Related papers: Random $k$-noncrossing RNA Structures
We explain the relation between certain random tiling models and interacting particle systems belonging to the anisotropic KPZ (Kardar-Parisi-Zhang) universality class in 2+1-dimensions. The link between these two \emph{a priori} disjoint…
I present an algorithm that, given a number $n \geq 1$, computes a compact representation of the set of all noncrossing acyclic digraphs with $n$ nodes. This compact representation can be used as the basis for a wide range of dynamic…
Many models for chaotic systems consist of joining two integrable systems with incompatible constants of motion. The quantum counterparts of such models have a propagator which factorizes into two integrable parts. Each part can be…
This short course offers a new perspective on randomized algorithms for matrix computations. It explores the distinct ways in which probability can be used to design algorithms for numerical linear algebra. Each design template is…
We propose a stochastic method to generate exactly the overdamped Langevin dynamics of semi-flexible Gaussian chains, conditioned to evolve between given initial and final conformations in a preassigned time. The initial and final…
We present an alternate formulation of the partial assignment problem as matching random clique complexes, that are higher-order analogues of random graphs, designed to provide a set of invariants that better detect higher-order structure.…
Given a set of well-formed terminal pairs on the external face of an undirected planar graph with unit edge weights, we give a linear-time algorithm for computing the union of non-crossing shortest paths joining each terminal pair, where…
Randomized iterative algorithms have attracted much attention in recent years because they can approximately solve large-scale linear systems of equations without accessing the entire coefficient matrix. In this paper, we propose two novel…
Schutzenberger's theorem for the ordinary RSK correspondence naturally extends to Chen et. al's correspondence for matchings and partitions. Thus the counting of bilaterally symmetric $k$-noncrossing partitions naturally arises as an…
An RNA molecule is structured on several layers. The primary and most obvious structure is its sequence of bases, i.e. a word over the alphabet {A,C,G,U}. The higher structure is a set of one-to-one base-pairings resulting in a…
Boltzmann samplers and the recursive method are prominent algorithmic frameworks for the approximate-size and exact-size random generation of large combinatorial structures, such as maps, tilings, RNA sequences or various tree-like…
We describe a dynamic programming algorithm for predicting optimal RNA secondary structure, including pseudoknots. The algorithm has a worst case complexity of ${\cal O}(N^6)$ in time and ${\cal O}(N^4)$ in storage. The description of the…
In this paper we study $\gamma$-structures filtered by topological genus. $\gamma$-structures are a class of RNA pseudoknot structures that plays a key role in the context of polynomial time folding of RNA pseudoknot structures. A…
We give an algorithm that generates a uniformly random contingency table with specified marginals, i.e. a matrix with non-negative integer values and specified row and column sums. Such algorithms are useful in statistics and combinatorics.…
We consider a two dimensional reflecting random walk on the nonnegative integer quadrant. It is assumed that this reflecting random walk has skip free transitions. We are concerned with its time reversed process assuming that the stationary…
Matching is a method of the design of experiments. If we had an even number of patients and wanted to form pairs of patients such that their ages, for example, in each pair be as close as possible, we would use nonbipartite matching. Not…
In this paper we show how to express RNA tertiary interactions via the concepts of tangled diagrams. Tangled diagrams allow to formulate RNA base triples and pseudoknot-interactions and to control the maximum number of mutually crossing…
Analysis of the sequence-structure relationship in RNA molecules are essential to evolutionary studies but also to concrete applications such as error-correction methodologies in sequencing technologies. The prohibitive sizes of the…
The primary structure of a ribonucleic acid (RNA) molecule can be represented as a sequence of nucleotides (bases) over the alphabet {A, C, G, U}. The secondary or tertiary structure of an RNA is a set of base pairs which form bonds between…
We propose to construct cross and joint ordinal pattern transition networks from multivariate time series for two coupled systems, where synchronizations are often present. In particular, we focus on phase synchronization, which is one of…