Related papers: LinearFold: linear-time approximate RNA folding by…

AI-based protein structure prediction pipelines, such as AlphaFold2, have achieved near-experimental accuracy. These advanced pipelines mainly rely on Multiple Sequence Alignments (MSAs) as inputs to learn the co-evolution information from…

Recurrent neural networks (RNNs) have recently achieved remarkable successes in a number of applications. However, the huge sizes and computational burden of these models make it difficult for their deployment on edge devices. A practically…

The kinetic folding of RNA sequences into secondary structures is modeled as a complex adaptive system, the components of which are possible RNA structural rearrangements (SRs) and their associated bases and base pairs. RNA bases and base…

RNA-sequencing (RNA-seq) has become an exemplar technology in modern biology and clinical applications over the past decade. It has gained immense popularity in the recent years driven by continuous efforts of the bioinformatics community…

This study employs scientific machine learning to identify transient time series of dynamical systems near a fold bifurcation of periodic solutions. The unique aspect of this work is that a convolutional neural network (CNN) is trained with…

In this paper, we consider tree decompositions, branch decompositions, and clique decompositions. We improve the running time of dynamic programming algorithms on these graph decompositions for a large number of problems as a function of…

We give an approximation algorithm for packing and covering linear programs (linear programs with non-negative coefficients). Given a constraint matrix with n non-zeros, r rows, and c columns, the algorithm computes feasible primal and dual…

RNA design is the search for a sequence or set of sequences that will fold into predefined structures, also known as the inverse problem of RNA folding. While numerous RNA design methods have been invented to find sequences capable of…

Nanopore sequencing enables real-time long-read DNA sequencing with reads exceeding 10 kilobases, but inherent error rates of 12-15 percent present significant computational challenges for read alignment. The critical seed chaining step…

A run in a string is a maximal periodic substring. For example, the string $\texttt{bananatree}$ contains the runs $\texttt{anana} = (\texttt{an})^{3/2}$ and $\texttt{ee} = \texttt{e}^2$. There are less than $n$ runs in any length-$n$…

Positive linear programs (LP), also known as packing and covering linear programs, are an important class of problems that bridges computer science, operations research, and optimization. Despite the consistent efforts on this problem, all…

Described are two algorithms to find long approximate palindromes in a string, for example a DNA sequence. A simple algorithm requires O(n)-space and almost always runs in $O(k.n)$-time where n is the length of the string and k is the…

We propose a new way of looking at global optimization of off-lattice protein models. We present a dual optimization concept of predicting optimal sequences as well as optimal folds. We validate the utility of the recently introduced…

We propose a new approach for calculating the Lempel-Ziv factorization of a string, based on run length encoding (RLE). We present a conceptually simple off-line algorithm based on a variant of suffix arrays, as well as an on-line algorithm…

Solving the RNA inverse folding problem is a critical prerequisite to RNA design, an emerging field in bioengineering with a broad range of applications from reaction catalysis to cancer therapy. Although significant progress has been made…

Motivated by the imminent growth of massive, highly redundant genomic databases, we study the problem of compressing a string database while simultaneously supporting fast random access, substring extraction and pattern matching to the…

All-atom simulations have become increasingly popular to study conformational and dynamical properties of nucleic acids as they are accurate and provide high spatial and time resolutions. This high resolution however comes at a heavy…

Electronic phased-array radars offer new possibilities for radar search pattern optimization by using bi-dimensional beam-forming and beam-steering. Radar search pattern optimization can be approximated as a set cover problem and solved…

Understanding the principles of protein folding is a cornerstone of computational biology, with implications for drug design, bioengineering, and the understanding of fundamental biological processes. Lattice protein folding models offer a…

Accurate prediction of RNA properties, such as stability and interactions, is crucial for advancing our understanding of biological processes and developing RNA-based therapeutics. RNA structures can be represented as 1D sequences, 2D…