Related papers: Time and Space Efficient Algorithms for RNA Foldin…
We study the computational complexity of approximately computing the partition function of a spin system. Techniques based on standard counting-to-sampling reductions yield $\tilde{O}(n^2)$-time algorithms, where $n$ is the size of the…
String Edit Distance is a more-than-classical problem whose behavior in the dynamic setting, where the strings are updated over time, is well studied. A single-character substitution, insertion, or deletion can be processed in time…
We give a stochastic optimization algorithm that solves a dense $n\times n$ real-valued linear system $Ax=b$, returning $\tilde x$ such that $\|A\tilde x-b\|\leq \epsilon\|b\|$ in time: $$\tilde O((n^2+nk^{\omega-1})\log1/\epsilon),$$ where…
Given a multiset $A = \{a_1, \dots, a_n\}$ of positive integers and a target integer $t$, the Subset Sum problem asks if there is a subset of $A$ that sums to $t$. Bellman's [1957] classical dynamic programming algorithm runs in $O(nt)$…
Makespan scheduling on identical machines is one of the most basic and fundamental packing problems studied in the discrete optimization literature. It asks for an assignment of $n$ jobs to a set of $m$ identical machines that minimizes the…
We consider the problem of finding a desired item out of $N$ items arranged on the sites of a two-dimensional lattice of size $\sqrt{N} \times \sqrt{N}$. The previous quantum walk based algorithms take $O(\sqrt{N}\log N)$ steps to solve…
Given a set of pairwise disjoint polygonal obstacles in the plane, finding an obstacle-avoiding Euclidean shortest path between two points is a classical problem in computational geometry and has been studied extensively. Previously,…
Recently, a new polynomial basis over binary extension fields was proposed such that the fast Fourier transform (FFT) over such fields can be computed in the complexity of order $\mathcal{O}(n\lg(n))$, where $n$ is the number of points…
Recently, Armstrong, Guzm\'an, and Sing Long (2021), presented an optimal $O(n^2)$ time algorithm for strict circular seriation (called also the recognition of strict quasi-circular Robinson spaces). In this paper, we give a very simple…
We study a general family of facility location problems defined on planar graphs and on the 2-dimensional plane. In these problems, a subset of $k$ objects has to be selected, satisfying certain packing (disjointness) and covering…
In this paper, we consider a generalized longest common subsequence problem with multiple substring inclusive constraints. For the two input sequences $X$ and $Y$ of lengths $n$ and $m$, and a set of $d$ constraints $P=\{P_1,\cdots,P_d\}$…
Folded Reed-Solomon codes are an explicit family of codes that achieve the optimal trade-off between rate and error-correction capability: specifically, for any $\eps > 0$, the author and Rudra (2006,08) presented an $n^{O(1/\eps)}$ time…
The structure-preserving doubling algorithm (SDA) is a fairly efficient method for solving problems closely related to Hamiltonian (or Hamiltonian-like) matrices, such as computing the required solutions to algebraic Riccati equations.…
Predicting the secondary structure of RNA is a core challenge in computational biology, essential for understanding molecular function and designing novel therapeutics. The field has evolved from foundational but accuracy-limited…
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…
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 consider the problem of augmenting an $n$-vertex tree with one shortcut in order to minimize the diameter of the resulting graph. The tree is embedded in an unknown space and we have access to an oracle that, when queried on a pair of…
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…
We consider low-space algorithms for the classic Element Distinctness problem: given an array of $n$ input integers with $O(\log n)$ bit-length, decide whether or not all elements are pairwise distinct. Beame, Clifford, and Machmouchi [FOCS…
We consider a bichromatic two-center problem for pairs of points. Given a set $S$ of $n$ pairs of points in the plane, for every pair, we want to assign a red color to one point and a blue color to the other, in such a way that the value…