15 papers · ranked by Valyu relevance
Eliézer Béczi, Noémi Gaskó, Lisu Yu
Determining the critical nodes in a complex network is an essential computation problem. Several variants of this problem have emerged due to its wide applicability in network analysis. In this article we study the bi-objective critical node detection problem (BOCNDP), which is a new variant of the well-known critical…
Jian Zhang, Jianan Sheng, Jiawei Lu, Ling Shen
The particle swarm optimization algorithm (PSO) is a meta-heuristic algorithm with swarm intelligence. It has the advantages of easy implementation, high convergence accuracy, and fast convergence speed. However, PSO suffers from falling into a local optimum or premature convergence, and a better performance of PSO is…
Verusca Severo, Felipe B. S. Ferreira, Rodrigo Spencer, Arthur Nascimento + 2 more
'Arthur Nascimento' 'Francisco Madeiro' 'Steve Vanlanduit'] Vector Quantization (VQ) is a technique with a wide range of applications. For example, it can be used for image compression. The codebook design for VQ has great significance in the quality of the quantized signals and can benefit from the use of swarm…
Rahib H. Abiyev, Mustafa Tunay
A novel learning algorithm for solving global numerical optimization problems is proposed. The proposed learning algorithm is intense stochastic search method which is based on evaluation and optimization of a hypercube and is called the hypercube optimization (HO) algorithm. The HO algorithm comprises the…
Nicolas Sauwen, Marjan Acou, Halandur N. Bharath, Diana M. Sima + 6 more
'Jelle Veraart' 'Frederik Maes' 'Uwe Himmelreich' 'Eric Achten' 'Sabine Van Huffel' 'Daniel Monleon'] Non-negative matrix factorization (NMF) has become a widely used tool for additive parts-based analysis in a wide range of applications. As NMF is a non-convex problem, the quality of the solution will depend on the…
Kaiyuan Zheng, Huiyong Liu, Bopeng Li
In engineering applications, many complex problems can be formulated as mathematical optimization challenges, and efficiently solving these problems is critical. Metaheuristic algorithms have proven highly effective in addressing a wide range of engineering issues. The Snake Optimization Algorithm (SO) is a novel…
Marius Pachitariu, Lin Zhong, Alexa Gracias, Amanda Minisi + 2 more
Artificial neural networks learn faster if they are initialized well. Good initializations can generate high-dimensional macroscopic dynamics with long timescales. It is not known if biological neural networks have similar properties. Here we show that the eigenvalue spectrum and dynamical properties of large-scale…
Abiy Tasissa, Rongjie Lai, Chunyu Wang
The problem of finding the configuration of points given partial information on pairwise inter-point distances, the Euclidean distance geometry problem, appears in multiple applications. In this paper, we propose an approach that integrates homology modeling and a nonconvex distance geometry algorithm for the protein…
Tomáš Flouri, Kassian Kobert, Torbjørn Rognes, Alexandros Stamatakis
Pairwise sequence alignment is perhaps the most fundamental bioinformatics operation. An optimal global alignment algorithm was described in 1970 by Needleman and Wunsch. In 1982 Gotoh presented an improved algorithm with lower time complexity. Gotoh’s algorithm is frequently cited (1447 citations, Google Scholar, May…
Neha Vinayak, Shandar Ahmad
A multi-layer perceptron (MLP) consists of a number of forward-connected weights (W_ijk_) from each feeding layer node (n_ij_) to the many initially equivalent nodes (n_i+1,k_) in the next layer. Exact a priori order and search space of these weights (W_ijk_) is random and prone to redundancy, irreproducibility and…
Jose Torres-Jimenez, Nelson Rangel-Valdez, Himer Avila-George, Oscar Carrizalez-Turrubiates + 1 more
'Oscar Carrizalez-Turrubiates' 'M. Sohel Rahman'] Software test suites based on the concept of interaction testing are very useful for testing software components in an economical way. Test suites of this kind may be created using mathematical objects called covering arrays. A covering array, denoted by CA(N; t, k, v)…
Mohammed Baragilly, Brian H Willis
Meta-analysis may be used to summarise a test’s accuracy. Often the sensitivity and specificity are the measures of interest and as these are correlated a bivariate random effects model is commonly used to fit the data. This model has five parameters and it may be optimised using a Newton-Raphson based algorithm…
Fabio F. de Oliveira, Leonardo A. Dias, Marcelo A. C. Fernandes
In bioinformatics, alignment is an essential technique for finding similarities between biological sequences. Usually, the alignment is performed with the Smith-Waterman (SW) algorithm, a well-known sequence alignment technique of high-level precision based on dynamic programming. However, given the massive data volume…
Koichi Miyamoto, Naoki Yamamoto, Yasubumi Sakakibara
We propose two quantum algorithms for a problem in bioinformatics, position weight matrix (PWM) matching, which aims to find segments (sequence motifs) in a biological sequence such as DNA and protein that have high scores defined by the PWM and are thus of informational importance related to biological function. The…
Nikolai Baudis, Pierre Barbera, Sebastian Graf, Sarah Lutteropp + 3 more
In the context of a master level programming practical at the computer science department of the Karlsruhe Institute of Technology, we developed and make available two independent and highly optimized open-source implementations for the pair-wise statistical alignment model, also known as TKF91, that was developed by…