Journal of Combinatorial Optimization最新文献

{"title":"Partial Fitch graphs: characterization, satisfiability and complexity","authors":"Marc Hellmuth, Annachiara Korchmaros, José Antonio Ramírez-Rafael, Bruno Schmidt, Peter F. Stadler, Sandhya Thekkumpadan Puthiyaveedu","doi":"10.1007/s10878-026-01452-1","DOIUrl":"https://doi.org/10.1007/s10878-026-01452-1","url":null,"abstract":"Horizontal gene transfer is an important contributor to evolution. Following Walter M. Fitch, two genes are xenologs if at least one HGT separates them. More formally, the directed Fitch graph has a set of genes as its vertices, and directed edges (<italic>x</italic>, <italic>y</italic>) for all pairs of genes <italic>x</italic> and <italic>y</italic> for which <italic>y</italic> has been horizontally transferred at least once since it diverged from the last common ancestor of <italic>x</italic> and <italic>y</italic>. Subgraphs of Fitch graphs can be inferred by comparative sequence analysis. In many cases, however, only partial knowledge about the “full” Fitch graph can be obtained. Here, we characterize Fitch-satisfiable graphs that can be extended to a biologically feasible “full” Fitch graph and derive a simple polynomial-time recognition algorithm. We then proceed to show that several versions of finding the Fitch graph with total maximum (confidence) edge-weights are NP-hard. In addition, we provide a greedy-heuristic for “optimally” recovering Fitch graphs from partial ones. Somewhat surprisingly, even if <inline-formula><alternatives><mml:math><mml:mrow><mml:mo>∼</mml:mo><mml:mn>80</mml:mn><mml:mo>%</mml:mo></mml:mrow></mml:math><tex-math>documentclass[12pt]{minimal} usepackage{amsmath} usepackage{wasysym} usepackage{amsfonts} usepackage{amssymb} usepackage{amsbsy} usepackage{mathrsfs} usepackage{upgreek} setlength{oddsidemargin}{-69pt} begin{document}$$sim 80%$$end{document}</tex-math></alternatives></inline-formula> of information of the underlying input Fitch-graph <italic>G</italic> is lost (i.e., the partial Fitch graph contains only <inline-formula><alternatives><mml:math><mml:mrow><mml:mo>∼</mml:mo><mml:mn>20</mml:mn><mml:mo>%</mml:mo></mml:mrow></mml:math><tex-math>documentclass[12pt]{minimal} usepackage{amsmath} usepackage{wasysym} usepackage{amsfonts} usepackage{amssymb} usepackage{amsbsy} usepackage{mathrsfs} usepackage{upgreek} setlength{oddsidemargin}{-69pt} begin{document}$$sim 20%$$end{document}</tex-math></alternatives></inline-formula> of the edges of <italic>G</italic>), it is possible to recover <inline-formula><alternatives><mml:math><mml:mrow><mml:mo>∼</mml:mo><mml:mn>90</mml:mn><mml:mo>%</mml:mo></mml:mrow></mml:math><tex-math>documentclass[12pt]{minimal} usepackage{amsmath} usepackage{wasysym} usepackage{amsfonts} usepackage{amssymb} usepackage{amsbsy} usepackage{mathrsfs} usepackage{upgreek} setlength{oddsidemargin}{-69pt} begin{document}$$sim 90%$$end{document}</tex-math></alternatives></inline-formula> of the original edges of <italic>G</italic> on average.","PeriodicalId":50231,"journal":{"name":"Journal of Combinatorial Optimization","volume":"26 1","pages":""},"PeriodicalIF":1.0,"publicationDate":"2026-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148715899","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}

{"title":"Efficient algorithms for computing the edit distance with non-overlapping inversions","authors":"Kuan-Lin Lai, Shie-Yan Lee, Chang-Biau Yang, Kuo-Tsung Tseng","doi":"10.1007/s10878-026-01448-x","DOIUrl":"https://doi.org/10.1007/s10878-026-01448-x","url":null,"abstract":"Given two sequences with lengths &lt;italic&gt;m&lt;/italic&gt; and &lt;italic&gt;n&lt;/italic&gt;, &lt;inline-formula&gt;&lt;alternatives&gt;&lt;mml:math&gt;&lt;mml:mrow&gt;&lt;mml:mi&gt;m&lt;/mml:mi&gt;&lt;mml:mo&gt;≤&lt;/mml:mo&gt;&lt;mml:mi&gt;n&lt;/mml:mi&gt;&lt;/mml:mrow&gt;&lt;/mml:math&gt;&lt;tex-math&gt;documentclass[12pt]{minimal} usepackage{amsmath} usepackage{wasysym} usepackage{amsfonts} usepackage{amssymb} usepackage{amsbsy} usepackage{mathrsfs} usepackage{upgreek} setlength{oddsidemargin}{-69pt} begin{document}$$m le n$$end{document}&lt;/tex-math&gt;&lt;/alternatives&gt;&lt;/inline-formula&gt;, the edit distance is the minimum cost required to transform one into the other. In the traditional edit distance problem, three standard operations are allowed: insertion, deletion and replacement (substitution). In 1992, Schöniger and Waterman (&lt;xref ref-type=\"bibr\"&gt;1992&lt;/xref&gt;) defined a new problem with non-overlapping inversions, in which two inversions cannot overlap each other, but the standard operations can be performed outside or within the inversions. The time complexity of their algorithm is O&lt;inline-formula&gt;&lt;alternatives&gt;&lt;mml:math&gt;&lt;mml:mrow&gt;&lt;mml:mo stretchy=\"false\"&gt;(&lt;/mml:mo&gt;&lt;mml:msup&gt;&lt;mml:mi&gt;n&lt;/mml:mi&gt;&lt;mml:mn&gt;4&lt;/mml:mn&gt;&lt;/mml:msup&gt;&lt;mml:mo stretchy=\"false\"&gt;)&lt;/mml:mo&gt;&lt;/mml:mrow&gt;&lt;/mml:math&gt;&lt;tex-math&gt;documentclass[12pt]{minimal} usepackage{amsmath} usepackage{wasysym} usepackage{amsfonts} usepackage{amssymb} usepackage{amsbsy} usepackage{mathrsfs} usepackage{upgreek} setlength{oddsidemargin}{-69pt} begin{document}$$(n^4)$$end{document}&lt;/tex-math&gt;&lt;/alternatives&gt;&lt;/inline-formula&gt;. In 2006, Vellozo et al. (&lt;xref ref-type=\"bibr\"&gt;2006&lt;/xref&gt;) reduced the time complexity to O(&lt;inline-formula&gt;&lt;alternatives&gt;&lt;mml:math&gt;&lt;mml:msup&gt;&lt;mml:mi&gt;n&lt;/mml:mi&gt;&lt;mml:mn&gt;3&lt;/mml:mn&gt;&lt;/mml:msup&gt;&lt;/mml:math&gt;&lt;tex-math&gt;documentclass[12pt]{minimal} usepackage{amsmath} usepackage{wasysym} usepackage{amsfonts} usepackage{amssymb} usepackage{amsbsy} usepackage{mathrsfs} usepackage{upgreek} setlength{oddsidemargin}{-69pt} begin{document}$$n^3$$end{document}&lt;/tex-math&gt;&lt;/alternatives&gt;&lt;/inline-formula&gt;). In this paper, we further simplify the problem of Schöniger and Waterman by restricting that the standard operations can be performed only outside the inversions, but cannot be performed within an inversion. We name this new simplified variant as the edit distance with non-overlapping inversion (EDI) problem, which is to determine the minimum edit distance with four operations: insertion, deletion, replacement and inversion. We first propose a brute-force algorithm for solving the EDI problem with O&lt;inline-formula&gt;&lt;alternatives&gt;&lt;mml:math&gt;&lt;mml:mrow&gt;&lt;mml:mo stretchy=\"false\"&gt;(&lt;/mml:mo&gt;&lt;mml:msup&gt;&lt;mml:mi&gt;m&lt;/mml:mi&gt;&lt;mml:mn&gt;2&lt;/mml:mn&gt;&lt;/mml:msup&gt;&lt;mml:mi&gt;n&lt;/mml:mi&gt;&lt;mml:mo stretchy=\"false\"&gt;)&lt;/mml:mo&gt;&lt;/mml:mrow&gt;&lt;/mml:math&gt;&lt;tex-math&gt;documentclass[12pt]{minimal} usepackage{amsmath} usepackage{wasysym} usepackage{amsfonts} usepackage{amssymb} usepackage{amsbsy} usepackage{mathrsfs} usepackage{upgreek} setlength{oddsidemargin}{-69pt} begin{document}$$(m^2n)$$end{document}&lt;/tex-math&gt;&lt;/alternatives&gt;&lt;/inline-f","PeriodicalId":50231,"journal":{"name":"Journal of Combinatorial Optimization","volume":"108 1","pages":""},"PeriodicalIF":1.0,"publicationDate":"2026-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148715901","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}

{"title":"Random Schreier graphs as expanders","authors":"Geoffroy Caillat-Grenier","doi":"10.1007/s10878-026-01445-0","DOIUrl":"https://doi.org/10.1007/s10878-026-01445-0","url":null,"abstract":"Expander graphs, due to their mixing properties, are useful in many algorithms and combinatorial constructions. One can produce an expander graph with high probability by taking a random graph (e.g., the union of <italic>d</italic> random bijections for a bipartite graph of degree <italic>d</italic>). This construction is much simpler than all known explicit constructions of expanders and gives graphs with good mixing properties (small second largest eigenvalue) with high probability. However, from the practical viewpoint, it uses too many random bits. The natural idea is to restrict the class of the bijections that we use. For example, if both sides are vector spaces <inline-formula><alternatives><mml:math><mml:msubsup><mml:mi mathvariant=\"double-struck\">F</mml:mi><mml:mi>q</mml:mi><mml:mi>k</mml:mi></mml:msubsup></mml:math><tex-math>documentclass[12pt]{minimal} usepackage{amsmath} usepackage{wasysym} usepackage{amsfonts} usepackage{amssymb} usepackage{amsbsy} usepackage{mathrsfs} usepackage{upgreek} setlength{oddsidemargin}{-69pt} begin{document}$$mathbb {F}_q^k$$end{document}</tex-math></alternatives></inline-formula> over a finite field <inline-formula><alternatives><mml:math><mml:msub><mml:mi mathvariant=\"double-struck\">F</mml:mi><mml:mi>q</mml:mi></mml:msub></mml:math><tex-math>documentclass[12pt]{minimal} usepackage{amsmath} usepackage{wasysym} usepackage{amsfonts} usepackage{amssymb} usepackage{amsbsy} usepackage{mathrsfs} usepackage{upgreek} setlength{oddsidemargin}{-69pt} begin{document}$$mathbb {F}_q$$end{document}</tex-math></alternatives></inline-formula>, we may consider only <italic>linear</italic> bijections, making the number of random bits polynomial in <italic>k</italic> (and not <inline-formula><alternatives><mml:math><mml:msup><mml:mi>q</mml:mi><mml:mi>k</mml:mi></mml:msup></mml:math><tex-math>documentclass[12pt]{minimal} usepackage{amsmath} usepackage{wasysym} usepackage{amsfonts} usepackage{amssymb} usepackage{amsbsy} usepackage{mathrsfs} usepackage{upgreek} setlength{oddsidemargin}{-69pt} begin{document}$$q^k$$end{document}</tex-math></alternatives></inline-formula>). In this paper we provide some experimental data that shows that this approach conserves the mixing properties (the second eigenvalue) for several types of graphs (undirected regular and biregular bipartite graphs). We also prove some upper bounds for the second eigenvalue (though they are quite weak compared with the experimental results) and a lower bound for a special class of graphs. Finally, we discuss the possibility to decrease the number of random bits further by using Toeplitz matrices; our experiments show that this change makes the mixing properties only marginally worse while the number of random bits decreases significantly.","PeriodicalId":50231,"journal":{"name":"Journal of Combinatorial Optimization","volume":"127 1","pages":""},"PeriodicalIF":1.0,"publicationDate":"2026-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148687777","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}

{"title":"Linear convergence property of a new projection algorithm for split feasibility problem with multiple output sets","authors":"Xiaojie Sun, Meixia Li, Biao Qu, Jingjing Tan","doi":"10.1007/s10878-026-01453-0","DOIUrl":"https://doi.org/10.1007/s10878-026-01453-0","url":null,"abstract":"","PeriodicalId":50231,"journal":{"name":"Journal of Combinatorial Optimization","volume":"453 1","pages":""},"PeriodicalIF":1.0,"publicationDate":"2026-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148682116","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}

{"title":"Exact and approximate algorithms for high-multiplicity scheduling with rejection on parallel machines","authors":"Ruiqing Sun","doi":"10.1007/s10878-026-01455-y","DOIUrl":"https://doi.org/10.1007/s10878-026-01455-y","url":null,"abstract":"","PeriodicalId":50231,"journal":{"name":"Journal of Combinatorial Optimization","volume":"69 1","pages":""},"PeriodicalIF":1.0,"publicationDate":"2026-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148682118","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}

{"title":"Fast Algorithms for Monotone Submodular Meta-Learning under the Cardinality Constraint","authors":"Shufang Gong, Bin Liu, Qizhi Fang, Weili Wu","doi":"10.1007/s10878-026-01446-z","DOIUrl":"https://doi.org/10.1007/s10878-026-01446-z","url":null,"abstract":"","PeriodicalId":50231,"journal":{"name":"Journal of Combinatorial Optimization","volume":"15 1","pages":""},"PeriodicalIF":1.0,"publicationDate":"2026-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148586779","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}

{"title":"Deterministic algorithms for k-submodular maximization with the chance constraint","authors":"Shufang Gong, Qiao Chen, Bin Liu","doi":"10.1007/s10878-026-01444-1","DOIUrl":"https://doi.org/10.1007/s10878-026-01444-1","url":null,"abstract":"","PeriodicalId":50231,"journal":{"name":"Journal of Combinatorial Optimization","volume":"12 1","pages":""},"PeriodicalIF":1.0,"publicationDate":"2026-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148586780","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}

{"title":"Mechanism design for facility location games under a prelocated facility","authors":"Genjie Qin, Qizhi Fang, Wenjing Liu","doi":"10.1007/s10878-026-01439-y","DOIUrl":"https://doi.org/10.1007/s10878-026-01439-y","url":null,"abstract":"","PeriodicalId":50231,"journal":{"name":"Journal of Combinatorial Optimization","volume":"32 1","pages":""},"PeriodicalIF":1.0,"publicationDate":"2026-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148428779","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}

{"title":"Neighbor-distinguishing index of IC-planar graphs","authors":"Zhengyue He, Weifan Wang, Lina Zheng","doi":"10.1007/s10878-026-01442-3","DOIUrl":"https://doi.org/10.1007/s10878-026-01442-3","url":null,"abstract":"","PeriodicalId":50231,"journal":{"name":"Journal of Combinatorial Optimization","volume":"29 1","pages":""},"PeriodicalIF":1.0,"publicationDate":"2026-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148428780","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}

{"title":"The latest developments in combinatorial optimization","authors":"Silvano Martello, Greet Vanden Berghe, Tony Wauters","doi":"10.1007/s10878-026-01433-4","DOIUrl":"https://doi.org/10.1007/s10878-026-01433-4","url":null,"abstract":"","PeriodicalId":50231,"journal":{"name":"Journal of Combinatorial Optimization","volume":"42 1","pages":""},"PeriodicalIF":1.0,"publicationDate":"2026-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148428839","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}