Related papers: Cutting an alignment with Ockham's razor
Counting the number of homomorphisms of a pattern graph H in a large input graph G is a fundamental problem in computer science. There are myriad applications of this problem in databases, graph algorithms, and network science. Often, we…
A physics-informed machine learning framework based on holomorphic neural networks is introduced for detecting cracks in two-dimensional solids from strain or displacement data. Crack detection is formulated as an inverse problem in which…
In recent years, several integer programming (IP) approaches were developed for maximum-likelihood decoding and minimum distance computation for binary linear codes. Two aspects in particular have been demonstrated to improve the…
Parameterized complexity theory has enabled a refined classification of the difficulty of NP-hard optimization problems on graphs with respect to key structural properties, and so to a better understanding of their true difficulties. More…
In evolutionary biology, genetic sequences carry with them a trace of the underlying tree that describes their evolution from a common ancestral sequence. The question of how many sequence sites are required to recover this evolutionary…
The Exact Circular Pattern Matching (ECPM) problem consists of reporting every occurrence of a rotation of a pattern $P$ in a text $T$. In many real-world applications, specifically in computational biology, circular rotations are of…
Identification of local structure in intensive data -- such as time series, images, and higher dimensional processes -- is an important problem in astronomy. Since the data are typically generated by an inhomogeneous Poisson process, an…
This work studies problems in data reconstruction, an important area with numerous applications. In particular, we examine the reconstruction of binary and non-binary sequences from synchronization (insertion/deletion-correcting) codes.…
Detectability of failures of linear programming (LP) decoding and its potential for improvement by adding new constraints motivate the use of an adaptive approach in selecting the constraints for the LP problem. In this paper, we make a…
We consider the problem of detecting multiple changes in multiple independent time series. The search for the best segmentation can be expressed as a minimization problem over a given cost function. We focus on dynamic programming…
Identifying palindromes in sequences has been an interesting line of research in combinatorics on words and also in computational biology, after the discovery of the relation of palindromes in the DNA sequence with the HIV virus. Efficient…
Detectability of failures of linear programming (LP) decoding and the potential for improvement by adding new constraints motivate the use of an adaptive approach in selecting the constraints for the underlying LP problem. In this paper, we…
Many problems arising in image processing and signal recovery with multi-regularization can be formulated as minimization of a sum of three convex separable functions. Typically, the objective function involves a smooth function with…
The Single Cut or Join (SCJ) operation on genomes, generalizing chromosome evolution by fusions and fissions, is the computationally simplest known model of genome rearrangement. While most genome rearrangement problems are already hard…
Dictionary learning is the task of determining a data-dependent transform that yields a sparse representation of some observed data. The dictionary learning problem is non-convex, and usually solved via computationally complex iterative…
This paper addresses the problem of registering multiple point sets. Solutions to this problem are often approximated by repeatedly solving for pairwise registration, which results in an uneven treatment of the sets forming a pair: a model…
3D reconstruction is a fundamental issue in many applications and the feature point matching problem is a key step while reconstructing target objects. Conventional algorithms can only find a small number of feature points from two images…
NP-hard problems such as the maximum clique or minimum vertex cover problems, two of Karp's 21 NP-hard problems, have several applications in computational chemistry, biochemistry and computer network security. Adiabatic quantum annealers…
Given a dictionary that consists of multiple blocks and a signal that lives in the range space of only a few blocks, we study the problem of finding a block-sparse representation of the signal, i.e., a representation that uses the minimum…
This paper presents a novel approach to address the constrained coding challenge of generating almost-balanced sequences. While strictly balanced sequences have been well studied in the past, the problem of designing efficient algorithms…