Related papers: Time and Space Efficient Algorithms for RNA Foldin…
The minimum degree algorithm is one of the most widely-used heuristics for reducing the cost of solving large sparse systems of linear equations. It has been studied for nearly half a century and has a rich history of bridging techniques…
In this work, we consider the Combinatorial RNA Design problem, a minimal instance of the RNA design problem which aims at finding a sequence that admits a given target as its unique base pair maximizing structure. We provide complete…
We consider the approximate pattern matching problem under the edit distance. Given a text $T$ of length $n$, a pattern $P$ of length $m$, and a threshold $k$, the task is to find the starting positions of all substrings of $T$ that can be…
We investigate dynamic algorithms for the interval scheduling problem. Our algorithm runs in amortised time $O(\log n)$ for query operation and $O(d\log^2 n)$ for insertion and removal operations, where $n$ and $d$ are the maximal numbers…
In the two-dimensional orthogonal colored range counting problem, we preprocess a set, $P$, of $n$ colored points on the plane, such that given an orthogonal query rectangle, the number of distinct colors of the points contained in this…
We give new sublinear and parallel algorithms for the extensively studied problem of approximating n-variable r-CSPs (constraint satisfaction problems with constraints of arity r up to an additive error. The running time of our algorithms…
We revisit a classical problem in computational geometry: finding the largest-volume axis-aligned empty box (inside a given bounding box) amidst $n$ given points in $d$ dimensions. Previously, the best algorithms known have running time…
We present an algorithm that given a linear program with $n$ variables, $m$ constraints, and constraint matrix $A$, computes an $\epsilon$-approximate solution in $\tilde{O}(\sqrt{rank(A)}\log(1/\epsilon))$ iterations with high probability.…
The RNA inverse folding problem aims to identify nucleotide sequences that preferentially adopt a given target secondary structure. While various heuristic and machine learning-based approaches have been proposed, many require a large…
The problem of P vs. NP is very serious, and solutions to the problem can help save lives. This article is an attempt at solving the problem using a computer algorithm. It is presented in a fashion that will hopefully allow for easy…
This paper presents constant-time and near-constant-time distributed algorithms for a variety of problems in the congested clique model. We show how to compute a 3-ruling set in expected $O(\log \log \log n)$ rounds and using this, we…
In the Max $r$-SAT problem, the input is a CNF formula with $n$ variables where each clause is a disjunction of at most $r$ literals. The objective is to compute an assignment which satisfies as many of the clauses as possible. While there…
Let $P=(P_1, P_2, \ldots, P_n)$, $P_i \in \field{R}$ for all $i$, be a signal and let $C$ be a constant. In this work our goal is to find a function $F:[n]\rightarrow \field{R}$ which optimizes the following objective function: $$ \min_{F}…
Given a set of $m$ points and a set of $n$ lines in the plane, we consider the problem of computing the faces of the arrangement of the lines that contain at least one point. In this paper, we present an $O(m^{2/3}n^{2/3}+(n+m)\log n)$ time…
We give a proof of the conjecture of Nelson and Nguyen [FOCS 2013] on the optimal dimension and sparsity of oblivious subspace embeddings, up to sub-polylogarithmic factors: For any $n\geq d$ and $\epsilon\geq d^{-O(1)}$, there is a random…
In this paper we show that two-dimensional nearest neighbor queries can be answered in optimal $O(\log n)$ time while supporting insertions in $O(\log^{1+\varepsilon}n)$ time. No previous data structure was known that supports $O(\log…
We devise a data structure that can answer shortest path queries for two query points in a polygonal domain $P$ on $n$ vertices. For any $\varepsilon > 0$, the space complexity of the data structure is $O(n^{10+\varepsilon })$ and queries…
In this paper we present a selfcontained analysis and description of the novel {\it ab initio} folding algorithm {\sf cross}, which generates the minimum free energy (mfe), 3-noncrossing, $\sigma$-canonical RNA structure. Here an RNA…
In this paper we examined an algorithm for the All-k-Nearest-Neighbor problem proposed in 1980s, which was claimed to have an $O(n\log{n})$ upper bound on the running time. We find the algorithm actually exceeds the so claimed upper bound,…
We give a spectral algorithm for decomposing overcomplete order-4 tensors, so long as their components satisfy an algebraic non-degeneracy condition that holds for nearly all (all but an algebraic set of measure $0$) tensors over…