Related papers: Time and Space Efficient Algorithms for RNA Foldin…
The problem of RNA secondary structure design (also called inverse folding) is the following: given a target secondary structure, one aims to create a sequence that folds into, or is compatible with, a given structure. In several practical…
RNA molecules are essential cellular machines performing a wide variety of functions for which a specific three-dimensional structure is required. Over the last several years, experimental determination of RNA structures through X-ray…
mRNA technology has revolutionized vaccine development, protein replacement therapies, and cancer immunotherapies, offering rapid production and precise control over sequence and efficacy. However, the inherent instability of mRNA poses…
We consider the inverse-folding problem for RNA secondary structures: for a given (pseudo-knot-free) secondary structure find a sequence that has that structure as its ground state. If such a sequence exists, the structure is called…
An RNA sequence is a string composed of four types of nucleotides, $A, C, G$, and $U$. The goal of the RNA folding problem is to find a maximum cardinality set of crossing-free pairs of the form $\{A,U\}$ or $\{C,G\}$ in a given RNA…
We extend an hypergraph representation, introduced by Finkelstein and Roytberg, to unify dynamic programming algorithms in the context of RNA folding with pseudoknots. Classic applications of RNA dynamic programming energy minimization,…
One of the most fundamental problems in Computer Science is the Knapsack problem. Given a set of n items with different weights and values, it asks to pick the most valuable subset whose total weight is below a capacity threshold T. Despite…
We present space efficient Monte Carlo algorithms that solve Subset Sum and Knapsack instances with $n$ items using $O^*(2^{0.86n})$ time and polynomial space, where the $O^*(\cdot)$ notation suppresses factors polynomial in the input size.…
In this paper, we present a novel algorithm and its three variations for solving the Rubik's cube more efficiently. This algorithm can be used to solve the complete $n \times n \times n$ cube in $O(\frac{n^2}{\log n})$ moves. This algorithm…
We consider the algorithm by Ferson et al. (Reliable computing 11(3), p. 207-233, 2005) designed for solving the NP-hard problem of computing the maximal sample variance over interval data, motivated by robust statistics (in fact, the…
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…
We study the Multiple Cluster Scheduling problem and the Multiple Strip Packing problem. For both problems, there is no algorithm with approximation ratio better than $2$ unless $P = NP$. In this paper, we present an algorithm with…
The generalized egg dropping problem is a classic challenge in sequential decision-making. Standard dynamic programming evaluates the minimax minimum number of tests in $\mathcal{O}(K \cdot N^2)$ time. A known approach formulates the…
Computational prediction of RNA structures is an important problem in computational structural biology. Studies of RNA structure formation often assume that the process starts from a fully synthesized sequence. Experimental evidence,…
Dual graphs have been applied to model RNA secondary structures with pseudoknots, or intertwined base pairs. In previous works, a linear-time algorithm was introduced to partition dual graphs into maximally connected components called…
An NP-hard graph problem may be intractable for general graphs but it could be efficiently solvable using dynamic programming for graphs with bounded width (or depth or some other structural parameter). Dynamic programming is a well-known…
Given in the plane a set of points and a set of halfplanes, we consider the problem of computing a smallest subset of halfplanes whose union covers all points. In this paper, we present an $O(n^{4/3}\log^{5/3}n\log^{O(1)}\log n)$-time…
Classical density functional theory (DFT) of fluids is a valuable tool to analyze inhomogeneous fluids. However, few numerical solution algorithms for three-dimensional systems exist. Here we present an efficient numerical scheme for fluids…
We propose faster algorithms for the following three optimization problems on $n$ collinear points, i.e., points in dimension one. The first two problems are known to be NP-hard in higher dimensions. 1- Maximizing total area of disjoint…
We study quantum algorithms for several fundamental string problems, including Longest Common Substring, Lexicographically Minimal String Rotation, and Longest Square Substring. These problems have been widely studied in the stringology…