相关论文: Faster exon assembly by sparse spliced alignment

Approximate string matching is the problem of finding all factors of a text t of length n that are at a distance at most k from a pattern x of length m. Approximate circular string matching is the problem of finding all factors of t that…

We present the Scalable Nucleotide Alignment Program (SNAP), a new short and long read aligner that is both more accurate (i.e., aligns more reads with fewer errors) and 10-100x faster than state-of-the-art tools such as BWA. Unlike recent…

In this paper we present linear time approximation schemes for several generalized matching problems on nonbipartite graphs. Our results include $O_\epsilon(m)$-time algorithms for $(1-\epsilon)$-maximum weight $f$-factor and…

Matching pursuits are a class of greedy algorithms commonly used in signal processing, for solving the sparse approximation problem. They rely on an atom selection step that requires the calculation of numerous projections, which can be…

The problem of identifying splice sites consists of two sub-problems: finding their boundaries, and characterizing their sequence markers. Other splicing elements---including, enhancers and silencers---that occur in the intronic and exonic…

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…

It has been shown that minimum free energy structure for RNAs and RNA-RNA interaction is often incorrect due to inaccuracies in the energy parameters and inherent limitations of the energy model. In contrast, ensemble based quantities such…

Aligning a sequence to a walk in a labeled graph is a problem of fundamental importance to Computational Biology. For finding a walk in an arbitrary graph with $|E|$ edges that exactly matches a pattern of length $m$, a lower bound based on…

The classical pattern matching asks for locating all occurrences of one string, called the pattern, in another, called the text, where a string is simply a sequence of characters. Due to the potential practical applications, it is desirable…

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…

We consider two problems that arise in machine learning applications: the problem of recovering a planted sparse vector in a random linear subspace and the problem of decomposing a random low-rank overcomplete 3-tensor. For both problems,…

The equidistant subsequence pattern matching problem is considered. Given a pattern string $P$ and a text string $T$, we say that $P$ is an \emph{equidistant subsequence} of $T$ if $P$ is a subsequence of the text such that consecutive…

We propose the first \emph{local search} algorithm for Euclidean clustering that attains an $O(1)$-approximation in almost-linear time. Specifically, for Euclidean $k$-Means, our algorithm achieves an $O(c)$-approximation in $\tilde{O}(n^{1…

We present an application of a genetic algorithmic computational method to the optimization of the concurrence measure of entanglement for the cases of one dimensional chains, as well as square and triangular lattices in a simple…

This papers studies multi-agent (convex and \emph{nonconvex}) optimization over static digraphs. We propose a general distributed \emph{asynchronous} algorithmic framework whereby i) agents can update their local variables as well as…

This paper demonstrates the utility of organized numerical representations of genes in research involving flat string gene formats (i.e., FASTA/FASTQ5). FASTA/FASTQ files have several current limitations, such as their large file sizes,…

This paper aims at providing extremely efficient algorithms for approximate query enumeration on sparse databases, that come with performance and accuracy guarantees. We introduce a new model for approximate query enumeration on classes of…

A phylogeny describes the evolutionary history of an evolving population. Evolutionary search algorithms can perfectly track the ancestry of candidate solutions, illuminating a population's trajectory through the search space. However,…

Given a text $T$ and a pattern $P$ over alphabet $\Sigma$, the classic exact matching problem searches for all occurrences of pattern $P$ in text $T$. Unlike exact matching problem, order-preserving pattern matching (OPPM) considers the…

We present a new scaling algorithm for maximum (or minimum) weight perfect matching on general, edge weighted graphs. Our algorithm runs in $O(m\sqrt{n}\log(nN))$ time, $O(m\sqrt{n})$ per scale, which matches the running time of the best…