A Method to Evaluate CFG Comparison Algorithms

2014 ◽  
Author(s):  
Patrick P.F. Chan ◽  
Christian Collberg
Keyword(s):  
Comparison Algorithms

Parallel Processing of Biological Sequence Comparison Algorithms

1988 ◽  
Author(s):  
Nolan G. Gore ◽  
Elizabeth W. Edmiston ◽  
Joel H. Saltz ◽  
Roger M. Smith
Keyword(s):  
Parallel Processing ◽  
Sequence Comparison ◽  
Biological Sequence ◽  
Biological Sequence Comparison ◽  
Comparison Algorithms

scholarly journals Computing nearest neighbour interchange distances between ranked phylogenetic trees

2021 ◽  
Vol 82 (1-2) ◽  
Author(s):  
Lena Collienne ◽  
Alex Gavryushkin
Keyword(s):  
Cancer Research ◽  
Computational Complexity ◽  
Phylogenetic Tree ◽  
Shortest Path ◽  
Phylogenetic Trees ◽  
Shortest Paths ◽  
Nearest Neighbour ◽  
Tree Inference ◽  
Subtree Prune And Regraft ◽  
Comparison Algorithms

AbstractMany popular algorithms for searching the space of leaf-labelled (phylogenetic) trees are based on tree rearrangement operations. Under any such operation, the problem is reduced to searching a graph where vertices are trees and (undirected) edges are given by pairs of trees connected by one rearrangement operation (sometimes called a move). Most popular are the classical nearest neighbour interchange, subtree prune and regraft, and tree bisection and reconnection moves. The problem of computing distances, however, is $${\mathbf {N}}{\mathbf {P}}$$ N P -hard in each of these graphs, making tree inference and comparison algorithms challenging to design in practice. Although anked phylogenetic trees are one of the central objects of interest in applications such as cancer research, immunology, and epidemiology, the computational complexity of the shortest path problem for these trees remained unsolved for decades. In this paper, we settle this problem for the ranked nearest neighbour interchange operation by establishing that the complexity depends on the weight difference between the two types of tree rearrangements (rank moves and edge moves), and varies from quadratic, which is the lowest possible complexity for this problem, to $${\mathbf {N}}{\mathbf {P}}$$ N P -hard, which is the highest. In particular, our result provides the first example of a phylogenetic tree rearrangement operation for which shortest paths, and hence the distance, can be computed efficiently. Specifically, our algorithm scales to trees with tens of thousands of leaves (and likely hundreds of thousands if implemented efficiently).

Suffix array for multi-pattern matching with variable length wildcards

2021 ◽  
Vol 25 (2) ◽  
pp. 283-303
Author(s):  
Na Liu ◽  
Fei Xie ◽  
Xindong Wu
Keyword(s):  
Dynamic Programming ◽  
Data Structure ◽  
Pattern Matching ◽  
Edit Distance ◽  
State Of The Art ◽  
Suffix Array ◽  
Variable Length ◽  
Distance Method ◽  
Efficient Data ◽  
Comparison Algorithms

Approximate multi-pattern matching is an important issue that is widely and frequently utilized, when the pattern contains variable-length wildcards. In this paper, two suffix array-based algorithms have been proposed to solve this problem. Suffix array is an efficient data structure for exact string matching in existing studies, as well as for approximate pattern matching and multi-pattern matching. An algorithm called MMSA-S is for the short exact characters in a pattern by dynamic programming, while another algorithm called MMSA-L deals with the long exact characters by the edit distance method. Experimental results of Pizza & Chili corpus demonstrate that these two newly proposed algorithms, in most cases, are more time-efficient than the state-of-the-art comparison algorithms.

Supercomputers and biological sequence comparison algorithms

1989 ◽  
Vol 22 (6) ◽  
pp. 497-515 ◽  
Author(s):  
Nolan G. Core ◽  
Elizabeth W. Edmiston ◽  
Joel H. Saltz ◽  
Roger M. Smith
Keyword(s):  
Sequence Comparison ◽  
Biological Sequence ◽  
Biological Sequence Comparison ◽  
Comparison Algorithms

scholarly journals Dynamic Pathfinding for Non-Player Character Follower on Game

2021 ◽  
Vol 13 (2) ◽  
pp. 55-63
Author(s):  
Paulus Harsadi ◽  
Siti Asmiatun ◽  
Astrid Novita Putri
Keyword(s):  
Video Game ◽  
Potential Field ◽  
Computation Time ◽  
Attractive Potential ◽  
Artificial Potential Field ◽  
Field Function ◽  
Particle Chain ◽  
Comparison Algorithms ◽  
Test Result ◽  
Flocking Behavior

Artificial Intellegences in video game are important things that can challenge game player. One of them is creating character or NPC Follower (Non-player character Follower) inside the video game, such as real human/animal attitude. Artificial Intelligences have some techniques in which pathfinding is one of Artificial Intellegence techniques that is more popular in research than other techniques. The ability to do dynamic pathfinding is Dynamic Particle Chain (DPC) algorithm. This algorithm has the ability of flocking behavior called boid to explore the environment. But, the algoritm method moves from one boid’s point to another according to the nearest radius, then it will be able to increase computation time or needed time toward the target. To finish higher computation problem in dynamic pathfinding, the researcher suggests an algorithm that is able to handle dynamic pathfinding process through attractive potential field function of Artificial Potential Field to start pathfinding toward the target and flocking behavior technique to avoid the obstacle. Based on the test result by simulation of moving environment and complex, the computation time of algorithm is faster than comparison algorithms, DPC and Astar. It concludes that the suggested method can be used to decrease computation level in dynamic pathfinding.

Evidence for the Emergence of β-Trefoils by ‘Peptide Budding’ from an IgG-like β-Sandwich

2021 ◽  
Author(s):  
Liam M. Longo ◽  
Rachel Kolodny ◽  
Shawn E. McGlynn
Keyword(s):  
De Novo ◽  
General Trend ◽  
Sequence Structure ◽  
Structure Comparison ◽  
Related Sequence ◽  
Structure Space ◽  
Protein Universe ◽  
Remote Islands ◽  
Comparison Algorithms ◽  
Hallmark Feature

AbstractAs sequence and structure comparison algorithms gain sensitivity, the intrinsic interconnectedness of the protein universe has become increasingly apparent. Despite this general trend, β-trefoils have emerged as an uncommon counterexample: They are an isolated protein lineage for which few, if any, sequence or structure associations to other lineages have been identified. If β-trefoils are, in fact, remote islands in sequence-structure space, it implies that the oligomerizing peptide that founded the β-trefoil lineage itself arose de novo. To better understand β-trefoil evolution, and to probe the limits of fragment sharing across the protein universe, we identified both ‘β-trefoil bridging themes’ (evolutionarily-related sequence segments) and ‘β-trefoil-like motifs’ (structure motifs with a hallmark feature of the β-trefoil architecture) in multiple, ostensibly unrelated, protein lineages. The success of the present approach stems, in part, from considering β-trefoil sequence segments or structure motifs rather than the β-trefoil architecture as a whole, as has been done previously. The newly uncovered inter-lineage connections presented here suggest a novel hypothesis about the origins of the β-trefoil fold itself – namely, that it is a derived fold formed by ‘budding’ from an Immunoglobulin-like β-sandwich protein. These results demonstrate how the emergence of a folded domain from a peptide need not be a signature of antiquity and underpin an emerging truth: few protein lineages escape nature’s sewing table.

Nature-Inspired Metaheuristics for Automatic Multilevel Image Thresholding

2014 ◽  
Vol 5 (4) ◽  
pp. 47-69 ◽  
Author(s):  
Salima Ouadfel ◽  
Souham Meshoul
Keyword(s):  
Cuckoo Search ◽  
Exhaustive Search ◽  
The Other ◽  
Multilevel Thresholding ◽  
Bee Colony ◽  
Individual Solution ◽  
Optimal Values ◽  
Comparison Algorithms ◽  
Nature Inspired Metaheuristics ◽  
Better Than

Thresholding is one of the most used methods of image segmentation. It aims to identify the different regions in an image according to a number of thresholds in order to discriminate objects in a scene from background as well to distinguish objects from each other. A great number of thresholding methods have been proposed in the literature; however, most of them require the number of thresholds to be specified in advance. In this paper, three nature-inspired metaheuristics namely Artificial Bee Colony, Cuckoo Search and Bat algorithms have been adapted for the automatic multilevel thresholding (AMT) problem. The goal is to determine the correct number of thresholds as well as their optimal values. For this purpose, the article adopts—for each metaheuristic—a new hybrid coding scheme such that each individual solution is represented by two parts: a real part which represents the thresholds values and a binary part which indicates if a given threshold will be used or not during the thresholding process. Experiments have been conducted on six real test images and the results have been compared with two automatic multilevel thresholding based PSO methods and the exhaustive search method for fair comparison. Empirical results reveal that AMT-HABC and AMT-HCS algorithms performed equally to the solution provided by the exhaustive search and are better than the other comparison algorithms. In addition, the results indicate that the ATM-HABC algorithm has a higher success rate and a speed convergence than the other metaheuristics.

Scalable Influence Maximization Meets Efficiency and Effectiveness in Large-Scale Social Networks

2020 ◽  
Vol 30 (08) ◽  
pp. 1079-1096
Author(s):  
Liqing Qiu ◽  
Shuang Zhang ◽  
Chunmei Gu ◽  
Xiangbo Tian
Keyword(s):  
Social Networks ◽  
Large Scale ◽  
Heuristic Algorithms ◽  
Influence Maximization ◽  
Scalable Algorithm ◽  
Influence Spread ◽  
Efficiency And Effectiveness ◽  
Spread Of Influence ◽  
Influential Nodes ◽  
Comparison Algorithms

Influence maximization is a problem that aims to select top [Formula: see text] influential nodes to maximize the spread of influence in social networks. The classical greedy-based algorithms and their improvements are relatively slow or not scalable. The efficiency of heuristic algorithms is fast but their accuracy is unacceptable. Some algorithms improve the accuracy and efficiency by consuming a large amount of memory usage. To overcome the above shortcoming, this paper proposes a fast and scalable algorithm for influence maximization, called K-paths, which utilizes the influence tree to estimate the influence spread. Additionally, extensive experiments demonstrate that the K-paths algorithm outperforms the comparison algorithms in terms of efficiency while keeping competitive accuracy.

scholarly journals Community Detection Based on a Preferential Decision Model

Information ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 53
Author(s):  
Jinfang Sheng ◽  
Ben Lu ◽  
Bin Wang ◽  
Jie Hu ◽  
Kai Wang ◽  
...  
Keyword(s):  
Community Structure ◽  
Complex Networks ◽  
Community Detection ◽  
Decision Model ◽  
Structural Characteristics ◽  
Real Life ◽  
Stable State ◽  
Ground Truth ◽  
Label Propagation ◽  
Comparison Algorithms

The research on complex networks is a hot topic in many fields, among which community detection is a complex and meaningful process, which plays an important role in researching the characteristics of complex networks. Community structure is a common feature in the network. Given a graph, the process of uncovering its community structure is called community detection. Many community detection algorithms from different perspectives have been proposed. Achieving stable and accurate community division is still a non-trivial task due to the difficulty of setting specific parameters, high randomness and lack of ground-truth information. In this paper, we explore a new decision-making method through real-life communication and propose a preferential decision model based on dynamic relationships applied to dynamic systems. We apply this model to the label propagation algorithm and present a Community Detection based on Preferential Decision Model, called CDPD. This model intuitively aims to reveal the topological structure and the hierarchical structure between networks. By analyzing the structural characteristics of complex networks and mining the tightness between nodes, the priority of neighbor nodes is chosen to perform the required preferential decision, and finally the information in the system reaches a stable state. In the experiments, through the comparison of eight comparison algorithms, we verified the performance of CDPD in real-world networks and synthetic networks. The results show that CDPD not only has better performance than most recent algorithms on most datasets, but it is also more suitable for many community networks with ambiguous structure, especially sparse networks.

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