Related papers: Algebraic double cut and join -- A group-theoretic…
Rotational symmetry is a defining feature of many tomography systems, including computed tomography (CT) and emission computed tomography (ECT), where detectors are arranged in a circular or periodically rotating configuration. This study…
Evolutionary algorithms usually explore a search space of solutions by means of crossover and mutation. While a mutation consists of a small, local modification of a solution, crossover mixes the genetic information of two solutions to…
Many models of genome rearrangement involve operations (e.g. inversions and translocations) that are self-inverse, and hence generate a group acting on the space of genomes. This gives a correspondence between genome arrangements and the…
We consider the problem of decomposing a multivariate polynomial as the difference of two convex polynomials. We introduce algebraic techniques which reduce this task to linear, second order cone, and semidefinite programming. This allows…
Genome rearrangements are events where large blocks of DNA exchange places during evolution. The analysis of these events is a promising tool for understanding evolutionary genomics, providing data for phylogenetic reconstruction based on…
In computer science, divide and conquer (D&C) is an algorithm design paradigm based on multi-branched recursion. A D&C algorithm works by recursively and monotonically breaking down a problem into sub problems of the same (or a related)…
In this paper, we study design of deep neural networks for tasks of image restoration. We propose a novel style of residual connections dubbed "dual residual connection", which exploits the potential of paired operations, e.g., up- and…
We develop an algorithm based on three basic DNA editing operations suggested by a model for ciliate micronuclear decryption, to transform a given permutation into another. The number of ciliate operations performed by our algorithm during…
Cell instance segmentation in cytology images has significant importance for biology analysis and cancer screening, while remains challenging due to 1) the extensive overlapping translucent cell clusters that cause the ambiguous boundaries,…
Density operators are one of the key ingredients of quantum theory. They can be constructed in two ways: via a convex sum of 'doubled kets' (i.e. mixing), and by tracing out part of a 'doubled' two-system ket (i.e. dilation). Both…
Conventional tomographic reconstruction typically depends on centralized servers for both data storage and computation, leading to concerns about memory limitations and data privacy. Distributed reconstruction algorithms mitigate these…
Gene conversion is a mechanism by which a double-strand break in a DNA molecule is repaired using a homologous DNA molecule as a template. As a result, one gene is 'copied and pasted' onto the other gene. It was recently reported that the…
Double machine learning is a statistical method for leveraging complex black-box models to construct approximately unbiased treatment effect estimates given observational data with high-dimensional covariates, under the assumption of a…
Inversions, also sometimes called reversals, are a major contributor to variation among bacterial genomes, with studies suggesting that those involving small numbers of regions are more likely than larger inversions. Deletions may arise in…
Dantzig-Wolfe (DW) decomposition is a well-known technique in mixed-integer programming (MIP) for decomposing and convexifying constraints to obtain potentially strong dual bounds. We investigate cutting planes that can be derived using the…
Reconstructing ancestral gene orders is an important step towards understanding genome evolution. The Small Parsimony Problem (SPP) has been extensively studied in this regard. The problem aims at finding the gene orders at internal nodes…
We demonstrate a physical motivation for extending color-dual or BCJ double-copy construction to include theories with kinematic numerators that obey the same algebraic relations as symmetric structure constants,…
We present a novel coupled two-way clustering approach to gene microarray data analysis. The main idea is to identify subsets of the genes and samples, such that when one of these is used to cluster the other, stable and significant…
Gene assembly in ciliates is an extremely involved DNA transformation process, which transforms a nucleus, the micronucleus, to another functionally different nucleus, the macronucleus. In this paper we characterize which loop recombination…
As two fundamental problems, graph cuts and graph matching have been investigated over decades, resulting in vast literature in these two topics respectively. However the way of jointly applying and solving graph cuts and matching receives…