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106
Music information retrieval
 Annual Review of Information Science and Technology
, 2003
"... International Symposium on ..."
A decomposition theorem for maximum weight bipartite matchings with applications to evolutionary trees
 in Proceedings of the 7th Annual European Symposium on Algorithms, Lecture Notes in Comput. Sci
, 1999
"... Abstract. Let G be a bipartite graph with positive integer weights on the edges and without isolated nodes. Let n, N, and W be the node count, the largest edge weight, and the total weight of G. Let k(x, y) be log x / log(x2 /y). We present a new decomposition theorem for maximum weight bipartite ma ..."
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Cited by 28 (2 self)
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Abstract. Let G be a bipartite graph with positive integer weights on the edges and without isolated nodes. Let n, N, and W be the node count, the largest edge weight, and the total weight of G. Let k(x, y) be log x / log(x2 /y). We present a new decomposition theorem for maximum weight bipartite matchings and use it to design an O ( √ nW/k(n, W/N))time algorithm for computing a maximum weight matching of G. This algorithm bridges a longstanding gap between the best known time complexity of computing a maximum weight matching and that of computing a maximum cardinality matching. Given G and a maximum weight matching of G, we can further compute the weight of a maximum weight matching of G −{u} for all nodes u in O(W) time. Key words. allcavity matchings, maximum weight matchings, minimum weight covers, graph algorithms, unfolded graphs
FACULTE DES SCIENCES ET DE GENIE
"... Highspeed VLSI design for turbo and LDPC codes used in broadband wireless networks Thèse présentée à la Faculté des études supérieures de l'Université Laval dans le cadre du programme de doctorat en génie électrique pour l'obtention du grade de Philosophiae Doctor (Ph.D.) ..."
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Highspeed VLSI design for turbo and LDPC codes used in broadband wireless networks Thèse présentée à la Faculté des études supérieures de l'Université Laval dans le cadre du programme de doctorat en génie électrique pour l'obtention du grade de Philosophiae Doctor (Ph.D.)
Fast Recovery of Evolutionary Trees with Thousands of Nodes
 RECOMB
, 2001
"... We present a novel distancebased algorithm for evolutionary tree reconstruction. Our algorithm reconstructs the topology of a tree with n leaves in O(n 2 ) time using O(n) working space. In the general Markov model of evolution, the algorithm recovers the topology successfully with (1o(1)) probabi ..."
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Cited by 23 (0 self)
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We present a novel distancebased algorithm for evolutionary tree reconstruction. Our algorithm reconstructs the topology of a tree with n leaves in O(n 2 ) time using O(n) working space. In the general Markov model of evolution, the algorithm recovers the topology successfully with (1o(1)) probability from sequences with polynomial length in n. Moreover, for almost all trees, our algorithm achieves the same success probability on polylogarithmic sample sizes. The theoretical results are supported by simulation experiments involving trees with 500, 1895, and 3135 leaves. The topologies of the trees are recovered with high success from 2000 bp DNA sequences.
Towards truthful mechanisms for binary demand games: a general framework
 In Proceedings of the 6th ACM conference on Electronic commerce
, 2005
"... The family of VickreyClarkeGroves (VCG) mechanisms is arguably the most celebrated achievement in truthful mechanism design. However, VCG mechanisms have their limitations. They only apply to optimization problems with a utilitarian objective function, and their output should optimize the objectiv ..."
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Cited by 17 (10 self)
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The family of VickreyClarkeGroves (VCG) mechanisms is arguably the most celebrated achievement in truthful mechanism design. However, VCG mechanisms have their limitations. They only apply to optimization problems with a utilitarian objective function, and their output should optimize the objective function. For many optimization problems, finding the optimal output is computationally intractable. If we apply VCG mechanisms to polynomialtime algorithms that approximate the optimal solution, the resulting mechanisms may no longer be truthful. In light of these limitations, it is useful to study whether we can design a truthful nonVCG payment scheme that is computationally tractable for a given output method O. In this paper, we focus our attention on binary demand games in which the agents’ only available actions are to take part in the a game or not to. For these problems, we prove that a truthful mechanism M = (O, P) exists (with proper payment method P) if and only if O satisfies a certain monotone property. We also provide several general algorithms to compute the payments efficiently for various types of output. In particular, we show how a truthful payment can be computed through “or/and ” combinations, roundbased combinations, and some more complex combinations of outputs from subgames.
Fast Optimal Genome Tiling with Applications to Microarray Design and Homology Search
, 2003
"... In this paper we consider several variations of the following basic tiling problem: given a sequence of real numbers with two size bound parameters, we want to find a set of tiles of maximum total weight such that each tiles satisfies the size bounds. A solution to this problem is important to a num ..."
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Cited by 9 (4 self)
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In this paper we consider several variations of the following basic tiling problem: given a sequence of real numbers with two size bound parameters, we want to find a set of tiles of maximum total weight such that each tiles satisfies the size bounds. A solution to this problem is important to a number of computational biology applications such as selecting genomic DNA fragments for PCRbased amplicon microarrays and performing homology searches with long sequence queries. Our goal is to design efficient algorithms with linear or nearlinear time and space in the normal range of parameter values for these problems. For this purpose, we first discuss the solution to a basic online interval maximum problem via a sliding window approach and show how to use this solution in a nontrivial manner for many of the tiling problems introduced. We also discuss NPhardness results and approximation algorithms for generalizing our basic tiling problem to higher dimensions. Finally, computational results from applying our tiling algorithms to genomic sequences of five model eukaryotes are reported.
Cavity matchings, label compressions, and unrooted evolutionary trees
 SIAM J. Comput
, 2000
"... Abstract. We present an algorithm for computing a maximum agreement subtree of two unrooted evolutionary trees. It takes O(n 1.5 log n) time for trees with unbounded degrees, matching the best known time complexity for the rooted case. Our algorithm allows the input trees to be mixed trees, i.e., tr ..."
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Cited by 6 (1 self)
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Abstract. We present an algorithm for computing a maximum agreement subtree of two unrooted evolutionary trees. It takes O(n 1.5 log n) time for trees with unbounded degrees, matching the best known time complexity for the rooted case. Our algorithm allows the input trees to be mixed trees, i.e., trees that may contain directed and undirected edges at the same time. Our algorithm adopts a recursive strategy exploiting a technique called label compression. The backbone of this technique is an algorithm that computes the maximum weight matchings over many subgraphs of a bipartite graph as fast as it takes to compute a single matching. 1. Introduction. An
Optimal bidding algorithms against cheating in multiple object auctions
 SIAM Journal on Computing
, 1999
"... Abstract. This paper studies some basic problems in a multipleobject auction model using methodologies from theoretical computer science. We are especially concerned with situations where an adversary bidder knows the bidding algorithms of all the other bidders. In the twobidder case, we derive an ..."
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Cited by 4 (2 self)
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Abstract. This paper studies some basic problems in a multipleobject auction model using methodologies from theoretical computer science. We are especially concerned with situations where an adversary bidder knows the bidding algorithms of all the other bidders. In the twobidder case, we derive an optimal randomized bidding algorithm, by which the disadvantaged bidder can procure at least half of the auction objects despite the adversary’s a priori knowledge of his algorithm. In the general kbidder case, if the number of objects is a multiple of k, an optimal randomized bidding algorithm is found. If the k − 1 disadvantaged bidders employ that same algorithm, each of them can obtain at least 1/k of the objects regardless of the bidding algorithm the adversary uses. These two algorithms are based on closedform solutions to certain multivariate probability distributions. In situations where a closedform solution cannot be obtained, we study a restricted class of bidding algorithms as an approximation to desired optimal algorithms.
Optimal Augmentation For Bipartite Componentwise Biconnectivity In Linear Time
, 1996
"... . A graph is componentwise fully biconnected if every connected component either is an isolated vertex or is biconnected. We consider the problem of adding the smallest number of edges to make a bipartite graph componentwise fully biconnected while preserving its bipartiteness. This problem has impo ..."
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Cited by 4 (1 self)
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. A graph is componentwise fully biconnected if every connected component either is an isolated vertex or is biconnected. We consider the problem of adding the smallest number of edges to make a bipartite graph componentwise fully biconnected while preserving its bipartiteness. This problem has important applications for protecting sensitive information in cross tabulated tables. This paper presents a lineartime algorithm for the problem. Key words. algorithm, linear time, bipartite graph augmentation, biconnectivity, data security AMS(MOS) subject classifications. 68Q20, 68R10, 94C15, 05C40, 05C90 1. Introduction. The problem of adding the minimum number of edges to make a given graph biconnected is called the smallest biconnectivity augmentation problem. This problem has been extensively studied for general graphs [4, 17, 18]. A simplified sequential algorithm which corrects an error in [18] and an efficient parallel algorithm are reported in [13]. Efficient algorithms for other v...
Specific activation of glucuronide prodrugs by antibodytargeted enzyme conjugates for cancer therapy. Cancer Res
, 1992
"... t" Cancer chemothempy rnay be improved by increasing antineoplastic drug specificity for tumor crclls. We have synthesized a glucuronide prodrug that can be enzymatically converted to an antineoplastic agent at tumor cells that are able to bind pglucuronidasemonoclonal antibody conjugates. T ..."
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Cited by 4 (1 self)
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t" Cancer chemothempy rnay be improved by increasing antineoplastic drug specificity for tumor crclls. We have synthesized a glucuronide prodrug that can be enzymatically converted to an antineoplastic agent at tumor cells that are able to bind pglucuronidasemonoclonal antibody conjugates. The glucuronide prodrug BHAMG ' the tetrazbutyl ammonium salt of (pdi2chloroethylaminophenylfogluqtpFanosid) uronic acid, was 150 times less toxic than the parent drug ' N,Ndi(2chloroethyl)4hydroxyaniline, to HepG2 human hepatoma cells and over 1000fold less toxic than the parent drug to AS30D rat hepatoma cells iz vitro. ln the presence of Bglucuronidase ' BHAMG was activated and became as toxic as the parent drug N,Ndi(2chloroethyl)4hydroxyaniline. A conjugate (RHlBG) was formed by linking pglucuronidase to a monoclonal antibody which binds to an antigen expressed on the surface of AS30D cells. The concentration of BI{AMG causing 50o/o inhibition of AS30D cellular protein synthesis was reduc.ed over lfiDfold, from>770 p.vto <0.74 pnr after these cells were preincubated with RHIPG. Specificity of BHAMG activation at antigenpositive cells was shown by monoclonal antibody RHl blocking of RHIpG conversion of BHAMG to toxic drug and by the inability of BHAMG to be cunverted to active drug when antigennegative control cells were preincubated with RHfPG. Our results show that the targetedBglucuronidase activation of BHAMG can increase the specificity of chemotherapy for rat hepatoma in vifio and suggest that the targeted activation of glucuronide prodrugs may be useful for cancer therapy.
Results 1  10
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106