Related papers: Implementing Suffix Array Algorithm Using Apache B…
Suffix trees are a fundamental data structure in stringology, but their space usage, though linear, is an important problem for its applications. We design and implement a new compressed suffix tree targeted to highly repetitive texts, such…
Suffix trees are one of the most versatile data structures in stringology, with many applications in bioinformatics. Their main drawback is their size, which can be tens of times larger than the input sequence. Much effort has been put into…
In the past thirty years, numerous algorithms for building the suffix array of a string have been proposed. In 2021, the notion of suffix array was extended from strings to DFAs, and it was shown that the resulting data structure can be…
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…
Data sizes that cannot be processed by conventional data storage and analysis systems are named as Big Data.It also refers to nex technologies developed to store, process and analyze large amounts of data. Automatic information retrieval…
String matching is the problem of finding all the occurrences of a pattern in a text. It has been intensively studied and the Boyer-Moore string matching algorithm is probably one of the most famous solution to this problem. This algorithm…
In order to associate complex traits with genetic polymorphisms, genome-wide association studies process huge datasets involving tens of thousands of individuals genotyped for millions of polymorphisms. When handling these datasets, which…
We introduce a new family of compressed data structures to efficiently store and query large string dictionaries in main memory. Our main technique is a combination of hierarchical Front-coding with ideas from longest-common-prefix…
Big data, encompassing extensive datasets, has seen rapid expansion, notably with a considerable portion being textual data, including strings and texts. Simple compression methods and standard data structures prove inadequate for…
The Suffix Array $SA_S[1\ldots n]$ of an $n$-length string $S$ is a lexicographically sorted array of the suffixes of $S$. The suffix array is one of the most well known and widely used data structures in string algorithms. We present a…
The Suffix Array SA(S) of a string S[1 ... n] is an array containing all the suffixes of S sorted by lexicographic order. The suffix array is one of the most well known indexing data structures, and it functions as a key tool in many string…
The term Big Data is usually used to describe huge amount of data that is generated by humans from digital media such as cameras, internet, phones, sensors etc. By building advanced analytics on the top of big data, one can predict many…
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"…
Analytic queries enable sophisticated large-scale data analysis within many commercial, scientific and medical domains today. Data skew is a ubiquitous feature of these real-world domains. In a retail database, some products are typically…
Traditionally, we usually utilize the method of shotgun to cut a DNA sequence into pieces and we have to reconstruct the original DNA sequence from the pieces, those are widely used method for DNA assembly. Emerging DNA sequence…
Recently, in the area of big data, some popular applications such as web search engines and recommendation systems, face the problem to diversify results during query processing. In this sense, it is both significant and essential to…
We present an algorithm for classification tasks on big data. Experiments conducted as part of this study indicate that the algorithm can be as accurate as ensemble methods such as random forests or gradient boosted trees. Unlike ensemble…
With the advent of large-scale heterogeneous search engines comes the problem of unified search control resulting in mismatches that could have otherwise avoided. A mechanism is needed to determine exact patterns in web mining and…
We present first algorithmic ideas for a practical and lightweight adaption of the DCX suffix array construction algorithm [Sanders et al., 2003] to the distributed-memory setting. Our approach relies on a bucketing technique which enables…
This study analyzes the impact of heterogeneity ("Variety") in Big Data by comparing classification strategies across structured (Epsilon) and unstructured (Rest-Mex, IMDB) domains. A dual methodology was implemented: evolutionary and…