相关论文: Faster exon assembly by sparse spliced alignment

String matching algorithm plays the vital role in the Computational Biology. The functional and structural relationship of the biological sequence is determined by similarities on that sequence. For that, the researcher is supposed to aware…

The suffix array is a fundamental data structure for many applications that involve string searching and data compression. Designing time/space-efficient suffix array construction algorithms has attracted significant attention and…

Computing $k$-Nearest Neighbors (KNN) is one of the core kernels used in many machine learning, data mining and scientific computing applications. Although kd-tree based $O(\log n)$ algorithms have been proposed for computing KNN, due to…

We study the Euclidean minimum weight perfect matching problem for $n$ points in the plane. It is known that any deterministic approximation algorithm whose approximation ratio depends only on $n$ requires at least $\Omega(n \log n)$ time.…

In this paper, we consider tree decompositions, branch decompositions, and clique decompositions. We improve the running time of dynamic programming algorithms on these graph decompositions for a large number of problems as a function of…

DBSCAN is a popular density-based clustering algorithm. It computes the $\epsilon$-neighborhood graph of a dataset and uses the connected components of the high-degree nodes to decide the clusters. However, the full neighborhood graph may…

In the restricted shortest paths problem, we are given a graph $G$ whose edges are assigned two non-negative weights: lengths and delays, a source $s$, and a delay threshold $D$. The goal is to find, for each target $t$, the length of the…

With the aggressive scaling of VLSI technology, the explosion of layout patterns creates a critical bottleneck for DFM applications like OPC. Pattern clustering is essential to reduce data complexity, yet existing methods struggle with…

We demonstrate that the best $k$-sparse approximation of a length-$n$ vector can be recovered within a $(1+\epsilon)$-factor approximation in $O((k/\epsilon) \log n)$ time using a non-adaptive linear sketch with $O((k/\epsilon) \log n)$…

We consider the problem of querying a string (or, a database) of length $N$ bits to determine all the locations where a substring (query) of length $M$ appears either exactly or is within a Hamming distance of $K$ from the query. We assume…

Edit distance is a measurement of similarity between two sequences such as strings, point sequences, or polygonal curves. Many matching problems from a variety of areas, such as signal analysis, bioinformatics, etc., need to be solved in a…

Given a digraph $G = (VG,AG)$, an \emph{even factor} $M \subseteq AG$ is a subset of arcs that decomposes into a collection of node-disjoint paths and even cycles. Even factors in digraphs were introduced by Geleen and Cunningham and…

The {\em maximum cardinality} and {\em maximum weight matching} problems can be solved in time $\tilde{O}(m\sqrt{n})$, a bound that has resisted improvement despite decades of research. (Here $m$ and $n$ are the number of edges and…

For many hard computational problems, simple algorithms that run in time $2^n \cdot n^{O(1)}$ arise, say, from enumerating all subsets of a size-$n$ set. Finding (exponentially) faster algorithms is a natural goal that has driven much of…

Given a point set $P$ in a metric space and a real number $t \geq 1$, an \emph{oriented $t$-spanner} is an oriented graph $\overrightarrow{G}=(P,\overrightarrow{E})$, where for every pair of distinct points $p$ and $q$ in $P$, the shortest…

Packing several characters into one computer word is a simple and natural way to compress the representation of a string and to speed up its processing. Exploiting this idea, we propose an index for a packed string, based on a {\em sparse…

We introduce an algorithm for the alignment of protein- coding sequences accounting for frameshifts. The main specificity of this algorithm as compared to previously published protein-coding sequence alignment methods is the introduction of…

Miller et al. \cite{MPVX15} devised a distributed\footnote{They actually showed a PRAM algorithm. The distributed algorithm with these properties is implicit in \cite{MPVX15}.} algorithm in the CONGEST model, that given a parameter $k =…

De novo genome assembly is challenging in highly repetitive regions; however, reference-guided assemblers often suffer from bias. We propose a framework for pangenome-guided sequence assembly, which can resolve short-read data in complex…

Calculating the similarities between a pair of genomic sequences is one of the most fundamental computational steps in genomic analysis. This step -- called sequence alignment -- is the computational bottleneck because: (1) it is…