Journal of Combinatorial Optimization最新文献_第9页

Phylogenetic network-assisted rooting of unrooted gene trees 系统发生网络辅助无根基因树生根

IF 1 4区数学

Journal of Combinatorial Optimization Pub Date : 2024-06-01 DOI: 10.1007/s10878-024-01181-3

Jerzy Tiuryn, Natalia Rutecka, Paweł Górecki

{"title":"Phylogenetic network-assisted rooting of unrooted gene trees","authors":"Jerzy Tiuryn, Natalia Rutecka, Paweł Górecki","doi":"10.1007/s10878-024-01181-3","DOIUrl":"https://doi.org/10.1007/s10878-024-01181-3","url":null,"abstract":"Gene trees inferred from molecular sequence alignments are typically unrooted, and determining the most credible rooting edge is a classical problem in computational biology. One approach to solve this problem is unrooted reconciliation, where the rooting edge is postulated based on the split of the root from a given species tree. In this paper, we propose a novel variant of the gene tree rooting problem, where the gene tree root is inferred using a phylogenetic network of the species present in the gene tree. To obtain the best rooting, unrooted reconciliation can be applied, where the unrooted gene tree is jointly reconciled with a set of splits inferred from the network. However, the exponential size of the set induced by display trees of the network makes this approach computationally prohibitive. To address this, we propose a broader and easier-to-control set of splits based on the structural properties of the network. We then derive exact mathematical formulas for the rooting problem and propose two general rooting algorithms to handle cases where the input network does not meet the initial requirements. Our experimental study based on simulated gene trees and networks demonstrates that our algorithms infer gene tree rootings correctly or with a small error in most cases.\u0000","PeriodicalId":50231,"journal":{"name":"Journal of Combinatorial Optimization","volume":"35 1","pages":""},"PeriodicalIF":1.0,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141187669","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Diabetic prediction and classification of risk level using ODDTADC method in big data analytics 在大数据分析中使用 ODDTADC 方法预测和划分糖尿病风险等级

IF 1 4区数学

Journal of Combinatorial Optimization Pub Date : 2024-05-21 DOI: 10.1007/s10878-024-01179-x

G. Geo Jenefer, A. J. Deepa, M. Mary Linda

{"title":"Diabetic prediction and classification of risk level using ODDTADC method in big data analytics","authors":"G. Geo Jenefer, A. J. Deepa, M. Mary Linda","doi":"10.1007/s10878-024-01179-x","DOIUrl":"https://doi.org/10.1007/s10878-024-01179-x","url":null,"abstract":"Diabetes is regarded as one of the deadliest chronic illnesses that increases blood sugar. But there is no reliable method for predicting diabetic severity that shows how the disease will affect various body organs in the future. Therefore, this paper introduced Optimized Dual Directional Temporal convolution and Attention based Density Clustering (ODDTADC) method for predicting and classifying risk level in diabetic patients. In the diabetic prediction stage, the prediction is done by using an Integrated Dual Directional Temporal Convolution and an Enriched Remora Optimization Algorithm. Here, dual directional temporal convolution is used to extract temporal features by integrating dilated convolution and casual convolution in the feature extraction layer. Then, the attention module is used instead of max-pooling to emphasize the various features' importance in the feature aggregation layer. The Enriched Remora Optimization Algorithm is used to find optimal hyper parameters for Integrated Dual Directional Temporal Convolution. In the classification of stages based on risk level, the values from stage-I are fed into the Attention based Density Spatial Clustering of Applications with Noise, which allocate various weights based on their density values in the Core Points. Based on the results, the Nested Long Short-Term Memory is utilized to classify the risk levels of diabetic patients over a period of two or three years. Experimental evaluations were performed on five datasets, including PIMA Indian Diabetics Database, UCI Machine Learning Repository Diabetics Dataset, Heart Diseases Dataset, Chronic Disease Dataset and Diabetic Retinopathy Debrecen Dataset. The proposed ODDTADC method demonstrates superior performance compared to existing methods, achieving remarkable results in accuracy (98.21%), recall (94.46%), kappa coefficient (98.95%), precision (98.74%), F1-score (99.01%) and Matthew’s correlation coefficient (MCC) (0.87%).","PeriodicalId":50231,"journal":{"name":"Journal of Combinatorial Optimization","volume":"64 1","pages":""},"PeriodicalIF":1.0,"publicationDate":"2024-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141079275","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The frustum network model based on clique extension 基于簇扩展的簇网络模型

IF 1 4区数学

Journal of Combinatorial Optimization Pub Date : 2024-05-20 DOI: 10.1007/s10878-024-01178-y

Anthony Bonato, Ryan Cushman, Trent G. Marbach, Zhiyuan Zhang

引用次数: 0

On the oriented diameter of planar triangulations 论平面三角形的定向直径

IF 1 4区数学

Journal of Combinatorial Optimization Pub Date : 2024-05-20 DOI: 10.1007/s10878-024-01177-z

Debajyoti Mondal, N. Parthiban, Indra Rajasingh

{"title":"On the oriented diameter of planar triangulations","authors":"Debajyoti Mondal, N. Parthiban, Indra Rajasingh","doi":"10.1007/s10878-024-01177-z","DOIUrl":"https://doi.org/10.1007/s10878-024-01177-z","url":null,"abstract":"The diameter of an undirected or a directed graph is defined to be the maximum shortest path distance over all pairs of vertices in the graph. Given an undirected graph G, we examine the problem of assigning directions to each edge of G such that the diameter of the resulting oriented graph is minimized. The minimum diameter over all strongly connected orientations is called the oriented diameter of G. The problem of determining the oriented diameter of a graph is known to be NP-hard, but the time-complexity question is open for planar graphs. In this paper we compute the exact value of the oriented diameter for triangular grid graphs. We then prove an n/3 lower bound and an (n/2+Oleft( sqrt{n}right) ) upper bound on the oriented diameter of planar triangulations, where n is the number of vertices in G. It is known that given a planar graph G with bounded treewidth and a fixed positive integer k, one can determine in linear time whether the oriented diameter of G is at most k. We consider a weighted version of the oriented diameter problem and show it to be weakly NP-complete for planar graphs with bounded pathwidth.","PeriodicalId":50231,"journal":{"name":"Journal of Combinatorial Optimization","volume":"80 1","pages":""},"PeriodicalIF":1.0,"publicationDate":"2024-05-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141074036","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Scheduling of elective operations with coordinated utilization of hospital beds and operating rooms 通过协调利用医院病床和手术室，安排择期手术

IF 1 4区数学

Journal of Combinatorial Optimization Pub Date : 2024-05-18 DOI: 10.1007/s10878-024-01167-1

Zhaohui Li, Haiyue Yu, Zhaowei Zhou

引用次数: 0

The maximum 3-star packing problem in claw-free cubic graphs 无爪立方图中的最大三星堆积问题

IF 1 4区数学

Journal of Combinatorial Optimization Pub Date : 2024-05-18 DOI: 10.1007/s10878-024-01115-z

Wenying Xi, Wensong Lin

{"title":"The maximum 3-star packing problem in claw-free cubic graphs","authors":"Wenying Xi, Wensong Lin","doi":"10.1007/s10878-024-01115-z","DOIUrl":"https://doi.org/10.1007/s10878-024-01115-z","url":null,"abstract":"A 3-star is a complete bipartite graph (K_{1,3}). A 3-star packing of a graph G is a collection of vertex-disjoint subgraphs of G in which each subgraph is a 3-star. The maximum 3-star packing problem is to find a 3-star packing of a given graph with the maximum number of 3-stars. A 2-independent set of a graph G is a subset S of V(G) such that for each pair of vertices (u,vin S), paths between u and v are all of length at least 3. In cubic graphs, the maximum 3-star packing problem is equivalent to the maximum 2-independent set problem. The maximum 2-independent set problem was proved to be NP-hard on cubic graphs (Kong and Zhao in Congressus Numerantium 143:65–80, 2000), and the best approximation algorithm of maximum 2-independent set problem for cubic graphs has approximation ratio (frac{8}{15}) (Miyano et al. in WALCOM 2017, Proceedings, pp 228–240). In this paper, we first prove that the maximum 3-star packing problem is NP-hard in claw-free cubic graphs and then design a linear-time algorithm which can find a 3-star packing of a connected claw-free cubic graph G covering at least (frac{3v(G)-8}{4}) vertices, where v(G) denotes the number of vertices of G.","PeriodicalId":50231,"journal":{"name":"Journal of Combinatorial Optimization","volume":"38 1","pages":""},"PeriodicalIF":1.0,"publicationDate":"2024-05-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140954640","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The critical node game 关键节点游戏

IF 1 4区数学

Journal of Combinatorial Optimization Pub Date : 2024-05-18 DOI: 10.1007/s10878-024-01173-3

Gabriele Dragotto, Amine Boukhtouta, Andrea Lodi, Mehdi Taobane

{"title":"The critical node game","authors":"Gabriele Dragotto, Amine Boukhtouta, Andrea Lodi, Mehdi Taobane","doi":"10.1007/s10878-024-01173-3","DOIUrl":"https://doi.org/10.1007/s10878-024-01173-3","url":null,"abstract":"In this work, we introduce a game-theoretic model that assesses the cyber-security risk of cloud networks and informs security experts on the optimal security strategies. Our approach combines game theory, combinatorial optimization, and cyber-security and aims to minimize the unexpected network disruptions caused by malicious cyber-attacks under uncertainty. Methodologically, we introduce the the critical node game, a simultaneous and non-cooperative attacker-defender game where each player solves a combinatorial optimization problem parametrized in the variables of the other player. Each player simultaneously commits to a defensive (or attacking) strategy with limited knowledge about the choices of their adversary. We provide a realistic model for the critical node game and propose an algorithm to compute its stable solutions, i.e., its Nash equilibria. Practically, our approach enables security experts to assess the security posture of the cloud network and dynamically adapt the level of cyber-protection deployed on the network. We provide a detailed analysis of a real-world cloud network and demonstrate the efficacy of our approach through extensive computational tests. ","PeriodicalId":50231,"journal":{"name":"Journal of Combinatorial Optimization","volume":"48 1","pages":""},"PeriodicalIF":1.0,"publicationDate":"2024-05-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140954671","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

An intensification approach based on fitness landscape characteristics for job shop scheduling problem 基于作业车间调度问题适配景观特征的强化方法

IF 1 4区数学

Journal of Combinatorial Optimization Pub Date : 2024-05-18 DOI: 10.1007/s10878-024-01176-0

Aparecida de Fátima Castello Rosa, Fabio Henrique Pereira

{"title":"An intensification approach based on fitness landscape characteristics for job shop scheduling problem","authors":"Aparecida de Fátima Castello Rosa, Fabio Henrique Pereira","doi":"10.1007/s10878-024-01176-0","DOIUrl":"https://doi.org/10.1007/s10878-024-01176-0","url":null,"abstract":"This work deals with the classical Job Shop Scheduling Problem (JSSP) of minimizing the makespan. Metaheuristics are often used on the JSSP solution, but a performance comparable to the state-of-the-art depends on an efficient exploration of the solutions space characteristics. Thus, it is proposed an intensification approach based on the concepts of attraction basins and big valley. Suboptimal solutions obtained by the metaheuristic genetic algorithm are selected and subjected to intensification, in which a binary Bidimensional Genetic Algorithm (BGA) is utilized to enlarge the search neighborhood from a current solution, to escape of attraction basins. Then, the best solution found in this neighborhood is used as the final point of the path relinking strategy derived from the initial suboptimal solution, for exploring possible big valleys. Finally, the best solution in the path is inserted into the population. Trials with usual instances of the literature show that the proposed approach yields greater results with regards to local search, based on permutation of operations on critical blocks, either on the makespan reduction or on the number of generations, and competitive results regarding the contemporary literature.","PeriodicalId":50231,"journal":{"name":"Journal of Combinatorial Optimization","volume":"40 1","pages":""},"PeriodicalIF":1.0,"publicationDate":"2024-05-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140954649","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Online learning under one sided $$sigma $$ -smooth function 单边 $$sigma $$ 平滑函数下的在线学习

IF 1 4区数学

Journal of Combinatorial Optimization Pub Date : 2024-05-18 DOI: 10.1007/s10878-024-01174-2

Hongxiang Zhang, Dachuan Xu, Ling Gai, Zhenning Zhang

{"title":"Online learning under one sided $$sigma $$ -smooth function","authors":"Hongxiang Zhang, Dachuan Xu, Ling Gai, Zhenning Zhang","doi":"10.1007/s10878-024-01174-2","DOIUrl":"https://doi.org/10.1007/s10878-024-01174-2","url":null,"abstract":"The online optimization model was first introduced in the research of machine learning problems (Zinkevich, Proceedings of ICML, 928–936, 2003). It is a powerful framework that combines the principles of optimization with the challenges of online decision-making. The present research mainly consider the case that the reveal objective functions are convex or submodular. In this paper, we focus on the online maximization problem under a special objective function (varPhi (x):[0,1]^nrightarrow mathbb {R}_{+}) which satisfies the inequality (frac{1}{2}langle u^{T}nabla ^{2}varPhi (x),urangle le sigma cdot frac{Vert uVert _{1}}{Vert xVert _{1}}langle u,nabla varPhi (x)rangle ) for any (x,uin [0,1]^n, xne 0). This objective function is named as one sided (sigma )-smooth (OSS) function. We achieve two conclusions here. Firstly, under the assumption that the gradient function of OSS function is L-smooth, we propose an ((1-exp ((theta -1)(theta /(1+theta ))^{2sigma })))- approximation algorithm with (O(sqrt{T})) regret upper bound, where T is the number of rounds in the online algorithm and (theta , sigma in mathbb {R}_{+}) are parameters. Secondly, if the gradient function of OSS function has no L-smoothness, we provide an (left( 1+((theta +1)/theta )^{4sigma }right) ^{-1})-approximation projected gradient algorithm, and prove that the regret upper bound of the algorithm is (O(sqrt{T})). We think that this research can provide different ideas for online non-convex and non-submodular learning.","PeriodicalId":50231,"journal":{"name":"Journal of Combinatorial Optimization","volume":"48 1","pages":""},"PeriodicalIF":1.0,"publicationDate":"2024-05-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140954645","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A novel local search approach with connected dominating degree-based incremental neighborhood evaluation for the minimum 2-connected dominating set problem 针对最小 2 连接支配集问题的基于连接支配度增量邻域评估的新型局部搜索方法

IF 1 4区数学

Journal of Combinatorial Optimization Pub Date : 2024-05-14 DOI: 10.1007/s10878-024-01175-1

Mao Luo, Huigang Qin, Xinyun Wu, Caiquan Xiong

{"title":"A novel local search approach with connected dominating degree-based incremental neighborhood evaluation for the minimum 2-connected dominating set problem","authors":"Mao Luo, Huigang Qin, Xinyun Wu, Caiquan Xiong","doi":"10.1007/s10878-024-01175-1","DOIUrl":"https://doi.org/10.1007/s10878-024-01175-1","url":null,"abstract":"The minimum connected dominating set problem is widely studied due to its applicability to mobile ad-hoc networks and sensor grids. Its variant the minimum 2-connected dominating set (M-2CDS) problem has become increasingly important because its critical role in designing fault-tolerant network. This paper presents a connected dominating degree-based local search (CDD-LS) tailored for solving the M-2CDS. The proposed algorithm implements an improved swap-based neighborhood structure as well as the corresponding fast neighborhood evaluation method using connected dominating degree data structure. The diversification techniques including tabu strategy and perturbaistion help the search jump out of the local optima improving the efficiency. This study investigates the performance of the CDD-LS algorithm on 38 publicly available benchmark datasets. The results demonstrate that the CDD-LS algorithm significantly improves the best runtime in 19 instances, while providing the equivalent performance in 8 instances. Furthermore, the CDD-LS is tested on 18 newly generated instances to check its capability on large-scale scenarios. To gain a deeper understanding of the algorithm’s effectiveness, an investigation into the key components of the CDD-LS algorithm is conducted.","PeriodicalId":50231,"journal":{"name":"Journal of Combinatorial Optimization","volume":"16 1","pages":""},"PeriodicalIF":1.0,"publicationDate":"2024-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140942693","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0