Oguzhan Kulekci

Algorithm Engineer, Security/Privacy Researcher, Combinatorial Problem Solver

Research Expertise

algorithms
pattern matching
data compression
bioinformatics
security & privacy
Cell Biology
Molecular Biology
Biotechnology
Biochemistry
Applied Mathematics
Genetics
Software
Theoretical Computer Science
Discrete Mathematics and Combinatorics
Computational Theory and Mathematics
Computational Mathematics
Law
Numerical Analysis
Modeling and Simulation
Electrical and Electronic Engineering
Library and Information Sciences

About

My main expertise is in solving computational challenges with an innovative algorithm engineering approach. For more than two decades, I have been studying on such challenges originating from different fields mainly in cryptography and data security, natural language processing, information retrieval, computational biology, data compression and coding, massive data management, and most recently focusing on scalability and security aspects of ML/AI algorithms. I have been devising efficient innovative solutions and/or improving current state-of-art in terms of resource usage, e.g., time, memory, energy, communication costs. I would like to provide a summary of my previous achievements in engineering, research, and administration. Engineering Expertise: After spending around two years on programming point-of-sales devices and regular database programming, I have spent 10+ years in cryptography, where the main focus had been efficient implementation and cryptanalysis of the security&privacy algorithms and protocols both in hardware and software. During those years, despite gaining experience on how to develop programs that run fast and/or with small memory footprint, I had the chance to work with talented mathematicians and hardware engineers, that gave me the opportunity to widen my knowledge on different dimensions, including reverse engineering and FPGA/ASIC design. I also learned a lot on how to develop projects with a team of talent coming from different disciplines. I have observed, and today strongly believe, that theoretical knowledge is vital, but never enough to built efficient systems in practice. The platform that the solution will be executed on and the properties of the input data should always be considered for ground-breaking progress in practical performance. Theory without practice, or vice versa, is akin to trying to fly with one wing. In that sense, the development of the fastest pattern matching solutions and innovating patents that are licensed to companies have been exemplary outcomes of my perspective. Academic Expertise: Following my 15+ years in industry, I joined academia and have been serving as a professor of computer sci- ence. I succeeded to get several research grants and have been also serving in the committees of conferences. Actually, I started publishing in scientific venues when I was with the industry as well. I did my phd on natu- ral language processing, after which I got more engaged with combinatorial algorithms. I mostly published on data compression, combinatorial pattern matching and applications of them on computational biol- ogy/bioinformatics. Most recently, I have been studying scalablity and security aspects in ML/AI systems as well as in information retrieval. I have also experience in massive data management and analysis. I have been teaching courses on algorithms, security/privacy, and related topics. Administrative Expertise: After engineering cryptography for many years, I changed my focus to computational biology, particularly the genomics area. I have served as the deputy director of the National Institute of Genetics and Biotechnology of Turkey for two years, during which I was responsible for the establishment of the first high-throughput DNA sequencing facility of the country. That leadership equipped me with a unique experience of leading an interdisciplinary project with people from computing and life sciences disciplines. The establishment of the lab was supported with more than 2 million dollars grant by the government and was successfully completed in two years. Another leadership experience I had was being the program coordinator of the graduate programs in my university for more than four years. I was responsible by curriculum development and hiring new faculty. I have also served previously as principal investigator in research projects, lead research labs, and delivered project lead positions in industry projects.

Legacy Map

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Publications

Sketching algorithms for genomic data analysis and querying in a secure enclave
Nature Methods
2020
Fast Multiple String Matching Using Streaming SIMD Extensions Technology
String Processing and Information Retrieval
2012
Fast Packed String Matching for Short Patterns
2013 Proceedings of the Fifteenth Workshop on Algorithm Engineering and Experiments (ALENEX)
2013
Efficient Maximal Repeat Finding Using the Burrows-Wheeler Transform and Wavelet Tree
IEEE/ACM Transactions on Computational Biology and Bioinformatics
2012
Efficient Algorithms for the Order Preserving Pattern Matching Problem
Algorithmic Aspects in Information and Management
2016
Engineering order‐preserving pattern matching with SIMD parallelism
Software: Practice and Experience
2016
Enhanced Variable-Length Codes: Improved Compression with Efficient Random Access
2014 Data Compression Conference
2014
Tara: An algorithm for fast searching of multiple patterns on text files
2007 22nd international symposium on computer and information sciences
2007
Turkish word segmentation using morphological analyzer
7th European Conference on Speech Communication and Technology (Eurospeech 2001)
2001
Rule-based prosody prediction for German text-to-speech synthesis
Speech Prosody 2006
2006
I/O-efficient data structures for non-overlapping indexing
Theoretical Computer Science
2021
Uniquely decodable and directly accessible non-prefix-free codes via wavelet trees
2013 IEEE International Symposium on Information Theory
2013
Nucleotide Sequence Alignment and Compression via Shortest Unique Substring
Bioinformatics and Biomedical Engineering
2015
Succinct Non-overlapping Indexing
Combinatorial Pattern Matching
2015
Time- and space-efficient maximal repeat finding using the burrows-wheeler transform and wavelet trees
2010 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
2010
Ranking Assisted Unsupervised Morphological Disambiguation of Turkish
Unknown Venue
2023
Dynamic Multi-Server Searchable Encryption Scheme Based on Concept Hierarchy
2018 9th International Symposium on Parallel Architectures, Algorithms and Programming (PAAP)
2018
Ψ-RA: a parallel sparse index for genomic read alignment
BMC Genomics
2011
Compressed Context Modeling for Text Compression
2011 Data Compression Conference
2011
Pronunciation Disambiguation in Turkish
Computer and Information Sciences - ISCIS 2005
2005
Range Selection Queries in Data Aware Space and Time
2015 Data Compression Conference
2015
A Method to Ensure the Confidentiality of the Compressed Data
2011 First International Conference on Data Compression, Communications and Processing
2011
An overview of natural language processing techniques in text-to-speech systems
Proceedings of the IEEE 12th Signal Processing and Communications Applications Conference, 2004.
Counting with Prediction: Rank and Select Queries with Adjusted Anchoring
2022 Data Compression Conference (DCC)
2022
Quality Assessment of High-throughput DNA Sequencing Data via Range analysis
Unknown Venue
2017
Preprint repository arXiv achieves milestone million uploads
Physics Today
2014
A System Architecture for Efficient Transmission of Massive DNA Sequencing Data
Journal of Computational Biology
2017
PSI-RA: A parallel sparse index for read alignment on genomes
2010 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
2010
A framework for assessing a country’s scientific productivity based on published articles by scientists affiliated with that country
Information Discovery and Delivery
2023
Memory–Efficient FM-Index Construction for Reference Genomes
2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
2022
The future of evaluation of child and adolescent psychiatric treatments
IACAPAP ArXiv
2021
GENCROBAT: Efficient transmission and processing of the massive genomic data
NOMS 2016 - 2016 IEEE/IFIP Network Operations and Management Symposium
2016
On stabbing queries for generalized longest repeat
2015 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
2015
Turkish Tweet Classification with Transformer Encoder
Proceedings - Natural Language Processing in a Deep Learning World
2019
IMPACTS: Results Summary for CY 2010
Unknown Venue
2013
Randomized Data Partitioning with Efficient Search, Retrieval and Privacy-Preservation
Lecture Notes in Computer Science
2023
A Survey on Shortest Unique Substring Queries
Algorithms
2020
The order-preserving pattern matching problem in practice
Discrete Applied Mathematics
2020
Applications of Non-Uniquely Decodable Codes to Privacy-Preserving High-Entropy Data Representation
Algorithms
2019
Optimizing Packed String Matching on AVX2 Platform
High Performance Computing for Computational Science – VECPAR 2018
2019
Privacy–Preserving Text Similarity via Non-Prefix-Free Codes
Similarity Search and Applications
2019
A Two-Level Scheme for Quality Score Compression
Journal of Computational Biology
2018
Quality Assessment of High-Throughput DNA Sequencing Data via Range Analysis
Bioinformatics and Biomedical Engineering
2018
Range selection and predecessor queries in data aware space and time
Journal of Discrete Algorithms
2017
Security analysis on the ADS-B technology
2017 25th Signal Processing and Communications Applications Conference (SIU)
2017
Inverse Range Selection Queries
String Processing and Information Retrieval
2016
A simple yet time-optimal and linear-space algorithm for shortest unique substring queries
Theoretical Computer Science
2015
Huffman Codes versus Augmented Non-Prefix-Free Codes
Experimental Algorithms
2015
Robustness of Massively Parallel Sequencing Platforms
PLOS ONE
2015
Fast and flexible packed string matching
Journal of Discrete Algorithms
2014
Shortest Unique Substring Query Revisited
Combinatorial Pattern Matching
2014
A time--memory trade-off approach for the solution of nonlinear equation systems
Turkish Journal of Electrical Engineering and Computer Sciences
2013
Fast Pattern-Matching via k-bit Filtering Based Text Decomposition
The Computer Journal
2010
On enumerating the DNA sequences
Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine
2012
On scrambling the Burrows–Wheeler transform to provide privacy in lossless compression
Computers & Security
2012
BLIM: A New Bit-Parallel Pattern Matching Algorithm Overcoming Computer Word Size Limitation
Mathematics in Computer Science
2010
Boosting Pattern Matching Performance via k-bit Filtering
Lecture Notes in Electrical Engineering
2010
A Method to Overcome Computer Word Size Limitation in Bit-Parallel Pattern Matching
Algorithms and Computation
2008

Education

Sabancı University

Ph.D., Computer Science / July, 2006

Istanbul

Experience

Indiana University

Visiting Professor / January, 2022Present

Istanbul Teknik Üniversitesi

Professor / November, 2015Present

national research institute of electronics and cryptology

Chief Researcher / January, 2007March, 2014

Design, analysis, and implementation of cryptographic security and privacy algorithms

Senior Researcher / June, 2004May, 2007

Design, analysis, and implementation of cryptographic security and privacy algorithms

Researcher / June, 1999June, 2004

Design, analysis, and implementation of cryptographic security and privacy algorithms

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