletion channel} which independently deletes each bit with some fixed probability $\delta$ and concatenates…
In this paper, we focus on triplet-based deep binary embedding networks for image retrieval task. The triplet loss has been shown to be most effective for the ranking problem. However, most of the previous works treat the triplets equally…
We consider the well-studied problem of finding a spanning tree with minimum average distance between vertex pairs (called a MAD tree). This is a classic network design problem which is known to be NP-hard. While approximation algorithms…
Mining for trees in a graph is shown to be NP-complete.
Graph isomorphism, subgraph isomorphism, and maximum common subgraphs are classical well-investigated objects. Their (parameterized) complexity and efficiently tractable cases have been studied. In the present paper, for a given set of…
We here investigate on the complexity of computing the \emph{tree-length} and the \emph{tree-breadth} of any graph $G$, that are respectively the best possible upper-bounds on the diameter and the radius of the bags in a tree decomposition…
This paper considers the problem of inferring the structure of a network from indirect observations. Each observation (a "trace") is the unordered set of nodes which are activated along a path through the network. Since a trace does not…
We generalize the problem of reconstructing strings from their substring compositions first introduced by Acharya et al. in 2015 motivated by polymer-based advanced data storage systems utilizing mass spectrometry. Namely, we see strings as…
We consider combinatorial problems that can be solved in polynomial time for graphs of bounded treewidth but where the order of the polynomial that bounds the running time is expected to depend on the treewidth bound. First we review some…
In molecular phylogeny, relationships among organisms are reconstructed using DNA or protein sequences and are displayed as trees. A linear increase in the number of sequences results in an exponential increase of possible trees. Thus,…
The early development of a zygote can be mathematically described by a developmental tree. To compare developmental trees of different species, we need to define distances on trees. If children cells after a division are not…
We consider a natural variant of the well-known Feedback Vertex Set problem, namely the problem of deleting a small subset of vertices or edges to a full binary tree. This version of the problem is motivated by real-world scenarios that are…
Poly-trees are singly connected causal networks in which variables may arise from multiple causes. This paper develops a method of recovering ply-trees from empirically measured probability distributions of pairs of variables. The method…
Background: Tree reconciliation problems have long been studied in phylogenetics. A particular variant of the reconciliation problem for a gene tree T and a species tree S assumes that for each interior vertex x of T it is known whether x…
The $(n-\ell)$-deck of an $n$-vertex graph is the multiset of (unlabeled) subgraphs obtained from it by deleting $\ell$ vertices. An $n$-vertex graph is $\ell$-reconstructible if it is determined by its $(n-\ell)$-deck, meaning that no…