Related papers: An Algorithm for RNA Pseudoknots
Define a "nuclear partition" to be an integer partition with no part equal to one. In this study we prove a simple formula to compute the partition function $p(n)$ by counting only the nuclear partitions of $n$, a vanishingly small subset…
We offer multiplication method for factoring big natural numbers which extends the group of the Fermat's and Lehman's factorization algorithms and has run-time complexity $O(n^{1/3})$. This paper is argued the finiteness of proposed…
The information-encoding molecules RNA and DNA form a combinatorially large set of secondary structures through nucleic acid base pairing. Thermodynamic prediction algorithms predict favoured, or minimum free energy (MFE), secondary…
A lattice model of RNA denaturation which fully accounts for the excluded volume effects among nucleotides is proposed. A numerical study shows that interactions forming pseudoknots must be included in order to get a sharp continuous…
In a previous paper (q-alg/9501022) we suggested some algorithms that could be useful in solving the problem of knot classification. Here we continue this discussion by answering questions raised in that paper and by commenting on practical…
We present a novel quantum algorithm for estimating Gibbs partition functions in sublinear time with respect to the logarithm of the size of the state space. This is the first speed-up of this type to be obtained over the seminal…
We describe an algorithm for comparing two RNA secondary structures coded in the form of trees that introduces two new operations, called node fusion and edge fusion, besides the tree edit operations of deletion, insertion, and relabeling…
The subject of this paper is the time complexity of approximating Knapsack, Subset Sum, Partition, and some other related problems. The main result is an $\widetilde{O}(n+1/\varepsilon^{5/3})$ time randomized FPTAS for Partition, which is…
Rook polynomials are a powerful tool in the theory of restricted permutations. It is known that the rook polynomial of any board can be computed recursively, using a cell decomposition technique of Riordan. In this paper, we give a new…
A poly-log time method to compute the truncated theta function, its derivatives, and integrals is presented. The method is elementary, rigorous, explicit, and suited for computer implementation. We repeatedly apply the Poisson summation…
In this paper we present the asymptotic enumeration of RNA structures with pseudoknots. We develop a general framework for the computation of exponential growth rate and the sub exponential factors for $k$-noncrossing RNA structures. Our…
In a previous paper [CSIAM Trans. Appl. Math. 2 (2021), 1-55], the authors proposed a theoretical framework for the analysis of RNA velocity, which is a promising concept in scRNA-seq data analysis to reveal the cell state-transition…
This paper presents a new method for pre-training neural networks that can decrease the total training time for a neural network while maintaining the final performance, which motivates its use on deep neural networks. By partitioning the…
Computational protein structure determination involves optimization in a problem space much too large to exhaustively search. Existing approaches include optimization algorithms such as gradient descent and simulated annealing, but these…
In this paper, we develop a polynomial time algorithm to compute a Dulmage-Mendelsohn-type decomposition of a matrix partitioned into submatrices of rank at most $1$.
RNA structure prediction is a challenging problem, especially with pseudoknots. Recently, there has been a shift from the classical minimum free energy-based methods (MFE) to partition function-based ones that assemble structures using…
We design a recursive algorithm to compute the partition function of the Ising model, summed over cubic maps with fixed size and genus. The algorithm runs in polynomial time, which is much faster than methods based on a Tutte-like, or…
As a partial answer to a question of Rao, a deterministic and customizable efficient algorithm is presented to test whether an arbitrary graphical degree sequence has a bipartite realization. The algorithm can be configured to run in…
This article introduces recursive relations allowing the calculation of the number of partitions with constraints on the minimum and/or on the maximum fragment size.
In this paper, we study the combinatorial set of RNA secondary structures of length $n$ with $m$ base-pairs. For a compact representation, we encode an RNA secondary structure by the corresponding Motzkin word. For this combinatorial set,…