Related papers: Random $k$-noncrossing RNA Structures

Classical methods such as Principal Component Analysis (PCA) and Canonical Correlation Analysis (CCA) are ubiquitous in statistics. However, these techniques are only able to reveal linear relationships in data. Although nonlinear variants…

In this paper we present an algorithm for enumerating without repetitions all the non-crossing generically minimally rigid bar-and-joint frameworks under edge constraints (also called constrained non-crossing Laman frameworks) on a given…

We introduce a new domain decomposition strategy for time harmonic Maxwell's equations that is valid in the case of automatically generated subdomain partitions with possible presence of cross-points. The convergence of the algorithm is…

The material gives a new combinatorial proof of the multiplicative property of the S-transform. In particular, several properties of the coefficients of its inverse are connected to non-crossing linked partitions and planar trees.

This paper motivates the use of random-bridges -- stochastic processes conditioned to take target distributions at fixed timepoints -- in the realm of generative modelling. Herein, random-bridges can act as stochastic transports between two…

We present a novel method for computing reachability probabilities of parametric discrete-time Markov chains whose transition probabilities are fractions of polynomials over a set of parameters. Our algorithm is based on two key…

We consider the problem of stochastic flow of multiple particles traveling on a closed loop, with a constraint that particles move without passing. We use a Markov chain description that reduces the problem to a generalized random walk on a…

The shortest secure path (routing) problem in communication networks has to deal with multiple attack layers e.g., man-in-the-middle, eavesdropping, packet injection, packet insertion, etc. Consider different probabilities for each such…

We extend our techniques developed in our earlier paper appeared in Computational Complexity, 2017 (preprint: arXiv:1508.00690) to obtain a deterministic polynomial time algorithm for computing the non-commutative rank together with…

In this paper an algorithm is given to determine all possible structurally different linearly conjugate realizations of a given kinetic polynomial system. The solution is based on the iterative search for constrained dense realizations…

A growing number of RNA sequences are now known to have distributions of multiple stable sequences. Recent algorithms use the list of nucleotides in a sequence and auxiliary experimental data to predict such distributions. Although the…

Pairwise ordered tree alignment are combinatorial objects that appear in RNA secondary structure comparison. However, the usual representation of tree alignments as supertrees is ambiguous, i.e. two distinct supertrees may induce identical…

We present results on the enumeration of crossings and nestings for matchings and set partitions. Using a bijection between partitions and vacillating tableaux, we show that if we fix the sets of minimal block elements and maximal block…

Crystal structure prediction has traditionally relied on prototype-based seeding, approaches that often bias sampling toward known low-energy basins and overlook metastable polymorphs with unconventional symmetries. Here, we introduce…

Understanding the local structure of a graph provides valuable insights about the underlying phenomena from which the graph has originated. Sampling and examining k-subgraphs is a widely used approach to understand the local structure of a…

Various specifiable combinatorial structures, with d extensive parameters, can be exactly sampled both by the recursive method, with linear arithmetic complexity if a heavy preprocessing is performed, or by the Boltzmann method, with…

We introduce the problem of Poisson sampling over joins: compute a sample of the result of a join query by conceptually performing a Bernoulli trial for each join tuple, using a non-uniform and tuple-specific probability. We propose an…

We propose a new approach for estimating the finite dimensional transition matrix of a Markov chain using a large number of independent sample paths observed at random times. The sample paths may be observed as few as two times, and the…

An RNA sequence is a word over an alphabet on four elements $\{A,C,G,U\}$ called bases. RNA sequences fold into secondary structures where some bases match one another while others remain unpaired. Pseudoknot-free secondary structures can…

Chen, Deng, Du, Stanley, and Yan introduced the notion of $k$-crossings and $k$-nestings for set partitions, and proved that the sizes of the largest $k$-crossings and $k$-nestings in the partitions of an $n$-set possess a symmetric joint…