Related papers: Polynomial algorithms for protein similarity searc…
A perfect matching in an undirected graph $G=(V,E)$ is a set of vertex disjoint edges from $E$ that include all vertices in $V$. The perfect matching problem is to decide if $G$ has such a matching. Recently Rothvo{\ss} proved the striking…
A linear inverse problem is proposed that requires the determination of multiple unknown signal vectors. Each unknown vector passes through a different system matrix and the results are added to yield a single observation vector. Given the…
We study the power of the bounded-width consistency algorithm in the context of the fixed-template Promise Constraint Satisfaction Problem (PCSP). Our main technical finding is that the template of every PCSP that is solvable in bounded…
We design new algorithms for approximating 2CSPs on graphs with bounded threshold rank, that is, whose normalized adjacency matrix has few eigenvalues larger than $\varepsilon$, smaller than $-\varepsilon$, or both. Unlike on worst-case…
Recurrent neural networks (RNNs) are a powerful approach for time series prediction. However, their performance is strongly affected by their architecture and hyperparameter settings. The architecture optimization of RNNs is a…
Tensor networks are powerful factorization techniques which reduce resource requirements for numerically simulating principal quantum many-body systems and algorithms. The computational complexity of a tensor network simulation depends on…
Sparse coding consists in representing signals as sparse linear combinations of atoms selected from a dictionary. We consider an extension of this framework where the atoms are further assumed to be embedded in a tree. This is achieved…
Many problems are NP-hard and, unless P = NP, do not admit polynomial-time exact algorithms. The fastest known exact algorithms exactly usually take time exponential in the input size. Much research effort has gone into obtaining faster…
Parameterized algorithms are a very useful tool for dealing with NP-hard problems on graphs. Yet, to properly utilize parameterized algorithms it is necessary to choose the right parameter based on the type of problem and properties of the…
Correspondence is a ubiquitous problem in computer vision and graph matching has been a natural way to formalize correspondence as an optimization problem. Recently, graph matching solvers have included higher-order terms representing…
Machine learning (ML) is revolutionizing protein structural analysis, including an important subproblem of predicting protein residue contact maps, i.e., which amino-acid residues are in close spatial proximity given the amino-acid sequence…
In comparative genomic, the first step of sequence analysis is usually to decompose two or more genomes into syntenic blocks that are segments of homologous chromosomes. For the reliable recovery of syntenic blocks, noise and ambiguities in…
In this paper we present an algorithmic framework for solving a class of combinatorial optimization problems on graphs with bounded pathwidth. The problems are NP-hard in general, but solvable in linear time on this type of graphs. The…
Nearest neighbor search is a fundamental data structure problem with many applications in machine learning, computer vision, recommendation systems and other fields. Although the main objective of the data structure is to quickly report…
Affordable, high-quality whole-genome assemblies have made it possible to construct rich pangenomes that capture haplotype diversity across many species. As these datasets grow, they motivate the development of specialized techniques…
Consider the problem of determining whether there exists a spanning hypertree in a given k-uniform hypergraph. This problem is trivially in P for k=2, and is NP-complete for k>= 4, whereas for k=3, there exists a polynomial-time algorithm…
Similarity graphs are an active research direction for the nearest neighbor search (NNS) problem. New algorithms for similarity graph construction are continuously being proposed and analyzed by both theoreticians and practitioners.…
A multitude of measures have been proposed to quantify the similarity between protein 3-D structure. Among these measures, contact map overlap (CMO) maximization deserved sustained attention during past decade because it offers a fine…
Brambles were introduced as the dual notion to treewidth, one of the most central concepts of the graph minor theory of Robertson and Seymour. Recently, Grohe and Marx showed that there are graphs G, in which every bramble of order larger…
We present approximation algorithms for the following NP-hard optimization problems related to bottleneck spanning trees in metric spaces. 1. The disjoint bottleneck spanning tree problem: Given $n$ pairs of points in a metric space, find…