On the combinatorics of sparsification

Background: We study the sparsification of dynamic programming folding algorithms of RNA structures. Sparsification applies to the mfe-folding of RNA structures and can lead to a significant reduction of time complexity. Results: We analyze the sparsification of a particular decomposition rule, $\Lambda^*$, that splits an interval for RNA secondary and pseudoknot structures of fixed topological genus. Essential for quantifying the sparsification is the size of its so called candidate set. We present a combinatorial framework which allows by means of probabilities of irreducible substructures to obtain the expected size of the set of $\Lambda^*$-candidates. We compute these expectations for arc-based energy models via energy-filtered generating functions (GF) for RNA secondary structures as well as RNA pseudoknot structures. For RNA secondary structures we also consider a simplified loop-energy model. This combinatorial analysis is then compared to the expected number of $\Lambda^*$-candidates obtained from folding mfe-structures. In case of the mfe-folding of RNA secondary structures with a simplified loop energy model our results imply that sparsification provides a reduction of time complexity by a constant factor of 91% (theory) versus a 96% reduction (experiment). For the "full" loop-energy model there is a reduction of 98% (experiment).Comment: 27 pages, 12 figure

Large components in random induced subgraphs of n-cubes

In this paper we study random induced subgraphs of the binary $n$-cube, $Q_2^n$. This random graph is obtained by selecting each $Q_2^n$-vertex with independent probability $\lambda_n$. Using a novel construction of subcomponents we study the largest component for $\lambda_n=\frac{1+\chi_n}{n}$, where $\epsilon\ge \chi_n\ge n^{-{1/3}+ \delta}$, $\delta>0$. We prove that there exists a.s. a unique largest component $C_n^{(1)}$. We furthermore show that $\chi_n=\epsilon$, $| C_n^{(1)}|\sim \alpha(\epsilon) \frac{1+\chi_n}{n} 2^n$ and for $o(1)=\chi_n\ge n^{-{1/3}+\delta}$, $| C_n^{(1)}| \sim 2 \chi_n \frac{1+\chi_n}{n} 2^n$ holds. This improves the result of \cite{Bollobas:91} where constant $\chi_n=\chi$ is considered. In particular, in case of $\lambda_n=\frac{1+\epsilon} {n}$, our analysis implies that a.s. a unique giant component exists.Comment: 18 Page

Random 3-noncrossing partitions

In this paper, we introduce polynomial time algorithms that generate random 3-noncrossing partitions and 2-regular, 3-noncrossing partitions with uniform probability. A 3-noncrossing partition does not contain any three mutually crossing arcs in its canonical representation and is 2-regular if the latter does not contain arcs of the form $(i,i+1)$. Using a bijection of Chen {\it et al.} \cite{Chen,Reidys:08tan}, we interpret 3-noncrossing partitions and 2-regular, 3-noncrossing partitions as restricted generalized vacillating tableaux. Furthermore, we interpret the tableaux as sampling paths of Markov-processes over shapes and derive their transition probabilities.Comment: 17 pages, 7 figure

Random induced subgraphs of Cayley graphs induced by transpositions

In this paper we study random induced subgraphs of Cayley graphs of the symmetric group induced by an arbitrary minimal generating set of transpositions. A random induced subgraph of this Cayley graph is obtained by selecting permutations with independent probability, $\lambda_n$. Our main result is that for any minimal generating set of transpositions, for probabilities $\lambda_n=\frac{1+\epsilon_n}{n-1}$ where $n^{-{1/3}+\delta}\le \epsilon_n0$, a random induced subgraph has a.s. a unique largest component of size $\wp(\epsilon_n)\frac{1+\epsilon_n}{n-1}n!$, where $\wp(\epsilon_n)$ is the survival probability of a specific branching process.Comment: 18 pages, 1 figur