Related papers: Upper Bounds to Genome Rearrangement Problem using…
In the past several years, the problem of genome assembly has received considerable attention from both biologists and computer scientists. An important component of current assembly methods is the scaffolding process. This process involves…
Proof terms are syntactic expressions that represent computations in term rewriting. They were introduced by Meseguer and exploited by van Oostrom and de Vrijer to study equivalence of reductions in (left-linear) first-order term rewriting…
We propose a framework for solving evolution equations within parametric function classes, especially ones that are specified by neural networks. We call this framework the minimal neural evolution (MNE) because it is motivated by the goal…
Frameshift mutations in protein-coding DNA sequences produce a drastic change in the resulting protein sequence, which prevents classic protein alignment methods from revealing the proteins' common origin. Moreover, when a large number of…
We propose masked particle modeling (MPM) as a self-supervised method for learning generic, transferable, and reusable representations on unordered sets of inputs for use in high energy physics (HEP) scientific data. This work provides a…
This work aims to study and explore the use of Gene Expression Programming (GEP) in solving the on-line Bin-Packing problem. The main idea is to show how GEP can automatically find acceptable heuristic rules to solve the problem efficiently…
We investigate the symmetry of circular genome rearrangement models, discuss the implementation of a new representation-theoretic method of calculating evolutionary distances between circular genomes, and give the results of some initial…
De novo genome assembly focuses on finding connections between a vast amount of short sequences in order to reconstruct the original genome. The central problem of genome assembly could be described as finding a Hamiltonian path through a…
We present ensemble methods in a machine learning (ML) framework combining predictions from five known motif/binding site exploration algorithms. For a given TF the ensemble starts with position weight matrices (PWM's) for the motif,…
Here we propose an evolutionary algorithm that self modifies its operators at the same time that candidate solutions are evolved. This tackles convergence and lack of diversity issues, leading to better solutions. Operators are represented…
The study of the fundamental limits of information systems is a central theme in information theory. Both the traditional analytical approach and the recently proposed computational approach have significant limitations, where the former is…
In order to survive, reproduce and (in multicellular organisms) differentiate, cells must control the concentrations of the myriad different proteins that are encoded in the genome. The precision of this control is limited by the inevitable…
Sorting is one of the most used and well investigated algorithmic problem [1]. Traditional postulation supposes the sorting data archived, and the elementary operation as comparisons of two numbers. In a view of appearance of new processors…
How robust is the natural genetic code with respect to mistranslation errors? It has long been known that the genetic code is very efficient in limiting the effect of point mutation. A misread codon will commonly code either for the same…
In a model of network communication based on a random walk in an undirected graph, what subset of nodes (subject to constraints on the set size), enable the fastest spread of information? The dynamics of spread is described by a process…
The Progressive Edge Growth (PEG) algorithm is one of the most widely-used method for constructing finite length LDPC codes. In this paper we consider the PEG algorithm together with a scheduling distribution, which specifies the order in…
Programmable arrays of optical traps enable the assembly of configurations of single atoms to perform controlled experiments on quantum many-body systems. Finding the sequence of control operations to transform an arbitrary configuration of…
In this paper, we present an algorithm that enumerates a certain class of signed permutations, referred to as grid signed permutation classes. In the case of permutations, the corresponding grid classes are of interest because they are…
Phylogenetic networks are increasingly used in evolutionary biology to represent the history of species that have undergone reticulate events such as horizontal gene transfer, hybrid speciation and recombination. One of the most fundamental…
Prolog's ability to return multiple answers on backtracking provides an elegant mechanism to derive reversible encodings of combinatorial objects as Natural Numbers i.e. {\em ranking} and {\em unranking} functions. Starting from a…