Combinatorial analysis of interacting RNA molecules

Recently several minimum free energy (MFE) folding algorithms for predicting the joint structure of two interacting RNA molecules have been proposed. Their folding targets are interaction structures, that can be represented as diagrams with two backbones drawn horizontally on top of each other such that (1) intramolecular and intermolecular bonds are noncrossing and (2) there is no "zig-zag" configuration. This paper studies joint structures with arc-length at least four in which both, interior and exterior stack-lengths are at least two (no isolated arcs). The key idea in this paper is to consider a new type of shape, based on which joint structures can be derived via symbolic enumeration. Our results imply simple asymptotic formulas for the number of joint structures with surprisingly small exponential growth rates. They are of interest in the context of designing prediction algorithms for RNA-RNA interactions.Comment: 22 pages, 15 figure

Associative spectra of graph algebras II: Satisfaction of bracketing identities, spectrum dichotomy

Funding Information: This work is funded by National Funds through the FCT—Fundação para a Ciência e a Tecnologia, I.P., under the scope of the Project UIDB/00297/2020 (Center for Mathematics and Applications) and the Project PTDC/MAT-PUR/31174/2017. Funding Information: Research partially supported by the Hungarian Research, Development and Innovation Office Grant K115518, and by Grant TUDFO/47138-1/2019-ITM of the Ministry for Innovation and Technology, Hungary. Publisher Copyright: © 2021, The Author(s).A necessary and sufficient condition is presented for a graph algebra to satisfy a bracketing identity. The associative spectrum of an arbitrary graph algebra is shown to be either constant or exponentially growing.publishersversionepub_ahead_of_prin

Minimizing and Computing the Inverse Geodesic Length on Trees

For any fixed measure H that maps graphs to real numbers, the MinH problem is defined as follows: given a graph G, an integer k, and a target tau, is there a set S of k vertices that can be deleted, so that H(G - S) is at most tau? In this paper, we consider the MinH problem on trees. We call H balanced on trees if, whenever G is a tree, there is an optimal choice of S such that the components of G - S have sizes bounded by a polynomial in n / k. We show that MinH on trees is Fixed-Parameter Tractable (FPT) for parameter n / k, and furthermore, can be solved in subexponential time, and polynomial space, whenever H is additive, balanced on trees, and computable in polynomial time. A particular measure of interest is the Inverse Geodesic Length (IGL), which is used to gauge the efficiency and connectedness of a graph. It is defined as the sum of inverse distances between every two vertices: IGL(G) = sum_{{u,v} subseteq V} 1/d_G(u,v). While MinIGL is W[1]-hard for parameter treewidth, and cannot be solved in 2^{o(k + n + m)} time, even on bipartite graphs with n vertices and m edges, the complexity status of the problem remains open in the case where G is a tree. We show that IGL is balanced on trees, to give a 2^O((n log n)^(5/6)) time, polynomial space algorithm. The distance distribution of G is the sequence {a_i} describing the number of vertex pairs distance i apart in G: a_i = |{{u, v}: d_G(u, v) = i}|. Given only the distance distribution, one can easily determine graph parameters such as diameter, Wiener index, and particularly, the IGL. We show that the distance distribution of a tree can be computed in O(n log^2 n) time by reduction to polynomial multiplication. We also extend the result to graphs with small treewidth by showing that the first p values of the distance distribution can be computed in 2^(O(tw(G))) n^(1 + epsilon) sqrt(p) time, and the entire distance distribution can be computed in 2^(O(tw(G))) n^{1 + epsilon} time, when the diameter of G is O(n^epsilon\u27) for every epsilon\u27 > 0

Smaller ACC0 Circuits for Symmetric Functions

What is the power of constant-depth circuits with $MOD_m$ gates, that can count modulo $m$? Can they efficiently compute MAJORITY and other symmetric functions? When $m$ is a constant prime power, the answer is well understood: Razborov and Smolensky proved in the 1980s that MAJORITY and $MOD_m$ require super-polynomial-size $MOD_q$ circuits, where $q$ is any prime power not dividing $m$. However, relatively little is known about the power of $MOD_m$ circuits for non-prime-power $m$. For example, it is still open whether every problem in $EXP$ can be computed by depth-$3$ circuits of polynomial size and only $MOD_6$ gates. We shed some light on the difficulty of proving lower bounds for $MOD_m$ circuits, by giving new upper bounds. We construct $MOD_m$ circuits computing symmetric functions with non-prime power $m$, with size-depth tradeoffs that beat the longstanding lower bounds for $AC^0[m]$ circuits for prime power $m$. Our size-depth tradeoff circuits have essentially optimal dependence on $m$ and $d$ in the exponent, under a natural circuit complexity hypothesis. For example, we show for every $\varepsilon > 0$ that every symmetric function can be computed with depth-3 $MOD_m$ circuits of $\exp(O(n^{\varepsilon}))$ size, for a constant $m$ depending only on $\varepsilon > 0$. That is, depth-$3$ $CC^0$ circuits can compute any symmetric function in \emph{subexponential} size. This demonstrates a significant difference in the power of depth-$3$ $CC^0$ circuits, compared to other models: for certain symmetric functions, depth-$3$ $AC^0$ circuits require $2^{\Omega(\sqrt{n})}$ size [H{\aa}stad 1986], and depth-$3$ $AC^0[p^k]$ circuits (for fixed prime power $p^k$) require $2^{\Omega(n^{1/6})}$ size [Smolensky 1987]. Even for depth-two $MOD_p \circ MOD_m$ circuits, $2^{\Omega(n)}$ lower bounds were known [Barrington Straubing Th\'erien 1990].Comment: 15 pages; abstract edited to fit arXiv requirement

Diagonalizations over polynomial time computable sets

AbstractA formal notion of diagonalization is developed which allows to enforce properties that are related to the class of polynomial time computable sets (the class of polynomial time computable functions respectively), like, e.g., p-immunity. It is shown that there are sets—called p-generic— which have all properties enforceable by such diagonalizations. We study the behaviour and the complexity of p-generic sets. In particular, we show that the existence of p-generic sets in NP is oracle dependent, even if we assume P ≠ NP