JetBrains Research
Highlights of 2020

Neurodevelopment and Neurophysiology Group

• Taught the Computational Neuroscience course to students of HSE and ITMO partner master's degrees.
• The paper BCNNM: a framework for in silico neural tissue development modeling was accepted for publication in the Frontiers in Computational Neuroscience journal.
• The modeling platform core was rewritten.
• A language was created for building model configurations.
• New experiments are under development.
• Held regular seminars on various topics in the field of neurogenesis, central nervous system development, and neuro-modeling.
• Formed a partnership with Uppsala University, Sweden.

List of Publications:

BCNNM: a framework for in silico neural tissue development modeling.

D. Bozhko, G. Galumov, A. Polovjan, S. Kolchanova, V. Myrov, V. Stelmakh, H. Schiöth.

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Bioinformatics Group

• Published 2 articles.
• Taught a course on systems biology at ITMO.
• The first-ever class of the Bioinformatics and Systems Biology Master's program graduated at ITMO.
• Organized the bioinformatics section at the 2nd Single-Cell Sequencing Workshop.

List of Publications:

Evaluation of haplotype callers for next-generation sequencing of viruses//Infection.

Eliseev A., Gibson K., Avdeyev P., Novik D., Bendall M., Perez-Losada M., Alexeev N., Crandall K.

Chain Monte Carlo for Active Module Identification Problem.

Alexeev N., Isomurodov J., Sukhov V., Korotkevich G., Sergushichev A. Markov.

HoTT and Dependent Types Group

• Coding advances are reflected on the project page.
• Released three versions of the language and its plugin.
• Valery Isaev hosted a seminar about the Arend proof assistant.
• Commit statistics: +136,830 (lines added) –101,573 (lines deleted). These numbers can be found here and here (note they do not include work on tutorials and the standard library).
• Created a tutorial.

Cryptographic Lab

• 53 publications:
  • 16 articles in journals, including 8 in Q1-Q2 Scopus-WoS and 8 in Q3-Q4.
  • 2 articles published in conference proceedings CORE (B).
  • 5 articles published in conference proceedings of international conferences.
  • 30 theses at international and Russian conferences.
• Video course "Foundations of cryptanalysis" by N. Tokareva.
• The International Olympiad in Cryptography 2020 was held.
• Video lecture by N. Mouha "Review of AES by NIST".
• Published the proceedings "Results of crypto laboratory from September 2019 to August 2020".
• Organized a summer school-conference "Cryptography and information security" (July 9–27, 2000). The results were published in the proceedings.
• Organized 8 lecture courses on cryptography.
• Regular "Cryptography and cryptanalysis" seminars.
• Out team members defended one Ph.D. dissertation, six MS theses, and three BS theses.
• Two Ph.D. dissertations were prepared for defense scheduled for 2021:
  • A. Kutsenko, "Self-dual bent functions and their metrical properties" (supervised by Natalia Tokareva).
  • A. Oblaukhov, "Metrically regular sets in the Boolean cube: constructions and properties" (supervised by Natalia Tokareva).
• Formed new partnerships:
  • University of Bergen (Norway).
  • University of Paris 8 (France).
  • Computer Security Division of NIST (USA).
  • CryptoExperts (France).
  • CNRS (France).
  • Belarus State University.

List of Publications:

On metric regularity of Reed-Muller codes.

Oblaukhov A.

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Metrical properties of self-dual bent functions.

Kutsenko A.

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A note on the properties of associated Boolean functions of quadratic APN functions.

Gorodilova A.

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The Fifth International Students' Olympiad in Cryptography – NSUCRYPTO: problems and their solutions.

Gorodilova A., Agievich S., Carlet C., Hou X., Idrisova V., Kolomeec N., Kutsenko A., Mariot L., Oblaukhov A., Picek S., Preneel B., Rosie R., Tokareva N.

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Development of a method for hiding private data for a blockchain-based tender system.

Kondyrev D.

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The group of automorphisms of the set of self-dual bent functions.

Kutsenko A.

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Metrical properties of the set of bent functions in view of duality.

Kutsenko A., Tokareva N.

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On metric complements and metric regularity in finite metric spaces.

Oblaukhov A.

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Maximums of the additive differential probability of exclusive-or.

Mouha N., Kolomeec N., Akhtyamov D., Bonich T., Ischukova E., Panferov M., Sutormin I., Titova K., Tokareva N., Zhantulikov B.

On constructions and properties of self-dual generalized bent functions.

Kutsenko A.

Тесты для SAT-решателей, основанные на криптографических задачах.

Kalgin K.V., Doronin A.E.

On properties of a bent function secondary construction.

Kolomeec N.

О шестой международной олимпиаде по криптографии NSUCRYPTO.

Gorodilova A., Tokareva N., Agievich S., Carlet K., Gorkunov E., Idrisova V., Kolomeec N., Kutsenko A., Lebedev R., Nikova S., Oblaukhov A., Pankratova I., Pudovkina M., Reimen V., Udovenko A.

On the Sixth International Olympiad in Cryptography NSUCRYPTO.

Gorodilova A., Tokareva N., Agievich S., Carlet C., Gorkunov E., Idrisova V., Kolomeec N., Kutsenko A., Lebedev R., Nikova S., Oblaukhov A., Pankratova I., Pudovkina M., Rijmen V., Udovenko A.

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On the number of unsuitable Boolean functions in constructions of filter and combining models of stream ciphers.

Bonich T., Panferov M., Tokareva N.

Connections between quaternary and Boolean bent functions.

Tokareva N., Shaporenko A., Sole P.

Publications in conference proceedings:

On combinatorial approaches to search for quadratic APN functions.

Kalgin K., Idrisova V.

On constructions and properties of self-dual generalized bent functions.

Kutsenko A.

On relationship between quaternary and Boolean bent functions.

Shaporenko A.

S-box construction based on a Boolean function and a permutation.

Zyubina D., Zapolskii M., Khilchuk I., Tokareva N.

Properties of the secret gamma in stream ciphers.

Bonich T., Panferov M., Tokareva N.

Metrical properties of the set of bent functions in view of duality.

Kutsenko A., Tokareva N.

The general universal model of blockchain technology based on an analysis of some implementations.

Sazonova P.

Nuclear Physics Methods Laboratory

• Launched a demo version of the VisionForge platform for visualizing various types of scientific data.
• Publicly released the plotly.kt library.
• Taught an open course "Statistical Methods in Experimental Physics".
• 14 publications, including one funded by JBR.
• Conference talks:
  • Alexander Nozik, ICPPA-2020, "Advanced multi-platform visualization framework for particle physics experiments".
  • Alexander Nozik, Timur Hamitov, 11th IAXO Collaboration Meeting, “Preliminary Slow Control system design”, CERN.
• Lecture by Roman Belov on kotlin-jupyter.
• Seminar on metasystem transition applied to software development.
• Seminar on using Kotlin in Monte Carlo modeling.
• An article preprint on modeling electron locking in a magnetic trap in Kotlin.
• Developed a segmented satellite detector prototype for studying solar activity.
• Developed a prototype API for Kotlin device servers for data collection systems.
• Added a number of new features to kmath. In particular, an abstract representation of mathematical operations (MST, Mathematical Syntax Tree) was added and used to implement automatic differentiation.
• Taught 3 courses:
  • "Introduction to Scientific Programming in the Kotlin Language" (MIPT).
  • "Statistical Methods in Experimental Physics" (MIPT, open).
  • "Mini-Course on Data Analysis in Python for Educators" (MIPT).
• Formed new partnerships:
  • Helmholtz-Zentrum Geesthacht Outstation at DESY.
  • HSE.
  • IAXO.

List of Publications:

Declarative analysis in «Troitsk nu-mass» experiment.

A. Nozik.

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Mobile Robot Algorithms Laboratory

• Published 10 articles.
• 7 presentations at various conferences.
• Held two open lectures in Yasnaya Polyana.
• Organized two open seminars, "STEAM education in the aspect of career guidance: problems and prospects of development" and "Guidance in IT projects for beginners".
• Organized a hackathon on the use of neurotechnologies and machine learning methods.
• Launched the JetBrains Advanced Training Program at LETI.
• Organized the "Mobile robot technologies" laboratory.
• A STEM winter school was held in collaboration with MIT.
• A winter school on "Software Engineering and the Internet of Things" was held in collaboration with LETI.
• Created four Android activities for schoolchildren: (1), (2), (3), (4).
• Taught 5 courses:
  • Self-driving cars (HSE).
  • Computer architecture (SPbSU SP, SPbSU MAAD, CSC and LETI).
  • Mobile development (ITMO, HSE).
  • STEM for 8th and 9th grade students of School 777 in St. Petersburg.
  • Introduction to Software Engineering (LETI).
• Duckietown:
  • Integration of a graphical map editor into the Duckietown project.
  • New presentation format for maps in Duckietown.
  • The Autonomous Driving Olympics.
  • A video greeting card for Halloween.
  • An online course was developed with tasks based on the Duckietown simulator.
  • An open lecture on Duckietown.
  • A team was created at NSU to develop algorithms within the Duckietown framework.
• Formed a partnership with Sirius.Leto.

List of Publications:

Research Challenges Of Industry 4.0.

K. Chaika

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A Simplistic Approach for Lightweight Multi-Agent SLAM Algorithm.

A. Filatov, K. Krinkin.

Imitation Learning Approach for AI Driving Olympics Trained on Real-world and Simulation Data Simultaneously.

M. Sazanovich, K. Chaika, K. Krinkin, A. Shpilman.

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Transferable Belief Models for Lightweight Simultaneous Localization and Mapping.

K. Krinkin.

Models of Telecommunications Network Monitoring Based on Knowledge Graphs.

K. Krinkin, A. Vodyaho, I. Kulikov, N. Zhukova.

Architecture of a Telecommunications Network Monitoring System Based on a Knowledge Graph.

K. Krinkin, I. Kulikov, A. Vodyaho, N. Zhukova.

Android Memory Inspection Techniques and Tools.

K. Krinkin, V. Dopira, O. Kochneva, S. Petrov, M. Kopylov.

Integration AI to a society. Threats, benefits, challenges. VIDEO, AUDIO SIGNAL PROCESSING IN THE CONTEXT OF NEUROTECHNOLOGY

K. Krinkin.

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Media Content Delivery Protocols Performance and Reliability Evaluation in Cellular Mobile Networks.

I. Dronnikov, K. Krinkin.

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Autonomous Wheels And Camera Calibration In Duckietown Project.

K. Krinkin, K. Chayka, A. Filatov, A. Filatov.

Learning Research Lab

• Gave 3 courses:
  • "Cognitive Psychology and Social Behavior".
  • "Gender inequality in STEM".
  • "Who is engaged in programming? IT workers according to international opinion polls".

Programming Languages and Tools Lab

• 15 publications.
• Regular open seminars on the scientific interests of the laboratory:
  • Global seminar.
  • Seminar on formal languages.
• Presentation at Hydra and the Computer Science Club with the lecture "Programming language memory models: Problems, solutions, and directions".
• Taught 14 unique courses at 6 different sites:
  • "Compilers" (Computer Science Center, MCS SPbU, HSE).
  • "Meta Computing" (HSE).
  • "Relational and logic programming" (ITMO).
  • "Theory of automata and formal languages" (LETI, ITMO, HSE, Math-Mech и MCS SPbU).
  • "Graph theory" (Math-Mech SPbU).
  • "Programming practice" (Math-Mech SPbU).
  • "Structures and algorithms for computer data processing" (Math-Mech SPbU).
  • "Fundamentals of machine learning" (Math-Mech SPbU).
  • "Fundamentals of programming" (practice, MCS SPbU).
  • "Introduction to OOP" (practice, MCS SPbU).
  • "Principles of organization and architecture of computer systems" (practice, MCS SPbU).
  • "Fundamentals of Linux" (MCS SPbU).
  • "Semantics of programming languages" (HSE, ITMO).
  • "Additional chapters of mathematical logic and algorithms theory" (Math-Mech SPbU).
• Formed new partnerships:
  • DIMAp/UFRN (The Department of Informatics and Applied Mathematics (DIMAp). Center of Exact and Earth Sciences, Federal University of Rio Grande do Norte (UFRN)).
  • Florida State University.

List of Publications:

PerSeVerE: Persistency Semantics for Verification under Ext4.

M. Kokologiannakis, I. Kaysin, A. Raad, V. Vafeiadis.

Reconciling Event Structures with Modern Multiprocessors.

E. Moiseenko, A. Podkopaev, O. Lahav, O. Melkonian, V. Vafeiadis

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Repairing and Mechanising the JavaScript Relaxed Memory Model.

C. Watt, C. Pulte, A. Podkopaev, G. Barbier, S. Dolan, S. Flur, J. Pichon-Pharabod Shu-yu Guo

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Promising 2.0: Global Optimizations in Relaxed Memory Concurrency.

S.-H. Lee, M. Cho, A. Podkopaev, S. Chakraborty, C.-K. Hur, O. Lahav, V. Vafeiadis.

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Efficient Fair Relational Conjunction for Structurally-Recursive Relations.

P. Lozov, D.Boulytchev.

Context-Free Path Querying by Kronecker Product.

E. Orachev, I. Epelbaum, R. Azimov, S. Grigorev.

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Recursive Expressions for SPARQL Property Paths.

C. Medeiros, U. Costa, S. Grigorev, M. Musicante.

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Modification of Valiant’s algorithm for the string-matching problem.

Susanina Y., Yaveyn A., Grigorev S.

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Context-Free Path Querying with Single-Path Semantics by Matrix Multiplication.

A. Terekhov, A. Khoroshev, R. Azimov, S. Grigorev.

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Context-Free Path Querying via Matrix Equations.

Y. Susanina.

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Optimizing GPU programs by partial evaluation.

A.Tyurin, D. Berezun, S. Grigorev.

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Binding-Time Analysis for Relational Programs.

I. Artemeva, E. Verbitskaya.

Certified Semantics for Relational Programming.

D. Rozplokhas, A. Vyatkin, D. Boulytchev.

Relational Synthesis for Pattern Matching.

D. Kosarev, P. Lozov, D. Boulytchev.

An Empirical Study of Partial Deduction for miniKanren.

E. Verbitskaya, D. Berezun, D. Boulytchev.

Verification or Program Analysis Lab

• After more than two years of hard work, the laboratory staff completed the Request for Comments version of the Kotlin language specification.
• While working on the "Fuzzing of Kotlin Compiler" project, team members identified multiple existing bugs in the current compiler.
• 3 publications.
• Gave 9 courses:
  • "Program Analysis" (HSE).
  • "Computer Network Technologies" (HSE, Polytech).
  • "Fundamentals of Software Engineering" (HSE, Polytech).
  • "Verification and Program Analysis" (Polytech).
  • "Functional Programming Languages" (Polytech).
  • "Software Development Technologies" (Polytech).
  • "Software Testing" (Polytech).
• Expanded the functionality of the Kotoed programming education automation system.
• Conference talks:
  • "Kotoed: how we taught programming online even before it went mainstream" at the IT Education in Modern World Conference.
  • "Teaching team software development on the cases of industrial partners: how we do it at Polytech" at the IT Education in Modern World Conference.
• Formed a partnership with NSU.

List of Publications:

Automated Cross-Language Integration Based on Formal Model of Components.

A. Aleksyuk, V. Itsykson.

Computing Automatic generation of software bug fixes based on analysis of software repositories.

A. Belskii, V. Itsykson

Partial Specifications of Libraries: Applications in Software Engineering.

V. Itsykson.

Machine Learning Methods in Software Engineering

• 10 publications.
• Held regular seminars throughout the year.
• Published a number of tools:
  • KInference – a library that makes possible execution of complex ML models (written via ONNX) in vanilla Kotlin.
  • Sosed – an embedding-based approach to detect similar software projects.
  • Buckwheat – a multi-language tokenizer for extracting classes, functions, and identifiers from source code.
  • IntelliJDeodorant – an IntelliJ IDEA plugin that detects code smells in Java code and recommends appropriate refactorings to resolve them.
  • RefactorInsight – a plugin for IntelliJ IDEA that enables the IDE to visualize refactorings in the commit history of Java projects.
  • KotlinRefMiner – a library that detects performed refactorings in code changes written in Kotlin.
  • Topias – an IntelliJ IDEA plugin for visualization of VCS changes frequency.
• Taught 5 courses at 3 sites:
  • "Programming Practice" (SPbU).
  • "Software Engineering" (SPbU, HSE, ITMO).
  • "Software Design" (HSE, ITMO).
  • "Functional Programming" (SPbU).
  • "Machine Learning in Software Engineering" (HSE).
• Formed new partnerships:
  • TU Delft (The Netherlands).
  • University of California, Irvine (USA).
  • Rochester Institute of Technology (USA).
  • Johannes Kepler University (Austria).
  • University of British Columbia (Canada).

List of Publications:

Comparing Block-based Programming Models for Two-armed Robots.

N. Ritschel, V. Kovalenko, R. Holmes, R. Garcia, D. Shepherd.

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Sosed: a tool for finding similar software projects.

E. Bogomolov, Y. Golubev, A. Lobanov, V. Kovalenko, T. Bryksin.

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Pandemic Programming: How COVID-19 affects software developers and how their organizations can help.

P. Ralph, S. Baltes, G. Adisaputri, R. Torkar, V. Kovalenko, M. Kalinowski, N. Novielli, S. Yoo, X. Devroey, X. Tan, M. Zhou, B. Turhan, R. Hoda, H. Hata, G. Robles, A. Milani Fard, R. Alkadhi.

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Recommendation of Move Method Refactoring Using Path-Based Representation of Code.

Z. Kurbatova, I. Veselov, Y. Golubev, T. Bryksin.

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Visualization of Methods Changeability Based on VCS Data.

S. Svitkov, T. Bryksin.

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A Study of Potential Code Borrowing and License Violations in Java Projects on GitHub.

Y. Golubev, M. Eliseeva, N. Povarov, T. Bryksin.

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Building Implicit Vector Representations of Individual Coding Style.

V. Kovalenko, E. Bogomolov, T. Bryksin, A. Bacchelli.

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Using Large-Scale Anomaly Detection on Code to Improve Kotlin Compiler.

T. Bryksin, V. Petukhov, I. Alexin, S. Prikhodko, A. Shpilman, V. Kovalenko, N. Povarov.

Multi-Objective Optimization for Token-Based Clone Detection.

Y. Golubev, V. Poletansky, N. Povarov, T. Bryksin.

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Authorship Attribution of Source Code: A Language-Agnostic Approach and Applicability in Software Engineering.

E. Bogomolov, V. Kovalenko, A. Bacchelli, T. Bryksin.

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Concurrent Computing Lab

• 2 poster presentations at conferences.
• Taught a course on parallel programming at ITMO.

List of Publications:

Restricted memory-friendly lock-free bounded queues.

Nikita Koval, Vitaly Aksenov.

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Testing concurrency on the JVM with lincheck.

N. Koval, M. Sokolova, A. Fedorov, D. Alistarh, D. Tsitelov.

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Cyber-Physical Systems Lab

• 7 publications.
• Gave conference talks:
  • "Process-Oriented Programming for Cyber-Physical System Software" at the Scientific Russia-India Webinar on Cyber-physical systems; Society 5.0; Artificial Intelligence.
  • "Event-Driven Temporal Logic for Control Software Requirements Specification" at the Workshop on Program Semantics, Specification and Verification: Theory and Applications PSSV-2020.
  • "Process-Oriented Technology for Reactive Software Design and Development" at Huawei's Modern Compilers and Languages Technologies 2020.
• 6 author courses:
  • "Theory and practice of scientific research".
  • "Engineering of modern information systems".
  • "Hybrid systems with ARM architecture".
  • "Modern problems of computer science and engineering".
  • "Formal methods in software engineering".
  • "Theory of parallelism".
• Formed a partnership with NSU.

List of Publications:

Verifying Reflex-software with SPIN: Hand Dryer Case Study.

T. Liakh, N. Garanina, I. Anureev, V. Zyubin.

The Post Language: Process-Oriented Extension for IEC 61131-3 Structured Text.

V. Bashev, I. Anureev, V. Zyubin.

Generating Process Diagrams for Control Software in the Reflex Language.

S. Belenkaia, V. Zyubin, A. Rozov.

Bias-Corrected Optical Measurement of Film Thickness for Vacuum Evaporation Coating.

V. Drobotun, A. Rozov.

Bio-Inspired End-Stopped Neuron Model for the Curves Segmentation.

A. Kugaevskikh

Dynamic Verification of Process-Oriented Control Software by the Case of Crossroad Control.

T. Liakh, A. Grivtsova.

An Ontology-Based Approach to Support Formal Verification of Concurrent Systems.

Garanina N., Anureev I., Sidorova E., Koznov D., Zyubin V., Gorlatch S.

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Machine Learning Applications and Deep Learning and Agent Systems and Reinforcement Learning

• 4 publications.
• First place in the RL category at the Flatland competition.
• Took third place in the Black Box Optimization competition.
• Organized the Machine Learning Summer School.
• Taught 6 courses:
  • "Machine learning" (5 different courses for HSE, ITMO, SPbU, EUSP, and BI).
  • "Deep reinforcement learning" (HSE+ITMO).
  • "Algorithms in bioinformatics" (BI).
  • "Information search" (HSE+ITMO).
  • "Unmanned vehicles" (HSE).
  • "Unsupervised learning" (HSE).

List of Publications:

Automatic generation of reviews of scientific papers.

A. Nikiforovskaya, N. Kapralov, A. Vlasova, O. Shpynov, A. Shpilman.

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Imitation Learning Approach for AI Driving Olympics Trained on Real-world and Simulation Data Simultaneously.

M. Sazanovich, K. Chaika, K. Krinkin, A. Shpilman.

Using Large-Scale Anomaly Detection on Code to Improve Kotlin Compiler.

T. Bryksin, V. Petukhov, I. Alexin, S. Prikhodko, A. Shpilman, V. Kovalenko, N. Povarov.

Lipophilicity Prediction with Multitask Learning and Molecular Substructures Representation.

N. Lukashina, A. Alenicheva, E. Vlasova, A. Kondiukov, A. Khakimova, E. Magerramov, N. Churikov, A. Shpilman.

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Paper-Analyzer

• Published one article on the results of participation in the BioASQ competition (the Relation Extraction model took 2nd place in the leaderboard).
• Taught the "Deep Learning" course (HSE+ITMO – spring and fall semesters).
• Gave lectures at the Summer School on Machine and Deep Learning.

List of Publications:

Transformer-Based Open Domain Biomedical Question Answering.

A. Kazaryan, U. Sazanovich, V. Belyaev.

Optimization Problems in Software Engineering

• One publication.
• Held the school "Discrete methods of synthesis and verification for cyber-physical systems".
• Vladimir Ulyantsev delivered a lecture "Genetic algorithms: an evolutionary approach in artificial intelligence" for Sirius.
• Vladimir Ulyantsev was invited to the AAAI'21 committee.

List of Publications:

GADMA: Genetic algorithm for inferring demographic history of multiple populations from allele frequency spectrum data.

Noskova E., Ulyantsev V., Koepfli K.P., O’Brien S.J., Dobrynin P.

Parameterized Algorithms Laboratory

• 2 publications.
• Participation of the HSE-SPb team in the international student Olympiad in Mathematics.
• 7 courses:
  • "Parameterized algorithms".
  • "Probabilistic algorithms".
  • "Exact exponential algorithms".
  • "Discrete mathematics" (HSE).
  • "Discrete mathematics" (SPbU).
  • "Algorithms" (standard course).
  • "Complexity theory".

List of Publications:

Diverse Pairs of Matchings.

F. Fomin, P. Golovach, L. Jaffke, Geevarghese P., D. Sagunov.

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Building Large k-Cores from Sparse Graphs.

F. Fomin, D. Sagunov, K. Simonov.

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