Related papers: An Algorithm for RNA Pseudoknots
The generating function for $p_N(n)$, the number of partitions of $n$ into at most $N$ parts, may be written as a product of $N$ factors. In part I, we studied the behavior of coefficients in the partial fraction decomposition of this…
We study two important operations on polynomials defined over complete discrete valuation fields: Euclidean division and factorization. In particular, we design a simple and efficient algorithm for computing slope factorizations, based on…
We state and analyze a generalization of the "truncation trick" suggested by Gourdon and Sebah to improve the performance of power series evaluation by binary splitting. It follows from our analysis that the values of D-finite functions…
Let $P$ be a set of $m$ points in ${\mathbb R}^2$, let $\Sigma$ be a set of $n$ semi-algebraic sets of constant complexity in ${\mathbb R}^2$, let $(S,+)$ be a semigroup, and let $w: P \rightarrow S$ be a weight function on the points of…
Computational RNA design tasks are often posed as inverse problems, where sequences are designed based on adopting a single desired secondary structure without considering 3D conformational diversity. We introduce gRNAde, a geometric RNA…
Repeated recursion unfolding is a new approach that repeatedly unfolds a recursion with itself and simplifies it while keeping all unfolded rules. Each unfolding doubles the number of recursive steps covered. This reduces the number of…
We consider a recently introduced fair repetitive scheduling problem involving a set of clients, each asking for their associated job to be daily scheduled on a single machine across a finite planning horizon. The goal is to determine a job…
RNAs self-interact through hydrogen-bond base-pairing between nucleotides and fold into specific, stable structures that substantially govern their biochemical behaviour. Experimental characterization of these structures remains difficult,…
We present an algorithm for recovering planted solutions in two well-known models, the stochastic block model and planted constraint satisfaction problems, via a common generalization in terms of random bipartite graphs. Our algorithm…
In this paper we introduce efficient algorithm for the multiplication of split-octonions. The direct multiplication of two split-octonions requires 64 real multiplications and 56 real additions. More effective solutions still do not exist.…
It has been well accepted that the RNA secondary structures of most functional non-coding RNAs (ncRNAs) are closely related to their functions and are conserved during evolution. Hence, prediction of conserved secondary structures from…
Given an approximation to a multiple isolated solution of a polynomial system of equations, we have provided a symbolic-numeric deflation algorithm to restore the quadratic convergence of Newton's method. Using first-order derivatives of…
Reducing the conditions under which a given set satisfies the stipulations of the subset sum proposition to a set of linear relationships, the question of whether a set satisfies subset sum may be answered in a polynomial number of steps by…
Exact numerical methods and stochastic simulation methods are developed to study the force stretching single RNA issue on the secondary structure level in equilibrium. By computing the force-extension curves on the constant force and the…
Estimating quantum partition functions is a critical task in a variety of fields. However, the problem is classically intractable in general due to the exponential scaling of the Hamiltonian dimension $N$ in the number of particles. This…
In this paper, based on the homotopy continuation method and the interval Newton method, an efficient algorithm is introduced to isolate the real roots of semi-algebraic system. Tests on some random examples and a variety of problems…
We study theoretically the denaturation of single RNA molecules by mechanical stretching, focusing on signatures of the (un)folding pathway in molecular fluctuations. Our model describes the interactions between nucleotides by incorporating…
We describe a new algorithm that computes the n-th Bernoulli number in n^(4/3 + o(1)) bit operations. This improves on previous algorithms that had complexity n^(2 + o(1)).
Deep neural networks (DNNs) are nowadays witnessing a major success in solving many pattern recognition tasks including skeleton-based classification. The deployment of DNNs on edge-devices, endowed with limited time and memory resources,…
Genome annotation is an important issue in biology which has long been addressed with gene prediction methods and manual experiments requiring biological expertise. The expanding Next Generation Sequencing technologies and their enhanced…