Combinatorial RNA Design: Designability and Structure-Approximating Algorithm

In this work, we consider the Combinatorial RNA Design problem, a minimal instance of the RNA design problem which aims at finding a sequence that admits a given target as its unique base pair maximizing structure. We provide complete characterizations for the structures that can be designed using restricted alphabets. Under a classic four-letter alphabet, we provide a complete characterization of designable structures without unpaired bases. When unpaired bases are allowed, we provide partial characterizations for classes of designable/undesignable structures, and show that the class of designable structures is closed under the stutter operation. Membership of a given structure to any of the classes can be tested in linear time and, for positive instances, a solution can be found in linear time. Finally, we consider a structure-approximating version of the problem that allows to extend bands (helices) and, assuming that the input structure avoids two motifs, we provide a linear-time algorithm that produces a designable structure with at most twice more base pairs than the input structure.Comment: CPM - 26th Annual Symposium on Combinatorial Pattern Matching, Jun 2015, Ischia Island, Italy. LNCS, 201

Fast Distributed Approximation for Max-Cut

Finding a maximum cut is a fundamental task in many computational settings. Surprisingly, it has been insufficiently studied in the classic distributed settings, where vertices communicate by synchronously sending messages to their neighbors according to the underlying graph, known as the $\mathcal{LOCAL}$ or $\mathcal{CONGEST}$ models. We amend this by obtaining almost optimal algorithms for Max-Cut on a wide class of graphs in these models. In particular, for any $\epsilon > 0$, we develop randomized approximation algorithms achieving a ratio of $(1-\epsilon)$ to the optimum for Max-Cut on bipartite graphs in the $\mathcal{CONGEST}$ model, and on general graphs in the $\mathcal{LOCAL}$ model. We further present efficient deterministic algorithms, including a $1/3$-approximation for Max-Dicut in our models, thus improving the best known (randomized) ratio of $1/4$. Our algorithms make non-trivial use of the greedy approach of Buchbinder et al. (SIAM Journal on Computing, 2015) for maximizing an unconstrained (non-monotone) submodular function, which may be of independent interest

Distributed Approximation of Maximum Independent Set and Maximum Matching

We present a simple distributed $\Delta$-approximation algorithm for maximum weight independent set (MaxIS) in the $\mathsf{CONGEST}$ model which completes in $O(\texttt{MIS}(G)\cdot \log W)$ rounds, where $\Delta$ is the maximum degree, $\texttt{MIS}(G)$ is the number of rounds needed to compute a maximal independent set (MIS) on $G$, and $W$ is the maximum weight of a node. %Whether our algorithm is randomized or deterministic depends on the \texttt{MIS} algorithm used as a black-box. Plugging in the best known algorithm for MIS gives a randomized solution in $O(\log n \log W)$ rounds, where $n$ is the number of nodes. We also present a deterministic $O(\Delta +\log^* n)$-round algorithm based on coloring. We then show how to use our MaxIS approximation algorithms to compute a $2$-approximation for maximum weight matching without incurring any additional round penalty in the $\mathsf{CONGEST}$ model. We use a known reduction for simulating algorithms on the line graph while incurring congestion, but we show our algorithm is part of a broad family of \emph{local aggregation algorithms} for which we describe a mechanism that allows the simulation to run in the $\mathsf{CONGEST}$ model without an additional overhead. Next, we show that for maximum weight matching, relaxing the approximation factor to ($2+\varepsilon$) allows us to devise a distributed algorithm requiring $O(\frac{\log \Delta}{\log\log\Delta})$ rounds for any constant $\varepsilon>0$. For the unweighted case, we can even obtain a $(1+\varepsilon)$-approximation in this number of rounds. These algorithms are the first to achieve the provably optimal round complexity with respect to dependency on $\Delta$