相关论文: Central and Local Limit Theorems for RNA Structure…
We modify and extend the recently developed statistical mechanical model for predicting the thermodynamic properties of chain molecules having noncovalent double-stranded conformations, as in RNA or ssDNA, and $\beta-$sheets in protein, by…
A new statistical method of alignment of two heteropolymers which can form hierarchical cloverleaf-like secondary structures is proposed. This offers a new constructive algorithm for quantitative determination of binding free energy of two…
The k-truss model is one of the most important models in cohesive subgraph analysis. The k-truss decomposition problem is to compute the trussness of each edge in a given graph, and has been extensively studied. However, the conventional…
Secondary structure plays an important role in determining the function of non-coding RNAs. Hence, identifying RNA secondary structures is of great value to research. Computational prediction is a mainstream approach for predicting RNA…
We establish central limit theorems (CLTs) for the linear spectral statistics of the adjacency matrix of inhomogeneous random graphs across all sparsity regimes, providing explicit covariance formulas under the assumption that the variance…
For $\alpha \in (1,2]$, the $\alpha$-stable graph arises as the universal scaling limit of critical random graphs with i.i.d. degrees having a given $\alpha$-dependent power-law tail behavior. It consists of a sequence of compact measured…
In this paper we enumerate $k$-noncrossing tangled-diagrams. A tangled-diagram is a labeled graph whose vertices are $1,...,n$ have degree $\le 2$, and are arranged in increasing order in a horizontal line. Its arcs are drawn in the upper…
This is the fourth in a series of articles devoted to showing that a typical covering map of large degree to a fixed, regular graph has its new adjacency eigenvalues within the bound conjectured by Alon for random regular graphs. In this…
The intricate network of interactions observed in RNA three-dimensional structures is often described in terms of a multitude of geometrical properties, including helical parameters, base pairing/stacking, hydrogen bonding and backbone…
We study the asymptotic distribution of the two following combinatorial parameters: the number of arc crossings in the linear representation, ${\mathrm cr^{(\ell)}$, and the number of chord crossings in the circular representation,…
Non-coding RNAs are ubiquitous, but the discovery of new RNA gene sequences far outpaces research on their structure and functional interactions. We mine the evolutionary sequence record to derive precise information about function and…
The linear algorithm of the the full non-linear large scale structure of Gaussian random fields is extended here to to perform non-linear CRs. The procedure consists of: (1) Using linear CR of low resolution data to construct a high…
Like simpler graphs, nested (hypernodal) graphs consist of two components: a set of nodes and a set of edges, where each edge connects a pair of nodes. In the hypernodal graph model, however, a node may contain other graphs, so that a node…
RNA forms elaborate secondary structures through intramolecular base pairing. These structures perform critical biological functions within each cell. Due to the availability of a polynomial algorithm to calculate the partition function…
Graph Neural Networks (GNNs) have emerged as a flexible and powerful approach for learning over graphs. Despite this success, existing GNNs are constrained by their local message-passing architecture and are provably limited in their…
Small non-coding RNAs can exert significant regulatory activity on gene expression in bacteria. In recent years, substantial progress has been made in understanding bacterial gene expression by sRNAs. However, recent findings that…
The ongoing effort to detect and characterize physical entanglement in biopolymers has so far established that knots are present in many globular proteins and also abound in viral DNA packaged inside bacteriophages. RNA molecules, on the…
The Kinetoplast DNA (kDNA) is a two-dimensional Olympic-ring-like network of mutually linked 2.5 kb-long DNA minicircles found in certain parasites called Trypanosomes. Understanding the self-assembly and replication of this structure are…
In cond-mat/9907125 the low-temperature behavior of a model for RNA secondary structure was studied. It is claimed that the model exhibits a breaking of the replica symmetry, since the width of the distribution P(q) of overlaps may converge…
In this paper we experiment with using neural network structures to predict a protein's secondary structure ({\alpha} helix positions) from only its primary structure (amino acid sequence). We implement a fully connected neural network…