Applied Informatics Programme Doctorate Courses

* Detailed information on the Financial Engineering and Business Analytics course group with the list of recommended courses can be found in the attached .pdf document. 

BLU 696/E Scientific Research, Ethic and Seminar, (0), (Type: Compulsory)
Definition and development of science, scientific research approach, literature survey, research design, quantitative and qualitative research methodologies, data gathering, writing techniques for thesis, project, and scientific article, ethical principles to be followed when conducting research, ethical principles to be followed when publishing, citation ethics, tips for a successful presentation, students presentations within the scope of their thesis topics/own engineering field.
[Course Catalogue Form with ECTS Credits]

BLU 602/E Smart Antennas for Wireless Communications, (3+0)
System requirements for implementation of an appropriate Smart Antenna implementation. Application of adaptive arrays to modern communication systems and remote sensing systems. Smart Antenna or sensor system design and performance evaluation. The operation and application of spatial filtering accomplished by adaptive array antenna systems. [Course Catalogue Form with ECTS Credits]

BLU 6**/E Advanced Modeling and Simulation of Markovian Sytems, (3+0)
Review of Probability Theory and Random Processes, Memoryless Property, Markov Property, Poisson Process, Pseudo-random Number Generation, Generation of Poisson Arrival Events, Simulation optimization, Confidence intervals, Simulation and performance measures of M/M/1, M/M/k, M/D/1, M/M/k/k, M/M/k/k/N systems, Erlang loss formulas, Queueing disciplines, Impatience Models, Batch Arrivals, Markovian Arrival Process (MAP), Phase-type service times, Aloha systems, Internet traffic, Router/switch simulation [Course Catalogue Form with ECTS Credits]

BLU 606/E Finite Element Method  in Electromagnetic Theory, (3+0)
Basic concepts of the Finite Element Method (FEM), Modeling of some one-, two- and three- dimensional boundary-value problem by using Finite Element Method, make an algorithms and computer’s program using of the FEM. [Course Catalogue Form with ECTS Credits]

BLU 605/E Large Scale Data Processing, (3+0)
Large scale data analysis, distributed data storage, modern approaches and emerging technologies in data storage, network infrastructures, cache management, high performance data access, distributed data processing, statistical analysis, statistical analysis on distributed data, failure management, working with incomplete and stale data. [Course Catalogue Form with ECTS Credits]

BLU 614/E Method of Moment in Electromagnetics, (3+0)
Basic concepts of the Moment Method (Mom), Modeling of some one-, two- and threedimensional boundary-value problem by using Moment Method, make an algorithms and computer’s program using of the MoM. Radiation and scattering. Solution of matrix equation.  Thin wires. Two dimensional problems. [Course Catalogue Form with ECTS Credits]

BLU 6**/E Finite Difference Time Domain Method in Electromagnetics, (3+0)
Numeric interpolation and extrapolation. Analytical formulation and numerical configurations. Theory of conducting bodies. Permitting and/or dissipating bodies. Numerical and semianalytical computational methods. Finite Differences method in Time Domain. Several FDTD applications for conducting, dielectric, lossless, and/or lossy cases. Several FDTD applications for dispersive cases. Up-to-date research problems.[Course Catalogue Form with ECTS Credits]

BLU 6**/E Financial Signal Processing, (3+0)
Sparse Markowitz portfolio. Temporal causal modeling. Mean reverting portfolios. Explicit kernel and sparsity of eigen subspace for the AR (1) process. Approaches to high-dimensional covariance and precision matrix estimation. Stochastic volatility. Statistical measures of dependence for financial data. Correlated Poisson process and their applications in financial modeling. CVar (Conditional Value at Risk) minimizations in support vector machines. Regression models in risk management.
[Course Catalogue Form with ECTS Credits]

BLU 6**/E Law of Cyber Security and Cyber Defense, (3+0)
Network and information security incidents. Legal framework of countering cybercrime Regulation of ICTs. National security law. Problems in national and international cybersecurity and defense. International and regional network and information security regulations. International cyber law and policy development. Application of international law to uses of ICTs: the UN Charter and international cybersecurity. Application of international law to uses of ICTs: the law of state responsibility. International humanitarian law and cyberspace. Non-binding rules in cybersecurity discourse.
[Course Catalogue Form with ECTS Credits]

BLU 6**/E Public E-Services, (3+0)
The use of ICTs and information society services in public sector. Concepts of e-governance and public administration of ICTs. The concepts of public Information Systems, public key infrastructure, public databases, public service models, and strategies. Introduce and optimization of uses of ICTs in the public sector. Applicable legal regimes and user-friendly, trusted and economically efficient public sector presence online.[Course Catalogue Form with ECTS Credits]

BLU 6**/E Biotechnology and Health Care Regulations, (3+0)
The scientific, ethical, and socio-economic risks of modern bio-technologies. Normative approaches to human bio-technologies. Biotechnology Regulations in Turkey. Comparison of European Union (EU) and the United States (USA) approach. Key concepts: intellectual property and other rights. Evaluation of biotechnology regulations. Case study in biotechnology regulation.
[Course Catalogue Form with ECTS Credits]

BLU 615/E Privacy and Data Protection, (3+0)
A thorough understanding of the concepts, principles and regulation of privacy and personal data protection within the European regulatory framework. The applicable legislation, court practice by the Court of Justice of the European Union and the European Court of Human Rights of privacy and data protection and the latest developments in the respective field. [Course Catalogue Form with ECTS Credits]

BLU 6**/E Cybercrimes, (3+0)
Descriptions of the forms of cyber-crime (typology) and ICT-related investigation powers. Knowledge of current and forthcoming international legislative initiatives regarding substantive and procedural criminal cyber-crime law. Insight into the problems surrounding cyber-crime. Insight into the imperfections in existing legislation. Insight into the influence of international developments on law. Provide insight into the regulatory possibilities to fight cyber-crime. Apply legal rules to cases of cyber-crime. An analysis of the abuse of new technological developments with regard to existing law.
[Course Catalogue Form with ECTS Credits]

BLU 608/E Contracts in Information and Communication Technologies, (3+0)
Types of Information Communication Technologies (ICT) contracts. Characteristics of ICT contracts. The negotiation process. The contents of various types of contracts (eg. hardware, software, outsourcing, cloud computing and telecommunications contracts). Dispute resolution mechanisms for ICT disputes. Drafting and assessing ICT contracts (starting points, methods and practice).
[Course Catalogue Form with ECTS Credits]

BLU 604/E Advanced Analysis Techniques for Molecular Dynamics Simulations, (3+0)
Applications of  MD Simulations in biomembrane dynamics and function studies . Performing MD Simulations with NAMD program. VMD: a MD simulation analysis program. Time series analysis of basic features: Hydrogen bond, secondary structure, angle and distance. Root Mean Square Deviation (RMSD) and Root Mean Square Fluctuation (RMSF) calculations. Radial distribution function (RDF) and radius of gyration calculations. Principal component analysis of MD trajectory. Cross-correlation analysis. Elastic Network analysis of MD trajectories. Methods for analyzing simulations of Biomembranes and Membrane proteins. Density and diffusion calculations. Interaction Energy calculations of MD trajectories. MD simulation analysis using Markov State models-1. MD simulation analysis using Markov State models-2 [Course Catalogue Form with ECTS Credits]

BLU 6**/E Free Energy Calculations in Chemistry and Biology, (3+0)
Applications of free energy calculations in biology. Applications of free energy calculations in drug discovery. Molecular Dynamics and Monte Carlo Simulations. Adaptive Biasing Force (ABF) simulations. Steered Molecular Dynamics Simulations. Replica exchange molecular dynamics simulations. Free energy perturbation calculations. Umbrella Sampling. implicit solvent methods for ligand binding affinities: MM/PBSA and MM/GBSA. Linear interaction energy: method and applications in drug design. Analysis of free energy calculations. Metadynamics. Transition Path Sampling. Best practices in Free Energy calculations [Course Catalogue Form with ECTS Credits]

BLU 6**/E Vehicular Communications from Physical Layer to Networking, (3+0)
Intra-vehicular communication: In-vehicle Ethernet, Wireless in-vehicle networks. Inter-vehicular communication, Intersection collision warning systems. Requirements and components: Application demands, Metrics to assess IVC solutions, Communicating entities, Communication principles. Concepts for inter-vehicle communication. Fundamental limits. Access Technologies: Wireless networks, Short-range radio Technologies, cognitive radio for IVC. Physical layer aspects of V2X communications: Wireless channel models, Cooperative communication systems. Information dissemination in vehicular networks: Ad-hoc routing, Geographic routing, Beaconing, Infrastructure support, DTN and peer-to-peer networks. Performance evaluation. [Course Catalogue Form with ECTS Credits]

BLU 610/E Advanced Topics in Applied Informatics), (3+0)
Aside from fields such as computer science, electronics and communications; informatics applications are encountered in very diverse areas such as biology, health, space technologies, astronomy, law, mathematics, linguistics, energy, social media, business and education. Therefore, the diversity of the courses given in the applied informatics doctoral program has great importance. Within this context, courses with different subjects that do not comprise subjects of other courses  will be given. Topics may chance depending on the new research activities in applied informatics.[Course Catalogue Form with ECTS Credits]

BLU 601/E Guided Research, (3+0)
Under the supervision of a faculty member, in weekly meetings, the investigation of scholarly publications that are in a research area of interest to the faculty member and recommended by the faculty member. The analysis of these publications as well as potential directions of research for the future are to be shared with the faculty member in these meetings. Every 3-4 weeks, a concise presentation of the acquired knowledge and background, significant results in the research area as well as potential directions of research is to be made to the supervising faculty member. A report that summarizes the work carried out during the term will be prepared.[Course Catalogue Form with ECTS Credits]

BLU 6**/E Applied Probability and Probabilistic Systems Analysis, (3+0)
Introduction to Probabilistic Modeling, Conditional Probability, Combinatorics. Discrete Random Variables, Extension to higher dimensions. Continuous Random Variables, Extension to higher dimensions. Derived Distributions; Convolution, Covariance, Correlation. Sums of a random number of random variables. Prediction, Estimation, Convergence in Probability. Signal-to-Noise Ratio. Random Processes (Bernoulli, Poisson, Gaussian), Markov Chains. Laws of Large Numbers. Bayesian Inference. Hypothesis Testing. Applications on Queueing Theory. Applications on Statistical Learning.  [Course Catalogue Form with ECTS Credits]

BLU 6**/E Multimodal Surveillance Systems, (3+0)
Introduction to multi-modal surveillance systems, history and types of surveillance systems. Visible-range cameras, image processing methods. Audio Acquisition and audio processing methods. Thermal, SWIR, MWIR, LWIR Cameras. Hyperspectral Imaging. Novel sensing approaches, vibration sensors. Inertial Measurement Unit (IMU). PIR sensors and flame and gas sensing using PIR sensors. Data fusion, decision fusion. Various applications of multi-modal sensor systems, Stereoscopy. Audio-assisted cameras, joint processing of audio and vision. Visible-thermal image processing. Distributed multi-modal surveillance systems. Low computational complexity, low energy processing. [Course Catalogue Form with ECTS Credits]


BLU 603/E Statistical Learning, (3+0)
Probability, Entropy and Inference. Clustering and regression. Unsupervised and reinforcement learning. Monte Carlo methods. Ising models. Sampling. Independent component analysis. Neural networks. Capacity of a single neuron. Learning as inference. Hopfield networks. Supervised learning. Gaussian processes. De-convolution. [Course Catalogue Form with ECTS Credits]

BLU 6**/E Smart Electric Power Distribution Systems, (3+0)

Features and components of electric power distribution systems, power flow, short circuit and reliability analysis, basic control and protection, communications and SCADA, new "smart" functionality such as integrated volt/var control, demand response and advanced metering infrastructure, integration of distributed generation and energy storage. [Course Catalogue Form with ECTS Credits]

BLU 6**/E Multi-Scale Thermal Modeling of Data Centers, (3+0)
Thermal and Energy Systems Modeling of Data Centers, Thermal Resistance and Capacitance, Thermal Circuits at Various Scales, Fan and Pump Theory, Flow Characteristics of Data Centers, Flow Network Modeling,  Thermodynamics of Data Center Cooling and Air Conditioning Systems, Thermodynamic Modeling, Fundamentals of Computational Fluid Dynamics (CFD), CFD Modeling of Datacenters [Course Catalogue Form with ECTS Credits]

BLU 611/E Signal Processing Methods in Wireless Communications - 1, (3+0)
Introduction to signal processing and its application in communications. Discrete-time signals. Introduction to Fourier analysis. Fourier series, discrete-time Fourier transform (DTFT), discrete Fourier transform (DFT). Fast Fourier transform (FFT). Discrete-Time Systems (LTI filters.  Convolution and modulation. Difference equations. FIR vs IIR, stability issues.) Interpolation and Sampling. Sampling theorem. Aliasing. Quantization. A/D and D/A converters. Z-transform. FIR design methods. IIR design methods. Filter structures. Stochastic Signal Processing. Random processes. Spectral representation. Multi-rate signal processing. Upsampling and downsampling. Oversampling. Digital communication system design. Introduction to channel estimation and equalization. Channel estimation and  equalization using higher order statistics. Performance bounds for blind channel estimation. Subspace method for blind identification and deconvolution. [Course Catalogue Form with ECTS Credits]

BLU 6**/E Signal Processing Methods in Wireless Communications - 2, (3+0)
Introduction to  signal processing advances in wireless communications. Time-frequency analysis techniques. Fading channel models and linear, time varying fading channels. Time-frequency analysis of LTV fading channels. Coding strategies for transmissions over LTV channels. Channel estimation and prediction for LTV channels. Signal processing framework for space-time diversity. Signal separation in a multi-user environment. Algebraic constant modulus algorithms for blind signal separation. Orthogonal frequency division multiplexing (OFDM) and alternative  modulation techniques for the next-generation communication systems, Generalized OFDM. Filterbank multi-carrier. Synchronization techniques and antenna arrays. [Course Catalogue Form with ECTS Credits]

BLU 6**/E Wireless Networks, (3+0)
Introduction to computer and communication networks. TCP/IP stack. Wireless medium characteristics and challenges. Aloha protocol. CSMA, Ethernet, IEEE802.11,  DCF and PCF modes. Hidden and exposed node problems. WLAN Security, WEP. Ad hoc and sensor networks, challenges in MAC and routing. Smart homes, smart cities. Vehicular networks, mobility. Satellite communications. Bluetooth, Personal Area Networks. Cellular networks, architecture and standards, small cells. Wireless broadband, WiMAX, LTE. Next generation systems, current trends. [Course Catalogue Form with ECTS Credits]

BLU 6**/E Selected Topics in Algorithms, (3+0)
Time/space complexity analysis of algorithms and basic algorithm design approaches, P versus NP concept, approximation algorithms, randomization, streaming algorithms,  external-memory algorithms and related data structures [Course Catalogue Form with ECTS Credits]

BLU 6**/E Selected Topics in Data Compression, (3+0)
Basic information theory concepts to measure the entropy of a sequence, universal codes, entropy coding with Huffman and arithmetic codes, compression algorithms with dictionary-, statistics-, or transformation-based modeling methods, compressed data structures and regarding applications, compressed self-text indexing, using compression as a classifier [Course Catalogue Form with ECTS Credits]

BLU 607/E Informatics applications in drug discovery and development, (3+0)

Fundementals of drug development and discovery. Protein structure. Fundamentals of drug actions. Basics of Cheminformatics and data analysis. Drug binding sites. Sequence analysis. Proteomics and Metabolics Approaches for Biomarker Discovery. Drug repositioning/Repurposing. Prediction of Drug Combinations. Network and Pathway Analysis of Compound–Protein Interactions. Data integration and mixture modeling. Proteochemometrics modeling. Computational Toxicology analysis. Proteokemometrik modelleme. [Course Catalogue Form with ECTS Credits]

BLU 618/E Boundary Value Problems in Electromagnetics and the Special Functions I, (3+0)
The standard classical theoretical physics equations and boundary conditions. Standard equations. Boundary conditions. Other conditions. General solution methods.  Separation of variable method. Integral transformations. Eigen-function system expansions and Sturm-Liouville problem. Special functions. [Course Catalogue Form with ECTS Credits]

BLU 6**/E Boundary Value Problems in Electromagnetics and the Special Functions II, (3+0)

Cartesian coordinates. The initial value problem. Mixed boundary value problems. Exponential and trigonometric functions. Circular cylindrical coordinates. Bessel functions. Spherical coordinates and Legendre functions. General solution of Legendre's equation. Toroid coordinates. Harmonics. Gamma function. [Course Catalogue Form with ECTS Credits]