Supervisors and Their Subject Areas

This page lists the supervisors available at the Faculty of Informatics together with a brief description of their subject specialism. Ph.D. study applicants will find this information useful when specifying their subject of study interest.

It is recommended that all applicants consult with an appropriate supervisor on the intended subject of their work. It is possible to agree on a theme that is not included in the list below. For each supervisor, a link to the webpage may be attached with more detailed information and currently offered dissertation topics.

Applicants may contact the Vice-Dean for doctoral studies should there be any doubt on the most appropriate supervisor to consult with.

prof. RNDr. Jiří Barnat, Ph.D.
Software tools for automated formal analysis and verification of large-scale systems.

Dr. rer. nat. Achim Blumensath
Logic, Algorithmic Model Theory, Automata Theory, Formal Language Theory.
More detailed information.

doc. RNDr. Tomáš Brázdil, Ph.D., MBA
Explainable artificial intelligence in biomedicine.

prof. Ing. Pavel Čeleda, Ph.D.
Cybersecurity operations, computer and network security, network situational awareness, simulation and emulation environments, interactive learning environments, learning technologies, cybersecurity education, learning analytics, and educational data mining.
More detailed information.

prof. RNDr. Ivana Černá, CSc.
Formal methods for verification of computer systems.

doc. RNDr. Vlastislav Dohnal, Ph.D.
Similarity data management. Organizing and searching in databases of complex data. Design of traditional indexing techniques and search algorithms. Applications of artificial intelligence methods for data management and indexing.

doc. RNDr. Jiří Filipovič, Ph.D.
GPU acceleration, software performance optimization, performance portability, autotuning (automatic software adaptability for performance or energy efficiency), and scientific computing (mainly computational chemistry and biology).

prof. RNDr. Petr Hliněný, Ph.D.
Combinatorial and parameterized algorithmics: parameterized complexity, combinatorial optimization, FO and MSO model checking, metatheorems.
Topological and structural graph theories: graph minors, width and depth parameters, sparsity, graph crossing number, drawings and representations of graphs.

doc. RNDr. Petr Holub, Ph.D.
Explainable AI methods in biomedicine. Traceability and reproducibility of biomedical data and analyses, provenance of sensitive data. Processing and compression of multimedia. Processing sensitive biomedical data and privacy risk analyses.

doc. RNDr. Aleš Horák, Ph.D.
Natural language processing (syntactic analysis, semantic analysis, knowledge extraction), knowledge representation and reasoning, artificial intelligence, multiagent systems.
More detailed information.

doc. RNDr. Barbora Kozlíková, Ph.D.
Visualization and visual analysis for the purpose of data exploration, analysis, and presentation.
More detailed information.

prof. RNDr. Michal Kozubek, Ph.D.
Digital image acquisition and analysis, automation of these processes and biomedical applications using optical microscopy. Optimization of critical algorithms with respect to output quality and/or quantity. Simulation of image formation in optical systems: blur, noise, artifacts and their correction using hardware and/or software means. Analysis of multi-dimensional image data. Segmentation of cells and their components. Tracking of moving objects in live cell imaging.
More detailed information.

Priv.-Doz. Dipl.-Ing. Dr. Simone Kriglstein
Human Computer Interaction, User Interface and Interaction Design, Human Centered Design, Game Design, Games User Research, Games Experience, Game Analytics, Gameplay Visualization, and Esports.
More detailed information.

prof. Dr. rer. nat. RNDr. Mgr. Bc. Jan Křetínský, Ph.D.
Formal verification and synthesis, probabilistic model checking, applications of machine learning in verification, verification of learnt systems (e.g. neural networks), explainable AI (e.g. explainable controllers of cyber-physical systems), temporal logics, automata theory.

prof. RNDr. Antonín Kučera, Ph.D.
Formal modeling and verification of computer systems (model checking, equivalence checking). Modal and temporal logics and their probabilistic extensions. Game theory and its applications in computer science (Markov decision processes, stochastic games). Effective analysis of stochastic systems with infinitely many states. Methods, algorithms and tools for analysis and verification of programs written in imperative languages.

doc. Ing. Matej Lexa, Ph.D.
Bioinformatics, computational DNA sequence and genome analysis, sequence repeats.
Examples of possible topics include:
- tools and algorithms for working with the pan-genomes and/or pan-repeatomes,
- simulation models of repeat dynamics in eukaryotic genomes,
- 3D organization of chromatin in the nucleus,
- detection and quantification of recombination events in and outside the repeatome,
- genotype-phenotype relationships in biobanks and other publicly available data.

doc. RNDr. Martin Maška, Ph.D.
Object tracking and cell fate profiling in large-scale bioimage data; analysis of multidimensional bioimage data using deep learning and well-founded methods; analysis and synthesis of multidimensional image data of cells with complex shapes.
More detailed information.

doc. RNDr. Zdeněk Matěj, Ph.D.
Digital data analysis in the field of ionizing radiation detectors; HW architecture design for data analysis using real-time machine learning methods; acceleration of simulation tools (e.g. Monte-Carlo methods).

doc. RNDr. Pavel Matula, Ph.D.
Digital image analysis and biomedical applications using optical microscopy. Analysis of higher-dimensional image data. Image segmentation using mathematically well founded methods (active contours, graph-cut minimalization, etc.). Object tracking in live cell imaging.
More detailed information.

doc. RNDr. Petr Matula, Ph.D.
Analysis of multi-dimensional biomedical image data mostly acquired using optical microscopes. Mathematical morphology.
More detailed information.

prof. RNDr. Václav Matyáš, M.Sc., Ph.D.
Applied cryptography, computer and communications security, privacy.
More detailed information.

prof. RNDr. Luděk Matyska, CSc.
Parallel and distributed systems (Grids, metacomputers), infrastructure, monitoring and management, including implications for robustness and fault tolerance; parallel and distributed applications.
High performance networks and their transport protocols, multimedia transports, including use-in (e-)learning support.
Scheduling in distributed systems, primary based on constrain (logic) programming.

doc. Mgr. Bc. Vít Nováček, PhD
Health informatics, Discovery informatics, Biomedical AI/ML applications, Knowledge graphs, Ontologies, Knowledge representation, Representation (graph) learning, Explainable AI, Interpretable ML, Text mining.
More detailed information.

doc. RNDr. Petr Novotný, Ph.D.
Risk-aware and safe reinforcement learning. Formal methods for analysis of probabilistic programs. Controller synthesis for probabilistic agents, stochastic games on graphs.

doc. Mgr. Jan Obdržálek, PhD.
Logics and algorithms for verification. Program verification and analysis. Graph width/depth parameters and related algorithmic topics (incl. model checking and parameterized complexity).

doc. RNDr. Radek Ošlejšek, Ph.D.
Data semantics and its interactive visual analytics. Software architectures for data analysis and visualizations.

doc. Ing. Václav Oujezský, Ph.D.
Cutting-edge networking technologies, Internet of Things (IoT), Software-defined Networking (SDN), wireless and mobile communication systems, programmable networks, artificial intelligence applications in networking technologies, network traffic analysis, and network security.
More detailed information.

doc. Mgr. Radek Pelánek, Ph.D.
Intelligent tutoring systems, computerized adaptive practice, recommendation systems with applications in education, automated methods for programming education.
More detailed information.

prof. Ing. Václav Přenosil, CSc.
Design and architecture of the digital systems. Dependability and diagnostics of the digital systems. Fault tolerant systems. Embedded systems. Training systems.

doc. Bruno Rossi, PhD
Software Systems Engineering; Simulations and Reliability Modelling of Software Systems; Software Engineering for AI; AI for Software Engineering; Software Evolution & Mining Software Repositories; Empirical Data-driven Software Engineering.

doc. Mgr. Hana Rudová, Ph.D.
Routing and logistics, vehicle routing, warehouse planning. Scheduling, planning, timetabling, scheduling in distributed environments. Search and metaheuristics, constraint programming, integer linear programming.

doc. Mgr. Pavel Rychlý, Ph.D.
Processing of text, natural language processing, information extraction, big data, machine translation, language modeling.
More detailed information.

doc. RNDr. Vojtěch Řehák, Ph.D.
Formal models of stochastic systems and their algortihmic analysis. Agent systems with randomized behavior. Game theory and its applications in computer science (Markov decision processes, stochastic games).

doc. RNDr. Jan Sedmidubský, Ph.D.
Similarity modeling using deep neural networks with the main emphasis on the domain of spatio-temporal human motion data (so-called motion-capture data). Action recognition, event detection, and explainability in the domain of spatio-temporal human motion data. General-purpose indexing algorithms for similarity searching in various application domains.

doc. RNDr. Petr Sojka, Ph.D.
Machine learning [of text and word representation]. Natural language processing. Classification of [mathematical] texts.
Information retrieval, text corpora. Digital libraries, digitisation, recognition (OCR) and indexing.
Digital typography, electronic publishing, visualization.

prof. RNDr. Jan Strejček, Ph.D.
Automated analysis and verification of software. Automata over infinite and finite words. SMT solcing (focused on bit-vector logic).

doc. RNDr. David Svoboda, Ph.D.
Image processing in biomedicine: image augmentation, image synthesis, generative modeling, simulation of time-lapse image sequences of living cells, checking the plausibility of synthetic image data, manipulation of higher-dimensional data.
More detailed information.

doc. RNDr. David Šafránek, Ph.D.
Development of computational methods for specification and analysis of models of complex systems. Modelling of signalling, metabolic, and gene regulatory networks. Algorithms for monitoring and control of complex dynamical processes.

prof. PhDr. David Šmahel, Ph.D.
Human Computer Interaction (HCI), Usable Security, Social Informatics, User Experience (UX), Risks of the Technology Usage (online addictions, online aggression), Digital Technology and Well-being

doc. RNDr. Petr Švenda, Ph.D.
Applied cryptography. Security analysis of cryptographic smartcards. Protocols for secure multiparty computation in limited environments. Security of cryptocurrency hardware wallets.
More detailed information.

prof. Ing. Tomáš Vojnar, Ph.D.
Static and dynamic program analysis, verification, and testing. Formal analysis and verification of primarily software but also cyber-physical systems and hardware. Static analysis in compiling. Efficient techniques of dealing with automata and logics mainly in verification but also in other applications (searching, design, optimisation). Usually involves both theory as well as implementation and experiments. Can be in collaboration with the industry.

doc. RNDr. Jan Vykopal, Ph.D.
Cybersecurity education, interactive learning environments, learning analytics, and educational data mining.
More detailed information.

prof. Ing. Pavel Zezula, CSc.
Database systems, storage and search structures, multimedia and XML data, distibuted index structures, similarity search, performance evaluation.
More detailed information.

prof. RNDr. Jiří Zlatuška, CSc.
Electronic publishing. Information society.