Computing directed Steiner path covers

Molecular computing has proved its possibility to solve weighted graph problem such as Hamiltonian Path Problem (HPP), Traveling Salesman Problem (TSP) and the Shortest Path Problem (SPP). Normally, in molecular computation, the DNA sequences used for the computation should be critically designed in order to reduce error that could occur during computation. In the previous paper, we have proposed a readout method tailored specifically to HPP in DNA Computing using real-time PCR for output visualization. Six nodes of HPP was considered. Based on the example instance, the method requires 11 oligonucleotides, where 6 oligonucleotides are for the nodes and 5 oligonucleotides are for the edges. Three TaqMan probes and five primers are required as well. In this study, a procedure for DNA sequence design is presented in order to obtain good sequences for those nodes, primers, and probes. The experiment is done based on the generated DNA sequences and the Hamiltonian Path can be determined successfully.

Finding a minimum path cover of a distance-hereditary graph in polynomial time

The Hamiltonian cycle and path problems are fundamental in graph theory and useful in modelling real-life problems. Research in this area is directed toward designing better and better algorithms for general problems, but also toward defining new special cases for which exact polynomial-time algorithms exist. In the paper, such new classes of digraphs are proposed. The classes include, among others, quasi-adjoint graphs, which are a superclass of adjoints, directed line graphs, and graphs modelling a DNA sequencing problem.

This dissertation is to illustrate the current state of the art of DNA computing achievements, especially of new approaches to solve theoretical 3-SAT problems and the hitting-set problem. Beginning with Adleman’s breakthrough which is an molecular algorithm for the solution of a NP-complete, combinatorial problem, the directed Hamiltonian path problem (HPP). Today, many researchers all over the world concentrate on proposing new methods to solve engineering or application problems with a DNA computing approach. Satisfiability problem is given a Boolean formula, and decide if a satisfying truth assignment exists. ( ) ( ) … ( ) ( ) is an example of Boolean formula. k-SAT problem means that each clause has exactly k literals. Not-All-Equal (NAE) 3-SAT problem and One-In-Three (1IN3) 3-SAT problem are both NP-complete problems. In this dissertation, we present molecular solutions to find all true assignments (3-SAT problem) and furthermore find Not-All-Equal (NAE) solutions and One-In-Three (1IN3) solutions in DNA-based Supercomputing. Hitting-set problem assume that there exists a collection C of subsets of a finite set S, and a positive integer K  |S|, and we need to know if there is a subset  S with | |  K such that contains at least one element of each subset in C. In other words, is the subset that intersects every subset in C and is called the hitting-set. In this dissertation, a DNA-based algorithm is proposed to solve the small hitting-set problem. A small hitting-set is a hitting-set with the smallest K value, i.e., the hitting-set with the smallest number of elements. Furthermore, an algorithm is introduced to find the number of ones from 2n combinations and minimum numbers of ones represents the small hitting-set since K is expected to be as small as possible. The complexity of all the presented DNA-based algorithms is also discussed. We describe time complexity and volume complexity of three Algorithms, numbers of test tube used and the longest library strand in solution space of all three Algorithms. Finally, the simulated experiment is applied to verify correctness of the proposed DNA-based algorithm for solving the One-In-Three (1IN3) 3-SAT problem, and simulation of Not-All-Equal (NAE) 3-SAT problem is similar. Also, another simulated experiment is applied to our proposed DNA-based algorithm 6-2, in order to solve the well-known hitting-set problem. This research has been motivated by the benefit and the application of DNA computing and gives new methods to solve two 3-SAT problems and the hitting-set problem which are NP-complete.

Improved shortest path algorithms for nearly acyclic graphs

A graph is called Hamiltonian connected if it contains a Hamiltonian path between any two distinct vertices. In the past, we proved the Hamiltonian path and cycle problems for general supergrid graphs to be NP-complete. However, they are still open for solid supergrid graphs. In this paper, first we will verify the Hamiltonian cycle property of C-shaped supergrid graphs, which are a special case of solid supergrid graphs. Next, we show that C-shaped supergrid graphs are Hamiltonian connected except in a few conditions. For these excluding conditions of Hamiltonian connectivity, we compute their longest paths. Then, we design a linear-time algorithm to solve the longest path problem in these graphs. The Hamiltonian connectivity of C-shaped supergrid graphs can be applied to compute the optimal stitching trace of computer embroidery machines, and construct the minimum printing trace of 3D printers with a C-like component being printed.

For graph $G(V,E)$, a minimum path cover (MPC) is a minimum cardinality set of vertex disjoint paths that cover $V$ (i.e., every vertex of $G$ is in exactly one path in the cover). This problem is a natural generalization of the Hamiltonian path problem. Cocomparability graphs (the complements of graphs that have an acyclic transitive orientation of their edge sets) are a well studied subfamily of perfect graphs that includes many popular families of graphs such as interval, permutation, and cographs. Furthermore, for every cocomparability graph $G$ and acyclic transitive orientation of the edges of $\overline{G}$ there is a corresponding poset $P_G$; it is easy to see that an MPC of $G$ is a linear extension of $P_G$ that minimizes the bump number of $P_G$. Although there are directly graph-theoretical MPC algorithms (i.e., algorithms that do not rely on poset formulations) for various subfamilies of cocomparability graphs, notably interval graphs, until now all MPC algorithms for cocomparability graphs themselves have been based on the bump number algorithms for posets. In this paper we present the first directly graph-theoretical MPC algorithm for cocomparability graphs; this algorithm is based on two consecutive graph searches followed by a certifying algorithm. Surprisingly, except for a lexicographic depth first search (LDFS) preprocessing step, this algorithm is identical to the corresponding algorithm for interval graphs. The running time of the algorithm is $O({\rm min}(n^2, n + {\rm mloglogn}))$, with the nonlinearity coming from LDFS.

Given four distinct vertices s1,s2,t1, and t2 of a graph G, the 2-disjoint paths problem is to determine two disjoint paths, p1 from s1 to t1 and p2 from s2 to t2, if such paths exist. Disjoint can mean vertex- or edge-disjoint. Both, the edge- and the vertex-disjoint version of the problem, are NP-hard in the case of directed graphs. For undirected graphs, we show that the O(mn)-time algorithm of Shiloach can be modified to solve the 2-vertex-disjoint paths problem in only O(n + mα(m,n)) time, where m is the number of edges in G, n is the number of vertices in G, and where α denotes the inverse of the Ackermann function. Our result also improves the running time for the 2-edge-disjoint paths problem on undirected graphs as well as the running times for the 2-vertex- and the 2-edge-disjoint paths problem on dags.

Previous chapter Next chapter Full AccessProceedings Proceedings of the 2022 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA)Sparsifying, Shrinking and Splicing for Minimum Path Cover in Parameterized Linear TimeManuel Cáceres, Massimo Cairo, Brendan Mumey, Romeo Rizzi, and Alexandru I. TomescuManuel Cáceres, Massimo Cairo, Brendan Mumey, Romeo Rizzi, and Alexandru I. Tomescupp.359 - 376Chapter DOI:https://doi.org/10.1137/1.9781611977073.18PDFBibTexSections ToolsAdd to favoritesExport CitationTrack CitationsEmail SectionsAboutAbstract A minimum path cover (MPC) of a directed acyclic graph (DAG) G = (V, E) is a minimum-size set of paths that together cover all the vertices of the DAG. Computing an MPC is a basic polynomial problem, dating back to Dilworth's and Fulkerson's results in the 1950s. Since the size k of an MPC (also known as the width) can be small in practical applications, research has also studied algorithms whose running time is parameterized on k. We obtain two new MPC parameterized algorithms for DAGs running in time O(k2|V| log |V| + |E|) and O(k3|V| + |E|). We also obtain a parallel algorithm running in O(k2|V| + |E|) parallel steps and using O(log |V|) processors (in the PRAM model). Our latter two algorithms are the first solving the problem in parameterized linear time. Finally, we show that we can transform (in O(k2|V|) time) a given MPC into another MPC that uses less than 2|V| distinct edges, which we prove to be asymptotically tight. As such, we also obtain edge sparsification algorithms preserving the width of the DAG with the same running time as our MPC algorithms. At the core of all our algorithms we interleave the usage of three techniques: transitive sparsification, shrinking of a path cover, and the splicing of a set of paths along a given path. Previous chapter Next chapter RelatedDetails Published:2022eISBN:978-1-61197-707-3 https://doi.org/10.1137/1.9781611977073Book Series Name:ProceedingsBook Code:PRDA22Book Pages:xvii + 3771

Given an edge-weighted graph and a set of known seed vertices of interest, a network scientist often desires to understand the graph relationships to explain connections between the seed vertices. If the size of the seed set is 2, shortest path calculations are an attractive computational kernel to explore the connections between the two vertices. When the seed set is 3 or larger (say up to 1,000s) Steiner minimal tree – min-weight acyclic connected subgraph (of the input graph) that contains all the seed vertices – is an attractive generalization of shortest weighted paths. In general, computing a Steiner minimal tree is NP-hard, but decades ago several polynomial-time algorithms were designed and proven to yield Steiner trees whose total weight is bounded within 2 times the minimal Steiner tree. Despite its rich theoretical literature, works related to parallel Steiner minimal tree computation and their scalable implementations are rather scarce. In this paper, we present a parallel 2-approximation Steiner minimal tree algorithm (with theoretical guarantees) and its MPI-based distributed implementation. In place of distance computation between all pairs of seed vertices, an expensive phase in many approximation algorithms, the solution we employ, exploits Voronoi cell computation. Also, this approach has higher parallel efficiency than others that involve minimum spanning tree computation on the entire graph. Furthermore, our distributed design exploits asynchronous processing and a message prioritization scheme to accelerate convergence of distance computation, employs techniques to avoid inefficient distributed spanning tree computation on the entire graph, and harnesses a combination of vertex and edge centric processing to offer fast time-to-solution. We demonstrate scalability and performance of our solution using real-world graphs with up to 128 billion edges and 512 compute nodes (8K processes), show the ability to find Steiner trees with up to 10K seed vertices in under one minute, and present in-depth analyses that highlight the benefits of our design choices. Using four real-world graphs and three seed sets for each, we compare our solution with the state-of-the-art exact Steiner minimal tree solver, SCIP-Jack, and two sequential algorithms with the same approximation bound as our algorithm. Our distributed solution comfortably outperforms these related works on graphs with 10s million edges and offers decent strong scaling – up to 90% efficient. We empirically show that, on average, the total distance (sum of edge weights) of the Steiner tree identified by our solution is 1.0527 times greater than the Steiner minimal tree (i.e., the optimal solution) – well within the theoretical bound of less than equal to 2.

Largescale scientific applications require using various system resources to execute complex computing pipelines in distributed networks to support collaborative research. System resources are typically shared in the Internet or over dedicated connections based on their location, availability, capability, and capacity. Optimizing the network performance of computing pipelines in such distributed environments is critical to the success of these applications. We consider two types of largescale distributed applications: (i) interactive applications where a single dataset is sequentially processed along a pipeline; and (ii) streaming applications where a series of datasets continuously flow through a pipeline. The computing pipelines of these applications consist of a number of modules executed in a linear order in network environments with heterogeneous resources under different constraints. Our goal is to find an efficient mapping scheme that allocates the modules of a pipeline to network nodes for minimum endtoend delay or maximum frame rate. We formulate the pipeline mappings in distributed environments as optimization problems and categorize them into six classes with different optimization goals and mapping constraints: (i) Minimum Endtoend Delay with No Node Reuse (MEDNNR), (ii) Minimum Endtoend Delay with Contiguous Node Reuse (MEDCNR), (iii) Minimum Endtoend Delay with Arbitrary Node Reuse (MEDANR), (iv) Maximum Frame Rate with No Node Reuse or Share (MFRNNRS), (v) Maximum Frame Rate with Contiguous Node Reuse and Share (MFRCNRS), and (vi) Maximum Frame Rate with Arbitrary Node Reuse and Share (MFRANRS). Here, “contiguous node reuse” means that multiple contiguous modules along the pipeline may run on the same node and “arbitrary node reuse” imposes no restriction on node reuse. Note that in interactive applications, a node can be reused but its resource is not shared. We prove that MEDANR is polynomially solvable and the rest are NP-complete. MEDANR, where either contiguous or noncontiguous modules in the pipeline can be mapped onto the same node, is essentially the Maximum n-hop Shortest Path problem, and can be solved using a dynamic programming method. In MEDNNR and MFRNNRS, any network node can be used only once, which requires selecting the same number of nodes for onetoone onto mapping. We show its NP-completeness by reducing from the Hamiltonian Path problem. Node reuse is allowed in MEDCNR, MFRCNRS and MFRANRS, which are similar to the Maximum n-hop Shortest Path problem that considers resource sharing. We prove their NP-completeness by reducing from the Disjoint-Connecting-Path Problem and Widest path with the Linear Capacity Constraints problem, respectively.

In the Steiner Tree problem, we are given as input a connected $n$-vertex graph with edge weights in $\{1,2,\ldots,W\}$, and a set of $k$ terminal vertices. Our task is to compute a minimum-weight tree that contains all of the terminals. The main result of the paper is an algorithm solving Steiner Tree in time $\mathcal{O}(7.97^k\cdot n^4\cdot \log{W})$ and using $\mathcal{O}(n^3\cdot \log{nW} \cdot \log k)$ space. This is the first single-exponential time, polynomial space FPT algorithm for the weighted Steiner Tree problem. Whereas our main result seeks to optimize the polynomial dependency in $n$ for both the running time and space usage, it is possible to trade between polynomial dependence in $n$ and the single-exponential dependence in $k$ to obtain faster running time as a function of $k$, but at the cost of increased running time and space usage as a function of $n$. In particular, we show that there exists a polynomial space algorithm for Steiner Tree running in $\mathcal{O}(6.751^kn^{O(1)}\log W)$ time. Finally, by pushing such a trade-off between a polynomial in $n$ and an exponential in $k$ dependencies, we show that for any $\epsilon>0$ there is an $n^{\mathcal{O}(f(\epsilon))}\log W$ space $4^{(1+\epsilon)k}n^{\mathcal{O}(f(\epsilon))}\log W$ time algorithm for Steiner Tree, where $f$ is a computable function depending only on $\epsilon$.

2-vertex connectivity in directed graphs

We study local symmetry breaking problems in the Congest model, focusing on ruling set problems, which generalize the fundamental Maximal Independent Set (MIS) problem. The time (round) complexity of MIS (and ruling sets) have attracted much attention in the Local model. Indeed, recent results (Barenboim et al., FOCS 2012, Ghaffari SODA 2016) for the MIS problem have tried to break the long-standing O(log n)-round "barrier" achieved by Luby's algorithm, but these yield o(log n)-round complexity only when the maximum degree Delta is somewhat small relative to n. More importantly, these results apply only in the Local model. In fact, the best known time bound in the Congest model is still O(log n) (via Luby's algorithm) even for moderately small Delta (i.e., for Delta = Omega(log n) and Delta = o(n)). Furthermore, message complexity has been largely ignored in the context of local symmetry breaking. Luby's algorithm takes O(m) messages on m-edge graphs and this is the best known bound with respect to messages. Our work is motivated by the following central question: can we break the Theta(log n) time complexity barrier and the Theta(m) message complexity barrier in the Congest model for MIS or closely-related symmetry breaking problems?
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\nThis paper presents progress towards this question for the distributed ruling set problem in the Congest model. A beta-ruling set is an independent set such that every node in the graph is at most beta hops from a node in the independent set. We present the following results:
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\n- Time Complexity: We show that we can break the O(log n) "barrier" for 2- and 3-ruling sets. We compute 3-ruling sets in O(log n/log log n) rounds with high probability (whp). More generally we show that 2-ruling sets can be computed in O(log Delta (log n)^(1/2 + epsilon) + log n/log log n) rounds for any epsilon > 0, which is o(log n) for a wide range of Delta values (e.g., Delta = 2^(log n)^(1/2-epsilon)). These are the first 2- and 3-ruling set algorithms to improve over the O(log n)-round complexity of Luby's algorithm in the Congest model.
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\n- Message Complexity: We show an Omega(n^2) lower bound on the message complexity of computing an MIS (i.e., 1-ruling set) which holds also for randomized algorithms and present a contrast to this by showing a randomized algorithm for 2-ruling sets that, whp, uses only O(n log^2 n) messages and runs in O(Delta log n) rounds. This is the first message-efficient algorithm known for ruling sets, which has message complexity nearly linear in n (which is optimal up to a polylogarithmic factor).

A bipartite graph G(X, Y) whose vertex set is partitioned into X and Y is a convex bipartite graph, if there is an ordering of $$X=(x_1,\ldots ,x_m)$$ such that for all $$y \in Y$$ , $$N_G(y)$$ is consecutive with respect to the ordering of X, and G is said to have convexity with respect to X. A k-star caterpillar is a tree with a collection of stars with each star having k vertices of degree one whose roots are joined by a path. For a bipartite graph with partitions X and Y, we associate a k-star caterpillar on X such that for each vertex in Y, its neighborhood induces a tree. The minimum Steiner tree problem (STREE) is defined as follows: given a connected graph $$G=(V,E)$$ and a subset of vertices $$R \subseteq V(G)$$ , the objective is to find a minimum cardinality set $$S \subseteq V(G)$$ such that the set $$R \cup S$$ induces a connected subgraph. In this paper, we present the following dichotomy result: we show that STREE is NP-complete for 1-star caterpillar convex bipartite graphs and polynomial-time solvable for 0-star caterpillar convex bipartite graphs (also known as convex bipartite graphs). We also strengthen the well-known result of Müller and Brandstädt (Theoret Comput Sci 53(2-3):257-265, 1987), which says STREE in chordal bipartite graphs is NP-complete (reduction instances are 3-star caterpillar convex bipartite graphs). As an application, we use our STREE results to solve: (i) the classical dominating set problem in convex bipartite graphs, (ii) STREE on interval graphs, linear time.