Related papers: Faster Repetition-Aware Compressed Suffix Trees ba…
Suffix trees have emerged to be very fast for pattern searching yielding O (m) time, where m is the pattern size. Unfortunately their high memory requirements make it impractical to work with huge amounts of data. We present a memory…
Suffix tree construction algorithms based on suffix links are popular because they are simple to implement, can operate online in linear time, and because the suffix links are often convenient for pattern matching. We present an approach…
We present an improved wavelet tree construction algorithm and discuss its applications to a number of rank/select problems for integer keys and strings. Given a string of length n over an alphabet of size $\sigma\leq n$, our method builds…
The dictionary matching problem is to locate occurrences of any pattern among a set of patterns in a given text. Massive data sets abound and at the same time, there are many settings in which working space is extremely limited. We…
Efficient spatial indexing is crucial for processing large-scale spatial data. Traditional spatial indexes, such as STR-Tree and Quad-Tree, organize spatial objects based on coarse approximations, such as their minimum bounding rectangles…
We propose a new outline for adaptive dictionary learning methods for sparse encoding based on a hierarchical clustering of the training data. Through recursive application of a clustering method, the data is organized into a binary…
In many modern applications, including analysis of gene expression and text documents, the data are noisy, high-dimensional, and unordered--with no particular meaning to the given order of the variables. Yet, successful learning is often…
Supervised hashing aims to map the original features to compact binary codes that are able to preserve label based similarity in the Hamming space. Non-linear hash functions have demonstrated the advantage over linear ones due to their…
The Simplex Tree (ST) is a recently introduced data structure that can represent abstract simplicial complexes of any dimension and allows efficient implementation of a large range of basic operations on simplicial complexes. In this paper,…
A Supertree synthesizes the topologies of a set of phylogenetic trees carrying overlapping taxa set. In process, conflicts in the tree topologies are aimed to be resolved with the consensus clades. Such a problem is proved to be NP-hard.…
Highly-concurrent system models with vast state spaces like Chemical Reaction Networks (CRNs) that model biological and chemical systems pose a formidable challenge to cutting-edge formal analysis tools. Although many symbolic approaches…
This paper presents a general technique for optimally transforming any dynamic data structure that operates on atomic and indivisible keys by constant-time comparisons, into a data structure that handles unbounded-length keys whose…
We study the design of efficient algorithms for combinatorial pattern matching. More concretely, we study algorithms for tree matching, string matching, and string matching in compressed texts.
A suffix tree is able to efficiently locate a pattern in an indexed string, but not in general the most recent copy of the pattern in an online stream, which is desirable in some applications. We study the most general version of the…
The suffix array is the key to efficient solutions for myriads of string processing problems in different applications domains, like data compression, data mining, or Bioinformatics. With the rapid growth of available data, suffix array…
The rise of repetitive datasets has lately generated a lot of interest in compressed self-indexes based on dictionary compression, a rich and heterogeneous family that exploits text repetitions in different ways. For each such compression…
We introduce K-tree in an information retrieval context. It is an efficient approximation of the k-means clustering algorithm. Unlike k-means it forms a hierarchy of clusters. It has been extended to address issues with sparse…
We propose a flexible and multi-scale method for organizing, visualizing, and understanding datasets sampled from or near stratified spaces. The first part of the algorithm produces a cover tree using adaptive thresholds based on a…
Phylogenetic trees represent evolutionary relationships among sets of organisms. Popular phylogenetic reconstruction approaches typically yield hundreds to thousands of trees on a common leafset. Storing and sharing such large collection of…
Linguists have long held that a key aspect of natural language syntax is the recursive organization of language units into constituent structures, and research has suggested that current state-of-the-art language models lack an inherent…