Related papers: Extending Common Intervals Searching from Permutat…
We study pattern matching problems on two major representations of uncertain sequences used in molecular biology: weighted sequences (also known as position weight matrices, PWM) and profiles (i.e., scoring matrices). In the simple version,…
Quantum Approximation Optimization Algorithm (QAOA) is a highly advocated variational algorithm for solving the combinatorial optimization problem. One critical feature in the quantum circuit of QAOA algorithm is that it consists of…
We describe a family of recursive methods for the synthesis of qubit permutations on quantum computers with limited qubit connectivity. Two objectives are of importance: circuit size and depth. In each case we combine a scalable heuristic…
We propose new filtering algorithms for the SEQUENCE constraint and some extensions of the SEQUENCE constraint based on network flows. We enforce domain consistency on the SEQUENCE constraint in $O(n^2)$ time down a branch of the search…
Permutations are usually enumerated by size, but new results can be found by enumerating them by inversions instead, in which case one must restrict one's attention to indecomposable permutations. In the style of the seminal paper by Simion…
The aim of this research is twofold: Firstly, to model and solve a complex nurse scheduling problem with an integer programming formulation and evolutionary algorithms. Secondly, to detail a novel statistical method of comparing and hence…
We present a general approach to the problem of determining the asymptotic order of the variance of the optimal score between two independent random sequences defined over an arbitrary finite alphabet. Our general approach is based on…
In this paper, we focus on the problem of dynamically analysing concurrent software against high-level temporal specifications. Existing techniques for runtime monitoring against such specifications are primarily designed for sequential…
We study the classical scheduling problem on parallel machines %with precedence constraints where the precedence graph has the bounded depth $h$. Our goal is to minimize the maximum completion time. We focus on developing approximation…
Identifying palindromes in sequences has been an interesting line of research in combinatorics on words and also in computational biology, after the discovery of the relation of palindromes in the DNA sequence with the HIV virus. Efficient…
Goemans and Rothvoss (SODA'14) gave a framework for solving problems which can be described as finding a point in int$.$cone$(P\cap\mathbb{Z}^N)\cap Q$, where $P,Q\subset\mathbb{R}^N$ are (bounded) polyhedra. The running time for solving…
Short integer linear programs are programs with a relatively small number of constraints. We show how recent improvements on the running-times of solvers for such programs can be used to obtain fast pseudo-polynomial time algorithms for…
In this note, we consider the problem of finding a step-by-step transformation between two longest increasing subsequences in a sequence, namely Longest Increasing Subsequence Reconfiguration. We give a polynomial-time algorithm for…
Which combinatorial sequences correspond to moments of probability measures on the real line? We present a generating function, in the form of a continued fraction, for a fourteen-parameter family of such sequences and interpret these in…
In this paper, we intend to present a new algorithm to factorize large numbers. According to the algorithm proposed here, we prove that there is a common factor between p and q. With this procedure, the time of factorization considerably…
Cumulative probability models (CPMs) are a robust alternative to linear models for continuous outcomes. However, they are not feasible for very large datasets due to elevated running time and memory usage, which depend on the sample size,…
An experimental comparison of two or more optimization algorithms requires the same computational resources to be assigned to each algorithm. When a maximum runtime is set as the stopping criterion, all algorithms need to be executed in the…
Using sequences of finite length with positive integer elements and the inversion statistic on such sequences, a collection of binomial and multinomial identities are extended to their $q$-analog form via combinatorial proofs. Using the…
Most protocols for the high-throughput directed evolution of enzymes rely on random encapsulation to link phenotype and genotype. In order to optimize these approaches, or compare one to another, one needs a measure of their performance at…
We study the problem of non-parametric clustering of data sequences, where each data sequence comprises independent and identically distributed (i.i.d.) samples generated from an unknown distribution. The true clusters are the clusters…