Selected Publications

From among the hundreds of papers annually published by scientists at FI, here is a brief overview of those published at the world's top CS conferences (A*), and in the top ten percent of scientific journals, as ranked by Journal Citation Reports.


Generative modeling of living cells with SO(3)-equivariant implicit neural representations

Wiesner, David — Suk, Julian — Dummer, Sven — Nečasová, Tereza — Vladimír, Ulman — Svoboda, David — Wolterink, Jelmer
Medical Image Analysis, 2024, DOI

Machine learning estimated probability of relapse in early-stage non-small-cell lung cancer patients with aneuploidy imputation scores and knowledge graph embeddings

Buosi, Samuele — Timilsina, Mohan — Janik, Adriann — Costabello, Luca — Torrente, Maria — Provencio, Mariano — Fey, Dirk — Nováček, Vít
Expert Systems with Applications, 2024, DOI

Using data clustering to reveal trainees’ behavior in cybersecurity education

Dočkalová Burská, KarolínaMlynárik, Jakub RudolfOšlejšek, Radek
Education and Information Technologies, 2024, DOI


Applications of deep language models for reflective writings

Nehyba, JanŠtefánik, Michal
EDUCATION AND INFORMATION TECHNOLOGIES, 2023, DOI

Automated Feedback for Participants of Hands-on Cybersecurity Training

Švábenský, ValdemarVykopal, JanČeleda, PavelDovjak, Ján
Education and Information Technologies, 2023, DOI

Calc-X and Calcformers: Empowering Arithmetical Chain-of-Thought through Interaction with Symbolic Systems

Kadlčík, MarekŠtefánik, MichalSotolář, OndřejMartinek, Vlastimil
Empirical Methods in Natural Language Processing (EMNLP 2023), DOI

Guessing Winning Policies in LTL Synthesis by Semantic Learning

Křetínský, Jan — Meggendorfer, Tobias — Prokop, MaximilianRieder, Sabine
Computer Aided Verification (CAV 2023), DOI

Kratos2: An SMT-Based Model Checker for Imperative Programs

Griggio, Alberto — Jonáš, Martin
Computer Aided Verification (CAV 2023), DOI

Mean Payoff Optimization for Systems of Periodic Service and Maintenance

Klaška, DavidKučera, AntonínMusil, VítŘehák, Vojtěch
International Joint Conference on Artificial Intelligence (IJCAI 2023), DOI

Optical Cryptanalysis: Recovering Cryptographic Keys from Power LED Light Fluctuations

Nassi, Ben — Vayner, Ofek — Iluz, Etay — Nassi, Dudi — Cohen, Or Hai — Jančár, Ján — Genkin, Daniel — Tromer, Eran — Zadov, Boris — Elovici, Yuval
Computer and Communications Security (CCS 2023), DOI

Optimal Sobolev embeddings for the Ornstein-Uhlenbeck operator

Cianchi, Andrea — Musil, VítPick, Luboš
Journal of Differential Equations, 2023, DOI

Segmentation and Tracking of Mammary Epithelial Organoids in Brightfield Microscopy

Hradecká, LuciaWiesner, DavidSumbal, JakubSumbalová Koledová, ZuzanaMaška, Martin
IEEE Transactions on Medical Imaging, 2023, DOI

Shielding in Resource-Constrained Goal POMDPs

Ajdarów, MichalBrlej, ŠimonNovotný, Petr
AAAI Conference on Artificial Intelligence (AAAI 2023), DOI

Soft Alignment Objectives for Robust Adaptation of Language Generation

Štefánik, MichalKadlčík, MarekSojka, Petr
Annual Meeting of the Association for Computational Linguistics (ACL 2023), DOI

Synthesizing Resilient Strategies for Infinite-Horizon Objectives in Multi-Agent Systems

Klaška, DavidKučera, AntonínKurečka, MartinMusil, VítNovotný, PetrŘehák, Vojtěch
International Joint Conference on Artificial Intelligence (IJCAI 2023), DOI

Tentacle-Based Shape Shifting of Metamorphic Robots Using Fast Inverse Kinematics

Mrázek, JanOndika, PatrickČerná, IvanaBarnat, Jiří
International Conference on Robotics and Automation (ICRA 2023), DOI

The Cell Tracking Challenge: 10 years of objective benchmarking

Maška, MartinUlman, Vladimír — Delgado-Rodriguez, Pablo — Gómez-de-Mariscal, Estibaliz — Nečasová, Tereza — Peña, Fidel A Guerrero — Ren, Tsang Ing — Meyerowitz, Elliot M — Scherr, Tim — Löffler, Katharina — Mikut, Ralf — Guo, Tianqi — Wang, Yin — Allebach, Jan P — Bao, Rina — Al-Shakarji, Noor M — Rahmon, Gani — Toubal, Imad Eddine — Palaniappan, Kannappan — Lux, FilipMatula, Petr — Sugawara, Ko — Magnusson, Klas E G — Aho, Layton — Cohen, Andrew R — Arbelle, Assaf — Ben-Haim, Tal — Raviv, Tammy Riklin — Isensee, Fabian — Jäger, Paul F — Maier-Hein, Klaus H — Zhu, Yanming — Ederra, Cristina — Urbiola, Ainhoa — Meijering, Erik — Cunha, Alexandre — Muñoz-Barrutia, Arrate — Kozubek, Michal — Ortiz-de-Solórzano, Carlos
Nature Methods, 2023, DOI


CATANA: an online modelling environment for proteins and nucleic acid nanostructures

Kuťák, David — Melo, Lucas — Schroeder, Fabian — Jelic-Matošević, Zoe — Mutter, Natalie — Bertoša, Branimir — Barišić, Ivan
Nucleic acids research, 2022, DOI

Even if users do not read security directives, their behavior is not so catastrophic

Matyáš, VáclavMalinka, KamilKraus, LydiaKnapová, LenkaKružíková, Agáta
Communications of the ACM, 2022, DOI

Federated learning enables big data for rare cancer boundary detection

Pati, Sarthak — Baid, Ujjwal — Edwards, Brandon — Sheller, Micah — Wang, Shih-Han — Reina, G Anthony — Foley, Patrick — Gruzdev, Alexey — Karkada, Deepthi — Davatzikos, Christos — Sako, Chiharu — Ghodasara, Satyam — Bilello, Michel — Mohan, Suyash — Vollmuth, Philipp — Brugnara, Gianluca — Preetha, Chandrakanth J — Sahm, Felix — Maier-Hein, Klaus — Zenk, Maximilian — Bendszus, Martin — Wick, Wolfgang — Calabrese, Evan — Rudie, Jeffrey — Villanueva-Meyer, Javier — Cha, Soonmee — Ingalhalikar, Madhura — Jadhav, Manali — Pandey, Umang — Saini, Jitender — Garrett, John — Larson, Matthew — Jeraj, Robert — Currie, Stuart — Frood, Russell — Fatania, Kavi — Huang, Raymond Y — Chang, Ken — Quintero, Carmen Balaña — Capellades, Jaume — Puig, Josep — Trenkler, Johannes — Pichler, Josef — Necker, Georg — Haunschmidt, Andreas — Meckel, Stephan — Shukla, Gaurav — Liem, Spencer — Alexander, Gregory S — Lombardo, Joseph — Palmer, Joshua D — Flanders, Adam E — Dicker, Adam P — Sair, Haris I — Jones, Craig K — Venkataraman, Archana — Jiang, Meirui — So, Tiffany Y — Chen, Cheng — Heng, Pheng Ann — Dou, Qi — Kozubek, MichalLux, FilipMichálek, JanMatula, PetrKeřkovský, MilošKopřivová, TerezaDostál, MarekVybíhal, Václav — Vogelbaum, Michael A — Mitchell, J Ross — Farinhas, Joaquim — Maldjian, Joseph A — Yogananda, Chandan Ganesh Bangalore — Pinho, Marco C — Reddy, Divya — Holcomb, James — Wagner, Benjamin C — Ellingson, Benjamin M — Cloughesy, Timothy F — Raymond, Catalina — Oughourlian, Talia — Hagiwara, Akifumi — Wang, Chencai — To, Minh-Son — Bhardwaj, Sargam — Chong, Chee — Agzarian, Marc — Falcão, Alexandre Xavier — Martins, Samuel B — Teixeira, Bernardo C A — Sprenger, Flávia — Menotti, David — Lucio, Diego R — LaMontagne, Pamela — Marcus, Daniel — Wiestler, Benedikt — Kofler, Florian — Ezhov, Ivan — Metz, Marie — Jain, Rajan
Nature Communications, 2022, DOI

General Optimization Framework for Recurrent Reachability Objectives

Klaška, DavidKučera, AntonínMusil, VítŘehák, Vojtěch
International Joint Conference on Artificial Intelligence (IJCAI 2022), DOI

“They’re not that hard to mitigate”: What Cryptographic Library Developers Think About Timing Attacks

Jančár, Ján — Fourné, Marcel — De Almeida Braga, Daniel — Sabt, Mohamed — Schwabe, Peter — Barthe, Gilles — Fouque, Pierre-Alain — Acar, Yasemin
Security and Privacy (S&P 2022), DOI


Biological applications of knowledge graph embedding models

Mohamed, Sameh K — Nounu, Ayah — Nováček, Vít
Briefings in Bioinformatics, 2021, DOI

CombOptNet: Fit the Right NP-Hard Problem by Learning Integer Programming Constraints

Paulus, Anselm — Rolínek, Michal — Musil, Vít — Amos, Brandon — Martius, Georg
International Conference on Machine Learning (ICML 2021), URL

Computing Bottom SCCs Symbolically Using Transition Guided Reduction

Beneš, NikolaBrim, LubošPastva, SamuelŠafránek, David
Computer Aided Verification (CAV 2021), DOI

Counting Maximal Satisfiable Subsets

Bendík, Jaroslav — Meel, Kuldeep S.
AAAI Conference on Artificial Intelligence (AAAI 2021), URL

Counting Minimal Unsatisfiable Subsets

Bendík, Jaroslav — Meel, Kuldeep S.
Computer Aided Verification (CAV 2021), DOI

Fast Computation of Strong Control Dependencies

Chalupa, MarekKlaška, DavidStrejček, JanTomovič, Lukáš
Computer Aided Verification (CAV 2021), DOI

Proving non-termination by program reversal

Chatterjee, Krishnendu — Goharshady, Ehsan Kafshdar — Novotný, Petr — Žikelić, Djordje
Programming Language Design and Implementation (PLDI 2021), DOI

Semantic-driven Watermarking of Relational Textual Databases

Làzaro Pèrez Gort, Maikel — Olliaro, Martina — Cortesi, Agostino — Feregrino Uribe, Claudia
Expert Systems with Applications, 2021, DOI

What Players Want: Information Needs of Players on Post-Game Visualizations

Wallner, Günter — Wijland, Marnix van — Bernhaupt, Regina — Kriglstein, Simone
Human Factors in Computing Systems (CHI 2021), DOI

Who Is Smart with Their Smartphones? Determinants of Smartphone Security Behavior

Knapová, LenkaKružíková, AgátaDědková, LenkaŠmahel, David
Cyberpsychology, Behavior, and Social Networking, 2021, DOI


Adversarial Patrolling with Drones

Klaška, DavidKučera, AntonínŘehák, Vojtěch
Autonomous Agents and Multiagent Systems (AAMAS 2020), DOI

AEON: Attractor Bifurcation Analysis of Parametrised Boolean Networks

Beneš, NikolaBrim, LubošKadlecaj, JakubPastva, SamuelŠafránek, David
Computer Aided Verification (CAV 2020), DOI

Approximate Counting of Minimal Unsatisfiable Subsets

Bendík, Jaroslav — Meel, Kuldeep S.
Computer Aided Verification (CAV 2020), DOI

BIAS: Transparent reporting of biomedical image analysis challenges

Maier-Hein, Lena — Reinke, Annika — Kozubek, Michal — Martel, Anne L. — Arbel, Tal — Eisenmann, Matthias — Hanbury, Allan — Jannin, Pierre — Müller, Henning — Onogur, Sinan — Saez-Rodriguez, Julio — van Ginneken, Bram — Kopp-Schneider, Annette — Landman, Bennett A.
Medical Image Analysis, 2020, DOI

Checking Qualitative Liveness Properties of Replicated Systems with Stochastic Scheduling

Blondin, Michael — Esparza, Javier — Helfrich, Martin — Kučera, Antonín — Meyer, Philipp
Computer Aided Verification (CAV 2020), DOI

Efficient Analysis of VASS Termination Complexity

Kučera, Antonín — Leroux, Jérôme — Velan, Dominik
Logic in Computer Science (LICS 2020), DOI

Improved bounds for centered colorings

Dębski, Michał Karol — Felsner, Stefan — Micek, Piotr — Schröder, Felix
Symposium on Discrete Algorithms (SODA 2020), DOI

Improving Orienteering-based Tourist Trip Planning with Social Sensing

Persia, Fabio — Pilato, Giovanni — Ge, Mouzhi — Bolzoni, Paolo — D'Auria, Daniela — Sven, Helmer
Future Generation Computer Systems, 2020, DOI

Multiple-Environment Markov Decision Processes: Efficient Analysis and Applications

Chatterjee, Krishnendu — Chmelík, Martin — Karkhanis, Deep — Novotný, Petr — Royer, Amélie
Automated Planning and Scheduling (ICAPS 2020), URL

pqsfinder web: G-quadruplex prediction using optimized pqsfinder algorithm

Labudová, Dominika — Hon, JiříLexa, Matej
Bioinformatics, 2020, DOI

Qualitative Controller Synthesis for Consumption Markov Decision Processes

Blahoudek, FrantišekBrázdil, TomášNovotný, Petr — Ornik, Melkior — Thangeda, Pranay — Topcu, Ufuk
Computer Aided Verification (CAV 2020), DOI

Reinforcement Learning of Risk-Constrained Policies in Markov Decision Processes

Brázdil, Tomáš — Chatterjee, Krishnendu — Novotný, PetrVahala, Jiří
AAAI Conference on Artificial Intelligence (AAAI 2020), DOI

Seminator 2 Can Complement Generalized Büchi Automata via Improved Semi-determinization

Blahoudek, František — Duret-Lutz, Alexandre — Strejček, Jan
Computer Aided Verification (CAV 2020), DOI

TE-greedy-nester: structure-based detection of LTR retrotransposons and their nesting

Lexa, Matej — Jedlicka, Pavel — Vanát, IvanČerveňanský, MichalKejnovský, Eduard
Bioinformatics, 2020, DOI

What Can Long Terminal Repeats Tell Us About the Age of LTR Retrotransposons, Gene Conversion and Ectopic Recombination?

Jedlicka, Pavel — Lexa, MatejKejnovský, Eduard
Frontiers in Plant Science, 2020, DOI

Would You Do It?: Enacting Moral Dilemmas in Virtual Reality for Understanding Ethical Decision-Making

Niforatos, Evangelos — Palma, Adam — Gluszny, Roman — Vourvopoulos, Athanasios — Liarokapis, Fotios
Human Factors in Computing Systems (CHI 2021), 2020, DOI


3-D Quantification of Filopodia in Motile Cancer Cells

Castilla, Carlos — Maška, MartinSorokin, Dmitry — Meijering, Erik — Ortiz-de-Solórzano, Carlos
IEEE Transactions on Medical Imaging, 2019, DOI

Compactness and finite forcibility of graphons

Glebov, Roman — Kráľ, Daniel — Volec, Jan
Journal of the European Mathematical Society, 2019, DOI

CytoPacq: A web-interface for simulating multi-dimensional cell imaging

Wiesner, DavidSvoboda, DavidMaška, MartinKozubek, Michal
Bioinformatics, 2019, DOI

Examining And Enhancing The Illusory Touch Perception In Virtual Reality Using Non-Invasive Brain Stimulation

Škola, FilipLiarokapis, Fotis
Human Factors in Computing Systems (CHI 2019), DOI

Labels on Levels: Labeling of Multi-Scale Multi-Instance and Crowded 3D Biological Environments

Kouřil, David — Čmolík, Ladislav — Kozlíková, Barbora — Wu, Hsiang-Yun — Johnson, Graham — Goodsell, David S. — Olson, Arthur — Groeller, Eduard M. — Viola, Ivan
IEEE Transactions on Visualization and Computer Graphics, 2019, DOI

Mistakes in UML Diagrams: Analysis of Student Projects in a Software Engineering Course

Chren, StanislavBühnová, BarboraMacák, MartinDaubner, LukášRossi, Bruno
Software Engineering (ICSE 2019), DOI

Optimal Probabilistic Storage and Retrieval of Unitary Channels

Sedlák, Michal — Bisio, Alessandro — Ziman, Mário
Physical Review Letters, 2019, DOI

PAC Statistical Model Checking for Markov Decision Processes and Stochastic Games

Ashok, Pranav — Křetínský, Jan — Weininger, Maximilian
Computer Aided Verification (CAV 2019), DOI

Postcards from the Post-HTTP World: Amplification of HTTPS Vulnerabilities in the Web Ecosystem

Calzavara, Stefano — Focardi, Riccardo — Nemec, Matúš — Rabitti, Alvise — Squarcina, Marco
Security and Privacy (S&P 2019), DOI

Q3B: An Efficient BDD-based SMT Solver for Quantified Bit-Vectors

Jonáš, MartinStrejček, Jan
Computer Aided Verification (CAV 2019), DOI

Solving Integer Quadratic Programming via Explicit and Structural Restrictions

Eiben, Eduard — Ganian, Robert — Knop, Dusan — Ordyniak, Sebastian
AAAI Conference on Artificial Intelligence (AAAI 2019), DOI

The Parameterized Complexity of Cascading Portfolio Scheduling

Eiben, Eduard — Ganian, Robert — Kanj, Iyad — Szeider, Stefan
Advances in Neural Information Processing Systems (NIPS 2019), URL

Unbounded Orchestrations of Transducers for Manufacturing

Alechina, Natasha — Brázdil, Tomáš — De Giacomo, Giuseppe — Felli, Paolo — Logan, Brian — Vardi, Moshe
AAAI Conference on Artificial Intelligence (AAAI 2019), DOI

Visualization of Large Molecular Trajectories

Duran, David — Hermosilla, Pedro — Ropinski, Timo — Kozlíková, Barbora — Vinacua, Álvar — Vazquez, Pere-Pau
IEEE Transactions on Visualization and Computer Graphics, 2019, DOI

Data updated on 2024/2/22.