Weighted Shortest Common Supersequence problem revisited

A weighted string, also known as a position weight matrix, is a sequence of probability distributions over some alphabet. We revisit the Weighted Shortest Common Supersequence (WSCS) problem, introduced by Amir et al. [SPIRE 2011], that is, the SCS problem on weighted strings. In the WSCS problem, we are given two weighted strings (Formula presented) and (Formula presented) and a threshold (Formula presented) on probability, and we are asked to compute the shortest (standard) string S such that both (Formula presented) and (Formula presented) match subsequences of S (not necessarily the same

A Proof of Entropy Minimization for Outputs in Deletion Channels via Hidden Word Statistics

From the output produced by a memoryless deletion channel from a uniformly random input of known length $n$, one obtains a posterior distribution on the channel input. The difference between the Shannon entropy of this distribution and that of the uniform prior measures the amount of information about the channel input which is conveyed by the output of length $m$, and it is natural to ask for which outputs this is extremized. This question was posed in a previous work, where it was conjectured on the basis of experimental data that the entropy of the posterior is minimized and maximized by the constant strings $\texttt{000}\ldots$ and $\texttt{111}\ldots$ and the alternating strings $\texttt{0101}\ldots$ and $\texttt{1010}\ldots$ respectively. In the present work we confirm the minimization conjecture in the asymptotic limit using results from hidden word statistics. We show how the analytic-combinatorial methods of Flajolet, Szpankowski and Vall\'ee for dealing with the hidden pattern matching problem can be applied to resolve the case of fixed output length and $n\rightarrow\infty$, by obtaining estimates for the entropy in terms of the moments of the posterior distribution and establishing its minimization via a measure of autocorrelation.Comment: 11 pages, 2 figure

The Loading Time Scheduling Problem

In this paper we study precedence constrained scheduling problems, where the tasks can only be executed on a specified subset of the machines. Each machine has a loading time that is incurred only for the first task that is scheduled on the machine in a particular run. This basic scheduling problem arises in the context of machining on numerically controlled machines, query optimization in databases, and in other artificial intelligence applications. We give the first non-trivial approximation algorithm for this problem. We also prove non-trivial lower bounds on best possible approximation ratios for these problems. These improve on the non-approximability results that are implied by the non-approximability results for the shortests common supersequence problem. We use the same algorithmic technique to obtain approximation algorithms for a problem arising in the context of code generation for parallel machines, and for the weighted shortest common supersequence problem