Related papers: Faster Algorithms for RNA-folding using the Four-R…
In this paper, we develop new algorithms for the basic RNA folding problem. Given an RNA sequence that contains $n$ nucleotides, the goal of the problem is to compute a pseudoknot-free secondary structure that maximizes the number of base…
Motivation: Predicting the secondary structure of an RNA sequence is useful in many applications. Existing algorithms (based on dynamic programming) suffer from a major limitation: their runtimes scale cubically with the RNA length, and…
We describe a dynamic programming algorithm for predicting optimal RNA secondary structure, including pseudoknots. The algorithm has a worst case complexity of ${\cal O}(N^6)$ in time and ${\cal O}(N^4)$ in storage. The description of the…
Ab initio RNA secondary structure predictions have long dismissed helices interior to loops, so-called pseudoknots, despite their structural importance. Here, we report that many pseudoknots can be predicted through long time scales RNA…
RNA secondary structure prediction is widely used to understand RNA function. Recently, there has been a shift away from the classical minimum free energy (MFE) methods to partition function-based methods that account for folding ensembles…
The classical Sankoff algorithm for the simultaneous folding and alignment of homologous RNA sequences is highly influential, but it suffers from two major limitations in efficiency and modeling power. First, it takes $O(n^6)$ for two…
The Kinfold and KFOLD programs for RNA folding kinetics implement the Gillespie algorithm to generate stochastic folding trajectories from an initial structure s to a target structure t, in which each intermediate secondary structure is…
It is the first step for understanding how RNA structure folds from base sequences that to know how its secondary structure is formed. Traditional energy-based algorithms are short of precision, particularly for non-nested sequences, while…
A class of second-order algorithms is proposed for minimizing smooth nonconvex functions that alternates between regularized Newton and negative curvature steps in an iteration-dependent subspace. In most cases, the Hessian matrix is…
RNA design aims to identify RNA sequences that fold into a target secondary structure. This task is challenging in terms of computational efficiency. Most existing methods focus on either minimum free energy (MFE)-based or ensemble-based…
An RNA sequence is a word over an alphabet on four elements $\{A,C,G,U\}$ called bases. RNA sequences fold into secondary structures where some bases match one another while others remain unpaired. Pseudoknot-free secondary structures can…
We show that the known list-decoding algorithms for univariate multiplicity and folded Reed-Solomon codes can be made to run in $\tilde{O}(n)$ time. Univariate multiplicity codes and FRS codes are natural variants of Reed-Solomon codes that…
Many ncRNAs function through RNA-RNA interactions. Fast and reliable RNA structure prediction with consideration of RNA-RNA interaction is useful. Some existing tools are less accurate due to omitting the competing of intermolecular and…
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…
We have developed a parallel algorithm for radial basis function (RBF) interpolation that exhibits O(N) complexity,requires O(N) storage, and scales excellently up to a thousand processes. The algorithm uses a GMRES iterative solver with a…
Kernel matrices appear in machine learning and non-parametric statistics. Given $N$ points in $d$ dimensions and a kernel function that requires $\mathcal{O}(d)$ work to evaluate, we present an $\mathcal{O}(dN\log N)$-work algorithm for the…
We present a method of computing with matrices over very small finite fields of size larger than 2. Specifically, we show how the Method of Four Russians can be efficiently adapted to these larger fields, and introduce a row-wise matrix…
For many hard computational problems, simple algorithms that run in time $2^n \cdot n^{O(1)}$ arise, say, from enumerating all subsets of a size-$n$ set. Finding (exponentially) faster algorithms is a natural goal that has driven much of…
Stencil computations are widely used to simulate the change of state of physical systems across a multidimensional grid over multiple timesteps. The state-of-the-art techniques in this area fall into three groups: cache-aware tiled looping…
We present an asymptotically faster algorithm for solving linear systems in well-structured 3-dimensional truss stiffness matrices. These linear systems arise from linear elasticity problems, and can be viewed as extensions of graph…