Related papers: FMtree: A fast locating algorithm of FM-indexes fo…
Recently Kubica et al. (Inf. Process. Let., 2013) and Kim et al. (submitted to Theor. Comp. Sci.) introduced order-preserving pattern matching. In this problem we are looking for consecutive substrings of the text that have the same "shape"…
Approximate nearest neighbor algorithms are used to speed up nearest neighbor search in a wide array of applications. However, current indexing methods feature several hyperparameters that need to be tuned to reach an acceptable…
We consider $m \times s$ matrices (with $m\geq s$) in a real affine subspace of dimension $n$. The problem of finding elements of low rank in such spaces finds many applications in information and systems theory, where low rank is…
We present a novel method for efficiently searching top-k neighbors for documents represented in high dimensional space of terms based on the cosine similarity. Mostly, documents are stored as bag-of-words tf-idf representation. One of the…
Protein Fragment Motif Finder (PFMFind) is a system that enables efficient discovery of relationships between short fragments of protein sequences using similarity search. It supports queries based on score matrices and PSSMs obtained…
Finding desired information from large data set is a difficult problem. Information retrieval is concerned with the structure, analysis, organization, storage, searching, and retrieval of information. Index is the main constituent of an IR…
Click-through rate (CTR) prediction plays a critical role in recommender systems and online advertising. The data used in these applications are multi-field categorical data, where each feature belongs to one field. Field information is…
A large fraction of an XML document typically consists of text data. The XPath query language allows text search via the equal, contains, and starts-with predicates. Such predicates can efficiently be implemented using a compressed…
Reconciling a gene tree with a species tree is an important task that reveals much about the evolution of genes, genomes, and species, as well as about the molecular function of genes. A wide array of computational tools have been devised…
Pedigrees, or family trees, are graphs of family relationships that are used to study inheritance. A fundamental problem in computational biology is to find, for a pedigree with $n$ individuals genotyped at every site, a set of…
Most of the fastest-growing string collections today are repetitive, that is, most of the constituent documents are similar to many others. As these collections keep growing, a key approach to handling them is to exploit their…
FastText has established itself as a fundamental algorithm for learning word representations, demonstrating exceptional capability in handling out-of-vocabulary words through character-level n-gram embeddings. However, its hash-based…
Efficient indexing and searching of high dimensional data has been an area of active research due to the growing exploitation of high dimensional data and the vulnerability of traditional search methods to the curse of dimensionality. This…
FM-index is an efficient data structure for string search and is widely used in next-generation sequencing (NGS) applications such as sequence alignment and de novo assembly. Recently, FM-indexing is even performed down to the read level,…
In this paper we present novel algorithmic techniques with a O(H(N)+N/H(N)) time complexity for performing several types of queries and updates on general rooted trees, binary search trees and lists of size N. For rooted trees we introduce…
Maximal frequent patterns superset checking plays an important role in the efficient mining of complete Maximal Frequent Itemsets (MFI) and maximal search space pruning. In this paper we present a new indexing approach, FastLMFI for local…
Suffix trees have recently become very successful data structures in handling large data sequences such as DNA or Protein sequences. Consequently parallel architectures have become ubiquitous. We present a novel alphabet-dependent parallel…
We present a distributed full-text index for big data applications in a distributed environment. Our index can answer different types of pattern matching queries (existential, counting and enumeration). We perform experiments on inputs up…
Random Indexing (RI) K-tree is the combination of two algorithms for clustering. Many large scale problems exist in document clustering. RI K-tree scales well with large inputs due to its low complexity. It also exhibits features that are…
Ranked document retrieval is a fundamental task in search engines. Such queries are solved with inverted indexes that require additional 45%-80% of the compressed text space, and take tens to hundreds of microseconds per query. In this…