Related papers: Faster Algorithms for RNA-folding using the Four-R…
This paper proposes to develop a new variant of the two-time-scale stochastic approximation to find the roots of two coupled nonlinear operators, assuming only noisy samples of these operators can be observed. Our key idea is to leverage…
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…
The secondary structure of ribonucleic acid (RNA) is more stable and accessible in the cell than its tertiary structure, making it essential for functional prediction. Although deep learning has shown promising results in this field,…
Nonnegative matrix factorization (NMF) is a powerful technique for dimension reduction, extracting latent factors and learning part-based representation. For large datasets, NMF performance depends on some major issues: fast algorithms,…
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…
We propose a novel framework for Russian Roulette and Splitting (RRS) tailored to wavefront path tracing, a highly parallel rendering architecture that processes path states in batched, stage-wise execution for efficient GPU utilization.…
RNA secondary structure folding kinetics is known to be important for the biological function of certain processes, such as the hok/sok system in E. coli. Although linear algebra provides an exact computational solution of secondary…
Motivation: Non-coding RNAs (ncRNAs) express their functions by adopting molecular structures. Specifically, RNA secondary structures serve as a relatively stable intermediate step before tertiary structures, offering a reliable signature…
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…
We present the first optimal randomized algorithm for constructing the order-$k$ Voronoi diagram of $n$ points in two dimensions. The expected running time is $O(n\log n + nk)$, which improves the previous, two-decades-old result of Ramos…
Accurate prediction of mRNA secondary structure is critical for understanding gene expression, translation efficiency, and advancing mRNA-based therapeutics. However, the combinatorial complexity of possible foldings, especially in long…
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…
We present a unified framework for accelerating edit-distance computation between two compressible strings using straight-line programs. For two strings of total length $N$ having straight-line program representations of total size $n$, we…
In [1], a new construction called red-black hierarchy characterizing Laman graphs and an algorithm for computing it were presented. For a Laman graph G=(V,E) with n vertices it runs in O(n^2) time assuming that a partition of (V,E+e) into…
It is a classical result of Stein and Waterman that the asymptotic number of RNA secondary structures is $1.104366 \cdot n^{-3/2} \cdot 2.618034^n$. Motivated by the kinetics of RNA secondary structure formation, we are interested in…
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…
Second-order optimization methods offer superior convergence rates but are often bottlenecked by the wall-clock cost of Hessian computation and factorization. In the moderate-dimensional regime where the full Hessian fits in memory,…
We describe an efficient implementation of a hierarchy of algorithms for multiplication of dense matrices over the field with two elements (GF(2)). In particular we present our implementation -- in the M4RI library -- of Strassen-Winograd…
The quest for an algorithm that solves an $n\times n$ linear system in $O(n^2)$ time complexity, or $O(n^2 \text{poly}(1/\epsilon))$ when solving up to $\epsilon$ relative error, is a long-standing open problem in numerical linear algebra…
We present an algorithm that, with high probability, generates a random spanning tree from an edge-weighted undirected graph in $\tilde{O}(n^{4/3}m^{1/2}+n^{2})$ time (The $\tilde{O}(\cdot)$ notation hides $\operatorname{polylog}(n)$…