Related papers: Chaining with overlaps revisited
This paper describes a new alignment algorithm for sequences that can be used for determination of deletions and substitutions. It provides several solutions out of which the best one can be chosen on the basis of minimization of gaps or…
A run in a string is a maximal periodic substring. For example, the string $\texttt{bananatree}$ contains the runs $\texttt{anana} = (\texttt{an})^{3/2}$ and $\texttt{ee} = \texttt{e}^2$. There are less than $n$ runs in any length-$n$…
Several biological problems require the identification of regions in a sequence where some feature occurs within a target density range: examples including the location of GC-rich regions, identification of CpG islands, and sequence…
In this paper we present algorithms for several string problems in the Congested Clique model. In the Congested Clique model, $n$ nodes (computers) are used to solve some problem. The input to the problem is distributed among the nodes, and…
Given an input $x$, and a search problem $F$, local computation algorithms (LCAs) implement access to specified locations of $y$ in a legal output $y \in F(x)$, using polylogarithmic time and space. Mansour et al., (2012), had previously…
We consider the classic problem of scheduling a set of n jobs non-preemptively on a single machine. Each job j has non-negative processing time, weight, and deadline, and a feasible schedule needs to be consistent with chain-like precedence…
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…
Network coding is known to improve the throughput and the resilience to losses in most network scenarios. In a practical network scenario, however, the accurate modeling of the traffic is often too complex and/or infeasible. The goal is…
In this paper, the problem of designing network codes that are both communicationally and computationally efficient over packet line networks with worst-case schedules is considered. In this context, random linear network codes (dense…
This paper performs the analysis necessary to bound the running time of known, efficient algorithms for generating all longest common subsequences. That is, we bound the running time as a function of input size for algorithms with time…
Mixed packing and covering problems are problems that can be formulated as linear programs using only non-negative coefficients. Examples include multicommodity network flow, the Held-Karp lower bound on TSP, fractional relaxations of set…
Encoding data structures store enough information to answer the queries they are meant to support but not enough to recover their underlying datasets. In this paper we give the first encoding data structure for the challenging problem of…
We consider the problem of sorting $n$ elements in the case of \emph{persistent} comparison errors. In this model (Braverman and Mossel, SODA'08), each comparison between two elements can be wrong with some fixed (small) probability $p$,…
In this paper, we propose a cross-layer scheduling algorithm that achieves a throughput "epsilon-close" to the optimal throughput in multi-hop wireless networks with a tradeoff of O(1/epsilon) in delay guarantees. The algorithm aims to…
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…
This simple note lays out a few observations which are well known in many ways but may not have been said in quite this way before. The basic idea is that when comparing two different Markov chains it is useful to couple them is such a way…
A correlation is a binary vector that encodes all possible positions of overlaps of two words, where an overlap for an ordered pair of words (u,v) occurs if a suffix of word u matches a prefix of word v. As multiple pairs can have the same…
In a classical problem in scheduling, one has $n$ unit size jobs with a precedence order and the goal is to find a schedule of those jobs on $m$ identical machines as to minimize the makespan. It is one of the remaining four open problems…
Genome assembly is a fundamental problem in Bioinformatics, where for a given set of overlapping substrings of a genome, the aim is to reconstruct the source genome. The classical approaches to solving this problem use assembly graphs, such…
In this paper we address the application of pre-processing techniques to multi-channel time series data with varying lengths, which we refer to as the alignment problem, for downstream machine learning. The misalignment of multi-channel…