Related papers: Topological language for RNA
In this paper, we use the biological domain knowledge incorporated into stochastic models for ab initio RNA secondary-structure prediction to improve the state of the art in joint compression of RNA sequence and structure data (Liu et al.,…
Learning language of protein sequences, which captures non-local interactions between amino acids close in the spatial structure, is a long-standing bioinformatics challenge, which requires at least context-free grammars. However, complex…
A natural next step in the evolution of constraint-based grammar formalisms from rewriting formalisms is to abstract fully away from the details of the grammar mechanism---to express syntactic theories purely in terms of the properties of…
Background: RNA exhibits a variety of structural configurations. Here we consider a structure to be tantamount to the noncrossing Watson-Crick and \pairGU-base pairings (secondary structure) and additional cross-serial base pairs. These…
We enumerate the number of RNA contact structures according to their genus, i.e. the topological character of their pseudoknots. By using a recently proposed matrix model formulation for the RNA folding problem, we obtain exact results for…
The "RNA world" represents a novel frontier for the study of fundamental biological processes and human diseases and is paving the way for the development of new drugs tailored to the patient's biomolecular characteristics. Although…
Inspired by the success of large language models (LLM) for DNA and proteins, several LLM for RNA have been developed recently. RNA-LLM uses large datasets of RNA sequences to learn, in a self-supervised way, how to represent each RNA base…
Our work is concerned with the generation and targeted design of RNA, a type of genetic macromolecule that can adopt complex structures which influence their cellular activities and functions. The design of large scale and complex…
Text-attributed graphs require models to effectively integrate both structural topology and semantic content. Recent approaches apply large language models to graphs by linearizing structures into token sequences through random walks. These…
Context-free S grammars are introduced, for arbitrary (storage) type S, as a uniform framework for recursion-based grammars, automata, and transducers, viewed as programs. To each occurrence of a nonterminal of a context-free S grammar an…
We present a network model in which words over a specific alphabet, called {\it structures}, are associated to each node and undirected edges are added depending on some distance between different structures. It is shown that this model can…
There exists many complicated $k$-noncrossing pseudoknot RNA structures in nature based on some special conditions. The special characteristic of RNA structures gives us great challenges in researching the enumeration, prediction and the…
Non-coding RNA structure and function are essential to understanding various biological processes, such as cell signaling, gene expression, and post-transcriptional regulations. These are all among the core problems in the RNA field. With…
In this paper we present a sampling framework for RNA structures of fixed topological genus. We introduce a novel, linear time, uniform sampling algorithm for RNA structures of fixed topological genus $g$, for arbitrary $g>0$. Furthermore…
Given usefulness of protein language models (LMs) in structure and functional inference, RNA LMs have received increased attentions in the last few years. However, these RNA models are often not compared against the same standard. Here, we…
Arc-annotated sequences are useful for representing structural information of RNAs and have been extensively used for comparing RNA structures in both terms of sequence and structural similarities. Among the many paradigms referring to…
RNA design, the task of finding a sequence that folds into a target secondary structure, has broad biological and biomedical impact but remains computationally challenging due to the exponentially large sequence space and exponentially many…
Computational prediction of RNA structures is an important problem in computational structural biology. Studies of RNA structure formation often assume that the process starts from a fully synthesized sequence. Experimental evidence,…
In this paper we study the distribution of stacks in $k$-noncrossing, $\tau$-canonical RNA pseudoknot structures ($<k,\tau> $-structures). An RNA structure is called $k$-noncrossing if it has no more than $k-1$ mutually crossing arcs and…
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…