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Differential Evolution (DE) proved to be one of the most successful evolutionary algorithms for global optimization purposes in continuous problems. The core operator in DE is mutation which can provide the algorithm with both exploration…
Considering a pair of genomes, the goal of rearrangement distance problems is to estimate how distant these genomes are from each other based on genome rearrangements. Seminal works in genome rearrangements assumed that both genomes being…
There has recently been great progress in automatic segmentation of medical images with deep learning algorithms. In most works observer variation is acknowledged to be a problem as it makes training data heterogeneous but so far no…
Modellers of large scale genome rearrangement events, in which segments of DNA are inverted, moved, swapped, or even inserted or deleted, have found a natural syntax in the language of permutations. Despite this, there has been a wide range…
A difficult step in the process of karyotyping is segmenting chromosomes that touch or overlap. In an attempt to automate the process, previous studies turned to Deep Learning methods, with some formulating the task as a semantic…
This article presents a physical biology approach to understanding organization and segregation of bacterial chromosomes. The author uses a "piston" analogy for bacterial chromosomes in a cell, which leads to a phase diagram for the…
We study the algebraic and analytic structure of Feynman integrals by proposing an operation that maps an integral into pairs of integrals obtained from a master integrand and a corresponding master contour. This operation is a coaction. It…
Many approaches to 3D image segmentation are based on hierarchical clustering of supervoxels into image regions. Here we describe a distributed algorithm capable of handling a tremendous number of supervoxels. The algorithm works…
We describe an implementation of a genetic algorithm on partially commutative groups and apply it to the double coset search problem on a subclass of groups. This transforms a combinatorial group theory problem to a problem of combinatorial…
The diagrammatic coaction encodes the analytic structure of Feynman integrals by mapping any given Feynman diagram into a tensor product of diagrams defined by contractions and cuts of the original diagram. Feynman integrals evaluate to…
A mechanism of double strand breaking (DSB) in DNA due to the action of two electrons is considered. These are the electrons produced in the vicinity of DNA molecules due to ionization of water molecules with a consecutive emission of two…
This paper proposes a novel module called middle spectrum grouped convolution (MSGC) for efficient deep convolutional neural networks (DCNNs) with the mechanism of grouped convolution. It explores the broad "middle spectrum" area between…
A new approach to large-scale nuclear structure calculations, based on the Density Matrix Renormalization Group (DMRG), is described. The method is tested in the context of a problem involving many identical nucleons constrained to move in…
One of the most computationally intensive tasks in computational biology is de novo genome assembly, the decoding of the sequence of an unknown genome from redundant and erroneous short sequences. A common assembly paradigm identifies…
Motivation: Cellular Electron CryoTomography (CECT) enables 3D visualization of cellular organization at near-native state and in sub-molecular resolution, making it a powerful tool for analyzing structures of macromolecular complexes and…
We present a reciprocal space technique for the calculation of the Coulomb integral in two dimensions in systems with reduced periodicity, i.e., finite systems, or systems that are periodic only in one dimension. The technique consists in…
The Neighbor-Joining algorithm is a popular distance-based phylogenetic method that computes a tree metric from a dissimilarity map arising from biological data. Realizing dissimilarity maps as points in Euclidean space, the algorithm…
This paper provides a short and transparent solution for the covering cost of white-grey trees which play a crucial role in the algorithm of Bergeron {\it et al.}\ to compute the rearrangement distance between two multichromosomal genomes…
Motivated by an ongoing project on computer aided derivation of asymptotic models governed by partial differential equations, we introduce a class of term transformations that consists of traversal strategies and insertion of contexts. We…
The Neighbor-Joining algorithm is a recursive procedure for reconstructing trees that is based on a transformation of pairwise distances between leaves. We present a generalization of the neighbor-joining transformation, which uses…