Related papers: A memory-efficient data structure representing exa…
This paper explores combinatorial optimization for problems of max-weight graph matching on multi-partite graphs, which arise in integrating multiple data sources. Entity resolution-the data integration problem of performing noisy joins on…
Repeat finding in strings has important applications in subfields such as computational biology. The challenge of finding the longest repeats covering particular string positions was recently proposed and solved by \.{I}leri et al., using a…
The classic problem of exact subgraph matching returns those subgraphs in a large-scale data graph that are isomorphic to a given query graph, which has gained increasing importance in many real-world applications. In this paper, we propose…
DNA storage is a promising archival data storage solution to today's big data problem. A DNA storage system encodes and stores digital data with synthetic DNA sequences and decodes DNA sequences back to digital data via sequencing. For…
We study the space complexity of sketching cuts and Laplacian quadratic forms of graphs. We show that any data structure which approximately stores the sizes of all cuts in an undirected graph on $n$ vertices up to a $1+\epsilon$ error must…
In this paper, we describe a new type of match between a pattern and a text that aren't necessarily maximal in the query, but still contain useful matching information: locally maximal exact matches (LEMs). There are usually a large amount…
We show how to chain maximal exact matches (MEMs) between a query string $Q$ and a labeled directed acyclic graph (DAG) $G=(V,E)$ to solve the longest common subsequence (LCS) problem between $Q$ and $G$. We obtain our result via a new…
Genome assembly from the high-throughput sequencing (HTS) reads is a fundamental yet challenging computational problem. An intrinsic challenge is the uncertainty caused by the widespread repetitive elements. Here we get around the…
We consider compact representations of collections of similar strings that support random access queries. The collection of strings is given by a rooted tree where edges are labeled by an edit operation (inserting, deleting, or replacing a…
We provide a compact data structure for representing polyominoes that supports neighborhood and visibility queries. Neighborhood queries concern reporting adjacent cells to a given cell, and visibility queries determine whether a straight…
In this paper, we present a new data structure called the packed compact trie (packed c-trie) which stores a set $S$ of $k$ strings of total length $n$ in $n \log\sigma + O(k \log n)$ bits of space and supports fast pattern matching queries…
DNA sequencing is the process of determining the exact order of the nucleotide bases of an individual's genome in order to catalogue sequence variation and understand its biological implications. Whole-genome sequencing techniques produce…
DNA-based storage offers unprecedented density and durability, but its scalability is fundamentally limited by the efficiency of parallel strand synthesis. Existing methods either allow unconstrained nucleotide additions to individual…
Pattern matching can be used to calculate the support of patterns, and is a key issue in sequential pattern mining (or sequence pattern mining). Nonoverlapping pattern matching means that two occurrences cannot use the same character in the…
Graph pattern matching is a routine process for a wide variety of applications such as social network analysis. It is typically defined in terms of subgraph isomorphism which is NP-Complete. To lower its complexity, many extensions of graph…
A matching is compatible to two or more labeled point sets of size $n$ with labels $\{1,\dots,n\}$ if its straight-line drawing on each of these point sets is crossing-free. We study the maximum number of edges in a matching compatible to…
Suffix trees are an important data structure at the core of optimal solutions to many fundamental string problems, such as exact pattern matching, longest common substring, matching statistics, and longest repeated substring. Recent lines…
We study fully dynamic algorithms for maximum matching. This is a well-studied problem, known to admit several update-time/approximation trade-offs. For instance, it is known how to maintain a 1/2-approximate matching in $\log^{O(1)} n$…
Motivated by the imminent growth of massive, highly redundant genomic databases, we study the problem of compressing a string database while simultaneously supporting fast random access, substring extraction and pattern matching to the…
A new network construction method is presented for building of scalable, high throughput, low latency networks. The method is based on the exact equivalence discovered between the problem of maximizing network throughput (measured as…