Related papers: Time and Space Efficient Algorithms for RNA Foldin…
In numerical linear algebra, considerable effort has been devoted to obtaining faster algorithms for linear systems whose underlying matrices exhibit structural properties. A prominent success story is the method of generalized nested…
The currently fastest algorithm for regular expression pattern matching and membership improves the classical O(nm) time algorithm by a factor of about log^{3/2}n. Instead of focussing on general patterns we analyse homogeneous patterns of…
The Nearest Neighbor model is the $\textit{de facto}$ thermodynamic model of RNA secondary structure formation and is a cornerstone of RNA structure prediction and sequence design. The current functional form (Turner 2004) contains…
We present a data structure that supports three-dimensional range reporting queries in $O(\log \log U + (\log \log n)^3+k)$ time and uses $O(n\log^{1+\eps} n)$ space, where $U$ is the size of the universe, $k$ is the number of points in the…
A modified dynamic programming algorithm rapidly and accurately solves large 0/1 knapsack problems. It has computational O(nlogn), space O(nlogn) and predictable maximum error. Experimentally it's accuracy increases faster than linearly…
It has recently been shown that starting with a classical query algorithm (decision tree) and a guessing algorithm that tries to predict the query answers, we can design a quantum algorithm with query complexity $O(\sqrt{GT})$ where $T$ is…
The worst-case fastest known algorithm for the Set Cover problem on universes with $n$ elements still essentially is the simple $O^*(2^n)$-time dynamic programming algorithm, and no non-trivial consequences of an $O^*(1.01^n)$-time…
Background: RNA exhibits a variety of structural configurations. Here we consider a structure to be tantamount to the noncrossing Watson-Crick and \pairGU-base pairings (secondary structure) and additional cross-serial base pairs. These…
Arising from structural graph theory, treewidth has become a focus of study in fixed-parameter tractable algorithms in various communities including combinatorics, integer-linear programming, and numerical analysis. Many NP-hard problems…
In this paper, we first consider the subpath convex hull query problem: Given a simple path $\pi$ of $n$ vertices, preprocess it so that the convex hull of any query subpath of $\pi$ can be quickly obtained. Previously, Guibas, Hershberger,…
Given a set $P$ of $n$ points and a set $S$ of $n$ weighted disks in the plane, the disk coverage problem is to compute a subset of disks of smallest total weight such that the union of the disks in the subset covers all points of $P$. The…
Alignment of structural RNAs is an important problem with a wide range of applications. Since function is often determined by molecular structure, RNA alignment programs should take into account both sequence and base-pairing information…
We introduce space-efficient plane-sweep algorithms for basic planar geometric problems. It is assumed that the input is in a read-only array of $n$ items and that the available workspace is $\Theta(s)$ bits, where $\lg n \leq s \leq n…
This article devotes to developing robust but simple correction techniques and efficient algorithms for a class of second-order time stepping methods, namely the shifted fractional trapezoidal rule (SFTR), for subdiffusion problems to…
We present linear time {\it in-place} algorithms for several basic and fundamental graph problems including the well-known graph search methods (like depth-first search, breadth-first search, maximum cardinality search), connectivity…
Predicting the three-dimensional (3D) structure of a protein from its primary sequence of amino acids is known as the protein folding (PF) problem. Due to the central role of proteins' 3D structures in chemistry, biology and medicine…
We consider the problem of scattering $n$ robots in a two dimensional continuous space. As this problem is impossible to solve in a deterministic manner, all solutions must be probabilistic. We investigate the amount of randomness (that is,…
We revisit the classic problem of simplex range searching and related problems in computational geometry. We present a collection of new results which improve previous bounds by multiple logarithmic factors that were caused by the use of…
We consider the canonical Subset Sum problem: given a list of positive integers $a_1,\ldots,a_n$ and a target integer $t$ with $t > a_i$ for all $i$, determine if there is an $S \subseteq [n]$ such that $\sum_{i \in S} a_i = t$. The…
In this paper we provide an $\tilde{O}(nd+d^{3})$ time randomized algorithm for solving linear programs with $d$ variables and $n$ constraints with high probability. To obtain this result we provide a robust, primal-dual…