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- Simone Faro, M. Oguzhan Külekci
- AAIM
- 2016

Given a pattern x of length m and a text y of length n, both over an ordered alphabet, the order-preserving pattern matching problem consists in finding all substrings of the text with the same relative order as the pattern. It is an approximate variant of the well known exact pattern matching problem which has gained attention in recent years. This… (More)

- Domenico Cantone, Simone Faro, M. Oguzhan Külekci
- Stringology
- 2015

Given a pattern and text, both over a common ordered alphabet, the orderpreserving pattern matching problem consists in finding all substrings of the text with the same relative order as the pattern. This problem, an approximate variant of the well-known exact pattern matching problem, finds applications in such fields as time series analysis (e.g., share… (More)

- Atalay Mert Ileri, M. Oguzhan Külekci, Bojian Xu
- CPM
- 2014

We revisit the problem of finding shortest unique substring (SUS) proposed recently by [6]. We propose an optimal O(n) time and space algorithm that can find an SUS for every location of a string of size n. Our algorithm significantly improves the O(n) time complexity needed by [6]. We also support finding all the SUSes covering every location, whereas the… (More)

- M. Oguzhan Külekci, Jeffrey Scott Vitter, Bojian Xu
- IEEE/ACM Transactions on Computational Biology…
- 2012

Finding repetitive structures in genomes and proteins is important to understand their biological functions. Many data compressors for modern genomic sequences rely heavily on finding repeats in the sequences. Small-scale and local repetitive structures are better understood than large and complex interspersed ones. The notion of maximal repeats captures… (More)

- Simone Faro, M. Oguzhan Külekci
- SPIRE
- 2012

Searching for all occurrences of a given set of patterns in a text is a fundamental problem in computer science with applications in many fields, like computational biology and intrusion detection systems. In the last two decades a general trend has appeared trying to exploit the power of the word RAM model to speed-up the performances of classical string… (More)

- M. Oguzhan Külekci
- Stringology
- 2009

- Tamanna Chhabra, M. Oguzhan Külekci, Jorma Tarhio
- Stringology
- 2015

The problem of order-preserving matching is to find all substrings in the text which have the same relative order and length as the pattern. Several online and one offline solution were earlier proposed for the problem. In this paper, we introduce three new solutions based on filtration. The two online solutions rest on the SIMD (Single Instruction Multiple… (More)

- M. Oguzhan Külekci
- 2014 Data Compression Conference
- 2014

We investigate the usage of the wavelet tree and the rank/select-dictionary data structures on hybrid-structured variable-length codes, which represent an integer in the form of a unary code section followed by a binary section. We propose to handle unary and binary partitions as separate streams and create wavelet trees or R/S dictionaries over the unary… (More)

- Simone Faro, M. Oguzhan Külekci
- ALENEX
- 2013

Searching for all occurrences of a pattern in a text is a fundamental problem in computer science with applications in many other fields, like natural language processing, information retrieval and computational biology. In the last two decades a general trend has appeared trying to exploit the power of the word RAM model to speed-up the performances of… (More)

- M. Oguzhan Külekci
- Computers & Security
- 2012

The usual way of ensuring the confidentiality of the compressed data is to encrypt it with a standard encryption algorithm. Although the computational cost of encryption is practically tolerable in most cases, the lack of flexibility to perform pattern matching on the compressed data due to the encryption level is the main disadvantage. Another alternative… (More)