9397376
Inferring a DNA Sequence from Erroneous Copies
Abstract We suggest a novel approach for efficiently reconstructing an original DNA sequence from erroneous copies.
34458462
Learning in the Presence of Malicious Errors
In this paper an extension of the distribution-free model of learning introduced by Valiant [Comm. ACM, 27(1984), pp. 1134–1142] that allows the presence of malicious errors in the examples given to a learning algorithm is studied. Such errors are generated by an adversary with unbounded computational power and access to the entire history of the learning algorithm’s computation. Thus, a worst-case model of errors is studied.The results of this research include general methods for bounding the rate of error tolerable by any learning algorithm, efficient algorithms tolerating nontrivial rates of malicious errors, and equivalences between problems of learning with errors and standard combinatorial optimization problems.
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.
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.
6593224
DNA sequencing and string learning
In laboratories the majority of large-scale DNA sequencing is done following theshotgun strategy, which is to sequence large amount of relatively short fragments randomly and then heuristically find a shortest common superstring of the fragments [26].We study mathematical frameworks, under plausible assumptions, suitable for massive automated DNA sequencing and for analyzing DNA sequencing algorithms. We model the DNA sequencing problem as learning a string from its randomly drawn substrings. Under certain restrictions, this may be viewed as string learning in Valiant's distribution-free learning model and in this case we give an efficient learning algorithm and a quantitative bound on how many examples suffice.One major obstacle to our approach turns out to be a quite well-known open question on how to approximate a shortest common superstring of a set of strings, raised by a number of authors in the last 10 years [9], [29], [30]. We give the firstprovably good algorithm which approximates a shortest superstring of lengthn by a superstring of lengthO(n logn). The algorithm works equally well even in the presence of negative examples, i.e., when merging of some strings is prohibited.
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.
53306617
Human-Machine Collaborative Systems for Microsurgical Applications
Human-machine collaborative systems (HMCSs) are systems that amplify or assist human capabilities during the performance of tasks that require both human judgment and robotic precision. We examine the design and performance of HMCSs in the context of microsurgical procedures such as vitreo-retinal eye surgery. Three specific problems considered are: (1) development of systems tools for describing and implementing HMCSs, (2) segmentation of complex tasks into logical components given sensor traces of human task execution, and (3) measurement and evaluation of HMCS performance. These components can be integrated into a complete workstation with the ability to automatically “parse” traces of user activities into task models, which are loaded into an execution environment to provide the user with assistance using on-line recognition of task states. The major contributions of this work include an XML task graph modeling framework and execution engine, an algorithm for real-time segmentation of user actions using continuous hidden Markov models, and validation techniques for analyzing the performance of HMCSs.
204992426
Hamiltonian cycles in regular 3-connected claw-free graphs
Abstract A known result by the author in 1991 is that every 3-connected claw-free graph on at most 6δ-11 vertices is Hamiltonian. In this paper it is proved that every 3-connected k -regular claw-free graph on at most 7 k — 19 vertices is Hamiltonian.
1558162
Monitoring Abnormal Patterns with Complex Semantics over ICU Data Streams
Monitoring abnormal patterns in data streams is an important research area for many applications. In this paper we present a new approach MAPS(Monitoring Abnormal Patterns over data Streams) to model and identify the abnormal patterns over the massive data streams. Compared with other data streams, ICU streaming data have their own features: pseudo-periodicity and polymorphism. MAPS first extracts patterns from the online arriving data streams and then normalizes them according to their pseudo-periodic semantics. Abnormal patterns will be detected if they are satisfied the predicates defined in the clinician-specifying normal patterns. At last, a real application demonstrates that MAPS is efficient and effective in several important aspects.
45496659
Migrating legacy codes to distributed computing environments: a CORBA approach
Abstract This paper describes techniques used to migrate legacy codes as CORBA components to a distributed problem solving environment (PSE). It presents a CORBA compliant wrapper generator (WG), which can be used to automatically wrap high performance legacy codes in C or Fortran as CORBA components for reuse in the PSE. Using WG, a finite element based computational fluid dynamics (CFD) legacy code has been wrapped as a CORBA component and a PSE for simulating incompressible Navier-Stokes flows has been implemented. A user can submit a task to the wrapped CFD component through a Web page without knowing the exact implementation of the component. In this way, a user's desktop computing environment can be extended to a computing environment using a cluster of workstations or a parallel computer.
10085490
Circumferences of regular claw-free graphs
A known result obtained independently by Fan and Jung is that every 3-connected k-regular graph on n vertices contains a cycle of length at least min{3k,n}. This raises the question of how much can be said about the circumferences of 3-connected k-regular claw-free graphs. In this paper, we show that every 3-connected k-regular claw-free graph on n vertices contains a cycle of length at least min{6k-17,n}.