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In this article we discuss a data structure, which combines advantages of two different ways for representing graphs: adjacency matrix and collection of adjacency lists. This data structure can fast add and search edges (advantages of adjacency matrix), use linear amount of memory, let to obtain adjacency list for certain vertex (advantages of collection of adjacency lists). Basic knowledge of linked lists and hash tables is required to understand this article. The article contains examples of implementation on Java. | Data structure for representing a graph: combination of linked list and
hash table | 4,300 |
The aim of power management policies is to reduce the amount of energy consumed by computer systems while maintaining satisfactory level of performance. One common method for saving energy is to simply suspend the system during the idle times. No energy is consumed in the suspend mode. However, the process of waking up the system itself requires a certain fixed amount of energy, and thus suspending the system is beneficial only if the idle time is long enough to compensate for this additional energy expenditure. In the specific problem studied in the paper, we have a set of jobs with release times and deadlines that need to be executed on a single processor. Preemptions are allowed. The processor requires energy L to be woken up and, when it is on, it uses one unit of energy per one unit of time. It has been an open problem whether a schedule minimizing the overall energy consumption can be computed in polynomial time. We solve this problem in positive, by providing an O(n^5)-time algorithm. In addition we provide an O(n^4)-time algorithm for computing the minimum energy schedule when all jobs have unit length. | Polynomial Time Algorithms for Minimum Energy Scheduling | 4,301 |
The main objective of this survey is to present the important theoretical and experimental results contributed till date in the area of online algorithms for the self organizing sequential search problem, also popularly known as the List Update Problem(LUP) in a chronological way. The survey includes competitiveness results of deterministic and randomized online algorithms and complexity results of optimal off line algorithms for the list update problem. We also present the results associated with list update with look ahead, list update with locality of reference and other variants of the list update problem. We investigate research issues, explore scope of future work associated with each issue so that future researchers can find it useful to work on. | Online Algorithms for Self-Organizing Sequential Search - A Survey | 4,302 |
We present an algorithm for the asymmetric traveling salesman problem on instances which satisfy the triangle inequality. Like several existing algorithms, it achieves approximation ratio O(log n). Unlike previous algorithms, it uses randomized rounding. | A Randomized Rounding Algorithm for the Asymmetric Traveling Salesman
Problem | 4,303 |
Suppose that a rooted tree T is given for preprocessing. The Level-Ancestor Problem is to answer quickly queries of the following form. Given a vertex v and an integer i > 0, find the i-th vertex on the path from the root to v. Algorithms that achieve a linear time bound for preprocessing and a constant time bound for a query have been published by Dietz (1991), Alstrup and Holm (2000), and Bender and Farach (2002). The first two algorithms address dynamic versions of the problem; the last addresses the static version only and is the simplest so far. The purpose of this note is to expose another simple algorithm, derived from a complicated PRAM algorithm by Berkman and Vishkin (1990,1994). We further show some easy extensions of its functionality, adding queries for descendants and level successors as well as ancestors, extensions for which the formerly known algorithms are less suitable. | The Euler Path to Static Level-Ancestors | 4,304 |
In this paper, we describe randomized Shellsort--a simple, randomized, data-oblivious version of the Shellsort algorithm that always runs in O(n log n) time and, as we show, succeeds in sorting any given input permutation with very high probability. Thus, randomized Shellsort is simultaneously simple, time-optimal, and data-oblivious. Taken together, these properties imply applications in the design of new efficient privacy-preserving computations based on the secure multi-party computation (SMC) paradigm. In addition, by a trivial conversion of this Monte Carlo algorithm to its Las Vegas equivalent, one gets the first version of Shellsort with a running time that is provably O(n log n) with very high probability. | Randomized Shellsort: A Simple Oblivious Sorting Algorithm | 4,305 |
This paper considers pairs of optimization problems that are defined from a single input and for which it is desired to find a good approximation to either one of the problems. In many instances, it is possible to efficiently find an approximation of this type that is better than known inapproximability lower bounds for either of the two individual optimization problems forming the pair. In particular, we find either a $(1+\epsilon)$-approximation to $(1,2)$-TSP or a $1/\epsilon$-approximation to maximum independent set, from a given graph, in linear time. We show a similar paired approximation result for finding either a coloring or a long path. However, no such tradeoff exists in some other cases: for set cover and hitting set problems defined from a single set family, and for clique and independent set problems on the same graph, it is not possible to find an approximation when both problems are combined that is better than the best approximation for either problem on its own. | Paired approximation problems and incompatible inapproximabilities | 4,306 |
Deletion from open-address hash table is not so easy as deletion from chained hash table, because in open-address table we can't simply mark a slot containing deleted key as empty. Search for keys may become incorrect. The classical method to implement deletion is to mark slots in hash table by three values: "free", "busy", "deleted". That method is easy to implement, but there are some disadvantages. In this article we consider alternative method of deletion keys, where we avoid using the mark "deleted". The article contains the implementation of the method in Java. | Simple implementation of deletion from open-address hash table | 4,307 |
Perhaps the two most significant theoretical questions about the programming of self-assembling agents are: (1) necessary and sufficient conditions to produce a unique terminal assembly, and (2) error correction. We address both questions, by reducing two well-studied models of tile assembly to models of distributed shared memory (DSM), in order to obtain results from the memory consistency systems induced by tile assembly systems when simulated in the DSM setting. The Abstract Tile Assembly Model (aTAM) can be simulated by a DSM system that obeys causal consistency, and the locally deterministic tile assembly systems in the aTAM correspond exactly to the concurrent-write free programs that simulate tile assembly in such a model. Thus, the detection of the failure of local determinism (which had formerly been an open problem) reduces to the detection of data races in simulating programs. Further, the Kinetic Tile Assembly Model can be simulated by a DSM system that obeys GWO, a memory consistency condition defined by Steinke and Nutt. (To our knowledge, this is the first natural example of a DSM system that obeys GWO, but no stronger consistency condition.) We combine these results with the observation that self-assembly algorithms are local algorithms, and there exists a fast conversion of deterministic local algorithms into deterministic self-stabilizing algorithms. This provides an "immediate" generalization of a theorem by Soloveichik et al. about the existence of tile assembly systems that simultaneously perform two forms of self-stabilization: proofreading and self-healing. Our reductions and proof techniques can be extended to the programming of self-assembling agents in a variety of media, not just DNA tiles, and not just two-dimensional surfaces. | Memory Consistency Conditions for Self-Assembly Programming | 4,308 |
We study the recently introduced Connected Feedback Vertex Set (CFVS) problem from the view-point of parameterized algorithms. CFVS is the connected variant of the classical Feedback Vertex Set problem and is defined as follows: given a graph G=(V,E) and an integer k, decide whether there exists a subset F of V, of size at most k, such that G[V F] is a forest and G[F] is connected. We show that Connected Feedback Vertex Set can be solved in time $O(2^{O(k)}n^{O(1)})$ on general graphs and in time $O(2^{O(\sqrt{k}\log k)}n^{O(1)})$ on graphs excluding a fixed graph H as a minor. Our result on general undirected graphs uses as subroutine, a parameterized algorithm for Group Steiner Tree, a well studied variant of Steiner Tree. We find the algorithm for Group Steiner Tree of independent interest and believe that it will be useful for obtaining parameterized algorithms for other connectivity problems. | FPT Algorithms for Connected Feedback Vertex Set | 4,309 |
We consider algorithms to schedule packets with values and deadlines in a size-bounded buffer. At any time, the buffer can store at most B packets. Packets arrive over time. Each packet has a non-negative value and an integer deadline. In each time step, at most one packet can be sent. Packets can be dropped at any time before they are sent. The objective is to maximize the total value gained by delivering packets no later than their respective deadlines. This model generalizes the well-studied bounded-delay model (Hajek. CISS 2001. Kesselman et al. STOC 2001). We first provide an optimal offline algorithm for this model. Then we present an alternative proof of the 2-competitive deterministic online algorithm (Fung. arXiv July 2009). We also prove that the lower bound of competitive ratio of a family of (deterministic and randomized) algorithms is 2 - 1 / B. | Packet Scheduling in a Size-Bounded Buffer | 4,310 |
We construct efficient data structures that are resilient against a constant fraction of adversarial noise. Our model requires that the decoder answers most queries correctly with high probability and for the remaining queries, the decoder with high probability either answers correctly or declares "don't know." Furthermore, if there is no noise on the data structure, it answers all queries correctly with high probability. Our model is the common generalization of a model proposed recently by de Wolf and the notion of "relaxed locally decodable codes" developed in the PCP literature. We measure the efficiency of a data structure in terms of its length, measured by the number of bits in its representation, and query-answering time, measured by the number of bit-probes to the (possibly corrupted) representation. In this work, we study two data structure problems: membership and polynomial evaluation. We show that these two problems have constructions that are simultaneously efficient and error-correcting. | Efficient and Error-Correcting Data Structures for Membership and
Polynomial Evaluation | 4,311 |
The lower and the upper irredundance numbers of a graph $G$, denoted $ir(G)$ and $IR(G)$ respectively, are conceptually linked to domination and independence numbers and have numerous relations to other graph parameters. It is a long-standing open question whether determining these numbers for a graph $G$ on $n$ vertices admits exact algorithms running in time less than the trivial $\Omega(2^n)$ enumeration barrier. We solve these open problems by devising parameterized algorithms for the dual of the natural parameterizations of the problems with running times faster than $O^*(4^{k})$. For example, we present an algorithm running in time $O^*(3.069^{k})$ for determining whether $IR(G)$ is at least $n-k$. Although the corresponding problem has been known to be in FPT by kernelization techniques, this paper offers the first parameterized algorithms with an exponential dependency on the parameter in the running time. Additionally, our work also appears to be the first example of a parameterized approach leading to a solution to a problem in exponential time algorithmics where the natural interpretation as an exact exponential-time algorithm fails. | Breaking the 2^n-Barrier for Irredundance: A Parameterized Route to
Solving Exact Puzzles | 4,312 |
In this paper we describe algorithms for computing the BWT and for building (compressed) indexes in external memory. The innovative feature of our algorithms is that they are lightweight in the sense that, for an input of size $n$, they use only ${n}$ bits of disk working space while all previous approaches use $\Th{n \log n}$ bits of disk working space. Moreover, our algorithms access disk data only via sequential scans, thus they take full advantage of modern disk features that make sequential disk accesses much faster than random accesses. We also present a scan-based algorithm for inverting the BWT that uses $\Th{n}$ bits of working space, and a lightweight {\em internal-memory} algorithm for computing the BWT which is the fastest in the literature when the available working space is $\os{n}$ bits. Finally, we prove {\em lower} bounds on the complexity of computing and inverting the BWT via sequential scans in terms of the classic product: internal-memory space $\times$ number of passes over the disk data. | Lightweight Data Indexing and Compression in External Memory | 4,313 |
We study the computability and complexity of the exploration problem in a class of highly dynamic graphs: periodically varying (PV) graphs, where the edges exist only at some (unknown) times defined by the periodic movements of carriers. These graphs naturally model highly dynamic infrastructure-less networks such as public transports with fixed timetables, low earth orbiting (LEO) satellite systems, security guards' tours, etc. We establish necessary conditions for the problem to be solved. We also derive lower bounds on the amount of time required in general, as well as for the PV graphs defined by restricted classes of carriers movements: simple routes, and circular routes. We then prove that the limitations on computability and complexity we have established are indeed tight. In fact we prove that all necessary conditions are also sufficient and all lower bounds on costs are tight. We do so constructively presenting two worst case optimal solution algorithms, one for anonymous systems, and one for those with distinct nodes ids. An added benefit is that the algorithms are rather simple. | Exploration of Periodically Varying Graphs | 4,314 |
We study the non-overlapping indexing problem: Given a text T, preprocess it so that you can answer queries of the form: given a pattern P, report the maximal set of non-overlapping occurrences of P in T. A generalization of this problem is the range non-overlapping indexing where in addition we are given two indexes i,j to report the maximal set of non-overlapping occurrences between these two indexes. We suggest new solutions for these problems. For the non-overlapping problem our solution uses O(n) space with query time of O(m + occ_{NO}). For the range non-overlapping problem we propose a solution with O(n\log^\epsilon n) space for some 0<\epsilon<1 and O(m + \log\log n + occ_{ij,NO}) query time. | Range Non-Overlapping Indexing | 4,315 |
Tensors naturally model many real world processes which generate multi-aspect data. Such processes appear in many different research disciplines, e.g, chemometrics, computer vision, psychometrics and neuroimaging analysis. Tensor decompositions such as the Tucker decomposition are used to analyze multi-aspect data and extract latent factors, which capture the multilinear data structure. Such decompositions are powerful mining tools, for extracting patterns from large data volumes. However, most frequently used algorithms for such decompositions involve the computationally expensive Singular Value Decomposition. In this paper we propose MACH, a new sampling algorithm to compute such decompositions. Our method is of significant practical value for tensor streams, such as environmental monitoring systems, IP traffic matrices over time, where large amounts of data are accumulated and the analysis is computationally intensive but also in "post-mortem" data analysis cases where the tensor does not fit in the available memory. We provide the theoretical analysis of our proposed method, and verify its efficacy in monitoring system applications. | MACH: Fast Randomized Tensor Decompositions | 4,316 |
In this paper we present a new problem, the fast set intersection problem, which is to preprocess a collection of sets in order to efficiently report the intersection of any two sets in the collection. In addition we suggest new solutions for the two-dimensional substring indexing problem and the document listing problem for two patterns by reduction to the fast set intersection problem. | Fast Set Intersection and Two Patterns Matching | 4,317 |
Potential maximal cliques and minimal separators are combinatorial objects which were introduced and studied in the realm of minimal triangulations problems including Minimum Fill-in and Treewidth. We discover unexpected applications of these notions to the field of moderate exponential algorithms. In particular, we show that given an n-vertex graph G together with its set of potential maximal cliques Pi_G, and an integer t, it is possible in time |Pi_G| * n^(O(t)) to find a maximum induced subgraph of treewidth t in G; and for a given graph F of treewidth t, to decide if G contains an induced subgraph isomorphic to F. Combined with an improved algorithm enumerating all potential maximal cliques in time O(1.734601^n), this yields that both problems are solvable in time 1.734601^n * n^(O(t)). | Finding Induced Subgraphs via Minimal Triangulations | 4,318 |
Given a k-uniform hypergraph on n vertices, partitioned in k equal parts such that every hyperedge includes one vertex from each part, the k-dimensional matching problem asks whether there is a disjoint collection of the hyperedges which covers all vertices. We show it can be solved by a randomized polynomial space algorithm in time O*(2^(n(k-2)/k)). The O*() notation hides factors polynomial in n and k. When we drop the partition constraint and permit arbitrary hyperedges of cardinality k, we obtain the exact cover by k-sets problem. We show it can be solved by a randomized polynomial space algorithm in time O*(c_k^n), where c_3=1.496, c_4=1.642, c_5=1.721, and provide a general bound for larger k. Both results substantially improve on the previous best algorithms for these problems, especially for small k, and follow from the new observation that Lovasz' perfect matching detection via determinants (1979) admits an embedding in the recently proposed inclusion-exclusion counting scheme for set covers, despite its inability to count the perfect matchings. | Exact Covers via Determinants | 4,319 |
Trevisan [SICOMP 2012] presented an algorithm for Max-Cut based on spectral partitioning techniques. This is the first algorithm for Max-Cut with an approximation guarantee strictly larger than 1/2 that is not based on semidefinite programming. Trevisan showed that its approximation ratio is of at least 0.531. In this paper we improve this bound up to 0.614247. We also define and extend this result for the more general Maximum Colored Cut problem. | Improved Analysis of a Max Cut Algorithm Based on Spectral Partitioning | 4,320 |
We consider the problem of exploring an anonymous unoriented ring of size $n$ by $k$ identical, oblivious, asynchronous mobile robots, that are unable to communicate, yet have the ability to sense their environment and take decisions based on their local view. Previous works in this weak scenario prove that $k$ must not divide $n$ for a deterministic solution to exist. Also, it is known that the minimum number of robots (either deterministic or probabilistic) to explore a ring of size $n$ is 4. An upper bound of 17 robots holds in the deterministic case while 4 probabilistic robots are sufficient. In this paper, we close the complexity gap in the deterministic setting, by proving that no deterministic exploration is feasible with less than five robots whenever the size of the ring is even, and that five robots are sufficient for any $n$ that is coprime with five. Our protocol completes exploration in O(n) robot moves, which is also optimal. | Optimal deterministic ring exploration with oblivious asynchronous
robots | 4,321 |
A generalized algorithm for multiplication is proposed through recursive application of the Nikhilam Sutra from Vedic Mathematics, operating in radix - 2 number system environment suitable for digital platforms. Statistical analysis has been carried out based on the number of recursions profile as a function of the smaller multiplicand. The proposed algorithm is efficient for smaller multiplicands as well, unlike most of the asymptotically fast algorithms. Further, a basic block schematic of Hardware Implementation of our algorithm is suggested to exploit parallelism and speed up the implementation of the algorithm in a multiprocessor environment. | A Generalized Recursive Algorithm for Binary Multiplication based on
Vedic Mathematics | 4,322 |
We prove that longest common prefix (LCP) information can be stored in much less space than previously known. More precisely, we show that in the presence of the text and the suffix array, o(n) additional bits are sufficient to answer LCP-queries asymptotically in the same time that is needed to retrieve an entry from the suffix array. This yields the smallest compressed suffix tree with sub-logarithmic navigation time. | Wee LCP | 4,323 |
We consider the problem of testing distribution identity. Given a sequence of independent samples from an unknown distribution on a domain of size n, the goal is to check if the unknown distribution approximately equals a known distribution on the same domain. While Batu, Fortnow, Fischer, Kumar, Rubinfeld, and White (FOCS 2001) proved that the sample complexity of the problem is O~(sqrt(n) * poly(1/epsilon)), the running time of their tester is much higher: O(n) + O~(sqrt(n) * poly(1/epsilon)). We modify their tester to achieve a running time of O~(sqrt(n) * poly(1/epsilon)). | Testing Distribution Identity Efficiently | 4,324 |
Given an arbitrary bitstream, we consider the problem of finding the longest substring whose ratio of ones to zeroes equals a given value. The central result of this paper is an algorithm that solves this problem in linear time. The method involves (i) reformulating the problem as a constrained walk through a sparse matrix, and then (ii) developing a data structure for this sparse matrix that allows us to perform each step of the walk in amortised constant time. We also give a linear time algorithm to find the longest substring whose ratio of ones to zeroes is bounded below by a given value. Both problems have practical relevance to cryptography and bioinformatics. | Searching a bitstream in linear time for the longest substring of any
given density | 4,325 |
We consider a variant of bin packing called multiple-choice vector bin packing. In this problem we are given a set of items, where each item can be selected in one of several $D$-dimensional incarnations. We are also given $T$ bin types, each with its own cost and $D$-dimensional size. Our goal is to pack the items in a set of bins of minimum overall cost. The problem is motivated by scheduling in networks with guaranteed quality of service (QoS), but due to its general formulation it has many other applications as well. We present an approximation algorithm that is guaranteed to produce a solution whose cost is about $\ln D$ times the optimum. For the running time to be polynomial we require $D=O(1)$ and $T=O(\log n)$. This extends previous results for vector bin packing, in which each item has a single incarnation and there is only one bin type. To obtain our result we also present a PTAS for the multiple-choice version of multidimensional knapsack, where we are given only one bin and the goal is to pack a maximum weight set of (incarnations of) items in that bin. | Vector Bin Packing with Multiple-Choice | 4,326 |
This paper deals with the multiobjective version of the optimal spanning tree problem. More precisely, we are interested in determining the optimal spanning tree according to an Ordered Weighted Average (OWA) of its objective values. We first show that the problem is weakly NP-hard. In the case where the weights of the OWA are strictly decreasing, we then propose a mixed integer programming formulation, and provide dedicated optimality conditions yielding an important reduction of the size of the program. Next, we present two bounds that can be used to prune subspaces of solutions either in a shaving phase or in a branch and bound procedure. The validity of these bounds does not depend on specific properties of the weights (apart from non-negativity). All these exact resolution algorithms are compared on the basis of numerical experiments, according to their respective validity scopes. | Exact algorithms for OWA-optimization in multiobjective spanning tree
problems | 4,327 |
In most of the shortest path problems like vehicle routing problems and network routing problems, we only need an efficient path between two points source and destination, and it is not necessary to calculate the shortest path from source to all other nodes. This paper concentrates on this very idea and presents an algorithm for calculating shortest path for (i) nonnegative weighted undirected graphs (ii) unweighted undirected graphs. The algorithm completes its execution in O(E) for all graphs except few in which longer path (in terms of number of edges) from source to some node makes it best selection for that node. The main advantage of the algorithms is its simplicity and it does not need complex data structures for implementations. | A O(E) Time Shortest Path Algorithm For Non Negative Weighted Undirected
Graphs | 4,328 |
This paper proposes a new view to algorithms, Algorithms as defining dynamic systems. This view extends the traditional, deterministic view that an algorithm is a step by step procedure with nondeterminism. As a dynamic system can be designed by a set of its defining laws, it is also desirable to design an algorithm by a (possibly nondeterministic) set of defining laws. This observation requires some changes to algorithm development. We propose a two step approach, the first step is to design an algorithm via a set of defining laws of dynamic system. The second step is to translate these laws (written in a natural language) into a formal language such as linear logic. | Algorithm as Defining Dynamic Systems | 4,329 |
An arc-annotated string is a string of characters, called bases, augmented with a set of pairs, called arcs, each connecting two bases. Given arc-annotated strings $P$ and $Q$ the arc-preserving subsequence problem is to determine if $P$ can be obtained from $Q$ by deleting bases from $Q$. Whenever a base is deleted any arc with an endpoint in that base is also deleted. Arc-annotated strings where the arcs are ``nested'' are a natural model of RNA molecules that captures both the primary and secondary structure of these. The arc-preserving subsequence problem for nested arc-annotated strings is basic primitive for investigating the function of RNA molecules. Gramm et al. [ACM Trans. Algorithms 2006] gave an algorithm for this problem using $O(nm)$ time and space, where $m$ and $n$ are the lengths of $P$ and $Q$, respectively. In this paper we present a new algorithm using $O(nm)$ time and $O(n + m)$ space, thereby matching the previous time bound while significantly reducing the space from a quadratic term to linear. This is essential to process large RNA molecules where the space is likely to be a bottleneck. To obtain our result we introduce several novel ideas which may be of independent interest for related problems on arc-annotated strings. | Fast Arc-Annotated Subsequence Matching in Linear Space | 4,330 |
In this paper we propose and study a new complexity model for approximation algorithms. The main motivation are practical problems over large data sets that need to be solved many times for different scenarios, e.g., many multicast trees that need to be constructed for different groups of users. In our model we allow a preprocessing phase, when some information of the input graph $G=(V,E)$ is stored in a limited size data structure. Next, the data structure enables processing queries of the form ``solve problem A for an input $S\subseteq V$''. We consider problems like {\sc Steiner Forest}, {\sc Facility Location}, {\sc $k$-Median}, {\sc $k$-Center} and {\sc TSP} in the case when the graph induces a doubling metric. Our main results are data structures of near-linear size that are able to answer queries in time close to linear in $|S|$. This improves over typical worst case reuniting time of approximation algorithms in the classical setting which is $\Omega(|E|)$ independently of the query size. In most cases, our approximation guarantees are arbitrarily close to those in the classical setting. Additionally, we present the first fully dynamic algorithm for the Steiner tree problem. | Fast Approximation in Subspaces by Doubling Metric Decomposition | 4,331 |
Genome-wide association studies generate very large datasets that require scalable analysis algorithms. In this report we describe the GEDI software package, which implements efficient algorithms for performing several common tasks in the analysis of population genotype data, including genotype error detection and correction, imputation of both randomly missing and untyped genotypes, and genotype phasing. Experimental results show that GEDI achieves high accuracy with a runtime scaling linearly with the number of markers and samples. The open source C++ code of GEDI, released under the GNU General Public License, is available for download at http://dna.engr.uconn.edu/software/GEDI/ | GEDI: Scalable Algorithms for Genotype Error Detection and Imputation | 4,332 |
The Pattern self-Assembly Tile set Synthesis (PATS) problem is to determine a set of coloured tiles that self-assemble to implement a given rectangular colour pattern. We give an exhaustive branch-and-bound algorithm to find tile sets of minimum cardinality for the PATS problem. Our algorithm makes use of a search tree in the lattice of partitions of the ambient rectangular grid, and an efficient bounding function to prune this search tree. Empirical data on the performance of the algorithm shows that it compares favourably to previously presented heuristic solutions to the problem. | Synthesizing Minimal Tile Sets for Patterned DNA Self-Assembly | 4,333 |
Kosaraju in ``Computation of squares in a string'' briefly described a linear-time algorithm for computing the minimal squares starting at each position in a word. Using the same construction of suffix trees, we generalize his result and describe in detail how to compute in O(k|w|)-time the minimal k-th power, with period of length larger than s, starting at each position in a word w for arbitrary exponent $k\geq2$ and integer $s\geq0$. We provide the complete proof of correctness of the algorithm, which is somehow not completely clear in Kosaraju's original paper. The algorithm can be used as a sub-routine to detect certain types of pseudo-patterns in words, which is our original intention to study the generalization. | A Minimal Periods Algorithm with Applications | 4,334 |
This paper discusses a new family of bounds for use in similarity search, related to those used in metric indexing, but based on Ptolemy's inequality, rather than the metric axioms. Ptolemy's inequality holds for the well-known Euclidean distance, but is also shown here to hold for quadratic form metrics in general, with Mahalanobis distance as an important special case. The inequality is examined empirically on both synthetic and real-world data sets and is also found to hold approximately, with a very low degree of error, for important distances such as the angular pseudometric and several Lp norms. Indexing experiments demonstrate a highly increased filtering power compared to existing, triangular methods. It is also shown that combining the Ptolemaic and triangular filtering can lead to better results than using either approach on its own. | Ptolemaic Indexing | 4,335 |
We consider the Degree-Bounded Survivable Network Design Problem: the objective is to find a minimum cost subgraph satisfying the given connectivity requirements as well as the degree bounds on the vertices. If we denote the upper bound on the degree of a vertex v by b(v), then we present an algorithm that finds a solution whose cost is at most twice the cost of the optimal solution while the degree of a degree constrained vertex v is at most 2b(v) + 2. This improves upon the results of Lau and Singh and that of Lau, Naor, Salavatipour and Singh. | Improved Algorithm for Degree Bounded Survivable Network Design Problem | 4,336 |
We present a data structure that stores a sequence $s[1..n]$ over alphabet $[1..\sigma]$ in $n\Ho(s) + o(n)(\Ho(s){+}1)$ bits, where $\Ho(s)$ is the zero-order entropy of $s$. This structure supports the queries \access, \rank\ and \select, which are fundamental building blocks for many other compressed data structures, in worst-case time $\Oh{\lg\lg\sigma}$ and average time $\Oh{\lg \Ho(s)}$. The worst-case complexity matches the best previous results, yet these had been achieved with data structures using $n\Ho(s)+o(n\lg\sigma)$ bits. On highly compressible sequences the $o(n\lg\sigma)$ bits of the redundancy may be significant compared to the the $n\Ho(s)$ bits that encode the data. Our representation, instead, compresses the redundancy as well. Moreover, our average-case complexity is unprecedented. Our technique is based on partitioning the alphabet into characters of similar frequency. The subsequence corresponding to each group can then be encoded using fast uncompressed representations without harming the overall compression ratios, even in the redundancy. The result also improves upon the best current compressed representations of several other data structures. For example, we achieve $(i)$ compressed redundancy, retaining the best time complexities, for the smallest existing full-text self-indexes; $(ii)$ compressed permutations $\pi$ with times for $\pi()$ and $\pii()$ improved to loglogarithmic; and $(iii)$ the first compressed representation of dynamic collections of disjoint sets. We also point out various applications to inverted indexes, suffix arrays, binary relations, and data compressors. ... | Efficient Fully-Compressed Sequence Representations | 4,337 |
The {\em longest common subsequence (LCS)} problem is a classic and well-studied problem in computer science. LCS is a central problem in stringology and finds broad applications in text compression, error-detecting codes and biological sequence comparison. However, in numerous contexts, words represent cyclic sequences of symbols and LCS must be generalized to consider all circular shifts of the strings. This occurs especially in computational biology when genetic material is sequenced form circular DNA or RNA molecules. This initiates the problem of {\em longest common cyclic subsequence (LCCS)} which finds the longest subsequence between all circular shifts of two strings. In this paper, we give an $O(n^2)$ algorithm for solving LCCS problem where $n$ is the number of symbols in the strings. | An $O(n^2)$ Algorithm for Computing Longest Common Cyclic Subsequence | 4,338 |
We give the first polynomial-time approximation scheme (PTAS) for the Steiner forest problem on planar graphs and, more generally, on graphs of bounded genus. As a first step, we show how to build a Steiner forest spanner for such graphs. The crux of the process is a clustering procedure called prize-collecting clustering that breaks down the input instance into separate subinstances which are easier to handle; moreover, the terminals in different subinstances are far from each other. Each subinstance has a relatively inexpensive Steiner tree connecting all its terminals, and the subinstances can be solved (almost) separately. Another building block is a PTAS for Steiner forest on graphs of bounded treewidth. Surprisingly, Steiner forest is NP-hard even on graphs of treewidth 3. Therefore, our PTAS for bounded treewidth graph needs a nontrivial combination of approximation arguments and dynamic programming on the tree decomposition. We further show that Steiner forest can be solved in polynomial time for series-parallel graphs (graphs of treewidth at most two) by a novel combination of dynamic programming and minimum cut computations, completing our thorough complexity study of Steiner forest in the range of bounded treewidth graphs, planar graphs, and bounded genus graphs. | Approximation Schemes for Steiner Forest on Planar Graphs and Graphs of
Bounded Treewidth | 4,339 |
We settle the question of tight thresholds for offline cuckoo hashing. The problem can be stated as follows: we have n keys to be hashed into m buckets each capable of holding a single key. Each key has k >= 3 (distinct) associated buckets chosen uniformly at random and independently of the choices of other keys. A hash table can be constructed successfully if each key can be placed into one of its buckets. We seek thresholds alpha_k such that, as n goes to infinity, if n/m <= alpha for some alpha < alpha_k then a hash table can be constructed successfully with high probability, and if n/m >= alpha for some alpha > alpha_k a hash table cannot be constructed successfully with high probability. Here we are considering the offline version of the problem, where all keys and hash values are given, so the problem is equivalent to previous models of multiple-choice hashing. We find the thresholds for all values of k > 2 by showing that they are in fact the same as the previously known thresholds for the random k-XORSAT problem. We then extend these results to the setting where keys can have differing number of choices, and provide evidence in the form of an algorithm for a conjecture extending this result to cuckoo hash tables that store multiple keys in a bucket. | Tight Thresholds for Cuckoo Hashing via XORSAT | 4,340 |
Submodularity is a fundamental phenomenon in combinatorial optimization. Submodular functions occur in a variety of combinatorial settings such as coverage problems, cut problems, welfare maximization, and many more. Therefore, a lot of work has been concerned with maximizing or minimizing a submodular function, often subject to combinatorial constraints. Many of these algorithmic results exhibit a common structure. Namely, the function is extended to a continuous, usually non-linear, function on a convex domain. Then, this relaxation is solved, and the fractional solution rounded to yield an integral solution. Often, the continuous extension has a natural interpretation in terms of distributions on subsets of the ground set. This interpretation is often crucial to the results and their analysis. The purpose of this survey is to highlight this connection between extensions, distributions, relaxations, and optimization in the context of submodular functions. We also present the first constant factor approximation algorithm for minimizing symmetric submodular functions subject to a cardinality constraint. | Submodular Functions: Extensions, Distributions, and Algorithms. A
Survey | 4,341 |
The second eigenvalue of the Laplacian matrix and its associated eigenvector are fundamental features of an undirected graph, and as such they have found widespread use in scientific computing, machine learning, and data analysis. In many applications, however, graphs that arise have several \emph{local} regions of interest, and the second eigenvector will typically fail to provide information fine-tuned to each local region. In this paper, we introduce a locally-biased analogue of the second eigenvector, and we demonstrate its usefulness at highlighting local properties of data graphs in a semi-supervised manner. To do so, we first view the second eigenvector as the solution to a constrained optimization problem, and we incorporate the local information as an additional constraint; we then characterize the optimal solution to this new problem and show that it can be interpreted as a generalization of a Personalized PageRank vector; and finally, as a consequence, we show that the solution can be computed in nearly-linear time. In addition, we show that this locally-biased vector can be used to compute an approximation to the best partition \emph{near} an input seed set in a manner analogous to the way in which the second eigenvector of the Laplacian can be used to obtain an approximation to the best partition in the entire input graph. Such a primitive is useful for identifying and refining clusters locally, as it allows us to focus on a local region of interest in a semi-supervised manner. Finally, we provide a detailed empirical evaluation of our method by showing how it can applied to finding locally-biased sparse cuts around an input vertex seed set in social and information networks. | A Local Spectral Method for Graphs: with Applications to Improving Graph
Partitions and Exploring Data Graphs Locally | 4,342 |
We show that, given a string $s$ of length $n$, with constant memory and logarithmic passes over a constant number of streams we can build a context-free grammar that generates $s$ and only $s$ and whose size is within an $\Oh{\min (g \log g, \sqrt{n \log g})}$-factor of the minimum $g$. This stands in contrast to our previous result that, with polylogarithmic memory and polylogarithmic passes over a single stream, we cannot build such a grammar whose size is within any polynomial of $g$. | Grammar-Based Compression in a Streaming Model | 4,343 |
It has been shown by Alon et al. that the so-called 'all-pairs shortest-path' problem can be solved in O((MV)^2.688 * log^3(V)) for graphs with V vertices, with integer distances bounded by M. We solve the more general problem for graphs in R (assuming no negative cycles), with expected-case running time O(V^2.5 * log(V)). While our result appears to violate the Omega(V^3) requirement of "Funny Matrix Multiplication" (due to Kerr), we find that it has a sub-cubic expected time solution subject to reasonable conditions on the data distribution. The expected time solution arises when certain sub-problems are uncorrelated, though we can do better/worse than the expected-case under positive/negative correlation (respectively). Whether we observe positive/negative correlation depends on the statistics of the graph in question. In practice, our algorithm is significantly faster than Floyd-Warshall, even for dense graphs. | An expected-case sub-cubic solution to the all-pairs shortest path
problem in R | 4,344 |
The general problem of robust optimization is this: one of several possible scenarios will appear tomorrow, but things are more expensive tomorrow than they are today. What should you anticipatorily buy today, so that the worst-case cost (summed over both days) is minimized? Feige et al. and Khandekar et al. considered the k-robust model where the possible outcomes tomorrow are given by all demand-subsets of size k, and gave algorithms for the set cover problem, and the Steiner tree and facility location problems in this model, respectively. In this paper, we give the following simple and intuitive template for k-robust problems: "having built some anticipatory solution, if there exists a single demand whose augmentation cost is larger than some threshold, augment the anticipatory solution to cover this demand as well, and repeat". In this paper we show that this template gives us improved approximation algorithms for k-robust Steiner tree and set cover, and the first approximation algorithms for k-robust Steiner forest, minimum-cut and multicut. All our approximation ratios (except for multicut) are almost best possible. As a by-product of our techniques, we also get algorithms for max-min problems of the form: "given a covering problem instance, which k of the elements are costliest to cover?". | Thresholded Covering Algorithms for Robust and Max-Min Optimization | 4,345 |
In this paper, we consider Steiner forest and its generalizations, prize-collecting Steiner forest and k-Steiner forest, when the vertices of the input graph are points in the Euclidean plane and the lengths are Euclidean distances. First, we present a simpler analysis of the polynomial-time approximation scheme (PTAS) of Borradaile et al. [12] for the Euclidean Steiner forest problem. This is done by proving a new structural property and modifying the dynamic programming by adding a new piece of information to each dynamic programming state. Next we develop a PTAS for a well-motivated case, i.e., the multiplicative case, of prize-collecting and budgeted Steiner forest. The ideas used in the algorithm may have applications in design of a broad class of bicriteria PTASs. At the end, we demonstrate why PTASs for these problems can be hard in the general Euclidean case (and thus for PTASs we cannot go beyond the multiplicative case). | Euclidean Prize-collecting Steiner Forest | 4,346 |
This paper presents a means with time complexity of at worst O(n^3) to compute the discrete logarithm on cyclic finite groups of integers modulo p. The algorithm makes use of reduction of the problem to that of finding the concurrent zeros of two periodic functions in the real numbers. The problem is treated as an analog to a form of analog rotor-code computed cipher. | Computing a Discrete Logarithm in O(n^3) | 4,347 |
In this paper, I proposed to utilize partial-order alignment technique as a heuristic method to cope with the state-space explosion problem in progressive near-optimal alignment. The key idea of my approach is a formal treatment of progressive partial order alignment based on the graph product construction. | Combining Partial Order Alignment and Progressive Near-Optimal Alignment | 4,348 |
In the uncapacitated facility location problem, given a graph, a set of demands and opening costs, it is required to find a set of facilities R, so as to minimize the sum of the cost of opening the facilities in R and the cost of assigning all node demands to open facilities. This paper concerns the robust fault-tolerant version of the uncapacitated facility location problem (RFTFL). In this problem, one or more facilities might fail, and each demand should be supplied by the closest open facility that did not fail. It is required to find a set of facilities R, so as to minimize the sum of the cost of opening the facilities in R and the cost of assigning all node demands to open facilities that did not fail, after the failure of up to \alpha facilities. We present a polynomial time algorithm that yields a 6.5-approximation for this problem with at most one failure and a 1.5 + 7.5\alpha-approximation for the problem with at most \alpha > 1 failures. We also show that the RFTFL problem is NP-hard even on trees, and even in the case of a single failure. | Robust Fault Tolerant uncapacitated facility location | 4,349 |
Multiplicative inverse is a crucial operation in public key cryptography, and been widely used in cryptography. Public key cryptography has given rise to such a need, in which we need to generate a related public and private pair of numbers, each of which is the inverse of the other. The basic method to find multiplicative inverses is Extended-Euclidean method. In this paper we will propose a new algorithm for computing the inverse, based on continues subtract fraction from integer and divide by fraction to obtain integer that will be used to compute the inverse d. The authors claim that the proposed method more efficient and faster than the existed methods. | Fast Fraction-Integer Method for Computing Multiplicative Inverse | 4,350 |
The past decade has witnessed many interesting algorithms for maintaining statistics over a data stream. This paper initiates a theoretical study of algorithms for monitoring distributed data streams over a time-based sliding window (which contains a variable number of items and possibly out-of-order items). The concern is how to minimize the communication between individual streams and the root, while allowing the root, at any time, to be able to report the global statistics of all streams within a given error bound. This paper presents communication-efficient algorithms for three classical statistics, namely, basic counting, frequent items and quantiles. The worst-case communication cost over a window is $O(\frac{k} {\epsilon} \log \frac{\epsilon N}{k})$ bits for basic counting and $O(\frac{k}{\epsilon} \log \frac{N}{k})$ words for the remainings, where $k$ is the number of distributed data streams, $N$ is the total number of items in the streams that arrive or expire in the window, and $\epsilon < 1$ is the desired error bound. Matching and nearly matching lower bounds are also obtained. | Continuous Monitoring of Distributed Data Streams over a Time-based
Sliding Window | 4,351 |
In this paper, we propose a framework to solve a demand-supply optimization problem of long-term water resource allocation on a multi-connection reservoir network which, in two aspects, is different to the problem considered in previous works. First, while all previous works consider a problem where each reservoir can transfer water to only one fixed reservoir, we consider a multi-connection network being constructed in Thailand in which each reservoir can transfer water to many reservoirs in one period of time. Second, a demand-supply plan considered here is static, in contrast to a dynamic policy considered in previous works. Moreover, in order to efficiently develop a long-term static plan, a severe loss (a risk) is taken into account, i.e. a risk occurs if the real amount of water stored in each reservoir in each time period is less than what planned by the optimizer. The multi-connection function and the risk make the problem rather complex such that traditional stochastic dynamic programming and deterministic/heuristic approaches are inappropriate. Our framework is based on a novel convex programming formulation in which stochastic information can be naturally taken into account and an optimal solution is guaranteed to be found efficiently. Extensive experimental results show promising results of the framework. | Demand-Supply Optimization with Risk Management for a Multi-Connection
Water Reservoir Network | 4,352 |
The performance of a dynamic dictionary is measured mainly by its update time, lookup time, and space consumption. In terms of update time and lookup time there are known constructions that guarantee constant-time operations in the worst case with high probability, and in terms of space consumption there are known constructions that use essentially optimal space. However, although the first analysis of a dynamic dictionary dates back more than 45 years ago (when Knuth analyzed linear probing in 1963), the trade-off between these aspects of performance is still not completely understood. In this paper we settle two fundamental open problems: - We construct the first dynamic dictionary that enjoys the best of both worlds: it stores n elements using (1+epsilon)n memory words, and guarantees constant-time operations in the worst case with high probability. Specifically, for any epsilon = \Omega((\log\log n / \log n)^{1/2} ) and for any sequence of polynomially many operations, with high probability over the randomness of the initialization phase, all operations are performed in constant time which is independent of epsilon. The construction is a two-level variant of cuckoo hashing, augmented with a "backyard" that handles a large fraction of the elements, together with a de-amortized perfect hashing scheme for eliminating the dependency on epsilon. - We present a variant of the above construction that uses only (1+o(1))B bits, where B is the information-theoretic lower bound for representing a set of size n taken from a universe of size u, and guarantees constant-time operations in the worst case with high probability, as before. This problem was open even in the amortized setting. One of the main ingredients of our construction is a permutation-based variant of cuckoo hashing, which significantly improves the space consumption of cuckoo hashing when dealing with a rather small universe. | Backyard Cuckoo Hashing: Constant Worst-Case Operations with a Succinct
Representation | 4,353 |
We develop a variable depth search heuristic for the quadratic assignment problem. The heuristic is based on sequential changes in assignments analogous to the Lin-Kernighan sequential edge moves for the traveling salesman problem. We treat unstructured problem instances of sizes 60 to 400. When the heuristic is used in conjunction with robust tabu search, we measure performance improvements of up to a factor of 15 compared to the use of robust tabu alone. The performance improvement increases as the problem size increases. | A Variable Depth Sequential Search Heuristic for the Quadratic
Assignment Problem | 4,354 |
A mobile robot represented by a point moving in the plane has to explore an unknown terrain with obstacles. Both the terrain and the obstacles are modeled as arbitrary polygons. We consider two scenarios: the unlimited vision, when the robot situated at a point p of the terrain explores (sees) all points q of the terrain for which the segment pq belongs to the terrain, and the limited vision, when we require additionally that the distance between p and q be at most 1. All points of the terrain (except obstacles) have to be explored and the performance of an exploration algorithm is measured by the length of the trajectory of the robot. For unlimited vision we show an exploration algorithm with complexity O(P + D?k), where P is the total perimeter of the terrain (including perimeters of obstacles), D is the diameter of the convex hull of the terrain, and k is the number of obstacles. We do not assume knowledge of these parameters. We also prove a matching lower bound showing that the above complexity is optimal, even if the terrain is known to the robot. For limited vision we show exploration algorithms with complexity O(P + A + ?Ak), where A is the area of the terrain (excluding obstacles). Our algorithms work either for arbitrary terrains, if one of the parameters A or k is known, or for c-fat terrains, where c is any constant (unknown to the robot) and no additional knowledge is assumed. (A terrain T with obstacles is c-fat if R/r ? c, where R is the radius of the smallest disc containing T and r is the radius of the largest disc contained in T .) We also prove a matching lower bound ?(P + A + ?Ak) on the complexity of exploration for limited vision, even if the terrain is known to the robot. | Optimal Exploration of Terrains with Obstacles | 4,355 |
Let $G=(V,E)$ be any undirected graph on $V$ vertices and $E$ edges. A path $\textbf{P}$ between any two vertices $u,v\in V$ is said to be $t$-approximate shortest path if its length is at most $t$ times the length of the shortest path between $u$ and $v$. We consider the problem of building a compact data structure for a given graph $G$ which is capable of answering the following query for any $u,v,z\in V$ and $t>1$: Report $t$-approximate shortest path between $u$ and $v$ when vertex $z$ fails We present data structures for the single source as well all-pairs versions of this problem. Our data structures guarantee optimal query time. Most impressive feature of our data structures is that their size {\em nearly} match the size of their best static counterparts. | Approximate Shortest Paths Avoiding a Failed Vertex: Optimal Size Data
Structures for Unweighted Graph | 4,356 |
We study the online clustering problem where data items arrive in an online fashion. The algorithm maintains a clustering of data items into similarity classes. Upon arrival of v, the relation between v and previously arrived items is revealed, so that for each u we are told whether v is similar to u. The algorithm can create a new cluster for v and merge existing clusters. When the objective is to minimize disagreements between the clustering and the input, we prove that a natural greedy algorithm is O(n)-competitive, and this is optimal. When the objective is to maximize agreements between the clustering and the input, we prove that the greedy algorithm is .5-competitive; that no online algorithm can be better than .834-competitive; we prove that it is possible to get better than 1/2, by exhibiting a randomized algorithm with competitive ratio .5+c for a small positive fixed constant c. | Online Correlation Clustering | 4,357 |
Grammar based compression, where one replaces a long string by a small context-free grammar that generates the string, is a simple and powerful paradigm that captures many popular compression schemes. In this paper, we present a novel grammar representation that allows efficient random access to any character or substring without decompressing the string. Let $S$ be a string of length $N$ compressed into a context-free grammar $\mathcal{S}$ of size $n$. We present two representations of $\mathcal{S}$ achieving $O(\log N)$ random access time, and either $O(n\cdot \alpha_k(n))$ construction time and space on the pointer machine model, or $O(n)$ construction time and space on the RAM. Here, $\alpha_k(n)$ is the inverse of the $k^{th}$ row of Ackermann's function. Our representations also efficiently support decompression of any substring in $S$: we can decompress any substring of length $m$ in the same complexity as a single random access query and additional $O(m)$ time. Combining these results with fast algorithms for uncompressed approximate string matching leads to several efficient algorithms for approximate string matching on grammar-compressed strings without decompression. For instance, we can find all approximate occurrences of a pattern $P$ with at most $k$ errors in time $O(n(\min\{|P|k, k^4 + |P|\} + \log N) + occ)$, where $occ$ is the number of occurrences of $P$ in $S$. Finally, we generalize our results to navigation and other operations on grammar-compressed ordered trees. All of the above bounds significantly improve the currently best known results. To achieve these bounds, we introduce several new techniques and data structures of independent interest, including a predecessor data structure, two "biased" weighted ancestor data structures, and a compact representation of heavy paths in grammars. | Random Access to Grammar Compressed Strings | 4,358 |
Genealogical information is the best histories resources for culture study and cultural heritage. The genealogical research generally presents family information and depict tree diagram. This paper presents Parent Bidirectional Breadth Algorithm (PBBA) to find consanguine relationship between two persons. In addition, the paper utilizes rules based system in order to identify consanguine relationship. The study reveals that PBBA is fast to solve the genealogical information search problem and the Rule Based Relationship provides more benefits in blood relationship identification. | Genealogical Information Search by Using Parent Bidirectional Breadth
Algorithm and Rule Based Relationship | 4,359 |
When augmented with the longest common prefix (LCP) array and some other structures, the suffix array can solve many string processing problems in optimal time and space. A compressed representation of the LCP array is also one of the main building blocks in many compressed suffix tree proposals. In this paper, we describe a new compressed LCP representation: the sampled LCP array. We show that when used with a compressed suffix array (CSA), the sampled LCP array often offers better time/space trade-offs than the existing alternatives. We also show how to construct the compressed representations of the LCP array directly from a CSA. | Sampled Longest Common Prefix Array | 4,360 |
The problem of dictionary matching is a classical problem in string matching: given a set S of d strings of total length n characters over an (not necessarily constant) alphabet of size sigma, build a data structure so that we can match in a any text T all occurrences of strings belonging to S. The classical solution for this problem is the Aho-Corasick automaton which finds all occ occurrences in a text T in time O(|T| + occ) using a data structure that occupies O(m log m) bits of space where m <= n + 1 is the number of states in the automaton. In this paper we show that the Aho-Corasick automaton can be represented in just m(log sigma + O(1)) + O(d log(n/d)) bits of space while still maintaining the ability to answer to queries in O(|T| + occ) time. To the best of our knowledge, the currently fastest succinct data structure for the dictionary matching problem uses space O(n log sigma) while answering queries in O(|T|log log n + occ) time. In this paper we also show how the space occupancy can be reduced to m(H0 + O(1)) + O(d log(n/d)) where H0 is the empirical entropy of the characters appearing in the trie representation of the set S, provided that sigma < m^epsilon for any constant 0 < epsilon < 1. The query time remains unchanged. | Succinct Dictionary Matching With No Slowdown | 4,361 |
In the Densest k-Subgraph problem, given a graph G and a parameter k, one needs to find a subgraph of G induced on k vertices that contains the largest number of edges. There is a significant gap between the best known upper and lower bounds for this problem. It is NP-hard, and does not have a PTAS unless NP has subexponential time algorithms. On the other hand, the current best known algorithm of Feige, Kortsarz and Peleg, gives an approximation ratio of n^(1/3-epsilon) for some specific epsilon > 0 (estimated at around 1/60). We present an algorithm that for every epsilon > 0 approximates the Densest k-Subgraph problem within a ratio of n^(1/4+epsilon) in time n^O(1/epsilon). In particular, our algorithm achieves an approximation ratio of O(n^1/4) in time n^O(log n). Our algorithm is inspired by studying an average-case version of the problem where the goal is to distinguish random graphs from graphs with planted dense subgraphs. The approximation ratio we achieve for the general case matches the distinguishing ratio we obtain for this planted problem. At a high level, our algorithms involve cleverly counting appropriately defined trees of constant size in G, and using these counts to identify the vertices of the dense subgraph. Our algorithm is based on the following principle. We say that a graph G(V,E) has log-density alpha if its average degree is Theta(|V|^alpha). The algorithmic core of our result is a family of algorithms that output k-subgraphs of nontrivial density whenever the log-density of the densest k-subgraph is larger than the log-density of the host graph. | Detecting High Log-Densities -- an O(n^1/4) Approximation for Densest
k-Subgraph | 4,362 |
In this paper we consider the mutual exclusion problem on a multiple access channel. Mutual exclusion is one of the fundamental problems in distributed computing. In the classic version of this problem, n processes perform a concurrent program which occasionally triggers some of them to use shared resources, such as memory, communication channel, device, etc. The goal is to design a distributed algorithm to control entries and exits to/from the shared resource in such a way that in any time there is at most one process accessing it. We consider both the classic and a slightly weaker version of mutual exclusion, called ep-mutual-exclusion, where for each period of a process staying in the critical section the probability that there is some other process in the critical section is at most ep. We show that there are channel settings, where the classic mutual exclusion is not feasible even for randomized algorithms, while ep-mutual-exclusion is. In more relaxed channel settings, we prove an exponential gap between the makespan complexity of the classic mutual exclusion problem and its weaker ep-exclusion version. We also show how to guarantee fairness of mutual exclusion algorithms, i.e., that each process that wants to enter the critical section will eventually succeed. | Dynamic sharing of a multiple access channel | 4,363 |
Geometric programming problem is a powerful tool for solving some special type non-linear programming problems. It has a wide range of applications in optimization and engineering for solving some complex optimization problems. Many applications of geometric programming are on engineering design problems where parameters are estimated using geometric programming. When the parameters in the problems are imprecise, the calculated objective value should be imprecise as well. In this paper we have developed a method to solve geometric programming problems where the exponent of the variables in the objective function, cost coefficients and right hand side are multiple parameters. The equivalent mathematical programming problems are formulated to find their corresponding value of the objective function based on the duality theorem. By applying a variable separable technique the multi-choice mathematical programming problem is transformed into multiple one level geometric programming problem which produces multiple objective values that helps engineers to handle more realistic engineering design problems. | Posynomial Geometric Programming Problems with Multiple Parameters | 4,364 |
We study recursive algorithm for computing DCT of lengths $N=q 2^m$ ($m,q \in \mathbb{N}$, $q$ is odd) due to C.W.Kok. We show that this algorithm has the same multiplicative complexity as theoretically achievable by the prime factor decomposition, when $m \leqslant 2$. We also show that C.W.Kok's factorization allows a simple conversion to a scaled form. We analyze complexity of such a scaled factorization, and show that for some lengths it achieves lower multiplicative complexity than one of known prime factor-based scaled transforms. | On Fast Algorithm for Computing Even-Length DCT | 4,365 |
We study the complexity of the popular one player combinatorial game known as Flood-It. In this game the player is given an n by n board of tiles where each tile is allocated one of c colours. The goal is to make the colours of all tiles equal via the shortest possible sequence of flooding operations. In the standard version, a flooding operation consists of the player choosing a colour k, which then changes the colour of all the tiles in the monochromatic region connected to the top left tile to k. After this operation has been performed, neighbouring regions which are already of the chosen colour k will then also become connected, thereby extending the monochromatic region of the board. We show that finding the minimum number of flooding operations is NP-hard for c>=3 and that this even holds when the player can perform flooding operations from any position on the board. However, we show that this "free" variant is in P for c=2. We also prove that for an unbounded number of colours, Flood-It remains NP-hard for boards of height at least 3, but is in P for boards of height 2. Next we show how a c-1 approximation and a randomised 2c/3 approximation algorithm can be derived, and that no polynomial time constant factor, independent of c, approximation algorithm exists unless P=NP. We then investigate how many moves are required for the "most demanding" n by n boards (those requiring the most moves) and show that the number grows as fast as Theta(n*c^0.5). Finally, we consider boards where the colours of the tiles are chosen at random and show that for c>=2, the number of moves required to flood the whole board is Omega(n) with high probability. | The Complexity of Flood Filling Games | 4,366 |
Inspired by online ad allocation, we study online stochastic packing linear programs from theoretical and practical standpoints. We first present a near-optimal online algorithm for a general class of packing linear programs which model various online resource allocation problems including online variants of routing, ad allocations, generalized assignment, and combinatorial auctions. As our main theoretical result, we prove that a simple primal-dual training-based algorithm achieves a (1 - o(1))-approximation guarantee in the random order stochastic model. This is a significant improvement over logarithmic or constant-factor approximations for the adversarial variants of the same problems (e.g. factor 1 - 1/e for online ad allocation, and \log m for online routing). We then focus on the online display ad allocation problem and study the efficiency and fairness of various training-based and online allocation algorithms on data sets collected from real-life display ad allocation system. Our experimental evaluation confirms the effectiveness of training-based primal-dual algorithms on real data sets, and also indicate an intrinsic trade-off between fairness and efficiency. | Online Stochastic Packing Applied to Display Ad Allocation | 4,367 |
This paper addresses the uniform random generation of words from a context-free language (over an alphabet of size $k$), while constraining every letter to a targeted frequency of occurrence. Our approach consists in a multidimensional extension of Boltzmann samplers \cite{Duchon2004}. We show that, under mostly \emph{strong-connectivity} hypotheses, our samplers return a word of size in $[(1-\varepsilon)n, (1+\varepsilon)n]$ and exact frequency in $\mathcal{O}(n^{1+k/2})$ expected time. Moreover, if we accept tolerance intervals of width in $\Omega(\sqrt{n})$ for the number of occurrences of each letters, our samplers perform an approximate-size generation of words in expected $\mathcal{O}(n)$ time. We illustrate these techniques on the generation of Tetris tessellations with uniform statistics in the different types of tetraminoes. | Multi-dimensional Boltzmann Sampling of Languages | 4,368 |
We develop, analyze and experiment with a new tool, called MADMX, which extracts frequent motifs, possibly including don't care characters, from biological sequences. We introduce density, a simple and flexible measure for bounding the number of don't cares in a motif, defined as the ratio of solid (i.e., different from don't care) characters to the total length of the motif. By extracting only maximal dense motifs, MADMX reduces the output size and improves performance, while enhancing the quality of the discoveries. The efficiency of our approach relies on a newly defined combining operation, dubbed fusion, which allows for the construction of maximal dense motifs in a bottom-up fashion, while avoiding the generation of nonmaximal ones. We provide experimental evidence of the efficiency and the quality of the motifs returned by MADMX | MADMX: A Novel Strategy for Maximal Dense Motif Extraction | 4,369 |
We present a new heuristic point-to-point routing algorithm based on contraction hierarchies (CH). Given an epsilon >= 0, we can prove that the length of the path computed by our algorithm is at most (1+epsilon) times the length of the optimal (shortest) path. CH is based on node contraction: removing nodes from a network and adding shortcut edges to preserve shortest path distances. Our algorithm tries to avoid shortcuts even when a replacement path is epsilon times longer. | Heuristic Contraction Hierarchies with Approximation Guarantee | 4,370 |
We address in this paper a new computational biology problem that aims at understanding a mechanism that could potentially be used to genetically manipulate natural insect populations infected by inherited, intra-cellular parasitic bacteria. In this problem, that we denote by \textsc{Mod/Resc Parsimony Inference}, we are given a boolean matrix and the goal is to find two other boolean matrices with a minimum number of columns such that an appropriately defined operation on these matrices gives back the input. We show that this is formally equivalent to the \textsc{Bipartite Biclique Edge Cover} problem and derive some complexity results for our problem using this equivalence. We provide a new, fixed-parameter tractability approach for solving both that slightly improves upon a previously published algorithm for the \textsc{Bipartite Biclique Edge Cover}. Finally, we present experimental results where we applied some of our techniques to a real-life data set. | Mod/Resc Parsimony Inference | 4,371 |
A natural way to deal with multiple, partially conflicting objectives is turning all the objectives but one into budget constraints. Some classical polynomial-time optimization problems, such as spanning tree and forest, shortest path, (perfect) matching, independent set (basis) in a matroid or in the intersection of two matroids, become NP-hard even with one budget constraint. Still, for most of these problems deterministic and randomized polynomial-time approximation schemes are known. In the case of two or more budgets, typically only multi-criteria approximation schemes are available, which return slightly infeasible solutions. Not much is known however for the case of strict budget constraints: filling this gap is the main goal of this paper. We show that shortest path, perfect matching, and spanning tree (and hence matroid basis and matroid intersection basis) are inapproximable already with two budget constraints. For the remaining problems, whose set of solutions forms an independence system, we present deterministic and randomized polynomial-time approximation schemes for a constant number k of budget constraints. Our results are based on a variety of techniques: 1. We present a simple and powerful mechanism to transform multi-criteria approximation schemes into pure approximation schemes. 2. We show that points in low dimensional faces of any matroid polytope are almost integral, an interesting result on its own. This gives a deterministic approximation scheme for k-budgeted matroid independent set. 3. We present a deterministic approximation scheme for 2-budgeted matching. The backbone of this result is a purely topological property of curves in R^2. | Optimization with More than One Budget | 4,372 |
Non-dominated Sorting Genetic Algorithm (NSGA) has established itself as a benchmark algorithm for Multiobjective Optimization. The determination of pareto-optimal solutions is the key to its success. However the basic algorithm suffers from a high order of complexity, which renders it less useful for practical applications. Among the variants of NSGA, several attempts have been made to reduce the complexity. Though successful in reducing the runtime complexity, there is scope for further improvements, especially considering that the populations involved are frequently of large size. We propose a variant which reduces the run-time complexity using the simple principle of space-time trade-off. The improved algorithm is applied to the problem of classifying types of leukemia based on microarray data. Results of comparative tests are presented showing that the improved algorithm performs well on large populations. | Improved NSGA-II Based on a Novel Ranking Scheme | 4,373 |
Given a metric space $(X,d_X)$, the earth mover distance between two distributions over $X$ is defined as the minimum cost of a bipartite matching between the two distributions. The doubling dimension of a metric $(X, d_X)$ is the smallest value $\alpha$ such that every ball in $X$ can be covered by $2^\alpha$ ball of half the radius. We study efficient algorithms for approximating earth mover distance over metrics with bounded doubling dimension. Given a metric $(X, d_X)$, with $|X| = n$, we can use $\tilde O(n^2)$ preprocessing time to create a data structure of size $\tilde O(n^{1 + \e})$, such that subsequently queried EMDs can be $O(\alpha_X/\e)$-approximated in $\tilde O(n)$ time. We also show a weaker form of sketching scheme, which we call "encoding scheme". Given $(X, d_X)$, by using $\tilde O(n^2)$ preprocessing time, every subsequent distribution $\mu$ over $X$ can be encoded into $F(\mu)$ in $\tilde O(n^{1 + \e})$ time. Given $F(\mu)$ and $F(\nu)$, the EMD between $\mu$ and $\nu$ can be $O(\alpha_X/\e)$-approximated in $\tilde O(n^\e)$ time. | On constant factor approximation for earth mover distance over doubling
metrics | 4,374 |
Every human likes choices. But today's fast route planning algorithms usually compute just a single route between source and target. There are beginnings to compute alternative routes, but this topic has not been studied thoroughly. Often, the aspect of meaningful alternative routes is neglected from a human point of view. We fill in this gap by suggesting mathematical definitions for such routes. As a second contribution we propose heuristics to compute them, as this is NP-hard in general. | Defining and Computing Alternative Routes in Road Networks | 4,375 |
We consider the following sample selection problem. We observe in an online fashion a sequence of samples, each endowed by a quality. Our goal is to either select or reject each sample, so as to maximize the aggregate quality of the subsample selected so far. There is a natural trade-off here between the rate of selection and the aggregate quality of the subsample. We show that for a number of such problems extremely simple and oblivious "threshold rules" for selection achieve optimal tradeoffs between rate of selection and aggregate quality in a probabilistic sense. In some cases we show that the same threshold rule is optimal for a large class of quality distributions and is thus oblivious in a strong sense. | Threshold rules for online sample selection | 4,376 |
We present the zipper tree, an $O(\log \log n)$-competitive online binary search tree that performs each access in $O(\log n)$ worst-case time. This shows that for binary search trees, optimal worst-case access time and near-optimal amortized access time can be guaranteed simultaneously. | An O(loglog n)-Competitive Binary Search Tree with Optimal Worst-Case
Access Times | 4,377 |
We consider the problem of constructing optimal decision trees: given a collection of tests which can disambiguate between a set of $m$ possible diseases, each test having a cost, and the a-priori likelihood of the patient having any particular disease, what is a good adaptive strategy to perform these tests to minimize the expected cost to identify the disease? We settle the approximability of this problem by giving a tight $O(\log m)$-approximation algorithm. We also consider a more substantial generalization, the Adaptive TSP problem. Given an underlying metric space, a random subset $S$ of cities is drawn from a known distribution, but $S$ is initially unknown to us--we get information about whether any city is in $S$ only when we visit the city in question. What is a good adaptive way of visiting all the cities in the random subset $S$ while minimizing the expected distance traveled? For this problem, we give the first poly-logarithmic approximation, and show that this algorithm is best possible unless we can improve the approximation guarantees for the well-known group Steiner tree problem. | Approximation Algorithms for Optimal Decision Trees and Adaptive TSP
Problems | 4,378 |
We investigate a special case of the Induced Subgraph Isomorphism problem, where both input graphs are interval graphs. We show the NP-hardness of this problem, and we prove fixed-parameter tractability of the problem with non-standard parameterization, where the parameter is the difference |V(G)|-|V(H)|, with G and H being the larger and the smaller input graph, respectively. Intuitively, we can interpret this problem as "cleaning" the graph G, regarded as a pattern containing extra vertices indicating errors, in order to obtain the graph H representing the original pattern. We also prove W[1]-hardness for the standard parameterization where the parameter is |V(H)|. | Cleaning Interval Graphs | 4,379 |
In a column-restricted covering integer program (CCIP), all the non-zero entries of any column of the constraint matrix are equal. Such programs capture capacitated versions of covering problems. In this paper, we study the approximability of CCIPs, in particular, their relation to the integrality gaps of the underlying 0,1-CIP. If the underlying 0,1-CIP has an integrality gap O(gamma), and assuming that the integrality gap of the priority version of the 0,1-CIP is O(omega), we give a factor O(gamma + omega) approximation algorithm for the CCIP. Priority versions of 0,1-CIPs (PCIPs) naturally capture quality of service type constraints in a covering problem. We investigate priority versions of the line (PLC) and the (rooted) tree cover (PTC) problems. Apart from being natural objects to study, these problems fall in a class of fundamental geometric covering problems. We bound the integrality of certain classes of this PCIP by a constant. Algorithmically, we give a polytime exact algorithm for PLC, show that the PTC problem is APX-hard, and give a factor 2-approximation algorithm for it. | On Column-restricted and Priority Covering Integer Programs | 4,380 |
We present an algorithm that on input of an $n$-vertex $m$-edge weighted graph $G$ and a value $k$, produces an {\em incremental sparsifier} $\hat{G}$ with $n-1 + m/k$ edges, such that the condition number of $G$ with $\hat{G}$ is bounded above by $\tilde{O}(k\log^2 n)$, with probability $1-p$. The algorithm runs in time $$\tilde{O}((m \log{n} + n\log^2{n})\log(1/p)).$$ As a result, we obtain an algorithm that on input of an $n\times n$ symmetric diagonally dominant matrix $A$ with $m$ non-zero entries and a vector $b$, computes a vector ${x}$ satisfying $||{x}-A^{+}b||_A<\epsilon ||A^{+}b||_A $, in expected time $$\tilde{O}(m\log^2{n}\log(1/\epsilon)).$$ The solver is based on repeated applications of the incremental sparsifier that produces a chain of graphs which is then used as input to a recursive preconditioned Chebyshev iteration. | Approaching optimality for solving SDD systems | 4,381 |
Iterative rounding and relaxation have arguably become the method of choice in dealing with unconstrained and constrained network design problems. In this paper we extend the scope of the iterative relaxation method in two directions: (1) by handling more complex degree constraints in the minimum spanning tree problem (namely, laminar crossing spanning tree), and (2) by incorporating `degree bounds' in other combinatorial optimization problems such as matroid intersection and lattice polyhedra. We give new or improved approximation algorithms, hardness results, and integrality gaps for these problems. | On Generalizations of Network Design Problems with Degree Bounds | 4,382 |
We study policy iteration for infinite-horizon Markov decision processes. It has recently been shown policy iteration style algorithms have exponential lower bounds in a two player game setting. We extend these lower bounds to Markov decision processes with the total reward and average-reward optimality criteria. | Exponential Lower Bounds For Policy Iteration | 4,383 |
Memetic Algorithms are known to be a powerful technique in solving hard optimization problems. To design a memetic algorithm one needs to make a host of decisions; selecting a population size is one of the most important among them. Most algorithms in the literature fix the population size to a certain constant value. This reduces the algorithm's quality since the optimal population size varies for different instances, local search procedures and running times. In this paper we propose an adjustable population size. It is calculated as a function of the running time of the whole algorithm and the average running time of the local search for the given instance. Note that in many applications the running time of a heuristic should be limited and therefore we use this limit as a parameter of the algorithm. The average running time of the local search procedure is obtained during the algorithm's run. Some coefficients which are independent with respect to the instance or the local search are to be tuned before the algorithm run; we provide a procedure to find these coefficients. The proposed approach was used to develop a memetic algorithm for the Multidimensional Assignment Problem (MAP or s-AP in the case of s dimensions) which is an extension of the well-known assignment problem. MAP is NP-hard and has a host of applications. We show that using adjustable population size makes the algorithm flexible to perform well for instances of very different sizes and types and for different running times and local searches. This allows us to select the most efficient local search for every instance type. The results of computational experiments for several instance families and sizes prove that the proposed algorithm performs efficiently for a wide range of the running times and clearly outperforms the state-of-the art 3-AP memetic algorithm being given the same time. | A New Approach to Population Sizing for Memetic Algorithms: A Case Study
for the Multidimensional Assignment Problem | 4,384 |
I will present a way to implement graph algorithms which is different from traditional methods. This work was motivated by the belief that some ideas from software engineering should be applied to graph algorithms. Re-usability of software is an important and difficult problem in general, and this is particularly true for graph algorithms. The scientific literature demonstrates plenty of applications of graph algorithms as subroutines for other algorithms. Moreover, many practical problems from various domains may be modeled as graph problems and hence solved by means of graph algorithms. Chapter 2 introduces some data structures that will be used in 5 basic graph algorithms in chapter 3. Chapter 4 discusses an implementation of a maximum cardinality matching algorithm for general graphs. Chapter 5 explains some techniques in C++, which are useful to implement the data structures and algorithms in an efficient way. Finally chapter 6 contains some concluding remarks. | Graph Iterators: Decoupling Graph Structures from Algorithms | 4,385 |
The Lin-Kernighan heuristic is known to be one of the most successful heuristics for the Traveling Salesman Problem (TSP). It has also proven its efficiency in application to some other problems. In this paper we discuss possible adaptations of TSP heuristics for the Generalized Traveling Salesman Problem (GTSP) and focus on the case of the Lin-Kernighan algorithm. At first, we provide an easy-to-understand description of the original Lin-Kernighan heuristic. Then we propose several adaptations, both trivial and complicated. Finally, we conduct a fair competition between all the variations of the Lin-Kernighan adaptation and some other GTSP heuristics. It appears that our adaptation of the Lin-Kernighan algorithm for the GTSP reproduces the success of the original heuristic. Different variations of our adaptation outperform all other heuristics in a wide range of trade-offs between solution quality and running time, making Lin-Kernighan the state-of-the-art GTSP local search. | Lin-Kernighan Heuristic Adaptations for the Generalized Traveling
Salesman Problem | 4,386 |
We propose an extension of tree-based space-partitioning indexing structures for data with low intrinsic dimensionality embedded in a high dimensional space. We call this extension an Angle Tree. Our extension can be applied to both classical kd-trees as well as the more recent rp-trees. The key idea of our approach is to store the angle (the "dihedral angle") between the data region (which is a low dimensional manifold) and the random hyperplane that splits the region (the "splitter"). We show that the dihedral angle can be used to obtain a tight lower bound on the distance between the query point and any point on the opposite side of the splitter. This in turn can be used to efficiently prune the search space. We introduce a novel randomized strategy to efficiently calculate the dihedral angle with a high degree of accuracy. Experiments and analysis on real and synthetic data sets shows that the Angle Tree is the most efficient known indexing structure for nearest neighbor queries in terms of preprocessing and space usage while achieving high accuracy and fast search time. | Angle Tree: Nearest Neighbor Search in High Dimensions with Low
Intrinsic Dimensionality | 4,387 |
We combine the work of Garg and Konemann, and Fleischer with ideas from dynamic graph algorithms to obtain faster (1-eps)-approximation schemes for various versions of the multicommodity flow problem. In particular, if eps is moderately small and the size of every number used in the input instance is polynomially bounded, the running times of our algorithms match - up to poly-logarithmic factors and some provably optimal terms - the Omega(mn) flow-decomposition barrier for single-commodity flow. | Faster Approximation Schemes for Fractional Multicommodity Flow Problems
via Dynamic Graph Algorithms | 4,388 |
We consider the problem of constructing a single spanning tree for the single-source buy-at-bulk network design problem for doubling-dimension graphs. We compute a spanning tree to route a set of demands (or data) along a graph to or from a designated root node. The demands could be aggregated at (or symmetrically distributed to) intermediate nodes where the fusion-cost is specified by a non-negative concave function $f$. We describe a novel approach for developing an oblivious spanning tree in the sense that it is independent of the number of data sources (or demands) and cost function at intermediate nodes. To our knowledge, this is the first paper to propose a single spanning tree solution to this problem (as opposed to multiple overlay trees). There has been no prior work where the tree is oblivious to both the fusion cost function and the set of sources (demands). We present a deterministic, polynomial-time algorithm for constructing a spanning tree in low doubling graphs that guarantees $\log^{3}D\cdot\log n$-approximation over the optimal cost, where $D$ is the diameter of the graph and $n$ the total number of nodes. With constant fusion-cost function our spanning tree gives a $O(\log^3 D)$-approximation for every Steiner tree to the root. | An Oblivious Spanning Tree for Buy-at-Bulk Network Design Problems | 4,389 |
Bit arrays, or bitmaps, are used to significantly speed up set operations in several areas, such as data warehousing, information retrieval, and data mining, to cite a few. However, bitmaps usually use a large storage space, thus requiring compression. Nevertheless, there is a space-time tradeoff among compression schemes. The Word Aligned Hybrid (WAH) bitmap compression trades some space to allow for bitwise operations without first decompressing bitmaps. WAH has been recognized as the most efficient scheme in terms of computation time. In this paper we present CONCISE (Compressed 'n' Composable Integer Set), a new scheme that enjoys significatively better performances than those of WAH. In particular, when compared to WAH, our algorithm is able to reduce the required memory up to 50%, by having similar or better performance in terms of computation time. Further, we show that CONCISE can be efficiently used to manipulate bitmaps representing sets of integral numbers in lieu of well-known data structures such as arrays, lists, hashtables, and self-balancing binary search trees. Extensive experiments over synthetic data show the effectiveness of our approach. | CONCISE: Compressed 'n' Composable Integer Set | 4,390 |
The {\em shortest common superstring} and the {\em shortest common supersequence} are two well studied problems having a wide range of applications. In this paper we consider both problems with resource constraints, denoted as the Restricted Common Superstring (shortly \textit{RCSstr}) problem and the Restricted Common Supersequence (shortly \textit{RCSseq}). In the \textit{RCSstr} (\textit{RCSseq}) problem we are given a set $S$ of $n$ strings, $s_1$, $s_2$, $\ldots$, $s_n$, and a multiset $t = \{t_1, t_2, \dots, t_m\}$, and the goal is to find a permutation $\pi : \{1, \dots, m\} \to \{1, \dots, m\}$ to maximize the number of strings in $S$ that are substrings (subsequences) of $\pi(t) = t_{\pi(1)}t_{\pi(2)}...t_{\pi(m)}$ (we call this ordering of the multiset, $\pi(t)$, a permutation of $t$). We first show that in its most general setting the \textit{RCSstr} problem is {\em NP-complete} and hard to approximate within a factor of $n^{1-\epsilon}$, for any $\epsilon > 0$, unless P = NP. Afterwards, we present two separate reductions to show that the \textit{RCSstr} problem remains NP-Hard even in the case where the elements of $t$ are drawn from a binary alphabet or for the case where all input strings are of length two. We then present some approximation results for several variants of the \textit{RCSstr} problem. In the second part of this paper, we turn to the \textit{RCSseq} problem, where we present some hardness results, tight lower bounds and approximation algorithms. | Restricted Common Superstring and Restricted Common Supersequence | 4,391 |
We consider the problem of fault-tolerance in nanoscale algorithmic self-assembly. We employ a variant of Winfree's abstract Tile Assembly Model (aTAM), the two-handed aTAM, in which square "tiles" -- a model of molecules constructed from DNA for the purpose of engineering self-assembled nanostructures -- aggregate according to specific binding sites of varying strengths, and in which large aggregations of tiles may attach to each other, in contrast to the seeded aTAM, in which tiles aggregate one at a time to a single specially-designated "seed" assembly. We focus on a major cause of errors in tile-based self-assembly: that of unintended growth due to "weak" strength-1 bonds, which if allowed to persist, may be stabilized by subsequent attachment of neighboring tiles in the sense that at least energy 2 is now required to break apart the resulting assembly; i.e., the errant assembly is stable at temperature 2. We study a common self-assembly benchmark problem, that of assembling an n x n square using O(log n) unique tile types, under the two-handed model of self-assembly. Our main result achieves a much stronger notion of fault-tolerance than those achieved previously. Arbitrary strength-1 growth is allowed (i.e., the temperature is "fuzzy" and may drift from 2 to 1 for arbitrarily long); however, any assembly that grows sufficiently to become stable at temperature 2 is guaranteed to assemble at temperature 2 into the correct final assembly of an n x n square. In other words, errors due to insufficient attachment, which is the cause of errors studied in earlier papers on fault-tolerance, are prevented absolutely in our main construction, rather than only with high probability and for sufficiently small structures, as in previous fault-tolerance studies. | Strong Fault-Tolerance for Self-Assembly with Fuzzy Temperature | 4,392 |
The edit distance problem is a classical fundamental problem in computer science in general, and in combinatorial pattern matching in particular. The standard dynamic programming solution for this problem computes the edit-distance between a pair of strings of total length O(N) in O(N^2) time. To this date, this quadratic upper-bound has never been substantially improved for general strings. However, there are known techniques for breaking this bound in case the strings are known to compress well under a particular compression scheme. The basic idea is to first compress the strings, and then to compute the edit distance between the compressed strings. As it turns out, practically all known o(N^2) edit-distance algorithms work, in some sense, under the same paradigm described above. It is therefore natural to ask whether there is a single edit-distance algorithm that works for strings which are compressed under any compression scheme. A rephrasing of this question is to ask whether a single algorithm can exploit the compressibility properties of strings under any compression method, even if each string is compressed using a different compression. In this paper we set out to answer this question by using straight line programs. These provide a generic platform for representing many popular compression schemes including the LZ-family, Run-Length Encoding, Byte-Pair Encoding, and dictionary methods. For two strings of total length N having straight-line program representations of total size n, we present an algorithm running in O(nN log(N/n)) time for computing the edit-distance of these two strings under any rational scoring function, and an O(n^{2/3}N^{4/3}) time algorithm for arbitrary scoring functions. Our new result, while providing a signi cant speed up for highly compressible strings, does not surpass the quadratic time bound even in the worst case scenario. | Unified Compression-Based Acceleration of Edit-Distance Computation | 4,393 |
In the vertex connectivity survivable network design problem we are given an undirected graph G = (V,E) and connectivity requirement r(u,v) for each pair of vertices u,v. We are also given a cost function on the set of edges. Our goal is to find the minimum cost subset of edges such that for every pair (u,v) of vertices we have r(u,v) vertex disjoint paths in the graph induced by the chosen edges. Recently, Chuzhoy and Khanna presented a randomized algorithm that achieves a factor of O(k^3 log n) for this problem where k is the maximum connectivity requirement. In this paper we derandomize their algorithm to get a deterministic O(k^3 log n) factor algorithm. Another problem of interest is the single source version of the problem, where there is a special vertex s and all non-zero connectivity requirements must involve s. We also give a deterministic O(k^2 log n) algorithm for this problem. | A Deterministic Algorithm for the Vertex Connectivity Survivable Network
Design Problem | 4,394 |
We present a new parameterized algorithm for the {feedback vertex set} problem ({\sc fvs}) on undirected graphs. We approach the problem by considering a variation of it, the {disjoint feedback vertex set} problem ({\sc disjoint-fvs}), which finds a feedback vertex set of size $k$ that has no overlap with a given feedback vertex set $F$ of the graph $G$. We develop an improved kernelization algorithm for {\sc disjoint-fvs} and show that {\sc disjoint-fvs} can be solved in polynomial time when all vertices in $G \setminus F$ have degrees upper bounded by three. We then propose a new branch-and-search process on {\sc disjoint-fvs}, and introduce a new branch-and-search measure. The process effectively reduces a given graph to a graph on which {\sc disjoint-fvs} becomes polynomial-time solvable, and the new measure more accurately evaluates the efficiency of the process. These algorithmic and combinatorial studies enable us to develop an $O^*(3.83^k)$-time parameterized algorithm for the general {\sc fvs} problem, improving all previous algorithms for the problem. | On Feedback Vertex Set: New Measure and New Structures | 4,395 |
There has been much progress on efficient algorithms for clustering data points generated by a mixture of $k$ probability distributions under the assumption that the means of the distributions are well-separated, i.e., the distance between the means of any two distributions is at least $\Omega(k)$ standard deviations. These results generally make heavy use of the generative model and particular properties of the distributions. In this paper, we show that a simple clustering algorithm works without assuming any generative (probabilistic) model. Our only assumption is what we call a "proximity condition": the projection of any data point onto the line joining its cluster center to any other cluster center is $\Omega(k)$ standard deviations closer to its own center than the other center. Here the notion of standard deviations is based on the spectral norm of the matrix whose rows represent the difference between a point and the mean of the cluster to which it belongs. We show that in the generative models studied, our proximity condition is satisfied and so we are able to derive most known results for generative models as corollaries of our main result. We also prove some new results for generative models - e.g., we can cluster all but a small fraction of points only assuming a bound on the variance. Our algorithm relies on the well known $k$-means algorithm, and along the way, we prove a result of independent interest -- that the $k$-means algorithm converges to the "true centers" even in the presence of spurious points provided the initial (estimated) centers are close enough to the corresponding actual centers and all but a small fraction of the points satisfy the proximity condition. Finally, we present a new technique for boosting the ratio of inter-center separation to standard deviation. | Clustering with Spectral Norm and the k-means Algorithm | 4,396 |
We give the first algorithm for testing the feasibility of a system of sporadic real-time tasks on a set of identical processors, solving one major open problem in the area of multiprocessor real-time scheduling [S.K. Baruah and K. Pruhs, Journal of Scheduling, 2009]. We also investigate the related notion of schedulability and a notion that we call online feasibility. Finally, we show that discrete-time schedules are as powerful as continuous-time schedules, which answers another open question in the above mentioned survey. | Feasibility Analysis of Sporadic Real-Time Multiprocessor Task Systems | 4,397 |
In the (discrete) CNN problem, online requests appear as points in $\mathbb{R}^2$. Each request must be served before the next one is revealed. We have a server that can serve a request simply by aligning either its $x$ or $y$ coordinate with the request. The goal of the online algorithm is to minimize the total $L_1$ distance traveled by the server to serve all the requests. The best known competitive ratio for the discrete version is 879 (due to Sitters and Stougie). We study the continuous version, in which, the request can move continuously in $\mathbb{R}^2$ and the server must continuously serve the request. A simple adversarial argument shows that the lower bound on the competitive ratio of any online algorithm for the continuous CNN problem is 3. Our main contribution is an online algorithm with competitive ratio $3+2 \sqrt{3} \approx 6.464$. Our analysis is tight. The continuous version generalizes the discrete orthogonal CNN problem, in which every request must be $x$ or $y$ aligned with the previous request. Therefore, Our result improves upon the previous best competitive ratio of 9 (due to Iwama and Yonezawa). | On the Continuous CNN Problem | 4,398 |
We consider the {\em clustering with diversity} problem: given a set of colored points in a metric space, partition them into clusters such that each cluster has at least $\ell$ points, all of which have distinct colors. We give a 2-approximation to this problem for any $\ell$ when the objective is to minimize the maximum radius of any cluster. We show that the approximation ratio is optimal unless $\mathbf{P=NP}$, by providing a matching lower bound. Several extensions to our algorithm have also been developed for handling outliers. This problem is mainly motivated by applications in privacy-preserving data publication. | Clustering with diversity | 4,399 |
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