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We address a fundamental problem arising from analysis of biomolecular sequences. The input consists of two numbers wmin and wmax and a sequence S of n number pairs (ai, wi) with wi > 0. Let segment S(i, j) of S be the consecutive subsequence of S between indices i and j. The density of S(i,j) is d(i,j) = (ai + ai+1 +…+ aj)/(wi + wi+1 + … + wj). The maximum-density segment problem is to find a maximum-density segment over all segments S(i, j) with wmin ≤ wi + wi+1 + … + wj ≤ wmax. The best previously known algorithm for the problem, due to Goldwasser, Kao, and Lu [Proceedings of the Second International Workshop on Algorithms in Bioinformatics, R. Guigó and D. Gusfield, eds., Lecture Notes in Comput. Sci. 2452, Springer-Verlag, New York, 2002, pp. 157-171], runs in O(n log(wmax - wmin + 1)) time. In the present paper, we solve the problem in O(n) time. Our approach bypasses the complicated right-skew decomposition, introduced by Lin, Jiang, and Chao [J. Comput. System Sci., 65 (2002), pp. 570-586]. As a result, our algorithm has the capability to process the input sequence in an online manner, which is an important feature for dealing with genome-scale sequences. Moreover, for a type of input sequences S representable in O(m) space, we show how to exploit the sparsity of S and solve the maximum-density segment problem for S in O(m) time. [ABSTRACT FROM AUTHOR]

A new packet routing model proposed by the Internet Engineering Task Force is MultiProtocol Label Switching, or MPLS [B. Davie and Y. Rekhter, MPLS: Technology and Applications, Morgan Kaufmann (Elsevier), New York, 2000]. Instead of each router's parsing the packet network layer header and doing its lookups based on that analysis (as in much of conventional packet routing), MPLS ensures that the analysis of the header is performed just once. The packet is then assigned a stack of labels, where the labels are usually much smaller than the packet headers themselves. When a router receives a packet, it examines the label at the top of the label stack and makes the decision of where the packet is forwarded based solely on that label. It can pop the top label off the stack if it so desires, and can also push some new labels onto the stack, before forwarding the packet. This scheme has several advantages over conventional routing protocols, the two primary ones being (a) reduced amount of header analysis at intermediate routers, which allows for faster switching times, and (b) better traffic engineering capabilities and hence easier handling of quality of service issues. However, essentially nothing is known at a theoretical level about the performance one can achieve with this protocol, or about the intrinsic trade-offs in its use of resources. This paper initiates a theoretical study of MPLS protocols, and routing algorithms and lower bounds are given for a variety of situations. We first study the routing problem on the line, a case which is already nontrivial, and give routing protocols whose trade-offs are close to optimality. We then extend our results for paths to trees, and thence onto more general graphs. These routing algorithms on general graphs are obtained by finding a tree cover of a graph, i.e., a small family of subtrees of the graph such that, for each pair of vertices, one of the trees in the family contains an (almost-)shortest path between them. Our results show tree covers of logarithmic size for planar graphs and graphs with bounded separators, which may be of independent interest. [ABSTRACT FROM AUTHOR]