Hamiltonian paths and cycles passing through a prescribed path in hypercubes

Assume that P is any path in a bipartite graph G of length k with 2?k?h, G is said to be h-path bipancyclic if there exists a cycle C in G of every even length from 2k to |V(G)| such that P lies in C. In this paper, the following result is obtained: The n-dimensional hypercube Qn with n?3 is (2n−3)-path bipancyclic but is not (2n−2)-path bipancyclic, moreover, a path P of length k with 2?k?2n−3 lies in a cycle of length 2k−2 if and only if P contains two edges of the same dimension. In order to prove the above result we first show that any path of length at most 2n−1 is a subpath of a Hamiltonian path in Qn with n?2, moreover, the upper bound 2n−1 is sharp when n?4.     

Exact and approximation algorithms for sorting by reversals,with application to genome rearrangement

Motivated by the problem in computational biology of reconstructing the series of chromosome inversions by which one organism evolved from another, we consider the problem of computing the shortest series of reversals that transform one permutation to another. The permutations describe the order of genes on corresponding chromosomes, and areversal takes an arbitrary substring of elements, and reverses their order.For this problem, we develop two algorithms: a greedy approximation algorithm, that finds a solution provably close to optimal inO(n ²) time and0(n) space forn-element permutations, and a branch- and-bound exact algorithm, that finds an optimal solution in0(mL(n, n)) time and0(n ²) space, wherem is the size of the branch- and-bound search tree, andL(n, n) is the time to solve a linear program ofn variables andn constraints. The greedy algorithm is the first to come within a constant factor of the optimum; it guarantees a solution that uses no more than twice the minimum number of reversals. The lower and upper bounds of the branch- and-bound algorithm are a novel application of maximum-weight matchings, shortest paths, and linear programming.In a series of experiments, we study the performance of an implementation on random permutations, and permutations generated by random reversals. For permutations differing byk random reversals, we find that the average upper bound on reversal distance estimatesk to within one reversal fork<1/2n andn<100. For the difficult case of random permutations, we find that the average difference between the upper and lower bounds is less than three reversals forn<50. Due to the tightness of these bounds, we can solve, to optimality, problems on 30 elements in a few minutes of computer time. This approaches the scale of mitochondrial genomes.This research was supported by a postdoctoral fellowship from the Program in Mathematics and Molecular Biology of the University of California at Berkeley under National Science Foundation Grant DMS-8720208, and by a fellowship from the Centre de recherches mathématiques of the Université de Montréal.This research was supported by grants from the Natural Sciences and Engineering Research Council of Canada, and the Fonds pour la formation de chercheurs et l'aide à la recherche (Québec). The author is a fellow of the Canadian Institute for Advanced Research.     

Fault-tolerant hamiltonian laceability of hypercubes

It is known that every hypercube Q_n is a bipartite graph. Assume that n?2 and F is a subset of edges with |F|?n−2. We prove that there exists a hamiltonian path in Q_n−F between any two vertices of different partite sets. Moreover, there exists a path of length 2ⁿ−2 between any two vertices of the same partite set. Assume that n?3 and F is a subset of edges with |F|?n−3. We prove that there exists a hamiltonian path in Q_n−{v}−F between any two vertices in the partite set without v. Furthermore, all bounds are tight.     

A study of fault tolerance in star graph

The bounds on f(n,k), the number of faulty nodes to make every (n−k)-dimensional substar Sn−k in an n-dimensional star network Sn, have been derived. The exact value for f(n,k) is determined when n is prime and k=2, or when n−2?k?n. For 2<k<n−2, a general method is presented to derive a set of faulty nodes which damage all Sn−k's in Sn.     

Path bipancyclicity of hypercubes

A bipartite graph is vertex-bipancyclic (respectively, edge-bipancyclic) if every vertex (respectively, edge) lies in a cycle of every even length from 4 to |V(G)| inclusive. It is easy to see that every connected edge-bipancyclic graph is vertex-bipancyclic. An n-dimensional hypercube, or n-cube denoted by Qn, is well known as bipartite and one of the most efficient networks for parallel computation. In this paper, we study a stronger bipancyclicity of hypercubes. We prove that every n-dimensional hypercube is (2n−4)-path-bipancyclic for n?3. That is, for any path P of length k with 1?k?2n−4 and any integer l with max{2,k}?l?²n−1, an even cycle C of length 2l can be found in Qn such that the path P is included in C for n?3.     

On path bipancyclicity of hypercubes

Assume that P is any path in a bipartite graph G of length k with 2?k?h, G is said to be h-path bipancyclic if there exists a cycle C in G of every even length from 2k to |V(G)| such that P lies in C. Based on Lemma 5, the authors of [C.-H. Tsai, S.-Y. Jiang, Path bipancyclicity of hypercubes, Inform. Process. Lett. 101 (2007) 93-97] showed that the n-cube Qn with n?3 is (2n−4)-path bipancyclicity. In this paper, counterexamples to the lemma are given, therefore, their proof fails. And we show the following result: The n-cube Qn with n?3 is (2n−4)-path bipancyclicity but is not (2n−2)-path bipancyclicity, moreover, and a path P of length k with 2?k?2n−4 lies in a cycle of length 2k−2 if and only if P contains two edges of dimension i for some i, 1?i?n. We conjecture that if 2n−4 is replaced by 2n−3, then the above result also holds.     

Constructing vertex-disjoint paths in (n, k)-star graphs

This work describes a novel routing algorithm for constructing a container of width n − 1 between a pair of vertices in an (n, k)-star graph with connectivity n − 1. Since Lin et al. [T.C. Lin, D.R. Duh, H.C. Cheng, Wide diameter of (n, k)-star networks, in: Proceedings of the International Conference on Computing, Communications and Control Technologies, vol. 5, 2004, pp. 160-165] already calculated the wide diameters in (n, n − 1)-star and (n, 1)-star graphs, this study only considers an (n, k)-star with 2 ? k ? n − 2. The length of the longest container among all constructed containers serves as the upper bound of the wide diameter of an (n, k)-star graph. The lower bound of the wide diameter of an (n, k)-star graph with 2 ? k ? ⌊n/2⌋ and the lower bound of the wide diameter of a regular graph with a connectivity of 2 or above are also computed. Measurement results indicate that the wide diameter of an (n, k)-star graph is its diameter plus 2 for 2 ? k ? ⌊n/2⌋, or its diameter plus a value between 1 and 2 for ⌊n/2⌋ + 1 ? k ? n − 2.     

Birth and growth of multicyclic components in random hypergraphs

Define an ?-component to be a connected b-uniform hypergraph with k edges and k(b−1)−? vertices. In this paper, we investigate the growth of size and complexity of connected components of a random hypergraph process. We prove that the expected number of creations of ?-components during a random hypergraph process tends to 1 as b is fixed and ? tends to infinity with the total number of vertices n while remaining ?=o(n^1/3). We also show that the expected number of vertices that ever belong to an ?-component is ∼12^1/3?^1/3n^2/3(b−1)^−1/3. We prove that the expected number of times hypertrees are swallowed by ?-components is ∼2^1/33^−1/3n^1/3?^−1/3(b−1)^−5/3. It follows that with high probability the largest ?-component during the process is of size of order O(?^1/3n^2/3(b−1)^−1/3). Our results give insight into the size of giant components inside the phase transition of random hypergraphs and generalize previous results about graphs.     

Improved algorithms for finding length-bounded two vertex-disjoint paths in a planar graph and minmax k vertex-disjoint paths in a directed acyclic graph

This paper is composed of two parts. In the first part, an improved algorithm is presented for the problem of finding length-bounded two vertex-disjoint paths in an undirected planar graph. The presented algorithm requires O(n³bmin) time and O(n²bmin) space, where bmin is the smaller of the two given length bounds. In the second part of this paper, we consider the minmax k vertex-disjoint paths problem on a directed acyclic graph, where k?2 is a constant. An improved algorithm and a faster approximation scheme are presented. The presented algorithm requires O(nk+1Mk−1) time and O(nkMk−1) space, and the presented approximation scheme requires O((1/?)^k−1n2klogk−1M) time and O((1/?)^k−1n2k−1logk−1M) space, where ? is the given approximation parameter and M is the length of the longest path in an optimal solution.     

Cycles passing through a prescribed path in a hypercube with faulty edges

Let Qn denote an n-dimensional hypercube with n?2, P be a path of length h in Qn and F⊂E(Qn)\E(P). Recently, Tsai proved that if 1?h?n−1 and |F|?n−1−h, then in the graph Qn−F the path P lies on a cycle of every even length from 2h+2 to n², and P also lies on a cycle of length 2h if |F|?h−2. In this paper, we show that if 1?h?2n−3 and |F|?n−2−⌊h/2⌋, then in Qn−F the path P lies on a cycle of every even length from 2h+2 to n², and P also lies on a cycle of length 2h if P contains two edges of the same dimension or P is a shortest path and |F∩E(Qh)|?h−2, where Qh is the h-dimensional subcube containing the path P. Moreover, the upper bound 2n−3 of h is sharp and the upper bound n−2−⌊h/2⌋ of |F| is sharp for any given h with 1?h?2n−3.     

A note on maximum independent sets in rectangle intersection graphs

Finding the maximum independent set in the intersection graph of n axis-parallel rectangles is NP-hard. We re-examine two known approximation results for this problem. For the case of rectangles of unit height, Agarwal, van Kreveld and Suri [Comput. Geom. Theory Appl. 11 (1998) 209-218] gave a (1+1/k)-factor algorithm with an O(nlogn+n^2k−1) time bound for any integer constant k?1; we describe a similar algorithm running in only O(nlogn+nΔ^k−1) time, where Δ?n denotes the maximum number of rectangles a point can be in. For the general case, Berman, DasGupta, Muthukrishnan and Ramaswami [J. Algorithms 41 (2001) 443-470] gave a ⌈log_kn⌉-factor algorithm with an O(n^k+1) time bound for any integer constant k?2; we describe similar algorithms running in O(nlogn+nΔ^k−2) and n^O(k/logk) time.     

Speedup of Vidyasankar's algorithm for the group k-exclusion problem

Vidyasankar introduced a combined problem of k-exclusion and group mutual exclusion, called the group k-exclusion problem, which occurs in a situation where philosophers with the same interest can attend a forum in a meeting room, and up to k meeting rooms are available. We propose an improvement to Vidyasankar's algorithm. Waiting times in the trying region in the original algorithm and in our algorithm are bounded by n(n−k)c+O(n³(n−k))l and (n−k)c+O(n(n−k)²)l, respectively, where n is the number of processes, l is an upper bound on the time between successive two atomic steps, and c is an upper bound on the time that any philosopher spends in a forum.     

Selection problems viaM-ary queries

It is well known that, for fixedk, to find thek-th largest ofn elementsn+(k?1)log₂ n+Θ(1) comparisons are necessary and sufficient. But do the same bounds apply if we use a different type of query? We show that the arity of the queries is relevant. In particular, we present upper and lower bounds for finding the maximum using 3-ary or 4-ary Boolean (YES/NO answers) queries. We also study general (e.g.,max, sort) 3-ary queries, and show bounds for finding the maximum and the second largest. For sort queries we show matching upper and lower bounds.     

On the number of higher order Delaunay triangulations

Higher order Delaunay triangulations are a generalization of the Delaunay triangulation that provides a class of well-shaped triangulations, over which extra criteria can be optimized. A triangulation is order-k Delaunay if the circumcircle of each triangle of the triangulation contains at most k points. In this paper we study lower and upper bounds on the number of higher order Delaunay triangulations, as well as their expected number for randomly distributed points. We show that arbitrarily large point sets can have a single higher order Delaunay triangulation, even for large orders, whereas for first order Delaunay triangulations, the maximum number is 2ⁿ⁻³. Next we show that uniformly distributed points have an expected number of at least 2^{ρ₁n(1+o(1))} first order Delaunay triangulations, where ρ₁ is an analytically defined constant (ρ₁≈0.525785), and for k>1, the expected number of order-k Delaunay triangulations (which are not order-i for any i<k) is at least 2^{ρ_kn(1+o(1))}, where ρ_k can be calculated numerically.     

Conditional diagnosability of hypermeshes under the comparison model

The hypermeshes are a family of promising optical interconnection topologies for multiprocessor systems. This paper is concerned with the conditional diagnosability of hypermeshes under the comparison model. We prove that, for n?3, k?4, the conditional diagnosability of kn-hypermesh is 3n(k−1)−2k−1. This result shows that the hypermeshes possess strong self-diagnosing ability.     

Edge-bipancyclicity of the k-ary n-cubes with faulty nodes and edges

The k-ary n-cube has been one of the most popular interconnection networks for massively parallel systems. In this paper, we investigate the edge-bipancyclicity of k-ary n-cubes with faulty nodes and edges. It is proved that every healthy edge of the faulty k-ary n-cube with f_v faulty nodes and f_e faulty edges lies in a fault-free cycle of every even length from 4 to kⁿ − 2f_v (resp. kⁿ − f_v) if k ? 4 is even (resp. k ? 3 is odd) and f_v + f_e ? 2n − 3. The results are optimal with respect to the number of node and edge faults tolerated.     

Minimal Adaptive Routing on the Mesh with Bounded Queue Size

An adaptive routing algorithm is one in which the path a packet takes from its source to its destination may depend on other packets it encounters. Such algorithms potentially avoid network bottlenecks by routing packets around “hot spots.” Minimal adaptive routing algorithms have the additional advantage that the path each packet takes is a shortest one. For a large class of minimal adaptive routing algorithms, we present an Ω(n²/k²) bound on the worst case time to route a static permutation of packets on ann×nmesh or torus with nodes that can hold up tok≥ 1 packets each. This is the first nontrivial lower bound on adaptive routing algorithms. The argument extends to more general routing problems, such as theh–hrouting problem. It also extends to a large class of dimension order routing algorithms, yielding an Ω(n²/k) time bound. To complement these lower bounds, we present two upper bounds. One is anO(n²/k+n) time dimension order routing algorithm that matches the lower bound. The other is the first instance of a minimal adaptive routing algorithm that achievesO(n) time with constant sized queues per node. We point out why the latter algorithm is outside the model of our lower bounds.     

Order-k voronoi diagrams of sites with additive weights in the plane

It is shown that the order-k Voronoi diagram of n sites with additive weights in the plane has at most (4k?2)(n?k) vertices, (6k?3)(n?k) edges, and (2k?1)(n?itk) + 1 regions. These bounds are approximately the same as the ones known for unweighted order-k Voronoi diagrams. Furthermore, tight upper bounds on the number of edges and vertices are given for the case that every weighted site has a nonempty region in the order-1 diagram. The proof is based on a new algorithm for the construction of these diagrams which generalizes a plane-sweep algorithm for order-1 diagrams developed by Steven Fortune. The new algorithm has time-complexityO(k ² n logn) and space-complexityO(kn). It is the only nontrivial algorithm known for constructing order-kc Voronoi diagrams of sites withadditive weights. It is fairly simple and of practical interest also in the special case of unweighted sites.     

Towards understanding optimal MIMD queueless routing of arbitrary permutations on hypercubes

This paper addresses the problem of the offline routing of arbitrary permutations on hypercubes under the MIMD queueless communication constraints which imposes that only one message can be located in each node of the hypercube right through the routing. According to e-cube routing, this kind of communication may require in the worst cases at least n exchanges steps on an n-dimensional hypercube. It has been conjectured that in the general case n steps suffice. The conjecture has been proved either by enumeration or by program for the particular cases of n??3. We revisit the problem through the k-partitioning paradigm based on maximum matching of bipartite graphs concept to take advantage of the recursive structure of the hypercube topology. The paradigm consists in looking for each message a transition node distant of at most say k<n hops from its current node such that all the messages can be routed to their transition nodes in k hops then finally routed to their final destination nodes in n?k hops on two disjoints hypercubes. In others words, the paradigm consists to determine an upstream permutation routable in k steps and which leads to two independent downstream permutations routable in n?k steps on two disjoint hypercubes. With this purpose, we give a characterization of the non-1-partitionable permutations from which the proof of the conjecture comes straightforwardly for n??2 and the non-1-partitionable permutations can be built whatever n may be. For n=3, we thus confirm the existence of exactly three classes of non-1-partitionable permutations and prove that there are two classes of upstream permutations to avoid when 2-partitioning any non-1-partitionable permutation. The process to avoid such upstream permutations is presented, and leads to a formal proof of the conjecture for n=3. For n>3, experiences gained in routing permutations on 4D-hypercubes allow conjecturing that in these cases, too, any non-1-partitionable permutation is 2-partitionable. Indeed, the analysis carried out for the 3D-hypercubes is repeatable to identify, certainly more laboriously given their combinatory, the upstream permutations to avoid when 2-partitioning a non-1-partitionable permutation on a 4D-hypercube. The proof that resulting downstream permutations on a 3D-hypercube can be routed in 2 steps is a consequence of the fact that for n=2 and 3 any permutation on a nD-hypercube can be routed in n steps.     

LCS approximation via embedding into locally non-repetitive strings

A classical measure of similarity between strings is the length of the longest common subsequence (LCS) between the two given strings. The search for efficient algorithms for finding the LCS has been going on for more than three decades. To date, all known algorithms may take quadratic time (shaved by logarithmic factors) to find large LCS. In this paper, the problem of approximating LCS is studied, while focusing on the hard inputs for this problem, namely, approximating LCS of near-linear size in strings over a relatively large alphabet (of size at least n^? for some constant ?>0, where n is the length of the string). We show that, any given string over a relatively large alphabet can be embedded into a locally non-repetitive string. This embedding has a negligible additive distortion for strings that are not too dissimilar in terms of the edit distance. We also show that LCS can be efficiently approximated in locally-non-repetitive strings. Our new method (the embedding together with the approximation algorithm) gives a strictly sub-quadratic time algorithm (i.e., of complexity O(n^2-?) for some constant ?) which can find common subsequences of linear (and near linear) size that cannot be detected efficiently by the existing tools.