publications

papers in Russian listed [here]

2022

  1. Hi-C Metagenomics in the ICU: Exploring Clinically Relevant Features of Gut Microbiome in Chronically Critically Ill Patients
    Ivanova Valeriia, Chernevskaya Ekaterina, Vasiluev Petr, Ivanov Artem, Tolstoganov Ivan, Shafranskaya Daria, Ulyantsev Vladimir, Korobeynikov Anton, Razin Sergey V., Beloborodova Natalia, Ulianov Sergey V., Tyakht Alexander
    Frontiers in Microbiology 2022
  2. Machine learning of phase transitions in nonlinear polariton lattices
    Zvyagintseva Daria, Sigurdsson Helgi, Kozin Valerii K., Iorsh Ivan, Shelykh Ivan A., Ulyantsev Vladimir, Kyriienko Oleksandr
    Communications Physics 2022
  3. GADMA2: more efficient and flexible demographic inference from genetic data
    Noskova Ekaterina, Abramov Nikita, Iliutkin Stanislav, Sidorin Anton, Dobrynin Pavel, Ulyantsev Vladimir
    bioRxiv 2022

2021

  1. Evaluating the Hardness of SAT Instances Using Evolutionary Optimization Algorithms
    Semenov Alexander, Chivilikhin Daniil, Pavlenko Artem, Otpuschennikov Ilya, Ulyantsev Vladimir, Ignatiev Alexey
    In 27th International Conference on Principles and Practice of Constraint Programming (CP 2021) 2021
  2. Separation of Donor and Recipient Microbial Diversity Allows Determination of Taxonomic and Functional Features of Gut Microbiota Restructuring following Fecal Transplantation
    Olekhnovich Evgenii, Ivanov Artem, Ulyantsev Vladimir, Ilina Elena
    mSystems 2021
  3. Multipole optimization of light focusing by silicon nanosphere structures
    Ustimenko Nikita, Baryshnikova Kseniia, Melnikov Roman, Kornovan Danil, Ulyantsev Vladimir, Chichkov Boris, Evlyukhin Andrey
    Journal of the Optical Society of America B 2021
  4. BeBoSy: Behavior Examples meet Bounded Synthesis
    Chivilikhin D., Zakirzyanov I., Ulyantsev V.
    IEEE Access 2021

2020

  1. GigaScience
    GADMA: Genetic algorithm for inferring demographic history of multiple populations from allele frequency spectrum data
    Noskova Ekaterina, Ulyantsev Vladimir, Koepfli Klaus-Peter, O’Brien Stephen J, Dobrynin Pavel
    GigaScience 2020
  2. Evolutionary and genetic algorithms for design of metadevices working on electric dipole resonance
    Melnikov Roman, Baryshnikova Kseniia, Petrov Mihail, Ulyantsev Vladimir, Evlyukhin Andrey, Chichkov Boris
    Journal of Physics: Conference Series 2020
  3. MoG-VQE: Multiobjective genetic variational quantum eigensolver
    Chivilikhin D., Samarin A., Ulyantsev V., Iorsh I., Oganov A. R., Kyriienko O.
    2020
  4. Gut microbiota alterations due to fecal transplant
    Olekhnovich Evgenii, Ivanov Artem, Ulyantsev Vladimir, Ilina Elena
    bioRxiv 2020
  5. A 4-lineage statistical suite to evaluate the support of large-scale retrotransposon insertion data to reconstruct evolutionary trees
    Churakov G, Kuritzin A, Chukharev K, Zhang F, Wünnemann F, Ulyantsev V, Schmitz J
    bioRxiv 2020
  6. Genome-wide sequence analyses of ethnic populations across Russia
    Zhernakova Daria V., Brukhin Vladimir, Malov Sergey, Oleksyk Taras K., Koepfli Klaus Peter, Zhuk Anna, Dobrynin Pavel, Kliver Sergei, Cherkasov Nikolay, Tamazian Gaik, Rotkevich Mikhail, Krasheninnikova Ksenia, Evsyukov Igor, Sidorov Sviatoslav, Gorbunova Anna, Chernyaeva Ekaterina, Shevchenko Andrey, Kolchanova Sofia, Komissarov Alexei, Simonov Serguei, Antonik Alexey, Logachev Anton, Polev Dmitrii E., Pavlova Olga A., Glotov Andrey S., Ulyantsev Vladimir, Noskova Ekaterina, Davydova Tatyana K., Sivtseva Tatyana M., Limborska Svetlana, Balanovsky Oleg, Osakovsky Vladimir, Novozhilov Alexey, Puzyrev Valery, O’Brien Stephen J.
    Genomics 2020

2019

  1. Efficient Symmetry Breaking for SAT-Based Minimum DFA Inference
    Zakirzyanov Ilya, Morgado Antonio, Ignatiev Alexey, Ulyantsev Vladimir, Marques-Silva Joao
    In Language and Automata Theory and Applications 2019
  2. Evolutionary Computation Techniques for Constructing SAT-Based Attacks in Algebraic Cryptanalysis
    Pavlenko Artem, Semenov Alexander, Ulyantsev Vladimir
    In Applications of Evolutionary Computation 2019
  3. Fitness Comparison by Statistical Testing in Construction of SAT-Based Guess-and-Determine Cryptographic Attacks
    Pavlenko Artem, Buzdalov Maxim, Ulyantsev Vladimir
    In Proceedings of the Genetic and Evolutionary Computation Conference 2019
  4. Function Block Finite-State Model Identification Using SAT and CSP Solvers
    IEEE Transactions on Industrial Informatics 2019
  5. Smart Contract Design Meets State Machine Synthesis: Case Studies
    Suvorov Dmitrii, Ulyantsev Vladimir
    2019

2018

  1. Bioinf
    MetaCherchant: analyzing genomic context of antibiotic resistance genes in gut microbiota
    Olekhnovich Evgenii, Vasilyev Artem, Ulyantsev Vladimir, Kostryukova Elena, Tyakht Alexander
    Bioinformatics 2018
  2. Exact finite-state machine identification from scenarios and temporal properties
    Ulyantsev Vladimir, Buzhinsky Igor, Shalyto Anatoly
    International Journal on Software Tools for Technology Transfer 2018
  3. Active Learning of Formal Plant Models For Cyber-Physical Systems
    Ovsiannikova P., Chivilikhin D., Ulyantsev V., Stankevich A., Zakirzyanov I., Vyatkin V., Shalyto A.
    In IEEE 16th International Conference on Industrial Informatics (INDIN) 2018
  4. Counterexample-guided inference of controller logic from execution traces and temporal formulas
    Chivilikhin D., Buzhinsky I., Ulyantsev V., Stankevich A., Shalyto A., Vyatkin V.
    In 2018 IEEE 23rd International Conference on Emerging Technologies and Factory Automation (ETFA) 2018
  5. BFS Enumeration for Breaking Symmetries in Graphs
    Moklev Vyacheslav, Ulyantsev Vladimir
    2018
  6. Finding All Minimum-Size DFA Consistent with Given Examples: SAT-Based Approach
    Zakirzyanov Ilya, Shalyto Anatoly, Ulyantsev Vladimir
    In Software Engineering and Formal Methods. SEFM 2017 2018

2017

  1. Applying Reinforcement Learning and Supervised Learning Techniques to Play Hearthstone
    Kachalsky I., Zakirzyanov I., Ulyantsev V.
    In 2017 16th IEEE International Conference on Machine Learning and Applications (ICMLA) 2017
  2. Closed-loop verification of a compensating group drive model using synthesized formal plant model
    Ovsiannikova P., Chivilikhin D., Ulyantsev V., Shalyto A.
    In 2017 22nd IEEE International Conference on Emerging Technologies and Factory Automation (ETFA) 2017
  3. Plant trace generation for formal plant model inference: Methods and case study
    Avdyukhin D., Chivilikhin D., Korneev G., Ulyantsev V., Shalyto A.
    In 2017 IEEE 15th International Conference on Industrial Informatics (INDIN) 2017
  4. CSP-based inference of function block finite-state models from execution traces
    In 2017 IEEE 15th International Conference on Industrial Informatics (INDIN) 2017

2016

  1. Bioinf
    MetaFast: fast reference-free graph-based comparison of shotgun metagenomic data
    Ulyantsev Vladimir, Kazakov Sergey, Dubinkina Veronika, Tyakht Alexander, Alexeev Dmitry
    Bioinformatics 2016
  2. Assessment of k-mer spectrum applicability for metagenomic dissimilarity analysis
    Dubinkina Veronika, Ischenko Dmitry, Ulyantsev Vladimir, Tyakht Alexander, Alexeev Dmitry
    BMC bioinformatics 2016
  3. Modified ant colony algorithm for constructing finite state machines from execution scenarios and temporal formulas
    Chivilikhin Daniil, Ulyantsev Vladimir, Shalyto Anatoly
    Automation and Remote Control 2016

2015

  1. Modification of the method of generation of control finite-state machines with continuous actions based on training examples
    Buzhinsky I, Kazakov S, Ulyantsev V, Tsarev F, Shalyto A
    Journal of Computer and Systems Sciences International 2015
  2. Constructing parsimonious hybridization networks from multiple phylogenetic trees using a SAT-solver
    Ulyantsev Vladimir, Melnik Mikhail
    In International Conference on Algorithms for Computational Biology. ALCoB 2015 2015
  3. Evolutionary approach to coverage testing of IEC 61499 function block applications
    Buzhinsky I., Ulyantsev V., Veijalainen J., Vyatkin V.
    In 2015 IEEE 13th International Conference on Industrial Informatics (INDIN) 2015
  4. BFS-based symmetry breaking predicates for DFA identification
    Ulyantsev Vladimir, Zakirzyanov Ilya, Shalyto Anatoly
    In International Conference on Language and Automata Theory and Applications 2015

2014

  1. Combining Exact and Metaheuristic Techniques for Learning Extended Finite-State Machines from Test Scenarios and Temporal Properties
    Chivilikhin D., Ulyantsev V., Shalyto A.
    In 2014 13th International Conference on Machine Learning and Applications 2014
  2. Inferring Automata-Based Programs from Specification with Mutation-Based Ant Colony Optimization
    Chivilikhin Daniil, Ulyantsev Vladimir
    In Proceedings of the Companion Publication of the 2014 Annual Conference on Genetic and Evolutionary Computation 2014
  3. Improving the Quality of Supervised Finite-State Machine Construction Using Real-Valued Variables
    Buzhinsky Igor, Chivilikhin Daniil, Ulyantsev Vladimir, Tsarev Fedor
    In Proceedings of the Companion Publication of the 2014 Annual Conference on Genetic and Evolutionary Computation 2014
  4. Inducing finite state machines from training samples using ant colony optimization
    Buzhinsky IP, Ulyantsev VI, Chivilikhin DS, Shalyto AA
    Journal of Computer and Systems Sciences International 2014
  5. Extended finite-state machine inference with parallel ant colony based algorithms
    Chivilikhin D, Ulyantsev V, Shalyto A
    In Proceedings of the Student Workshop on Bioinspired Optimization Methods and their Applications, BIOMA 2014 2014

2013

  1. Learning Finite-State Machines: Conserving Fitness Function Evaluations by Marking Used Transitions
    Chivilikhin D., Ulyantsev V.
    In 2013 12th International Conference on Machine Learning and Applications 2013
  2. Learning Finite-State Machines with Classical and Mutation-Based Ant Colony Optimization: Experimental Evaluation
    Chivilikhin D., Ulyantsev V.
    In 2013 BRICS Congress on Computational Intelligence and 11th Brazilian Congress on Computational Intelligence 2013
  3. Search-Based Construction of Finite-State Machines with Real-Valued Actions: New Representation Model
    Buzhinsky Igor, Ulyantsev Vladimir, Tsarev Fedor, Shalyto Anatoly
    In Proceedings of the 15th Annual Conference Companion on Genetic and Evolutionary Computation 2013
  4. MuACOsm: A New Mutation-Based Ant Colony Optimization Algorithm for Learning Finite-State Machines
    Chivilikhin Daniil, Ulyantsev Vladimir
    In Proceedings of the 15th Annual Conference on Genetic and Evolutionary Computation 2013
  5. Test-Based Induction of Finite-State Machines with Continuous Output Actions
    Buzhinsky Igor, Ulyantsev Vladimir, Shalyto Anatoly
    IFAC Proceedings Volumes 2013
  6. Solving Five Instances of the Artificial Ant Problem with Ant Colony Optimization
    Chivilikhin Daniil S., Ulyantsev Vladimir I., Shalyto Anatoly A.
    IFAC Proceedings Volumes 2013

2012

  1. Learning finite-state machines with ant colony optimization
    Chivilikhin Daniil, Ulyantsev Vladimir
    In International Conference on Swarm Intelligence. ANTS 2012. 2012
  2. Test-Based Extended Finite-State Machines Induction with Evolutionary Algorithms and Ant Colony Optimization
    Chivilikhin Daniil, Ulyantsev Vladimir, Tsarev Fedor
    In Proceedings of the 14th Annual Conference Companion on Genetic and Evolutionary Computation 2012
  3. Extended Finite-State Machine Induction using SAT-Solver
    Ulyantsev Vladimir I., Tsarev Fedor N.
    IFAC Proceedings Volumes 2012

2011

  1. Extended Finite-State Machine Induction Using SAT-Solver
    Ulyantsev V., Tsarev F.
    In 2011 10th International Conference on Machine Learning and Applications and Workshops 2011