Projects

Internationally Funded Projects:

• New methods for systems biology diagram construction
  Sponsored by Luxembourg Centre for Systems Biomedicine (LCSB)
• AI EDIH Türkiye: AI-Enabled Manufacturing for Twin Transition
  Sponsored by the European Union
• Processing-in-memory architectures and programming libraries for bioinformatics
  Sponsored by the European Innovation Council. 
• Spatio-Temporal Gene Discovery for Autism Spectrum Disorder.
  Sponsored by Simons Foundation. 
• Visual analysis of microservices-based cloud environments.
  Sponsored by Cyber ARMO Ltd, Israel.
• Speeding up autism gene discovery via multitask learning on comorbid neuropsychiatric disorders.
  Sponsored by Simons Foundation
• A High-Level Design Methodology for Developing Graph Algorithms on Xeon + FPGA Platforms.
  Sponsored by Intel Corporation
• CUDA Research Center (CRC).
  Sponsored by NVIDIA
• Using Accelerator Technologies in Graph Parallel Applications
  Sponsored by Intel Corp.
• Elastic and transparent scaling for stream processing applications
  Sponsored by European Commission, Marie Curie Actions
• Development and application of computational methods to analyze next generation sequence data
  Sponsored by European Molecular Biology Organization
• Novel algorithms and hardware designs for ultra-fast next-gen sequence analysis
  Sponsored by United States of America National Institutes of Health
• Integrated approaches for genomic variation discovery using high throughput sequencing
  Sponsored by European Commission, Marie Curie Actions
• FIRESENSE: Fire Detection and Management through a Multi-Sensor Network for the Protection of Cultural Heritage Areas from the Risk of Fire and Extreme Weather Conditions
  Sponsored by European Commission, 7th Framework Programme
• Heterogeneous Chip Multiprocessor Design (HTCMP)
  Sponsored by European Commission FP7-People Marie Curie Actions
• Training, Research and Innovations in Computing Education
  Sponsored by Lifelong Learning Programme of the European Commission
• Parallelizing for IBM Cell, Sponsored by HPC-Europa2
• 3DPHONE
  Sponsored by European Commission, 7th Framework Programme
• NEWCOM++ – Opportunistic Networks
  Sponsored by European Commission, 7th Framework Programme
• Automatic Detection and Segmentation of Hazelnut Orchards in Northern Turkey
  Sponsored by European Commission, Joint Research Centre
• Automatic Mapping of Linear Woody Vegetation Features in Agricultural Landscapes
  Sponsored by European Commission, Joint Research Centre
• CILL: Constrained Intuitionistic Linear Logic
  Sponsored by European Commission FP6 Marie Curie Actions
• Wireless Networking Curriculum Enhancement
  Sponsored by Intel Higher Education Program
• Hierarchical Classification, Mining and Semantic Retrieval in Remote Sensing Image Archives
  Sponsored by European Commission FP6 Marie Curie Actions
• MUSCLE-Multimedia Understanding, Through Semantics, Computation, and Learning
  Sponsored by The European Community Sixth Framework Programme (FP6)
• 3DTV-Integrated 3-D Television: Capture, Transmission and Display
  Sponsored by The European Community Sixth Framework Programme (FP6)
• South Eastern GRid Enabled eInfrastructure Development
  Sponsored by TheEuropean Community Sixth Framework Programme (FP6)
• NEWCOM – Ad Hoc and Sensor Networks
  Sponsored by The European Community Sixth Framework Programme (FP6)
• European Thematic Network for Doctoral Education in Computing
  Sponsored by Socrates Erasmus Programme of the European Commission
• Utilizing Heterogeneous CMPs through Efficient Parallelization, Sponsored by IBM Corporation
• Network Middleware for Environmental Monitoring and Control with Wireless Ad hoc, Mesh and Sensor Networks, Sponsored by IBM Corporation
• A Tool for Visually Handicapped People
  Sponsored by Microsoft Research Ltd., Cambridge, UK.
• Kronecker Operations to Define Large Markov Chains Underlying Structured Representations
  Sponsored by AvH (Alexander von Humboldt) Foundation, Germany
• Complexity Management Techniques in Graph Visualization
  Sponsored by Tom Sawyer Software, Berkeley, CA.
• Turkish Natural Language Processing Initiative
  Sponsored by NATO Science for Stability Program.
• Unstructured Domain Mapping for Distributed Memory Architectures
  Sponsored by Commission of the European Communities.
• Time-Cognizant Trigger Processing In Mobile Distributed Systems
  Sponsored by NATO Collaborative Research Grant Program.
• Detecting and preventing fraud in financial transaction networks through graph based modeling, querying, and visualization. Sponsored by TÜBITAK (Scientific and Technological Research Council of Turkey) and Turkcell Technology. 
• BacGenTrack – An integrated system for Bacterial Genome Tracking using high throughput sequencing technology: from identification to visualization. (115E596)
  Sponsored by TÜBITAK (Scientific and Technological Research Council of Turkey) and FCT (The Foundation of Science and Technology, Portugal)
• Big graph visualization and analysis using advanced querying, fast layout and complexity management techniques (5180088).  Sponsored by TÜBITAK (Scientific and Technological Research Council of Turkey) and Huawei. 
• Energy efficient FPGA accelerators for graph analytics, Sponsored by European Commission (H2020-MSCA-IF) and in collaboration with Intel Corp.
• Heterogenous parallel and distributed computing with Java (HPDCJ)
  Sponsored by CHIST-ERA (European Coordinated Research on Long-term Challenges in Information and Communication Sciences & Technologies)
• Leonardo Mobility Project
  Sponsored by European Union Leonardo Program and State Planning Organization of Turkey
• Semantic Multimodal Analysis of Digital Media
  Sponsored by TÜBITAK (Scientific and Technical Research Council of Turkey) and European Commission COST 292 Action
• Data Mining Techniques for the Location and Air-Cache management Problems
  Sponsored by TÜBITAK (Scientific and Technical Research Council of Turkey) and GSRT (The General Secretariat for Research and Technology of Greece).
• Storing and Querying Multimedia Presentations from XML Documents
  Sponsored by TÜBITAK (Scientific and Technical Research Council of Turkey) and NSF (National Science Foundation).
• New Methods for Large State Spaces in Performance Evaluation with Markovian Modeling – II
  Sponsored by TÜBITAK (Scientific and Technical Research Council of Turkey) and CNRS (Center National de la Recherche Scientifique of France).
• New Methods for Large State Spaces in Performance Evaluation with Markovian Modeling – I.
  Sponsored by TÜBITAK (Scientific and Technical Research Council of Turkey) and CNRS (Center National de la Recherche Scientifique of France).

Nationally Funded Projects:

• Açık Uçlu Sınavların Yapay Zekâ Aracılığıyla Değerlendirilmesi Projesi (3257002)
• 3D Mesh Parameterization with Cut-Distortion-Packing Optimizations (125E724)
• AI Assisted Bug Reporting and Validity Analysis (125E371)
• Continual stream learning: A comprehensive framework for continual model training and evaluation in streaming environments with a case study (125E060)
• Translating Natural Language Queries into Structured Query Language (SQL) Using Large Language Models (LLM) (125E386)
• Static and incremental automatic layout algorithms for compound graphs (125E061)
• 3D Scan Registration and Reconstruction for Digital Twin Creation (124E183)
• SAA: Supporting the software development process with visualization-based methods using software analytics (123E492)
• Personality-invariant Detection of Deceit Level through Multimodal Analysis of Speech Videos (122E134)
• Supervised and semi-supervised classification of concept drifting multi-label data data streams using novel neural network approaches (122E271)
• Personality Analysis through Human Animation with Deep Learning-based Methods and Transferring Learned Personality Traits to Human Animation (122E123)
• A System and Tool to Find, Assess and Eliminate Process Smells in software Engineering (5200078)
• Investigation and Modeling of Audio-Visual Hereditary Patterns of Speech, and Their Use in Kinship Verification (118C015)
• Applying Information Retrieval Paradigms in Natural Language to SQL Translation (118E724)
• Energy efficient processor architectures for big data graph applications
• Efficient Layout Algorithms for Compound Graphs With Support for Ports and Constraints (118E131)
• Processor Design for Graph Applications
• Rendering Three-Dimensional Scenes with Tetrahedral Meshes (117E881)
• Weakly Supervised Learning and Content-Based Retrieval for Whole Slide Breast Histopathology (117E172)
• Software and Hardware Solutions for Safety Critical Applications (117E870)
• Online Classification of Multi-Source Parallel Data Streams in Big Data Environments (117E870)
• DNA’nın 3 Boyutlu Yapısının Genetik Varyasyonların Otizm ile İlişkilendirilmesinde Kullanılması (116E148)
• Deep Learning for Histopathological Image Analysis (116E075)
• Wireless Network Topologies and Algorithms for Cloud Datacenters (116E028)
• Predicting Social Reaction and Its Labels for a Given News Article by Using Microblogs (215E169)
• Genom Çapında Yeniden İnşa Edilmiş Metabolik Ağları Barındıran Çevrimiçi Veritabanının Dizaynı ve Geliştirilmesi(115C128)
• Kolorektal Kanserin Nanomekanik Sistemlerle Erken Teşhisi Projesi (213E036)
• Algorithms for structural variation discovery using hybrid sequencing technologies and library preparation protocols. (215E172)
• Computer Vision and Machine Learning Techniques for Automated Classification of Whole-Slide Breast Histopathology Images (113E602)
• Hardware/Software Mechanisms to Enhance the Effectiveness of Directory Based Cache Coherence in Tiled Chip Multiprocessors (113E258)
• Methods and Tools for Effective Analysis of Biological Processes with SBGN (EEEAG 113E161)
• News Chain Discovery in News Articles (EEEAG 113E274)
• Efficient Resource Allocation in Heterogeneous Cloud Infrastructures (EEEAG 113E249)
• An Augmented Reality Environment for Interactive Crowd Simulation (EEEAG 112E110)
• Reliability-Aware Network on Chip (NoC) Architecture Design (112E360)
• Diverse Matching based Browsing in Large-scale Multi-dimensional Databases (EEEAG 111E217)
• Application-aware, system-level load management and shedding techniques for stream processing (112E271)
• Development and application of novel genome assembly algorithms that use multiple data sources (112E135)
• CHISIO: Querying, layout, and visualization of clustered or hierarchical relational information (111E036)
• Content-Based Retrieval of Histopathological Images using Relational Tissue Graphs (110E232)
• Refreshment Strategies for Query Result Caching in Web Search Engines (110E135)
• Mining of Very High Resolution Satellite Images Using Hierarchical Graph Models (109E193)
• Intelligent System Design for Automated Classification and Indexing of Cell Deaths in Cancerous Cell Cultures and Image based Anticancer Drug Screening Method Development (109E206)
• Novelty Detection in Topic Tracking for Turkish and its Application to a Large-Scale News Portal (108E074)
• Energy Efficient Application Mapping onto NoCs with Different Topologies (108E233)
• Exploiting Semantic Relationships for the Scalability and Efficiency of Web Search Engines (108E008)
• Biocomputational Cancer Modeling and Intelligent Medical Decision-Making System Design for Objective Cancer Diagnosis and Grading (CAREER Grant 106E118)
• Instant new event detection and tracking and retrospective event clustering in Turkish news using Web resources (106E014)
• State estimation and dynamic feedback behaviors for a legged robot (106E089)
• BTT-TÜRKIYE: Türkiye için Yeni Bilgi Toplumu Teknolojileri (105E065)
• Supporting Real-Time Traffic in Wireless Ad Hoc and Sensor Networks (CAREER Grant 104E028)
• Automatic Construction and Sophisticated Querying of Domain-Specific Web Search Engines (105E024)
• PATIKA: A Project on Modeling and Analysis of Biological Pathways to Aid Rapid Knowledge Acquisition, Drug Development and Disease Identification (CAREER Grant 104E049)
• Developing an Urban Visualization System for Virtual Environments using Computer Graphics (CAREER Grant 104E029)
• Probabilistic and Structural Approaches to Image Understanding, Classification and Retrieval, and Applications to Remote Sensing and Medical Image Analysis(CAREER Grant 104E074)
• Multimedia Data Mining: Integration of Multi-modal Data for a Better Retrieval and Analysis (CAREER Grant 104E065)
• Efficient Parallel Crawling of Web Content (103E028)
• Bluetooth Scatternet Construction and Bluetooth Applications (103E014)
• Development of Benefit Maximization and Interesting Rule Learning Algorithms for Feature Projection Based Classification Systems (101E044)
• Data Modelling and Querying for Video Databases (199E025)
• Polygonal Approximation Algorithms for Multiresolution Modeling (198E018)
• Continuous Function Approximation Using Feature Projections (198E015)
• Development of algorithms and parallel object-oriented programming techniques for SMP clusters (EEEAG-247)
• Real-Time Data Management in Mobile Computer Systems (EEEAG-246)
• Learning Translation Templates from Bilingual Translation Examples Using Machine Learning Techniques (EEEAG-244)
• Investigation of Numerical Solution Methods for Computing the Stationary Distribution of Markov Chains (EEEAG-161)
• Development of Batch Machine Learning Techniques for Multi-concept Descriptions in the form of Feature Partitioning and Overlapping Feature Intervals (EEEAG-153)
• Real-Time Database Transaction Scheduling (EEEAG-137)
• Fast pathogen screening using DNA sequencing in disaster-stricken areas
  Sponsored by Bridge to Türkiye, 2023-2025.
• Developing rapid diagnostic kit for sepsis (Sepsi-Fast).
  Sponsored by Afyon Health Sciences University, 2021-2022.
• Processor Emulator for Safety Critical Applications,
  Sponsored by Turkish Aviation Industries (TAI), 2017-2018.
• Safe Computer Design.
  Sponsored by ASELSAN, 2015-2017.
• Utilizing Accelerator Technologies in the Cloud.
  Sponsored by Turk Telekom, 2012-1013.
• E-DEVLET Icin Bilgisayar Destekli Gorsel Dokumantasyon, Arsiv ve Yonetim Sistemi Gerceklestirilmesi (in Turkish),
  Sponsored by Devlet Planlama Teskilati (YUUP: Yayginlastirilmis Ulusal ve Uluslararasi Proje) (E_DEVLET)