52151541
Linear approximation of shortest superstrings
We consider the following problem: given a collection of strings <italic>s<subscrpt>1</subscrpt></italic>,…, <italic>s<subscrpt>m</subscrpt></italic>, find the shortest string <italic>s</italic> such that each <italic>s<subscrpt>i</subscrpt></italic> appears as a substring (a consecutive block) of <italic>s</italic>. Although this problem is known to be NP-hard, a simple greedy procedure appears to do quite well and is routinely used in DNA sequencing and data compression practice, namely: repeatedly merge the pair of (distinct) strings with maximum overlap until only one string remains. Let <italic>n</italic> denote the length of the optimal superstring. A common conjecture states that the above greedy procedure produces a superstring of length <italic>O(n)</italic> (in fact, 2<italic>n</italic>), yet the only previous nontrivial bound known for any polynomial-time algorithm is a recent <italic>O(n</italic> log <italic>n</italic>) result.
We show that the greedy algorithm does in fact achieve a constant factor approximation, proving an upper bound of 4<italic>n</italic>. Furthermore, we present a simple modified version of the greedy algorithm that we show produces a superstring of length at most 3<italic>n</italic>. We also show the superstring problem to be MAXSNP-hard, which implies that a polynomial-time approximation scheme for this problem is unlikely.
43310555
Twist-Rotation Transformations of Binary Trees and Arithmetic Expressions
The paper studies the computational complexity and efficient algorithms for the twist?rotation transformations of binary trees, which is equivalent to the transformation of arithmetic expressions over an associative and commutative binary operation. The main results are (1) a full binary tree with n labeled leaves can be transformed into any other in at most 3nlogn+2n twist and rotation operations, (2) deciding the twist?rotation distance between two binary trees is NP-complete, and (3) the twist?rotation transformation can be approximated with ratio 6logn+4 in polynomial time for full binary trees with n uniquely labeled leaves.
553776
Linear approximation of shortest superstrings
We consider the following problem: given a collection of strings s1, ••• ,sm, find the shortest string s such that each s; appears as a substring (a consecutive block) of s. Although this problem is known to be NP-hard, a simple greedy procedure appears to do quite well and is routinely used in DNA sequencing and data compression practice, namely: repeatedly merge the pair of (distinct) strings with maximum overlap until only one string remains. Let n denote the A. Blum was supported by a National Science Foundation (NSF) Graduate Fellowship. Part of this work was done while A. Blum was visiting AT & T Bell Labs. T. Jiang was supported in part by a grant from SERB, McMaster University and NSERC Operating Grant OGP0046613. M. Li was supported in part by the NSERC Operating Grants OGP0036747 and OGP0046506. J. Tromp was supported in part by NSERC Grant OGP0036747 while the author was visiting at the University of Waterloo. Authors' present addresses: A. Blum, School of Computer Science, Carnegie-Mellon University, 5000 Forbes Avenue, Pittsburgh, PA 15213. E-mail: avrim@theory.cs.cmu.edu; T. Jiang, Department of Computer Science, McMaster University, Hamilton, Ont., Canada L8S 4Kl. E-mail: jiang<Q•maccs. mcmaster.ca; M. Li, Department of Computer Science, University of Waterloo, Waterloo, Ont., Canada N3L 30 I. E-mail: mli@watmath.waterloo.edu; J. Tromp, CWI, P.O. Box 4079, 1009 AB Amsterdam, The Netherlands. E-mail: tromp@cwi.nl; M. Yannakakis, Room 2C-319, AT&T Bell Labs, 600 Mountain Avenue, Murray Hill, NJ 07974. E-mail: mihalis@research.att.com. Permission to copy without fee all or part of this material is granted provided that the copies arc not made or distributed for direct commercial advantage, the ACM copyright notice and the title of the publication and its date appear, and notice is given that copying is by permission of the Association for Computing Machinery. To copy otherwise, or to republish, requires a fee and/or specific permission. © 1994 ACM 0004-5411/94/0700-0630$03.50 Journal of the Association for Computing Machinery, Vol. 41, No. 4, July 1994, pages 630-647. Linear Approximation of Shortest Superstrings 631 length of the optimal superstring. A common conjecture states that the above greedy procedure produces a superstring of length O(n) (in fact, 2n), yet the only previous nontrivial bound known for any polynomial-time algorithm is a recent O(n log n) result. We show that the greedy algorithm does in fact achieve a constant factor approximation, proving an upper bound of 4n. Furthermore, we present a simple modified version of the greedy algorithm that we show produces a superstring of length at most 3n. We also show the superstring problem to be MAX SNP-hard, which implies that a polynomial-time approximation scheme for this problem is unlikely.
9397376
Inferring a DNA Sequence from Erroneous Copies
Abstract We suggest a novel approach for efficiently reconstructing an original DNA sequence from erroneous copies.
871253
Kolmogorov Complexity Arguments in Combinatorics
Abstract The utility of a Kolmogorov complexity method in combinatorial theory is demonstrated by several examples.
14168735
Inductive Reasoning and Kolmogorov Complexity
Abstract Reasoning to obtain the “truth” about reality, from external data, is an important, controversial, and complicated issue in man's effort to understand nature. (Yet, today, we try to make machines do this.) There have been old useful principles, new exciting models, and intricate theories scattered in vastly different areas including philosophy of science, statistics, computer science, and psychology. We focus on inductive reasoning in correspondence with ideas of R. J. Solomonoff. While his proposals result in perfect procedures, they involve the noncomputable notion of Kolmogorov complexity. In this paper we develop the thesis that Solomonoff's method is fundamental in the sense that many other induction principles can be viewed as particular ways to obtain computable approximations to it. We demonstrate this explicitly in the cases of Gold's paradigm for inductive inference, Rissanen's minimum description length (MDL) principle, Fisher's maximum likelihood principle, and Jaynes' maximum entropy principle. We present several new theorems and derivations to this effect. We also delimit what can be learned and what cannot be learned in terms of Kolmogorov complexity, and we describe an experiment in machine learning of handwritten characters. We also give an application of Kolmogorov complexity in Valiant style learning, where we want to learn a concept probably approximately correct in feasible time and examples.
12322208
Gemini: Probabilistic Routing Algorithm in Structured P2P Overlay
In this paper, we propose a new structured overlay protocol, which is more efficient and scalable than previous ones. We call it Gemini, because its routing table consists of two parts, one containing nodes with common prefix and the other containing nodes with common suffix. Gemini routes messages to their destinations in just 2 hops, with a very high probability of 0.99. When running in a p2p network of 5,000,000 peers, each Gemini node consumes only 6 messages per second for maintenance. This cost, as well as routing table size, varies as a \(O {\sqrt{N}}\) function to the overlay scale, so Gemini can also run well in an even larger environment.
5906681
Circumferences of 2-Connected Claw-Free Graphs
15861046
A Survey on Topology issues in Wireless Sensor Network
Topology issues have received more and more attentions in Wireless Sensor Networks (WSN). While WSN applications are normally optimized by the given underlying network topology, another trend is to optimize WSN by means of topology control. A number of approaches have been invested in this area, such as topology directed routing, cooperating schemes, sensor coverage based topology control and network connectivity based topology control. Most of the schemes have proven to be able to provide a better network monitoring and communication performance with prolonged system lifetime. In this survey paper, we provide a full view of the studies in this area. By summarizing previous achievements and analyzing existed problems, we also point out possible research directions for future work .
751784
An Efficient Algorithm for Computing Optimal Discrete Voltage Schedules
We consider the problem of job scheduling on a variable voltage processor with d discrete voltage/speed levels. We give an algorithm which constructs a minimum energy schedule for n jobs in O(dnlogn) time. Previous approaches solve this problem by first computing the optimal continuous solution in O(n 3 ) time and then adjusting the speed to discrete levels. In our approach, the optimal discrete solution is characterized and computed directly from the inputs. We also show that O(n log n) time is required, hence the algorithm is optimal for fixed d.
20792301
An Efficient Algorithm for Computing Optimal Discrete Voltage Schedules
We consider the problem of job scheduling on a variable voltage processor with d discrete voltage/speed levels. We give an algorithm which constructs a minimum energy schedule for n jobs in O(dnlog n) time. Previous approaches solve this problem by first computing the optimal continuous solution in O(n3) time and then adjusting the speed to discrete levels. In our approach, the optimal discrete solution is characterized and computed directly from the inputs. We also show that O(nlog n) time is required, hence the algorithm is optimal for fixed d.