Related papers: Canonical RNA pseudoknot structures
RNA is a fundamental class of biomolecules that mediate a large variety of molecular processes within the cell. Computational algorithms can be of great help in the understanding of RNA structure-function relationship. One of the main…
Over the past few years, trace regression models have received considerable attention in the context of matrix completion, quantum state tomography, and compressed sensing. Estimation of the underlying matrix from regularization-based…
Let n_g denote the number of numerical semigroups of genus g. Bras-Amoros conjectured that n_g possesses certain Fibonacci-like properties. Almost all previous attempts at proving this conjecture were based on analyzing the semigroup tree.…
Let k be a positive integer. A sequence s over an n-element alphabet A is called a k-radius sequence if every two symbols from A occur in s at distance of at most k. Let f_k(n) denote the length of a shortest k-radius sequence over A. We…
Accurate RNA structure modeling remains difficult because RNA backbones are highly flexible, non-canonical interactions are prevalent, and experimentally determined 3D structures are comparatively scarce. We introduce \emph{RiboSphere}, a…
We study the triangular array defined by the Graham--Knuth--Patashnik recurrence $T(n,k) = (\alpha n + \beta k + \gamma)\, T(n-1,k)+(\alpha' n + \beta' k + \gamma') \, T(n-1,k-1)$ with initial condition $T(0,k) = \delta_{k0}$ and parameters…
We study the problem of column selection in large-scale kernel canonical correlation analysis (KCCA) using the Nystr\"om approximation, where one approximates two positive semi-definite kernel matrices using "landmark" points from the…
A Seifert surface for a knot K is called canonical if it can be built by applying Seifert's algorithm to some projection of K. The canonical genus of K is the smallest genus of a surface so obtained. In this paper we show that there is a…
We study canonical filtrations of finite-dimensional associative algebras and Lie algebras. These filtrations are defined via optimal destabilizing one-parameter subgroups in the sense of geometric invariant theory (GIT), and appear to be a…
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…
Motivation: Non-coding RNAs (ncRNAs) express their functions by adopting molecular structures. Specifically, RNA secondary structures serve as a relatively stable intermediate step before tertiary structures, offering a reliable signature…
Selection comparator networks have been studied for many years. Recently, they have been successfully applied to encode cardinality constraints for SAT-solvers. To decrease the size of generated formula there is a need for constructions of…
In array-based DNA synthesis, multiple strands of DNA are synthesized in parallel to reduce the time cost from the sum of their lengths to the length their shortest common supersequences. To maximize the amount of information that can be…
An endhered (end-adhered) pattern is a subset of arcs in matchings, such that the corresponding starting points are consecutive and the same holds for the ending points. Such patterns are in one-to-one correspondence with the permutations.…
Canonical Correlation Analysis (CCA) is a classical tool for finding correlations among the components of two random vectors. In recent years, CCA has been widely applied to the analysis of genomic data, where it is common for researchers…
We focus on N = 3 chiral supergravity (SUGRA) which is the lowest N theory involving a spin-1/2 field, and derive the Ashtekar's canonical formulation of N = 3 SUGRA starting with the chiral Lagrangian constructed by closely following the…
In previous work, we gave asymptotic counting results for the number of tree-child and normal networks with $k$ reticulation vertices and explicit exponential generating functions of the counting sequences for $k=1,2,3$. The purpose of this…
We show that the SL(2,C)-character variety of the (-2,3,n) pretzel knot consists of two (respectively three) algebraic curves when 3 does not divide n (respectively 3 divides n) and give an explicit calculation of the Culler-Shalen…
Canonical orders, introduced in the minimal model program for orders, are simultaneous generalisations of Kleinian singularities and their associated skew group rings. In this paper, we construct minimal resolutions of canonical orders via…
This paper contains linear systems of equations which can distinguish knots without knot invariants. Let $M_n$ be the topological moduli space of all n-component string links and such that a fixed projection into the plane is an immersion.…