Related papers: Polynomial algorithms for protein similarity searc…
We investigate the complexity of several fundamental polynomial-time solvable problems on graphs and on matrices, when the given instance has low treewidth; in the case of matrices, we consider the treewidth of the graph formed by non-zero…
We give the first approximation algorithm for mixed packing and covering semidefinite programs (SDPs) with polylogarithmic dependence on width. Mixed packing and covering SDPs constitute a fundamental algorithmic primitive with recent…
We introduce a new parameter, called stretch-width, that we show sits strictly between clique-width and twin-width. Unlike the reduced parameters [BKW '22], planar graphs and polynomial subdivisions do not have bounded stretch-width. This…
Nuclear Magnetic Resonance (NMR) Spectroscopy is a widely used technique to predict the native structure of proteins. However, NMR machines are only able to report approximate and partial distances between pair of atoms. To build the…
In the longest plane spanning tree problem, we are given a finite planar point set $\mathcal{P}$, and our task is to find a plane (i.e., noncrossing) spanning tree for $\mathcal{P}$ with maximum total Euclidean edge length. Despite more…
We show NP-completeness for several planar variants of the monotone satisfiability problem with bounded variable appearances. With one exception the presented variants have an associated bipartite graph where the vertex degree is bounded by…
We consider scheduling on identical and unrelated parallel machines with job assignment restrictions. These problems are NP-hard and they do not admit polynomial time approximation algorithms with approximation ratios smaller than $1.5$…
The problem of computing all maximal induced subgraphs of a graph G that have a graph property P, also called the maximal P-subgraphs problem, is considered. This problem is studied for hereditary, connected-hereditary and rooted-hereditary…
A graph class is monotone if it is closed under taking subgraphs. It is known that a monotone class defined by finitely many obstructions has bounded treewidth if and only if one of the obstructions is a so-called tripod, that is, a…
Inferring probabilistic networks from data is a notoriously difficult task. Under various goodness-of-fit measures, finding an optimal network is NP-hard, even if restricted to polytrees of bounded in-degree. Polynomial-time algorithms are…
We consider the stochastic geometry model where the location of each node is a random point in a given metric space, or the existence of each node is uncertain. We study the problems of computing the expected lengths of several…
Best match graphs (BMGs) are a class of colored digraphs that naturally appear in mathematical phylogenetics and can be approximated with the help of similarity measures between gene sequences, albeit not without errors. The corresponding…
Query plans are compared according to multiple cost metrics in multi-objective query optimization. The goal is to find the set of Pareto plans realizing optimal cost tradeoffs for a given query. So far, only algorithms with exponential…
We present a new algorithm for enumerating bubbles with length constraints in directed graphs. This problem arises in transcriptomics, where the question is to identify all alternative splicing events present in a sample of mRNAs sequenced…
We give the first polynomial-time algorithms on graphs of bounded maximum induced matching width (mim-width) for problems that are not locally checkable. In particular, we give $n^{\mathcal{O}(w)}$-time algorithms on graphs of mim-width at…
In the last decade, algorithmic frameworks based on a structural graph parameter called mim-width have been developed to solve generally NP-hard problems. However, it is known that the frameworks cannot be applied to the Clique problem, and…
Despite significant research efforts, the state-of-the-art algorithm for maintaining an approximate matching in fully dynamic graphs has a polynomial {worst-case} update time, even for very poor approximation guarantees. In a recent…
Finding coarse representations of large graphs is an important computational problem in the fields of scientific computing, large scale graph partitioning, and the reduction of geometric meshes. Of particular interest in all of these fields…
The minimum-cost arborescence problem is a well-studied problem in the area of graph theory, with known polynomial-time algorithms for solving it. Previous literature introduced new variations on the original problem with different…
Questions in computational molecular biology generate various discrete optimization problems, such as DNA sequence alignment and RNA secondary structure prediction. However, the optimal solutions are fundamentally dependent on the…