Acta Informatica最新文献

{"title":"Homeostasis tissue-like P systems with cell separation","authors":"Yueguo Luo,&nbsp;Yuzhen Zhao,&nbsp;Wenqin Li,&nbsp;Ping Guo","doi":"10.1007/s00236-024-00470-y","DOIUrl":"10.1007/s00236-024-00470-y","url":null,"abstract":"<div><p>P systems are distributed, parallel computing models inspired by biology. Tissue-like P systems are an important variant of P systems, where the environment can provide objects for cells. Hence, the environment plays a critical role. Nevertheless, in actual biological tissues, there exists a peculiar biological phenomenon called “homeostasis”; that is, the internal organisms maintain stable, thereby reducing their dependence on external conditions (i.e., the environment). In this work, considering cell separation, we construct a novel variant to simulate the mechanism of biological homeostasis, called homeostasis tissue-like P systems with cell separation. In this variant, the number of object is finite, and certain substance changes occur inside the cells; moreover, an exponential workspace can be obtained with cell separation in feasible time. The computational power of this model is studied by simulating register machines, and the results show that the variant is computationally complete as number computing devices. Furthermore, to explore the computational efficiency of the model, we use the variant to solve a classic <span>(textbf{NP})</span>-complete problem, the SAT problem, obtaining a uniform solution with a rule length of at most 3.</p></div>","PeriodicalId":7189,"journal":{"name":"Acta Informatica","volume":"62 1","pages":""},"PeriodicalIF":0.4,"publicationDate":"2024-11-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142714232","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Connected feedback vertex set on AT-free graphs","authors":"Joydeep Mukherjee,&nbsp;Tamojit Saha","doi":"10.1007/s00236-024-00469-5","DOIUrl":"10.1007/s00236-024-00469-5","url":null,"abstract":"<div><p>A connected feedback vertex set of a graph is a connected subgraph of the graph whose removal makes the graph cycle free. In this paper, we provide an approximation algorithm for connected feedback vertex set in AT-free graphs. Given an <span>(alpha )</span>-approximate solution for feedback vertex set on 2-connected AT-free graph, our algorithm produces a solution of size <span>(((alpha +0.9091)OPT+6))</span> for connected feedback vertex set on the same graph. The complexity of our algorithm is <span>(O(f(n)+(m+n)))</span>, where the time required to obtain the <span>(alpha )</span>-approximate solution is <i>O</i>(<i>f</i>(<i>n</i>)). Our result leads to the following two observations. The optimal feedback vertex set algorithm for AT-free graphs combined with our result provides an algorithm which produces a solution of size <span>((1.9091OPT+6))</span> with running time <span>(O(n^8m^2))</span> for 2-connected AT-free graphs. The 2-approximation algorithm for feedback vertex set in general graphs along with our result provides an algorithm which produces a solution of size <span>((2.9091OPT+6))</span> with running time <span>(O(min{m(log(n)),n^2}))</span>. Using the same method we also obtain a <span>(((alpha +1)OPT+6))</span>-approximation for this problem on general AT-free graphs. We note that, the complexity status of this problem is not known.</p></div>","PeriodicalId":7189,"journal":{"name":"Acta Informatica","volume":"62 1","pages":""},"PeriodicalIF":0.4,"publicationDate":"2024-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142714182","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative genomics with succinct colored de Bruijn graphs","authors":"Lucas P. Ramos,&nbsp;Felipe A. Louza,&nbsp;Guilherme P. Telles","doi":"10.1007/s00236-024-00467-7","DOIUrl":"10.1007/s00236-024-00467-7","url":null,"abstract":"<div><p>DNA technologies have evolved significantly in the past years enabling the sequencing of a large number of genomes in a short time. Nevertheless, the underlying problem of assembling sequence fragments is computationally hard and many technical factors and limitations complicate obtaining the complete sequence of a genome. Many genomes are left in a draft state, in which each chromosome is represented by a set of sequences with partial information on their relative order. Recently, some approaches have been proposed to compare draft genomes by comparing paths in de Bruijn graphs, which are constructed by many practical genome assemblers. In this article we describe in more detail a method for comparing genomes represented as succinct colored de Bruijn graphs directly and without resorting to sequence alignments, called <span>(texttt {gcBB})</span>, that evaluates the entropy and expectation measures based on the Burrows-Wheeler Similarity Distribution. We also introduce an improved version of <span>(texttt {gcBB})</span>, called <span>(texttt {multi-gcBB})</span>, that improves the time and space performance considerably through the selection of different data structures. We have compared phylogenies of 12 Drosophila species obtained by other methods to those obtained with <span>(texttt {gcBB})</span>, achieving promising results.</p></div>","PeriodicalId":7189,"journal":{"name":"Acta Informatica","volume":"62 1","pages":""},"PeriodicalIF":0.4,"publicationDate":"2024-11-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142679814","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Editorial 2024: moving forwards in the electronic age","authors":"Henning Fernau","doi":"10.1007/s00236-024-00466-8","DOIUrl":"10.1007/s00236-024-00466-8","url":null,"abstract":"","PeriodicalId":7189,"journal":{"name":"Acta Informatica","volume":"61 4","pages":"331 - 332"},"PeriodicalIF":0.4,"publicationDate":"2024-10-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142579477","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Serial and parallel algorithms for order-preserving pattern matching based on the duel-and-sweep paradigm","authors":"Davaajav Jargalsaikhan,&nbsp;Diptarama Hendrian,&nbsp;Yohei Ueki,&nbsp;Ryo Yoshinaka,&nbsp;Ayumi Shinohara","doi":"10.1007/s00236-024-00464-w","DOIUrl":"10.1007/s00236-024-00464-w","url":null,"abstract":"<div><p>Given a text and a pattern over an alphabet, the classic exact matching problem searches for all occurrences of the pattern in the text. Unlike exact matching, <i>order-preserving pattern matching</i> (OPPM) considers the relative order of elements, rather than their exact values. In this paper, we propose efficient algorithms for the OPPM problem using the “duel-and-sweep” paradigm. For a pattern of length <i>m</i> and a text of length <i>n</i>, our serial algorithm runs in <span>(O(n + mlog m))</span> time, and our parallel algorithm runs in <span>(O(log ^2 m))</span> time and <span>(O(n log ^2 m))</span> work with <span>(O(log m))</span> time and <span>(O(m log m))</span> work pattern preprocessing on the Priority Concurrent Read Concurrent Write Parallel Random-Access Machines (P-CRCW PRAM).</p></div>","PeriodicalId":7189,"journal":{"name":"Acta Informatica","volume":"61 4","pages":"415 - 444"},"PeriodicalIF":0.4,"publicationDate":"2024-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142209514","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Linear-size suffix tries and linear-size CDAWGs simplified and improved","authors":"Shunsuke Inenaga","doi":"10.1007/s00236-024-00465-9","DOIUrl":"10.1007/s00236-024-00465-9","url":null,"abstract":"<div><p>The <i>linear-size suffix tries</i> (<i>LSTries</i>) (Crochemore et al. in Theor Comput Sci 638:171–178, 2016) are a version of suffix trees in which the edge labels are single characters, yet are able to perform pattern matching queries in optimal time. Instead of explicitly storing the input text, LSTries have some extra non-branching internal nodes called <i>type-2</i> nodes. The extended techniques are then used in the <i>linear-size compact directed acyclic word graphs</i> (<i>LCDAWGs</i>) (Takagi et al., in: SPIRE 2017, pp. 304–316, 2017), which can be stored with <span>(O(textsf{el}(T)+textsf{er}(T)))</span> space (i.e. without the text), where <span>(textsf{el}(T))</span> and <span>(textsf{er}(T))</span> are the numbers of left- and right-extensions of the maximal repeats in the input text string <i>T</i>, respectively. In this paper, we present simpler alternatives to the aforementioned indexing structures, called the <i>simplified LSTries</i> (<i>simLSTries</i>) and the <i>simplified LCDAWGs</i> (<i>simLCDAWGs</i>), in which most of the type-2 nodes are removed. In particular, our simLCDAWGs require only <span>(O(textsf{er}(T)))</span> space and work in a weaker model of computation (i.e. the pointer machine model). This contrasts the <span>(O(textsf{er}(T)))</span>-space CDAWG representation of Belazzougui and Cunial (in: Proceedings of the 24th international symposium on string processing and information retrieval, pp. 161–175, 2017), which works on the word RAM model.</p></div>","PeriodicalId":7189,"journal":{"name":"Acta Informatica","volume":"61 4","pages":"445 - 468"},"PeriodicalIF":0.4,"publicationDate":"2024-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142209384","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Parameterized aspects of distinct Kemeny rank aggregation","authors":"Koustav De,&nbsp;Harshil Mittal,&nbsp;Palash Dey,&nbsp;Neeldhara Misra","doi":"10.1007/s00236-024-00463-x","DOIUrl":"10.1007/s00236-024-00463-x","url":null,"abstract":"<div><p>The Kemeny method is one of the popular tools for rank aggregation. However, computing an optimal Kemeny ranking is <span>(textsf{NP})</span>-hard. Consequently, the computational task of finding a Kemeny ranking has been studied under the lens of parameterized complexity with respect to many parameters. We study the parameterized complexity of the problem of computing all distinct Kemeny rankings. We consider the target Kemeny score, number of candidates, average distance of input rankings, maximum range of any candidate, and unanimity width as our parameters. For all these parameters, we already have <span>(textsf{FPT})</span> algorithms. We find that any desirable number of Kemeny rankings can also be found without substantial increase in running time. We also present <span>(textsf{FPT})</span> approximation algorithms for Kemeny rank aggregation with respect to these parameters.</p></div>","PeriodicalId":7189,"journal":{"name":"Acta Informatica","volume":"61 4","pages":"401 - 414"},"PeriodicalIF":0.4,"publicationDate":"2024-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142209385","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Word-representable graphs from a word’s perspective","authors":"Pamela Fleischmann,&nbsp;Lukas Haschke,&nbsp;Tim Löck,&nbsp;Dirk Nowotka","doi":"10.1007/s00236-024-00462-y","DOIUrl":"10.1007/s00236-024-00462-y","url":null,"abstract":"<div><p>Word-representable graphs were introduced in 2008 by Kitaev and Pyatkin in the context of semigroup theory. Graphs are called word-representable if there exists a word with the graph’s nodes as letters such that the letters in the word alternate iff there is an edge between them in the graph. Until today numerous works investigated the word-representability of graphs but mostly from the graph perspective. In this work, we change the perspective to the words, i.e., we take classes of words and investigate the represented graphs. Our first subject of interest are the conjugates of words: we determine exactly which graphs are represented if we rotate the word. Afterwards, we look at <i>k</i>-local words introduced by Day et al. (FSTTCS LIPIcs, 2017) in order to gain more insights into this class of words. Here, we investigate especially which graphs are represented by 1-local words. Lastly, we prove that the language of all words representing a graph is regular. We were also able to characterise <i>k</i>-representable graphs, solving an open problem.\u0000</p></div>","PeriodicalId":7189,"journal":{"name":"Acta Informatica","volume":"61 4","pages":"383 - 400"},"PeriodicalIF":0.4,"publicationDate":"2024-08-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s00236-024-00462-y.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141937303","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A closer look at Hamiltonicity and domination through the lens of diameter and convexity","authors":"R. Mahendra Kumar,&nbsp;N. Sadagopan","doi":"10.1007/s00236-024-00461-z","DOIUrl":"10.1007/s00236-024-00461-z","url":null,"abstract":"&lt;div&gt;&lt;p&gt;A bipartite graph &lt;i&gt;G&lt;/i&gt;(&lt;i&gt;X&lt;/i&gt;, &lt;i&gt;Y&lt;/i&gt;) is called a star-convex bipartite graph with convexity on &lt;i&gt;X&lt;/i&gt; if there is an associated star &lt;i&gt;T&lt;/i&gt;(&lt;i&gt;X&lt;/i&gt;, &lt;i&gt;F&lt;/i&gt;), such that for each vertex in &lt;i&gt;Y&lt;/i&gt;, its neighborhood in &lt;i&gt;X&lt;/i&gt; induces a subtree in &lt;i&gt;T&lt;/i&gt;. A graph &lt;i&gt;G&lt;/i&gt; is said to be a split graph if &lt;i&gt;G&lt;/i&gt; can be partitioned into a clique (&lt;i&gt;K&lt;/i&gt;) and an independent set (&lt;i&gt;I&lt;/i&gt;). The objective of this study is twofold: (i) to strengthen the complexity results presented in Chen et al. (J Comb Optim 32(1):95–110, 2016) for the Hamiltonian cycle (HCYCLE), the Hamiltonian path (HPATH), and the Domination (DS) problems on star-convex bipartite graphs (ii) to reinforce the results of Müller (Discret Math 156(1–3):291–298, 1996) for HCYCLE, and HPATH on split graphs by introducing a convex ordering on one of the partitions (&lt;i&gt;K&lt;/i&gt; or &lt;i&gt;I&lt;/i&gt;). As part of our fine-grained analysis study with the diameter being the parameter, we first show that the diameter of star-convex bipartite graphs is at most six. Next, we observe that the reduction instances of Chen et al. (J Comb Optim 32(1):95–110, 2016) are star-convex bipartite graphs with at most diameter 4, and hence HCYCLE and HPATH are NP-complete on star-convex bipartite graphs with at most diameter 4. We strengthen this result and establish the following results on star-convex bipartite graphs: (i) HCYCLE is NP-complete for diameter 3, and polynomial-time solvable for diameters 2, 5, and 6 (a transformation in complexity: P to NPC to P) (ii) HPATH is polynomial-time solvable for diameter 2, and NP-Complete, otherwise (a dichotomy). Further, with convexity being the parameter, for split graphs with convexity on &lt;i&gt;K&lt;/i&gt; (resp. &lt;i&gt;I&lt;/i&gt;), we show that HCYCLE and HPATH are NP-complete on star-convex (resp. comb) split graphs with convexity on &lt;i&gt;K&lt;/i&gt; (resp. &lt;i&gt;I&lt;/i&gt;). Further, we show that HCYCLE is NP-complete on &lt;span&gt;(k_{1,r})&lt;/span&gt;-free star-convex split graphs with convexity on &lt;i&gt;I&lt;/i&gt;, &lt;span&gt;(rge 6)&lt;/span&gt;. On the positive side, we show that for &lt;span&gt;(K_{1,5})&lt;/span&gt;-free star-convex split graphs with convexity on &lt;i&gt;I&lt;/i&gt;, HCYCLE is polynomial-time solvable. Thus, we establish a dichotomy for HCYCLE on star-convex split graphs with convexity on &lt;i&gt;I&lt;/i&gt;. We further show that the dominating set problem (DS) and its variants (resp. Connected, Total, Outer-Connected, and Dominating biclique) are NP-complete on star-convex bipartite graphs with diameter 3 (resp. diameter 5, and diameter 6). On the parameterized complexity front, we prove that the parameterized version of the domination problem and its variants, with the parameter being the solution size, is not fixed-parameter tractable for star-convex bipartite graphs with diameter 3 (resp. diameter 5, and diameter 6), whereas it is fixed-parameter tractable when the parameter is the number of leaves in the associated star. Further, we show that for star-convex bipartite graphs with diameters 5, and 6, the domin","PeriodicalId":7189,"journal":{"name":"Acta Informatica","volume":"61 4","pages":"357 - 382"},"PeriodicalIF":0.4,"publicationDate":"2024-08-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141937307","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cycle encoding-based parameter synthesis for timed automata safety","authors":"Burkay Sucu,&nbsp;Ebru Aydin Gol","doi":"10.1007/s00236-024-00460-0","DOIUrl":"10.1007/s00236-024-00460-0","url":null,"abstract":"<div><p>Parametric timed automata (PTA) extend timed automata (TA) with parameters instead of fixed timing constraints, providing the flexibility to accommodate uncertainties during the design phase. Once a parametric model is obtained, the next step is finding the optimal parameters such that the resulting TA satisfies the specifications. This paper introduces a new algorithm for determining parameters from safety specifications for PTA with bounded integer parameters and no nested cycles. The algorithm searches for unsafe paths through a depth-first search and generates parameter constraints. In particular, the realizability of simple and cyclic paths are encoded via mixed integer linear programming and non-linear programming problems. Then, the parameter constraints rendering the path unrealizable are derived via quantifier elimination. The accumulated constraints through the depth-first search guarantee that a parameter valuation satisfying these constraints solves the synthesis problem. The results are illustrated over benchmarks.\u0000</p></div>","PeriodicalId":7189,"journal":{"name":"Acta Informatica","volume":"61 4","pages":"333 - 356"},"PeriodicalIF":0.4,"publicationDate":"2024-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141868296","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}