相关论文: Faster exon assembly by sparse spliced alignment
Motivation: New long read sequencers promise to transform sequencing and genome assembly by producing reads tens of kilobases long. However their high error rate significantly complicates assembly and requires expensive correction steps to…
The algorithmic tasks of computing the Hamming distance between a given pattern of length $m$ and each location in a text of length $n$ is one of the most fundamental algorithmic tasks in string algorithms. Unfortunately, there is evidence…
We study polynomial-time approximation algorithms for (edge/vertex) Sparsest Cut and Small Set Expansion in terms of $k$, the number of edges or vertices cut in the optimal solution. Our main results are $\mathcal{O}(\text{polylog}\,…
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…
We provide an algorithm for properly learning mixtures of two single-dimensional Gaussians without any separability assumptions. Given $\tilde{O}(1/\varepsilon^2)$ samples from an unknown mixture, our algorithm outputs a mixture that is…
We study the problem of indexing text with wildcard positions, motivated by the challenge of aligning sequencing data to large genomes that contain millions of single nucleotide polymorphisms (SNPs)---positions known to differ between…
In the \emph{trace reconstruction problem}, an unknown source string $x \in \{0,1\}^n$ is transmitted through a probabilistic \emph{deletion channel} which independently deletes each bit with some fixed probability $\delta$ and concatenates…
We give a new probabilistic algorithm for interpolating a "sparse" polynomial f given by a straight-line program. Our algorithm constructs an approximation f* of f, such that their difference probably has at most half the number of terms of…
We consider the approximate pattern matching problem under the edit distance. Given a text $T$ of length $n$, a pattern $P$ of length $m$, and a threshold $k$, the task is to find the starting positions of all substrings of $T$ that can be…
We consider the problem of efficiently designing sets (codes) of equal-length DNA strings (words) that satisfy certain combinatorial constraints. This problem has numerous motivations including DNA computing and DNA self-assembly. Previous…
In this paper, we present a linear-time approximation scheme for $k$-means clustering of \emph{incomplete} data points in $d$-dimensional Euclidean space. An \emph{incomplete} data point with $\Delta>0$ unspecified entries is represented as…
We consider a natural generalization of scheduling $n$ jobs on $m$ parallel machines so as to minimize the makespan. In our extension the set of jobs is partitioned into several classes and a machine requires a setup whenever it switches…
Finding cohesive subgraphs in a large graph has many important applications, such as community detection and biological network analysis. Clique is often a too strict cohesive structure since communities or biological modules rarely form as…
We consider the standard message passing model; we assume the system is fully synchronous: all processes start at the same time and time proceeds in synchronised rounds. In each round each vertex can transmit a different message of size…
We develop a time-optimal $O(mn^2)$-time algorithm to construct the subtree prune-regraft (SPR) graph on a collection of m phylogenetic trees with n leaves. This improves on the previous bound of $O(mn^3)$. Such graphs are used to better…
In projective clustering we are given a set of n points in $R^d$ and wish to cluster them to a set $S$ of $k$ linear subspaces in $R^d$ according to some given distance function. An $\eps$-coreset for this problem is a weighted (scaled)…
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…
To store and search genomic databases efficiently, researchers have recently started building compressed self-indexes based on grammars. In this paper we show how, given a straight-line program with $r$ rules for a string (S [1..n]) whose…
The {Congested Clique} is a distributed-computing model for single-hop networks with restricted bandwidth that has been very intensively studied recently. It models a network by an $n$-vertex graph in which any pair of vertices can…
Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently. However, it is well-known that the evolution of gene families…