Related papers: Estimating Genome Reversal Distance by Genetic Alg…
Problems with solutions represented by permutations are very prominent in combinatorial optimization. Thus, in recent decades, a number of evolutionary algorithms have been proposed to solve them, and among them, those based on probability…
In this paper we present genetic algorithms based search technique for the linear optics schemes, performing two-qubit quantum gates. We successfully applied this technique for finding heralded two-qubit gates and obtained the new schemes…
The last decade brought a significant increase in the amount of data and a variety of new inference methods for reconstructing the detailed evolutionary history of various cancers. This brings the need of designing efficient procedures for…
In this work, we show how a genetic algorithm (GA) can be used to find step-by-step solutions to introductory physics problems. Our perspective is that the underlying task for this is one of finding a sequence of equations that will lead to…
Unbalanced translocations are among the most frequent chromosomal alterations, accounted for 30\% of all losses of heterozygosity, a major genetic event causing inactivation of tumor suppressor genes. Despite of their central role in…
Permutation patterns and pattern avoidance have been intensively studied in combinatorics and computer science, going back at least to the seminal work of Knuth on stack-sorting (1968). Perhaps the most natural algorithmic question in this…
During the course of evolution, an organism's genome can undergo changes that affect the large-scale structure of the genome. These changes include gene gain, loss, duplication, chromosome fusion, fission, and rearrangement. When gene gain…
Best-Fit is one of the most prominent and practically used algorithms for the bin packing problem, where a set of items with associated sizes needs to be packed in the minimum number of unit-capacity bins. Kenyon [SODA '96] studied online…
Motivated by comparative genomics, Chen et al. [9] introduced the Maximum Duo-preservation String Mapping (MDSM) problem in which we are given two strings $s_1$ and $s_2$ from the same alphabet and the goal is to find a mapping $\pi$…
In this paper, two approximation algorithms are given. Let N be an odd composite number. The algorithms give new directions regarding primality test of given N. The first algorithm is given using a new method called digital coding method.…
In this paper, we look at the complexity of designing algorithms without any bank conflicts in the shared memory of Graphical Processing Units (GPUs). Given input of size $n$, $w$ processors and $w$ memory banks, we study three fundamental…
We study sorting of permutations by random swaps if each comparison gives the wrong result with some fixed probability $p<1/2$. We use this process as prototype for the behaviour of randomized, comparison-based optimization heuristics in…
We give optimal sorting algorithms in the evolving data framework, where an algorithm's input data is changing while the algorithm is executing. In this framework, instead of producing a final output, an algorithm attempts to maintain an…
Clustering is a difficult and widely-studied data mining task, with many varieties of clustering algorithms proposed in the literature. Nearly all algorithms use a similarity measure such as a distance metric (e.g. Euclidean distance) to…
The quantum analogue of the equality function, known as the quantum state identity problem, is the task of deciding whether $n$ unknown quantum states are equal or unequal, given the promise that all states are either pairwise orthogonal or…
Sequence Alignment is the process of aligning biological sequences in order to identify similarities between multiple sequences. In this paper, a Quantum Algorithm for finding the optimal alignment between DNA sequences has been…
One approach for reducing run time and improving efficiency of machine learning is to reduce the convergence rate of the optimization algorithm used. Shuffling is an algorithm technique that is widely used in machine learning, but it only…
Surface registration is a technique that is used in various areas such as object recognition and 3D model reconstruction. Problem of surface registration can be analyzed as an optimization problem of seeking a rigid motion between two…
With small-scale quantum processors transitioning from experimental physics labs to industrial products, these processors allow us to efficiently compute important algorithms in various fields. In this paper, we propose a quantum algorithm…
The Transposition Distance Problem (TDP) is a classical problem in genome rearrangements which seeks to determine the minimum number of transpositions needed to transform a linear chromosome into another represented by the permutations…