Related papers: RNA Folding and Large N Matrix Theory
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…
DNA sequences are prone to creating secondary structures by folding back on themselves by non-specific hybridization among its nucleotides. The formation of secondary structures makes the sequences chemically inactive towards synthesis and…
We prove a conjecture of W.~Hackbusch in a bigger generality than in our previous article. Here we consider Tensor Train (TT) model with an arbitrary number of leaves and a corresponding "almost binary tree" for Hierarchical Tucker (HT)…
The main purpose of this paper is to present a kneading theory for two-dimensional triangular maps. This is done by defining a tensor product between the polynomials and matrices corresponding to the one-dimensional basis map and fiber map.…
Nonnegative matrix factorization (NMF) has found many applications including topic modeling and document analysis. Hierarchical NMF (HNMF) variants are able to learn topics at various levels of granularity and illustrate their hierarchical…
We consider a certain abstract of RNA secondary structures, which is closely related to RNA shapes. The generating function counting the number of the abstract structures is obtained by means of Narayana numbers and 2-Motzkin paths, through…
In this note, we first explain the equivalence between the interaction Hamiltonian of Green-Schwarz light-cone gauge superstring field theory and the twist field formalism known from matrix string theory. We analyze the role of the large N…
We study mass-deformed N=2 gauge theories from various points of view. Their partition functions can be computed via three dual approaches: firstly, (p,q)-brane webs in type II string theory using Nekrasov's instanton calculus, secondly,…
A linear external perturbation is introduced in the action of the partition function of the random matrix model of RNA [G. Vernizzi, H. Orland and A. Zee, Phys. Rev. Lett. 94, 168103 (2005)]. It is seen that (i). the perturbation…
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…
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…
Data often comes in the form of an array or matrix. Matrix factorization techniques attempt to recover missing or corrupted entries by assuming that the matrix can be written as the product of two low-rank matrices. In other words, matrix…
Random contractions (sub-unitary random matrices) appear naturally when considering quantized chaotic maps within a general theory of open linear stationary systems with discrete time. We analyze statistical properties of complex…
It has been shown that minimum free energy structure for RNAs and RNA-RNA interaction is often incorrect due to inaccuracies in the energy parameters and inherent limitations of the energy model. In contrast, ensemble based quantities such…
Given a random RNA secondary structure, $S$, we study RNA sequences having fixed ratios of nuclotides that are compatible with $S$. We perform this analysis for RNA secondary structures subject to various base pairing rules and minimum arc-…
We present a general setting for structure-sequence comparison in a large class of RNA structures that unifies and generalizes a number of recent works on specific families on structures. Our approach is based on tree decomposition of…
Neural networks are typically represented as data structures that are traversed either through iteration or by manual chaining of method calls. However, a deeper analysis reveals that structured recursion can be used instead, so that…
Background: In the Nearest-Neighbor Thermodynamic Model, a standard approach for RNA secondary structure prediction, the energy of the multiloops is modeled using a linear entropic penalty governed by three branching parameters. Although…
This paper presents a method of reconstruction a primary structure of a protein that folds into a given geometrical shape. This method predicts the primary structure of a protein and restores its linear sequence of amino acids in the…
We introduce the notion of a restricted exchangeable partition of $\mathbb{N}$. We obtain integral representations, consider associated fragmentations, embeddings into continuum random trees and convergence to such limit trees. In…