Related papers: Inverse folding of RNA pseudoknot structures
The alignment between RNA sequences and structures in foundation models (FMs) has yet to be thoroughly investigated. Existing FMs have struggled to establish sequence-structure alignment, hindering the free flow of genomic information…
RNA folding is a kinetic process governed by the competition of a large number of structures stabilized by the transient formation of base pairs that may induce complex folding pathways and the formation of misfolded structures. Despite of…
Recent model inversion attack algorithms permit adversaries to reconstruct a neural network's private and potentially sensitive training data by repeatedly querying the network. In this work, we develop a novel network architecture that…
Recent advancements in machine learning techniques for protein folding motivate better results in its inverse problem -- protein design. In this work we introduce a new graph mimetic neural network, MimNet, and show that it is possible to…
Neural networks functions are supposed to be able to encode the desired solution of an inverse problem very efficiently. In this paper, we consider the problem of solving linear inverse problems with neural network coders. First we…
We introduce a neural network architecture to solve inverse problems linked to a one-dimensional integral operator. This architecture is built by unfolding a forward-backward algorithm derived from the minimization of an objective function…
Rising costs in recent years of developing new drugs and treatments have led to extensive research in optimization techniques in biomolecular design. Currently, the most widely used approach in biomolecular design is directed evolution,…
The topological framework of circuit topology has recently been introduced to complement knot theory and to help in understanding the physics of molecular folding. Naturally evolved linear molecular chains, such as proteins and nucleic…
The primary structure of a ribonucleic acid (RNA) molecule can be represented as a sequence of nucleotides (bases) over the alphabet {A, C, G, U}. The secondary or tertiary structure of an RNA is a set of base pairs which form bonds between…
The inverse mapping of GANs'(Generative Adversarial Nets) generator has a great potential value.Hence, some works have been developed to construct the inverse function of generator by directly learning or adversarial learning.While the…
We develop a physics-informed neural networks (PINNs) framework for the inverse scattering problem in nuclear physics and apply it to the $P_{3/2}$ partial wave of neutron-alpha elastic scattering. The radial potential is represented by a…
Due to the hierarchical organization of RNA structures and their pivotal roles in fulfilling RNA functions, the formation of RNA secondary structure critically influences many biological processes and has thus been a crucial research topic.…
Long non-coding RNA, microRNA, and messenger RNA enable key regulations of various biological processes through a variety of diverse interaction mechanisms. Identifying the interactions and cross-talk between these heterogeneous RNA classes…
This paper has presented inversely determining the resonant configuration of the bilateral nanostructures for periodic metallic slits with extraordinary optical transmission performance. The topology optimization approach is utilized to…
In this paper we study $k$-noncrossing, canonical RNA pseudoknot structures with minimum arc-length $\ge 4$. Let ${\sf T}_{k,\sigma}^{[4]} (n)$ denote the number of these structures. We derive exact enumeration results by computing the…
The RNA inverse folding problem aims to identify nucleotide sequences that preferentially adopt a given target secondary structure. While various heuristic and machine learning-based approaches have been proposed, many require a large…
The paper proposes to employ deep convolutional neural networks (CNNs) to classify noncoding RNA (ncRNA) sequences. To this end, we first propose an efficient approach to convert the RNA sequences into images characterizing their…
In this paper we study irreducibility in RNA structures. By RNA structure we mean RNA secondary as well as RNA pseudoknot structures. In our analysis we shall contrast random and minimum free energy (mfe) configurations. We compute various…
The high-throughput short-reads RNA-seq protocols often produce paired-end reads, with the middle portion of the fragments being unsequenced. We explore if the full-length fragments can be computationally reconstructed from the sequenced…
The Human Genome Project has led to an exponential increase in data related to the sequence, structure, and function of biomolecules. Bioinformatics is an interdisciplinary research field that primarily uses computational methods to analyze…