A Branch-Checking Algorithm for All-Pairs Shortest Paths

We formulate and study an algorithm for all-pairs shortest paths in a network with $n $ nodes and $m $ arcs of positive length. Using the dynamic programming principle of optimality of subpaths the algorithm avoids redundant updates of distance labels. A shortest $v$--$w$ path, say $\langle v, r_{1} , r_{2} , \ldots , r_{k } = w \rangle$ with $k $ arcs ($k \geq 1$), is only then combined with an arc $(w,t) \in A$ to update the distance label of pair $v$--$t$, if $(w,t) $ is present on the shortest $r_{\ell } $--$ t$ path for each node $r_{\ell}$ $(\ell=k- 1 , k- 2, \ldots, 1) $. The algorithm extracts shortest paths in order of length from a data structure and builds two shortest path trees per node, an extra effort of $O(n^{2})$. This way it can execute efficiently only the aforementioned distance updates, by picking the arcs $(w,t)$ out of these trees. The time complexity order per distance update and path extraction is similar as in other algorithms. An implementation with a data structure of heaps is possible, but a bucket-type data structure may be more appropriate. The implied number of distance updates does not exceed $nm_{0}$ ($m_{0}$ being the total number of shortest path arcs), but is frequently much lower. In extreme cases the new algorithm applies $O(n^{2})$ distance updates, whereas known algorithms require $\Omega( n ^{3})$ updates. The algorithm is especially suited for undirected graphs; here the construction of one tree per node is sufficient and the computation times halve.     

Matching Polyhedral Terrains Using Overlays of Envelopes

For a collection $\F$ of $d$-variate piecewise linear functions of overall combinatorial complexity $n$, the lower envelope $\E(\F)$ of $\F$ is the pointwise minimum of these functions. The minimization diagram $\M(\F)$ is the subdivision of $\reals^d$ obtained by vertically (i.e., in direction $x_{d+1}$) projecting $\E(\F)$. The overlay $\O(\F,\G)$ of two such subdivisions $\M(\F)$ and $\M(\G)$ is their superposition. We extend and improve the analysis of de Berg et al. \cite{bgh-vdt3s-96} by showing that the combinatorial complexity of $\O(\F,\G)$ is $\Omega(n^d \alpha^{2}(n))$ and $O(n^{d+\eps})$ for any $\eps>0$ when $d \ge 2$, and $O(n^2 \alpha(n) \log n)$ when $d=2$. We also describe an algorithm that constructs $\O(\F,\G)$ in this time. We apply these results to obtain efficient general solutions to the problem of matching two polyhedral terrains in higher dimensions under translation. That is, given two piecewise linear terrains of combinatorial complexity $n$ in $\reals^{d+1}$, we wish to find a translation of the first terrain that minimizes its distance to the second, according to some distance measure. For the perpendicular distance measure, which we adopt from functional analysis since it is natural for measuring the similarity of terrains, we present a matching algorithm that runs in time $O(n^{2d+\eps})$ for any $\eps>0$. Sharper running time bounds are shown for $d \le 2$. For the directed and undirected \Hd\ distance measures, we present a matching algorithm that runs in time $O(n^{d^2+d+\eps})$ for any $\eps>0$.     

Fast Algorithms for Computing the Smallest k-Enclosing Circle

For a set $P$ of $n$ points in the plane and an integer $k \leq n$, consider the problem of finding the smallest circle enclosing at least $k$ points of $P$. We present a randomized algorithm that computes in $O( n k )$ expected time such a circle, improving over previously known algorithms. Further, we present a linear time $\delta$-approximation algorithm that outputs a circle that contains at least $k$ points of $P$ and has radius less than $(1+\delta)r_{opt}(P,k)$, where $r_{opt}(P,k)$ is the radius of the minimum circle containing at least $k$ points of $P$. The expected running time of this approximation algorithm is $O(n + n \cdot\min((1/k\delta^3) \log^2 (1/\delta), k))$.     

Rooted Maximum Agreement Supertrees

Given a set $\T$ of rooted, unordered trees, where each $T_i \in \T$ is distinctly leaf-labeled by a set $\Lambda(T_i)$ and where the sets $\Lambda(T_i)$ may overlap, the maximum agreement supertree problem~(MASP) is to construct a distinctly leaf-labeled tree $Q$ with leaf set $\Lambda(Q) \subseteq $\cup$_{T_i \in \T} \Lambda(T_i)$ such that $|\Lambda(Q)|$ is maximized and for each $T_i \in \T$, the topological restriction of $T_i$ to $\Lambda(Q)$ is isomorphic to the topological restriction of $Q$ to $\Lambda(T_i)$. Let $n = \left| $\cup$_{T_i \in \T} \Lambda(T_i)\right|$, $k = |\T|$, and $D = \max_{T_i \in \T}\{\deg(T_i)\}$. We first show that MASP with $k = 2$ can be solved in $O(\sqrt{D} n \log (2n/D))$ time, which is $O(n \log n)$ when $D = O(1)$ and $O(n^{1.5})$ when $D$ is unrestricted. We then present an algorithm for MASP with $D = 2$ whose running time is polynomial if $k = O(1)$. On the other hand, we prove that MASP is NP-hard for any fixed $k \geq 3$ when $D$ is unrestricted, and also NP-hard for any fixed $D \geq 2$ when $k$ is unrestricted even if each input tree is required to contain at most three leaves. Finally, we describe a polynomial-time $(n/\!\log n)$-approximation algorithm for MASP.     

Approximating Node Connectivity Problems via Set Covers

Given a graph (directed or undirected) with costs on the edges, and an integer $k$, we consider the problem of finding a $k$-node connected spanning subgraph of minimum cost. For the general instance of the problem (directed or undirected), there is a simple $2k$-approximation algorithm. Better algorithms are known for various ranges of $n,k$. For undirected graphs with metric costs Khuller and Raghavachari gave a $( 2+{2(k-1)}/{n})$-approximation algorithm. We obtain the following results: (i) For arbitrary costs, a $k$-approximation algorithm for undirected graphs and a $(k+1)$-approximation algorithm for directed graphs. (ii) For metric costs, a $(2+({k-1})/{n})$-approximation algorithm for undirected graphs and a $(2+{k}/{n})$-approximation algorithm for directed graphs. For undirected graphs and $k=6,7$, we further improve the approximation ratio from $k$ to $\lceil (k+1)/2 \rceil=4$; previously, $\lceil (k+1)/2 \rceil$-approximation algorithms were known only for $k \leq 5$. We also give a fast $3$-approximation algorithm for $k=4$. The multiroot problem generalizes the min-cost $k$-connected subgraph problem. In the multiroot problem, requirements $k_u$ for every node $u$ are given, and the aim is to find a minimum-cost subgraph that contains $\max\{k_u,k_v\}$ internally disjoint paths between every pair of nodes $u,v$. For the general instance of the problem, the best known algorithm has approximation ratio $2k$, where $k=\max k_u$. For metric costs there is a 3-approximation algorithm. We consider the case of metric costs, and, using our techniques, improve for $k \leq 7$ the approximation guarantee from $3$ to $2+{\lfloor (k-1)/2 \rfloor}/{k} < 2.5$.     

Subquadratic Algorithms for 3SUM

We obtain subquadratic algorithms for 3SUM on integers and rationals in several models. On a standard word RAM with w-bit words, we obtain a running time of . In the circuit RAM with one nonstandard AC ⁰ operation, we obtain . In external memory, we achieve O(n ²/(MB)), even under the standard assumption of data indivisibility. Cache-obliviously, we obtain a running time of . In all cases, our speedup is almost quadratic in the “parallelism” the model can afford, which may be the best possible. Our algorithms are Las Vegas randomized; time bounds hold in expectation, and in most cases, with high probability.     

Finding Pathway Structures in Protein Interaction Networks

The increased availability of data describing biological interactions provides important clues on how complex chains of genes and proteins interact with each other. Most previous approaches either restrict their attention to analyzing simple substructures such as paths or trees in these graphs, or use heuristics that do not provide performance guarantees when general substructures are analyzed. We investigate a formulation to model pathway structures directly and give a probabilistic algorithm to find an optimal path structure in time and space, where n and m are respectively the number of vertices and the number of edges in the given network, k is the number of vertices in the path structure, and t is the maximum number of vertices (i.e., "width") at each level of the structure. Even for the case t = 1 which corresponds to finding simple paths of length k, our time complexity is a significant improvement over previous probabilistic approaches. To allow for the analysis of multiple pathway structures, we further consider a variant of the algorithm that provides probabilistic guarantees for the top suboptimal path structures with a slight increase in time and space. We show that our algorithm can identify pathway structures with high sensitivity by applying it to protein interaction networks in the DIP database.     

A note on reverse scheduling with maximum lateness objective

The inverse and reverse counterparts of the single-machine scheduling problem $1||L_{\max }$ are studied in [2], in which the complexity classification is provided for various combinations of adjustable parameters (due dates and processing times) and for five different types of norm: $\ell _{1},\ell _{2},\ell _{\infty },\ell _{H}^{\Sigma } $ , and $\ell _{H}^{\max }$ . It appears that the $O(n^{2})$ -time algorithm for the reverse problem with adjustable due dates contains a flaw. In this note, we present the structural properties of the reverse model, establishing a link with the forward scheduling problem with due dates and deadlines. For the four norms $\ell _{1},\ell _{\infty },\ell _{H}^{\Sigma }$ , and $ \ell _{H}^{\max }$ , the complexity results are derived based on the properties of the corresponding forward problems, while the case of the norm $\ell _{2}$ is treated separately. As a by-product, we resolve an open question on the complexity of problem $1||\sum \alpha _{j}T_{j}^{2}$ .     

Approximation Algorithms for Quickest Spanning Tree Problems

Let $G=(V,E)$ be an undirected multigraph with a special vertex ${\it root} \in V$, and where each edge $e \in E$ is endowed with a length $l(e) \geq 0$ and a capacity $c(e) > 0$. For a path $P$ that connects $u$ and $v$, the {\it transmission time} of $P$ is defined as $t(P)=\mbox{\large$\Sigma$}_{e \in P} l(e) + \max_{e \in P}\!{(1 / c(e))}$. For a spanning tree $T$, let $P_{u,v}^T$ be the unique $u$--$v$ path in $T$. The {\sc quickest radius spanning tree problem} is to find a spanning tree $T$ of $G$ such that $\max _{v \in V} t(P^T_{root,v})$ is minimized. In this paper we present a 2-approximation algorithm for this problem, and show that unless $P =NP$, there is no approximation algorithm with a performance guarantee of $2 - \epsilon$ for any $\epsilon >0$. The {\sc quickest diameter spanning tree problem} is to find a spanning tree $T$ of $G$ such that $\max_{u,v \in V} t(P^T_{u,v})$ is minimized. We present a ${3 \over 2}$-approximation to this problem, and prove that unless $P=NP$ there is no approximation algorithm with a performance guarantee of ${3 \over 2}-\epsilon$ for any $\epsilon >0$.     

Approximation Algorithms for Quickest Spanning Tree Problems

Let $G=(V,E)$ be an undirected multigraph with a special vertex ${\it root} \in V$, and where each edge $e \in E$ is endowed with a length $l(e) \geq 0$ and a capacity $c(e) > 0$. For a path $P$ that connects $u$ and $v$, the {\it transmission time} of $P$ is defined as $t(P)=\mbox{\large$\Sigma$}_{e \in P} l(e) + \max_{e \in P}\!{(1 / c(e))}$. For a spanning tree $T$, let $P_{u,v}^T$ be the unique $u$--$v$ path in $T$. The {\sc quickest radius spanning tree problem} is to find a spanning tree $T$ of $G$ such that $\max _{v \in V} t(P^T_{root,v})$ is minimized. In this paper we present a 2-approximation algorithm for this problem, and show that unless $P =NP$, there is no approximation algorithm with a performance guarantee of $2 - \epsilon$ for any $\epsilon >0$. The {\sc quickest diameter spanning tree problem} is to find a spanning tree $T$ of $G$ such that $\max_{u,v \in V} t(P^T_{u,v})$ is minimized. We present a ${3 \over 2}$-approximation to this problem, and prove that unless $P=NP$ there is no approximation algorithm with a performance guarantee of ${3 \over 2}-\epsilon$ for any $\epsilon >0$.     

Approximating Rooted Connectivity Augmentation Problems

A graph is called {\em $\el$-connected from $U$ to $r$} if there are $\el$ internally disjoint paths from every node $u \in U$ to $r$. The {\em Rooted Subset Connectivity Augmentation Problem} ({\em RSCAP}) is as follows: given a graph $G=(V+r,E)$, a node subset $U \subseteq V$, and an integer $k$, find a smallest set $F$ of new edges such that $G+F$ is $k$-connected from $U$ to $r$. In this paper we consider mainly a restricted version of RSCAP in which the input graph $G$ is already $(k-1)$-connected from $U$ to $r$. For this version we give an $O(\ln\! |U|)$-approximation algorithm, and show that the problem cannot achieve a better approximation guarantee than the Set Cover Problem (SCP) on $|U|$ elements and with $|V|-|U|$ sets. For the general version of RSCAP we give an $O(\ln k \ln\!|U|)$-approximation algorithm. For $U=V$ we get the {\em Rooted Connectivity Augmentation Problem} ({\em RCAP}). For directed graphs RCAP is polynomially solvable, but for undirected graphs its complexity status is not known: no polynomial algorithm is known, and it is also not known to be NP-hard. For undirected graphs with the input graph $G$ being $(k-1)$-connected from $V$ to $r$, we give an algorithm that computes a solution of size at most ${\it opt}+\min\{opt,k\}/2$, where {\it opt} denotes the optimal solution size.     

Augmenting a (k - 1)-Vertex-Connected Multigraph ℓ-Edge-Connected and k-Vertex-Connected Multigraph

For two integers $k,\ell > 0$ and an undirected multigraph $G=(V,E)$, we consider the problem of augmenting $G$ by the smallest number of new edges to obtain an $\ell$-edge-connected and $k$-vertex-connected multigraph. In this paper we show that a $(k-1)$-vertex-connected multigraph $G$ can be made $\ell$-edge-connected and $k$-vertex-connected by adding at most $\bound$ surplus edges over the optimum in $O(\tm)$ time, where $n=|V|$.     

Theory Of A B-Spline Basis Function

This paper extends the work of a previous paper of the author. A theoretical argument is provided to justify the heuristic algorithm used in the former paper. On the basis of the theory one derives, the previous algorithm can be further simplified. In the simplified basis function algorithm, the regular basis function (where $N_i^1(t)$ is 1 for $t_i \le t \lt t_{i + 1}$ and zero elsewhere) can be used for all cases except the case of the last point of a clamped B-spline where the basis function is modified to $N_{i,1} (t)$ where is 1 for $t_i \le t \le t_{i + 1}$ and zero elsewhere. Under this simplified algorithm, the knots ( i.e. , $t_{0}$ , $t_{1}, \ldots, t_{n+k}$ ) are a k -extended partition in the interior of the knot vector with a possibility that two ends of the knot vector could be a $(k + 1)$ -extended partition (case of clamped B-spline). It is shown that given a set of $(n + 1)$ control points, $V_{0}$ , $V_{1}, \ldots, V_{n}$ , the order of k , and the knots $(t_{0}, t_{1}, \ldots, t_{n+k})$ , the B-spline $P(t) = \sum_{i = 0}^{n} N_{i}^{k}(t)V_{i}$ is a continuous function for $t \in [t_{k - 1}, t_{n + 1}]$ and maintains the partition of unity. This algorithm circumvents the problem of generating a spike at the last point of a clamped B-spline. The constraint of having k -extended partition interior knots overcomes the problem of disconnecting the B-spline at the k repeated knot.     

Efficient Algorithms for k Maximum Sums

We study the problem of computing the k maximum sum subsequences. Given a sequence of real numbers and an integer parameter k, the problem involves finding the k largest values of for The problem for fixed k = 1, also known as the maximum sum subsequence problem, has received much attention in the literature and is linear-time solvable. Recently, Bae and Takaoka presented a -time algorithm for the k maximum sum subsequences problem. In this paper we design an efficient algorithm that solves the above problem in time in the worst case. Our algorithm is optimal for and improves over the previously best known result for any value of the user-defined parameter k < 1. Moreover, our results are also extended to the multi-dimensional versions of the k maximum sum subsequences problem; resulting in fast algorithms as well.     

Sum Coloring of Bipartite Graphs with Bounded Degree

We consider the Chromatic Sum Problem on bipartite graphs which appears to be much harder than the classical Chromatic Number Problem. We prove that the Chromatic Sum Problem is NP-complete on planar bipartite graphs with $\Delta \leq 5$, but polynomial on bipartite graphs with $\Delta \leq 3$, for which we construct an $O(n^{2})$-time algorithm. Hence, we tighten the borderline of intractability for this problem on bipartite graphs with bounded degree, namely: the case $\Delta =3$ is easy, $% \Delta =5$ is hard. Moreover, we construct a $27/26$-approximation algorithm for this problem thus improving the best known approximation ratio of $10/9$.     

Polynomial-Time Algorithms for the Ordered Maximum Agreement Subtree Problem

For a set of rooted, unordered, distinctly leaf-labeled trees, the NP-hard maximum agreement subtree problem (MAST) asks for a tree contained (up to isomorphism or homeomorphism) in all of the input trees with as many labeled leaves as possible. We study the ordered variants of MAST where the trees are uniformly or non-uniformly ordered. We provide the first known polynomial-time algorithms for the uniformly and non-uniformly ordered homeomorphic variants as well as the uniformly and non-uniformly ordered isomorphic variants of MAST. Our algorithms run in time , , , and , respectively, where n is the number of leaf labels and k is the number of input trees.     

Deterministic Resource Discovery in Distributed Networks

The resource discovery problem was introduced by Harchol-Balter, Leighton, and Lewin. They developed a number of algorithms for the problem in the weakly connected directed graph model. This model is a directed logical graph that represents the vertices’ knowledge about the topology of the underlying communication network. The current paper proposes a deterministic algorithm for the problem in the same model, with improved time, message, and communication complexities. Each previous algorithm had a complexity that was higher at least in one of the measures. Specifically, previous deterministic solutions required either time linear in the diameter of the initial network, or communication complexity $O(n^3)$ (with message complexity $O(n^2)$), or message complexity $O(|E_0| \log n)$ (where $E_0$ is the arc set of the initial graph $G_0$). Compared with the main randomized algorithm of Harchol-Balter, Leighton, and Lewin, the time complexity is reduced from $O(\log^2n)$ to\pagebreak[4] $O(\log n )$, the message complexity from $O(n \log^2 n)$ to $O(n \log n )$, and the communication complexity from $O(n^2 \log^3 n)$ to $O(|E_0|\log ^2 n )$. \par Our work significantly extends the connectivity algorithm of Shiloach and Vishkin which was originally given for a parallel model of computation. Our result also confirms a conjecture of Harchol-Balter, Leighton, and Lewin, and addresses an open question due to Lipton.     

The Cache Complexity of Multithreaded Cache Oblivious Algorithms

We present a technique for analyzing the number of cache misses incurred by multithreaded cache oblivious algorithms on an idealized parallel machine in which each processor has a private cache. We specialize this technique to computations executed by the Cilk work-stealing scheduler on a machine with dag-consistent shared memory. We show that a multithreaded cache oblivious matrix multiplication incurs cache misses when executed by the Cilk scheduler on a machine with P processors, each with a cache of size Z, with high probability. This bound is tighter than previously published bounds. We also present a new multithreaded cache oblivious algorithm for 1D stencil computations incurring cache misses with high probability, one for Gaussian elimination and back substitution, and one for the length computation part of the longest common subsequence problem incurring cache misses with high probability. This work was supported in part by the Defense Advanced Research Projects Agency (DARPA) under contract No. NBCH30390004.     

Branching Time Logics \mathcal {BTL}^{\mathrm {U,S}}_{\mathrm {N},\mathrm {N}^{-1}}(\mathcal {Z})_{\alpha } with Operations Until and Since Based on Bundles of Integer Numbers, Logical Consecutions, Deciding Algorithms

This paper is intended as an attempt to describe logical consequence in branching time logics. We study temporal branching time logics $\mathcal {BTL}^{\mathrm {U,S}}_{\mathrm {N},\mathrm {N}^{-1}}(\mathcal {Z})_{\alpha }$ which use the standard operations Until and Next and dual operations Since and Previous (LTL, as standard, uses only Until and Next). Temporal logics $\mathcal {BTL}^{\mathrm {U,S}}_{\mathrm {N},\mathrm {N}^{-1}}(\mathcal {Z})_{\alpha }$ are generated by semantics based on Kripke/Hinttikka structures with linear frames of integer numbers $\mathcal {Z}$ with a single node (glued zeros). For $\mathcal {BTL}^{\mathrm {U,S}}_{\mathrm {N},\mathrm {N}^{-1}}(\mathcal {Z})_{\alpha }$ , the permissible branching of the node is limited by α (where 1≤α≤ω). We prove that any logic $\mathcal {BTL}^{\mathrm {U,S}}_{\mathrm {N},\mathrm {N}^{-1}}(\mathcal {Z})_{\alpha }$ is decidable w.r.t. admissible consecutions (inference rules), i.e. we find an algorithm recognizing consecutions admissible in $\mathcal {BTL}^{\mathrm {U,S}}_{\mathrm {N},\mathrm {N}^{-1}}(\mathcal {Z})_{\alpha }$ . As a consequence, it implies that $\mathcal {BTL}^{\mathrm {U,S}}_{\mathrm {N},\mathrm {N}^{-1}}(\mathcal {Z})_{\alpha }$ itself is decidable and solves the satisfiability problem.     

Finding Induced Paths of Given Parity in Claw-Free Graphs

The Parity Path problem is to decide if a given graph contains both an induced path of odd length and an induced path of even length between two specified vertices. In the related problems Odd Induced Path and Even Induced Path, the goal is to determine whether an induced path of odd, respectively even, length between two specified vertices exists. Although all three problems are NP-complete in general, we show that they can be solved in $\mathcal{O}(n^{5})$ time for the class of claw-free graphs. Two vertices s and t form an even pair in G if every induced path from s to t in G has even length. Our results imply that the problem of deciding if two specified vertices of a claw-free graph form an even pair, as well as the problem of deciding if a given claw-free graph has an even pair, can be solved in $\mathcal{O}(n^{5})$ time and $\mathcal{O}(n^{7})$ time, respectively. We also show that we can decide in $\mathcal{O}(n^{7})$ time whether a claw-free graph has an induced cycle of given parity through a specified vertex. Finally, we show that a shortest induced path of given parity between two specified vertices of a claw-free perfect graph can be found in $\mathcal {O}(n^{7})$ time.