Related papers: Practical colinear chaining on sequences revisited
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…
A single-commodity congestion approximator for a graph is a compact data structure that approximately predicts the edge congestion required to route any set of single-commodity flow demands in a network. A hierarchical congestion…
In this paper, we present a generalized version of the matrix chain algorithm to generate efficient code for linear algebra problems, a task for which human experts often invest days or even weeks of works. The standard matrix chain problem…
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…
A minimum chain cover (MCC) of a $k$-width directed acyclic graph (DAG) $G = (V, E)$ is a set of $k$ chains (paths in the transitive closure) of $G$ such that every vertex appears in at least one chain in the cover. The state-of-the-art…
Allen's interval algebra is one of the most well-known calculi in qualitative temporal reasoning with numerous applications in artificial intelligence. Recently, there has been a surge of improvements in the fine-grained complexity of…
Given a sequence $s_1$ of $n$ letters drawn i.i.d. from an alphabet of size $\sigma$ and a mutated substring $s_2$ of length $m < n$, we often want to recover the mutation history that generated $s_2$ from $s_1$. Modern sequence aligners…
Finding the length of the longest increasing subsequence (LIS) is a classic algorithmic problem. Let $n$ denote the size of the array. Simple $O(n\log n)$ algorithms are known for this problem. We develop a polylogarithmic time randomized…
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…
Partitioning a sequence of length $n$ into $k$ coherent segments (Seg) is one of the classic optimization problems. As long as the optimization criterion is additive, Seg can be solved exactly in $O(n^2k)$ time using a classic dynamic…
We study quantum algorithms for several fundamental string problems, including Longest Common Substring, Lexicographically Minimal String Rotation, and Longest Square Substring. These problems have been widely studied in the stringology…
Auctions are widely used in exchanges to match buy and sell requests. Once the buyers and sellers place their requests, the exchange determines how these requests are to be matched. The two most popular objectives used while determining the…
Numerical algorithms have two kinds of costs: arithmetic and communication, by which we mean either moving data between levels of a memory hierarchy (in the sequential case) or over a network connecting processors (in the parallel case).…
Graph partitioning schedules parallel calculations like sparse matrix-vector multiply (SpMV). We consider contiguous partitions, where the $m$ rows (or columns) of a sparse matrix with $N$ nonzeros are split into $K$ parts without…
The current best practice for computing optimal transport (OT) is via entropy regularization and Sinkhorn iterations. This algorithm runs in quadratic time as it requires the full pairwise cost matrix, which is prohibitively expensive for…
The cost-distance Steiner tree problem seeks a Steiner tree that minimizes the total congestion cost plus the weighted sum of source-sink delays. This problem arises as a subroutine in timing-constrained global routing with a linear delay…
In this paper, we have developed a fully-dynamic algorithm for maintaining cardinality of maximum-matching in a tree using the construction of top-trees. The time complexities are as follows: 1. Initialization Time: $O(n(log(n)))$ to build…
Similar subtrajectory search is a finer-grained operator that can better capture the similarities between one query trajectory and a portion of a data trajectory than the traditional similar trajectory search, which requires the two checked…
This paper presents a new approach to statistical similarity assessment based on sequence alignment. The algorithm performs mutual matching of two random sequences by successively searching for common elements and by applying sequence…
We consider the problem of finding \textit{semi-matching} in bipartite graphs which is also extensively studied under various names in the scheduling literature. We give faster algorithms for both weighted and unweighted case. For the…