Related papers: MaxSSmap: A GPU program for mapping divergent shor…

The fitting of spectral lines is a common step in the analysis of line observations and simulations. However, the observational noise, the presence of multiple velocity components, and potentially large data sets make it a non-trivial task.…

Graph neural networks (GNNs) are powerful tools for learning from graph data and are widely used in various applications such as social network recommendation, fraud detection, and graph search. The graphs in these applications are…

This paper presents a framework that supports the implementation of parallel solutions for the widespread parametric maximum flow computational routines used in image segmentation algorithms. The framework is based on supergraphs, a special…

Developing high-performance and energy-efficient algorithms for maximum matchings is becoming increasingly important in social network analysis, computational sciences, scheduling, and others. In this work, we propose the first maximum…

The MAX BISECTION problem seeks a maximum-size cut that evenly divides the vertices of a given undirected graph. An open problem raised by Austrin, Benabbas, and Georgiou is whether MAX BISECTION can be approximated as well as MAX CUT,…

Repeat finding in strings has important applications in subfields such as computational biology. The challenge of finding the longest repeats covering particular string positions was recently proposed and solved by \.{I}leri et al., using a…

Although the matrix multiplication plays a vital role in computational linear algebra, there are few efficient solutions for matrix multiplication of the near-sparse matrices. The Sparse Approximate Matrix Multiply (SpAMM) is one of the…

Gaussian Processes are widely used for regression tasks. A known limitation in the application of Gaussian Processes to regression tasks is that the computation of the solution requires performing a matrix inversion. The solution also…

This paper studies a classic maximum entropy sampling problem (MESP), which aims to select the most informative principal submatrix of a prespecified size from a covariance matrix. MESP has been widely applied to many areas, including…

The class $(r,2)$-CSP, or simply Max 2-CSP, consists of constraint satisfaction problems with at most two $r$-valued variables per clause. For instances with $n$ variables and $m$ binary clauses, we present an $O(n r^{5+19m/100})$-time…

Much effort has been directed at algorithms for obtaining the highest probability configuration in a probabilistic random field model known as the maximum a posteriori (MAP) inference problem. In many situations, one could benefit from…

Given a graph $G$, the NP-hard Maximum Planar Subgraph problem (MPS) asks for a planar subgraph of $G$ with the maximum number of edges. There are several heuristic, approximative, and exact algorithms to tackle the problem, but---to the…

In this paper, we propose an inexact multi-block ADMM-type first-order method for solving a class of high-dimensional convex composite conic optimization problems to moderate accuracy. The design of this method combines an inexact 2-block…

Motivation: We introduce SneakySnake, a highly parallel and highly accurate pre-alignment filter that remarkably reduces the need for computationally costly sequence alignment. The key idea of SneakySnake is to reduce the approximate string…

Huge numbers of short reads are being generated for mapping back to the genome to discover the frequency of transcripts, miRNAs, DNAase hypersensitive sites, FAIRE regions, nucleosome occupancy, etc. Since these reads are typically short…

Bayesian spectral deconvolution provides a data-driven framework for mathematical model selection and parameter estimation from spectral data. Although highly versatile, it becomes computationally expensive as the number of model…

The limits of molecular dynamics (MD) simulations of macromolecules are steadily pushed forward by the relentless developments of computer architectures and algorithms. This explosion in the number and extent (in size and time) of MD…

The Max-Cut problem is a well known combinatorial optimization problem. In this paper we describe a fast approximation method. Given a graph G, we want to find a cut whose size is maximal among all possible cuts. A cut is a partition of the…

Softassign is a pivotal method in graph matching and other learning tasks. Many softassign-based algorithms exhibit performance sensitivity to a parameter in the softassign. However, tuning the parameter is challenging and almost done…

Metagenome assembly is the process of transforming a set of short, overlapping, and potentially erroneous DNA segments from environmental samples into the accurate representation of the underlying microbiomes's genomes. State-of-the-art…