An Efficient Dynamic Programming Algorithm for the Generalized LCS Problem with Multiple Substring Exclusion Constrains

In this paper, we consider a generalized longest common subsequence problem with multiple substring exclusion constrains. For the two input sequences $X$ and $Y$ of lengths $n$ and $m$, and a set of $d$ constrains $P=\{P_1,...,P_d\}$ of total length $r$, the problem is to find a common subsequence $Z$ of $X$ and $Y$ excluding each of constrain string in $P$ as a substring and the length of $Z$ is maximized. The problem was declared to be NP-hard\cite{1}, but we finally found that this is not true. A new dynamic programming solution for this problem is presented in this paper. The correctness of the new algorithm is proved. The time complexity of our algorithm is $O(nmr)$.Comment: arXiv admin note: substantial text overlap with arXiv:1301.718

Sublinear Space Algorithms for the Longest Common Substring Problem

Given $m$ documents of total length $n$, we consider the problem of finding a longest string common to at least $d \geq 2$ of the documents. This problem is known as the \emph{longest common substring (LCS) problem} and has a classic $O(n)$ space and $O(n)$ time solution (Weiner [FOCS'73], Hui [CPM'92]). However, the use of linear space is impractical in many applications. In this paper we show that for any trade-off parameter $1 \leq \tau \leq n$, the LCS problem can be solved in $O(\tau)$ space and $O(n^2/\tau)$ time, thus providing the first smooth deterministic time-space trade-off from constant to linear space. The result uses a new and very simple algorithm, which computes a $\tau$-additive approximation to the LCS in $O(n^2/\tau)$ time and $O(1)$ space. We also show a time-space trade-off lower bound for deterministic branching programs, which implies that any deterministic RAM algorithm solving the LCS problem on documents from a sufficiently large alphabet in $O(\tau)$ space must use $\Omega(n\sqrt{\log(n/(\tau\log n))/\log\log(n/(\tau\log n)})$ time.Comment: Accepted to 22nd European Symposium on Algorithm

Free Energy Approximations for CSMA networks

In this paper we study how to estimate the back-off rates in an idealized CSMA network consisting of $n$ links to achieve a given throughput vector using free energy approximations. More specifically, we introduce the class of region-based free energy approximations with clique belief and present a closed form expression for the back-off rates based on the zero gradient points of the free energy approximation (in terms of the conflict graph, target throughput vector and counting numbers). Next we introduce the size $k_{max}$ clique free energy approximation as a special case and derive an explicit expression for the counting numbers, as well as a recursion to compute the back-off rates. We subsequently show that the size $k_{max}$ clique approximation coincides with a Kikuchi free energy approximation and prove that it is exact on chordal conflict graphs when $k_{max} = n$. As a by-product these results provide us with an explicit expression of a fixed point of the inverse generalized belief propagation algorithm for CSMA networks. Using numerical experiments we compare the accuracy of the novel approximation method with existing methods