Related papers: Cutting an alignment with Ockham's razor
This paper explores the enhancement of solution diversity in evolutionary algorithms (EAs) for the maximum matching problem, concentrating on complete bipartite graphs and paths. We adopt binary string encoding for matchings and use Hamming…
Array-Based Comparative Genomic Hybridization (aCGH) is a method used to search for genomic regions with copy numbers variations. For a given aCGH profile, one challenge is to accurately segment it into regions of constant copy number.…
Sequence alignment is a cornerstone technique in computational biology for assessing similarities and differences among biological sequences. A key variant, sequence-to-graph alignment, plays a crucial role in effectively capturing genetic…
Tomography is an imaging technique that works by reconstructing a scene from acquired data in the form of line integrals of the imaging domain. A fundamental underlying assumption in the reconstruction procedure is the precise alignment of…
We consider string matching with variable length gaps. Given a string $T$ and a pattern $P$ consisting of strings separated by variable length gaps (arbitrary strings of length in a specified range), the problem is to find all ending…
We consider the following basic problem: given an $n$-variate degree-$d$ homogeneous polynomial $f$ with real coefficients, compute a unit vector $x \in \mathbb{R}^n$ that maximizes $|f(x)|$. Besides its fundamental nature, this problem…
Background: Haplotypes, the ordered lists of single nucleotide variations that distinguish chromosomal sequences from their homologous pairs, may reveal an individual's susceptibility to hereditary and complex diseases and affect how our…
Phylogenetic networks are used to display the relationship of different species whose evolution is not treelike, which is the case, for instance, in the presence of hybridization events or horizontal gene transfers. Tree inference methods…
Over the past two decades, a series of works have aimed at studying the problem of genome assembly: the process of reconstructing a genome from sequence reads. An early formulation of the genome assembly problem showed that genome…
Pairwise compatibility calculation is at the core of most fragments-reconstruction algorithms, in particular those designed to solve different types of the jigsaw puzzle problem. However, most existing approaches fail, or aren't designed to…
Efficient optimal prefix coding has long been accomplished via the Huffman algorithm. However, there is still room for improvement and exploration regarding variants of the Huffman problem. Length-limited Huffman coding, useful for many…
The (Perfect) Matching Cut problem is to decide if a graph $G$ has a (perfect) matching cut, i.e., a (perfect) matching that is also an edge cut of $G$. Both Matching Cut and Perfect Matching Cut are known to be NP-complete. A perfect…
The abelian pattern matching problem consists in finding all substrings of a text which are permutations of a given pattern. This problem finds application in many areas and can be solved in linear time by a naive sliding window approach.…
All fields of science depend on mathematical models. Occam's razor refers to the principle that good models should exclude parameters beyond those minimally required to describe the systems they represent. This is because redundancy can…
In this paper, we develop two new randomized block-coordinate optimistic gradient algorithms to approximate a solution of nonlinear equations in large-scale settings, which are called root-finding problems. Our first algorithm is…
We extend a primal-dual fixed point algorithm (PDFP) proposed in [5] to solve two kinds of separable multi-block minimization problems, arising in signal processing and imaging science. This work shows the flexibility of applying PDFP…
Fully Convolutional Networks have been achieving remarkable results in image semantic segmentation, while being efficient. Such efficiency results from the capability of segmenting several voxels in a single forward pass. So, there is a…
We study the problem of change point localization in dynamic networks models. We assume that we observe a sequence of independent adjacency matrices of the same size, each corresponding to a realization of an unknown inhomogeneous Bernoulli…
The NP-hard Distinct Vectors problem asks to delete as many columns as possible from a matrix such that all rows in the resulting matrix are still pairwise distinct. Our main result is that, for binary matrices, there is a complexity…
Binary size reduction is an increasingly important optimization objective for compilers. One emerging technique is function merging, where multiple similar functions are merged into one, thereby eliminating redundancy. The SOTA approach to…