Related papers: Time and Space Efficient Algorithms for RNA Foldin…
We present a fully dynamic data structure for the maintenance of lower envelopes of pseudo-lines. The structure has $O(\log^2 n)$ update time and $O(\log n)$ vertical ray shooting query time. To achieve this performance, we devise a new…
In this paper we present a new algorithm for solving linear programs that requires only $\tilde{O}(\sqrt{rank(A)}L)$ iterations to solve a linear program with $m$ constraints, $n$ variables, and constraint matrix $A$, and bit complexity…
Let $\mathcal{D}$ be a collection of $D$ documents, which are strings over an alphabet of size $\sigma$, of total length $n$. We describe a data structure that uses linear space and and reports $k$ most relevant documents that contain a…
Packing and covering linear programs belong to the narrow class of linear programs that are efficiently solvable in parallel and distributed models of computation, yet are a powerful modeling tool for a wide range of fundamental problems in…
In the classical interval scheduling type of problems, a set of $n$ jobs, characterized by their start and end time, need to be executed by a set of machines, under various constraints. In this paper we study a new variant in which the jobs…
In this paper, we propose an end-to-end deep learning model, called E2Efold, for RNA secondary structure prediction which can effectively take into account the inherent constraints in the problem. The key idea of E2Efold is to directly…
Solving linear systems and quadratic programming (QP) problems are both ubiquitous tasks in the engineering and computing fields. Direct methods for solving systems, such as Cholesky, LU, and QR factorizations, exhibit data-independent time…
We consider the problem of reconstructing a rank-$k$ $n \times n$ matrix $M$ from a sampling of its entries. Under a certain incoherence assumption on $M$ and for the case when both the rank and the condition number of $M$ are bounded, it…
We present the first linear time algorithm to construct the $2n$-bit version of the Lyndon array for a string of length $n$ using only $o(n)$ bits of working space. A simpler variant of this algorithm computes the plain ($n\lg n$-bit)…
Recent work by Elmasry et al. (STACS 2015) and Asano et al. (ISAAC 2014), reconsidered classical fundamental graph algorithms focusing on improving the space complexity. We continue this line of work focusing on space. Our first result is a…
We design a space-efficient algorithm for performing depth-first search traversal(DFS) of a graph in $O(m+n\log^* n)$ time using $O(n)$ bits of space. While a normal DFS algorithm results in a DFS-tree (in case the graph is connected), our…
A large number of NP-hard graph problems can be solved in $f(w)n^{O(1)}$ time and space when the input graph is provided together with a tree decomposition of width $w$, in many cases with a modest exponential dependence $f(w)$ on $w$.…
Given $m$ documents of total length $n$, we consider the problem of finding a longest string common to at least $d \geq 2$ of the documents. This problem is known as the \emph{longest common substring (LCS) problem} and has a classic $O(n)$…
We present an efficient and elementary algorithm for computing the number of primes up to $N$ in $\tilde{O}(\sqrt N)$ time, improving upon the existing combinatorial methods that require $\tilde{O}(N ^ {2/3})$ time. Our method has a similar…
We study fundamental problems in linear algebra, such as finding a maximal linearly independent subset of rows or columns (a basis), solving linear regression, or computing a subspace embedding. For these problems, we consider input…
Recently, a framework considering RNA sequences and their RNA secondary structures as pairs, led to some information-theoretic perspectives on how the semantics encoded in RNA sequences can be inferred. In this context, the pairing arises…
We develop fast spectral algorithms for tensor decomposition that match the robustness guarantees of the best known polynomial-time algorithms for this problem based on the sum-of-squares (SOS) semidefinite programming hierarchy. Our…
In this paper we revisit the classical regular expression matching problem, namely, given a regular expression $R$ and a string $Q$, decide if $Q$ matches one of the strings specified by $R$. Let $m$ and $n$ be the length of $R$ and $Q$,…
Many signal processing problems can be solved by maximizing the fitness of a segmented model over all possible partitions of the data interval. This letter describes a simple but powerful algorithm that searches the exponentially large…
Given an array A of $n$ elements, we wish to support queries for the most frequent and least frequent element in a subrange $[l, r]$ of $A$. We also wish to support updates that change a particular element at index $i$ or insert/ delete an…