Избранные публикации сотрудников факультета

2021 

A Simple Approach for Handling Out-of-Vocabulary Identifiers in Deep Learning for Source Code
Chirkova N., Troshin S.
Conference of the North American Chapter of the Association for Computational Linguistics (NAACL 2021), 278-288

A Systematic Evaluation of Transfer Learning and Pseudo-labeling with BERT-based Ranking Models
Mokrii Iu., Boytsov L., Braslavski P.
International ACM Conference on Research and Development in Information Retrieval (SIGIR 2021)

Histone dynamics mediate DNA unwrapping and sliding in nucleosomes
Armeev G., Shaytan A. et al.
Nature Communications 12:2387

Moments of L-functions and the Liouville-Green method
Balkanova O., Frolenkov D.
Journal of the European Mathematical Society 23, 1333–1380

Density deconvolution under general assumptions on the distribution of measurement errors
Belomestny D., Goldenshluger A.
Annals of Statistics 49, 615–649

Comprehensive analysis of cancer breakpoints reveals signatures of genetic and epigenetic contribution to cancer genome rearrangements
Cheloshkina K., Poptsova M.
PLOS Computational Biology 17

Switching systems with dwell time: Computing the maximal Lyapunov exponent
Chitour Y., Protasov V. et al.
Nonlinear Analysis: Hybrid Systems 40:101021

Molecular Mechanisms of Oncogenesis through the Lens of Nucleosomes and Histones
Espiritu D., Shaytan A. et al.
Journal of Physical Chemistry B 125, 3963-3976

MEG signatures of long-term effects of agreement and disagreement with the majority
Gorin A., Ossadtchi A. et al.
Scientific Reports 11:3297

Linear functions preserving Green's relations over fields
Guterman A., Maksaev A. et al.
Linear Algebra and its Applications 611, 310-333

Automatic Kolmogorov complexity, normality, and finite-state dimension revisited
Kozachinskiy A., Shen A.
Journal of Computer and System Sciences 118, 75-107

Modified covariance beamformer for solving MEG inverse problem in the environment with correlated sources
Kuznetsova A., Nurislamova Y., Ossadtchi A.
NeuroImage 228:117677

A game-theoretical model of the landscape theory
Le Breton M., Shapoval A., Weber S.
Journal of Mathematical Economics 92, 41-46

Survey on graph embeddings and their applications to machine learning problems on graphs
Makarov I., Kiselev D., Nikitinsky N. et al.
PeerJ Computer Science 7

Earth's Magnetotail as the Reservoir of Accelerated Single- and Multicharged Oxygen Ions Replenishing Radiation Belts
Panasyuk M., Popov V. et al.
Journal of Geophysical Research: Space Physics 126

Decoding and interpreting cortical signals with a compact convolutional neural network
Petrosyan A., Sinkin M., Ossadtchi A. et al.
Journal of Neural Engineering 18

Robust alternating direction implicit solverin quantized tensor formats for athree-dimensional elliptic PDE
Rakhuba M.
SIAM Journal of Scientific Computing 43, A800-A827

Neuropsychiatric disease classification using functional connectomics- results of the connectomics in neuroimaging transfer learning challenge
Schirmer M., Levchenko E. et al.
Medical Image Analysis 70

2020 

Information Distance Revisited
Bauwens B.
International Symposium on Theoretical Aspects of Computer Science (STACS 2020):46

Separating variables in bivariate polynomial ideals 
Buchacher M., Kauers M., Pogudin G.
International Symposium on Symbolic and Algebraic Computation (ISSAC 2020), 54-61

Re-pairing brackets
Chistikov D., Vyalyi M.   
Symposium on Logic in Computer Science (LICS 2020), 312-326

Low-variance black-box gradient estimates for the Plackett-Luce distribution
Gadetsky A., Struminsky K., Robinson C., Quadrianto N., Vetrov D. 
AAAI Conference on Artificial Intelligence (AAAI 2020), 10126-10135

A data complexity and rewritability tetrachotomy of ontology-mediated queries with a covering axiom
Gerasimova O., Podolskii V. et al.
International Conference of Principles of Knowledge Representation and Reasoning (KR 2020), 403-413

Finite time analysis of linear two-timescale stochastic approximation with markovian noise 
Kaledin M., Moulines E., Naumov A. et al.
Annual Conference on Computational Learning Theory (COLT 2020), 2144-2203

Controlling overestimation bias with truncated mixture of continuous distribution quatile critics
Kuznetsov A., Schvechikov P., Grishin A., Vetrov D. 
International Conference on Machine Learning (ICML 2020), 11615-11625

Structured sparsifiction of gated reccurent neural networks
Lobacheva E., Chirkova N., Markovich A., Vetrov D. 
AAAI Conference Artificial Intelligence (AAAI 2020), 4989-4996

On Power Laws in Deep Ensembles
Lobacheva E., Chirkova N., Vetrov D., Kodryan M.
Neural Information Processing Systems (NeurIPS 2020)

Greedy policy search: a simple baseline for learnable test-time augmentation
Molchanov D., Lyzhov A., Molchanova Y., Ashukha A., Vetrov D.
Conference on Uncertainty in Artificial Intelligence (UAI 2020)

Involutive MCMC: a unifying framework
Neklyudov D., Vetrov D. et al.
International Conference on Machine Learning (ICML 2020), 7634-7643

Deterministic Decoding for Discrete Data in Variational Autoencoders
Polykovskiy D., Vetrov D.
International Conference on Artificial Intelligence and Statistics (AISTATS 2020), 3046-3055

BPE-dropout: Simple and effective subword regularization
Provilkov I., Emelianenko D., Volta E.
Annual Meeting of the Association for Computational Linguistics (ACL 2020), 1882-1892

Prediction of 3D Chromatin Structure Using Recurrent Neural Networks
Rozenwald M., Khrameeva E. et al.
IEEE International Conference on Bioinformatics and (BIBM 2018):18399259

Towards Crowdsourced Training of Large Neural Networks using Decentralized Mixture-of-Experts
Ryabinin M., Gusev A.
Neural Information Processing Systems (NeurIPS 2020)

Black-Box Optimization with Local Generative Surrogates
Shirobokov S., Belavin V., Ustyuzhanin A. et al.
Neural Information Processing Systems (NeurIPS 2020)

Revisiting bounded-suboptimal safe interval path planning
Yakovlev K., Andreychuk A., Stern R.
International Conference on Automated Planning and Scheduling (ICAPS 2020), 300-304

First observation of excited Ωb-states
Aaij R., Derkach D., Maevskiy A., Kazeev N., Ratnikov F., Boldyrev A., Gushchin M., Ustyuzhanin A. et al. (The LHCb collaboration)  
Physical Review Letters 124:082002

*and 28 other publications prepared within the framework of CERN collaborations

Coloring hypergraphs with bounded cardinalities of edge intersections 
Akhmejanova M., Shabanov D.  
Discrete Mathematics 343:111692 

SANgo: A storage infrastructure simulator with reinforcement learning support
Arzymatov K., Sapronov A., Belavin V., Gremyachikh L., Karpov M., Ustyuzhanin A. et al. 
PeerJ Computer Science 2020:271

Spherical actions on isotropic flag varieties and related branching rules
Avdeev R., Petukhov A. 
Transformation Groups. In press

Space of isospectral periodic tridiagonal matrices
Ayzenberg A.
Algebr. Geom. Topol. 20, 2957-2994

Draft genome sequences of Hirudo medicinalis and salivary transcriptome of three closely related medicinal leeches 
Babenko V., Gelfand M. et al. 
BMC Genomics 21:331

Gaussian processes with multidimensional distribution inputs via optimal transport and hilbertian embedding
Bachoc F., Spokoiny V. et al.
Electronic Journal of Statistics 14, 2742-2772

Mixed moment of GL(2) and GL(3) L-functions
Balkanova O., Bhowmik G., Frolenkov D., Raulf N. 
Proceedings of the London Mathematical Society 121, 177-219

Short-delay neurofeedback facilitates training of the parietal alpha rhythm
Belinskaia A., Smetanin N., Lebedev M., Ossadtchi A.
Journal of Neural Engineering 17:066012

Fourier transform MCMC, heavy-tailed distributions, and geometric ergodicity 
Belomestny D., Iosipoi L. 
Mathematics and computers in simulation 181, 351-363

Quasiperiods of biinfinite words 
Barbero D., Gamard G., Grandjean A.   
European Journal of Combinatorics 85:103046

On stochastic gradient Langevin dynamics with dependent data streams in the logconcave case 
Barkhagen M., Moulines E. et al. 
Bernoulli 27, 1-33

Solving linear parabolic rough partial differential equations
Bayer C., Belomestny D. et al. 
Journal of Mathematical Analysis and Applications 490:124236

Deep learning approach for predicting functional Z-DNA regions using omics data
Beknazarov N., Jin S., Poptsova M.
Scientific Reports 10:19134

On pattern setups and pattern multistructures
Belfodil A., Kuznetsov S., Kaytoue M.
International Journal of General Systems, 785-818

Nonparametric density estimation from observations with multiplicative measurement errors
Belomestny D., Goldenshluger A.  
Annales de l'institut Henri Poincare (B) Probability and Statistics 56, 36-67

Variance reduction for Markov chains with application to MCMC 
Belomestny D., Iosipoi L., Moulines E., Naumov A., Samsonov S. 
Statistics and Computing 30, 973-997

Semitractability of optimal stopping problems via a weighted stochastic mesh algorithm
Belomestny D., Kaledin M., Schoenmakers J. 
Mathematical Finance 30, 1591-1616

Optimal stopping via reinforced regression
Belomestny D., Schoenmakers J., Spokoiny V., Zharkynbay B. 
Communications in Mathematical Sciences 18, 109-121

ML-assisted versatile approach to Calorimeter R&D
Boldyrev A., Derkach D., Ratnikov F., Shevelev A. 
Journal of Instrumentation 15:C09030

Adaptive divergence for rapid adversarial optimization
Borisyak M., Gaintseva T., Ustyuzhanin A. 
PeerJ Computer Science 6:е274

(1+epsilon)-class classification: an anomaly detection method for higly imbalanced or incomplete data sets  
Borisyak M., Ryzhikov A., Ustyuzhanin A., Derkach D., Ratnikov F., Mineeva O. 
Journal of Machine Learning Research 21, 1-22

On the Sprague-Grundy function of extensions of proper NIM 
Boros E., Gurvich V., Bao Ho N. et al. 
International Journal of Game Theory. In press

Characterizing and decomposing classes of threshold, split, and bipartite graphs via 1-Sperner hypergraphs
Boros E., Gurvich V., Milanic M. 
Journal of Graph Theory 94, 364-397 

High entropy random selection protocols
Buhrman H., Vereshchagin N. et al.
Algorithmica 83, 667-694

Maximal acyclic subgraphs and closest stable matrices
Cvetkovic A., Protasov V. 
SIAM Journal on Matrix Analysis and Applications 41, 1167-1182

Brief Report: Classification of Autistic Traits According to Brain Activity Recoded by fNIRS Using ε-Complexity Coefficients
Dahan A., Dubnov Y.. et al.
Journal of Autism and Developmental Disorders. In press

NEXTPRIORITYCONCEPT: A new and generic algorithm computing concepts from complex and heterogeneous data
Demko C., Kuznetsov S. et al. 
Theoretical Computer Science 845, 1-20 

Cherenkov detectors fast simulation using neural networks   
Derkach D., Kazeev N., Ratnikov F., Ustyuzhanin A., Volokhova A.   
Nuclear Instruments and Methods in Physics Research, Section A: Accelerators, Spectrometers, Detectors and Associated Equipment 952:161804

Irreducibility and geometric ergodicity of Hamiltonian Monte Carlo
Durmus A., Moulines E., Saksman E.
Annals of Statistics 48, 3545-3564

Random hypergraphs and property B  
Duraj L., Kozik J., Shabanov D. 
European Journal of Combinatorics 91:103205 

An accelerated directional derivative method for smooth stochastic convex optimization  
Dvurechensky P., Gorbunov E., Gasnikov A. 
European Journal of Operational Research 290, 601-621

The cubic moment of automorphic L-functions in the weight aspect  
Frolenkov D.   
Journal of Number Theory 207, 247-281 

Parsimonious generalization of fuzzy thematic sets in taxonomies applied to the analysis of tendencies of research in data science 
Frolov D., Nascimento S., Fenner T., Mirkin B.    
Information Sciences 512, 595-615

Studying RNA-DNA interactome by Red-C identifies noncoding RNAs associated with various chromatin types and reveals transcription dynamics
Gavrilov A., Mironov A.   et al. 
Nucleic Acids Resrarch 48, 6699-6714   

An explicit solution for a multimarginal mass transportation problem  
Gladkov N., Zimin A.  
SIAM Journal on Mathematical Analysis 52, 3666-3696

On the occupancy problem for a regime-switching model
Grabchak M., Kelbert M., Paris Q. 
Journal of Applied Probability 57, 53-77

Zinc binds to RRM2 peptide of TDP-43
Golovin A.. Devred F., Yatoui D. et al.
International Journal of Molecular Sciences: 9080

Global Identifiability of differential models 
Hong H., Ovchinnikov A., Pogudin G., Yap C. 
Communications on Pure and Applied Mathematics 73, 1831-1879 

On the Lp-Brunn-Minkowski and dimensional Brunn–Minkowski conjectures for log-concave measures
Hosle J., Kolesnikov A., Livshyts G.
Journal of Geometric Analysis. In press

Composite optimization for the resource allocation problem 
Ivanova A., Dvurechensky P., Gasnikov A., Kamzolov D. 
Optimization Methods and Software. In press

Universal intermediate gradient method for convex problems with inexact oracle
Kamzolov D., Dvurechensky P., Gasnikov A.     
Optimization Methods and Software. In press

The Multiplicative-Additive Lambek Calculus with Subexponential and Bracket Modalities
Kanovich M., Kuznetsov S., Scedrov A.
Journal of Logic, Language and Information 30, 89-89

A P300 Brain-Computer Interface With a Reduced Visual Field
Kirasirova L., Ossadtchi A. et al.
Frontiers in Neuroscience 14, 1246

The scalability analysis of a parallel tree search algorithm
Kolpakov R., Posypkin M. 
Optimization Letters 14, 2211–2226

Spherical and geodesic growth rates of right-angled Coxeter and Artin groups are Perron numbers
Kolpakov A., Talambutsa A.      
Discrete Mathematics 343:3 

Influence of the spacer region between the Shine–Dalgarno box and the start codon for fine-tuning of the translation efficiency in Escherichia coli
Komarova E., Gelfand M. et al. 
Microbial Biotechnology 13, 1254-1261

Optimizing connectivity-driven brain parcellation using ensemble clustering
Kurmukov A., Mussabaeva A., Denisova Y.  et al.  
Brain Connectivity 10:4

Origin of the nuclear proteome on the basis of pre-existing nuclear localization signals in prokaryotic proteins 
Lisitsyna O., Mironov A. et al. 
Biology Direct 15:9

Magnetohydrodynamic modeling of the solar wind key parameters and current sheets in the heliosphere: radial and solar cycle evolution
Maiewski E., Popov Y. et al. 
Astrophysical Journal 892:12

From-below Boolean matrix factorization algorithm based on MDL
Makhalova T., Trnecka M. 
Advances in Data Analysis and Classification. In press

Online supervised attention-based recurrent depth estimation from monocular video
Maslov D., Makarov I.
Peerj computer science 6:e317

Robust covariance estimation under L4 - L2 norm equivalence
Mendelson S., Zhivotovskiy N.
Annals of Statistics 48, 1648-1664

NeuroPycon: An open-source python toolbox for fast multi-modal and reproducible brain connectivity pipelines 
Meunier D., Pascarella A., Altukhov D. et al. 
NeuroImage 219:117020

Test-time augmentation for deep learning-based cell segmentation on microscopy images 
Moshkov N., Mathe B., Kertesz-Farkas A. et al. 
Scientific Reports 10:5068

Generation of the Reactive Oxygen Species on the surface of nanosized titanium(IV) oxides particles under UV-irradiation and their connection with photocatalytic properties
Mulakov S., Gotovtsev P., Gainanova A., Kravchenko G., Kuz'micheva G., Podbel'skii V. 
Journal of Photochemistry and Photobiology A: Chemistry 393:112424

Primal–dual accelerated gradient methods with small-dimensional relaxation oracle
Nesterov Y., Gasnikov A., Guminov S., Dvurechensky P. 
Optimization Methods and Software. In press

Tensor train decomposition on tensorflow (T3F) 
Novikov A., Izmailov P., Khrulkov V., Figurnov M. et al. 
Journal of Machine Learning Research 21:30

Multi-dimensional interpretations of Presburger arithmetic in itself
Pakhomov F., Zapryagaev A.
Journal of Logic and Computation 30, 1681–1693

The Dynamics of Canalizing Boolean Networks
Paul E., Pogudin G. et al.    
Complexity 2020:3687961

Modern view of the solar wind from micro to macro scales
Petrukovich A., Popov V., Maiewski E. et al.
Physics-Uspekhi 63, 801-811

Software tools for 3D nuclei segmentation and quantitative analysis in multicellular aggregates
Piccinini F., Moshkov N. et al.
Computational and Structural Biotechnology Journal 18, 1287-1300

Is there any intron sliding in mammals?
Poverennaya I., Potapova N., Spirin S.
BMC evolutionary biology 20:164

Using machine learning to speed up and improve calorimeter R&D
Ratnikov F.    
Journal of Instrumentation 15:C05032

A randomized coordinate descent method with volume sampling
Rodomanov A., Kropotov D.     
SIAM Journal on Optimization 30, 1878-1904

BitFun: Fast Answers to Queries with Tunable Functions in Geospatial Array DBMS
Rodriges Zalipynis R.
Proceedings of the VLDB Endowment 13, 2150-8097

A machine learning framework for the prediction of chromatin folding in Drosophila using epigenetic features
Rozenwald M., Galitsyna A.; Sapunov G. et al.
PeerJ Computer Science 6:e307

Reconstruction of the coupling between solar proxies: When approaches based on Kuramoto and Van der Pol models agree with each other
Savostyanov A., Shapoval A., Shnirman M.  
Communications in Nonlinear Science and Numerical Simulation 83:105149

The inverse problem for the Kuramoto model of two nonlinear coupled oscillators driven by applications to solar activity
Savostyanov A., Shapoval A., Shnirman M.  
Physica D: Nonlinear Phenomena 401:132160

Industry equilibrium and welfare in monopolistic competition under uncertainty
Shapoval A. , Goncharenko V. 
Journal of Economics 130, 187-218

Influence of very large spatial heterogeneity on estimates of sea-level trends
Shapoval A.  et al. 
Applied Mathematics and Computation 386:125485

Digital filters for low-latency quantification of brain rhythms in real time
Smetanin N., Belinskaya A., Lebedev M.,  Ossadtchi A.
Journal of Neural Engineering 17:4

On the Joint Usage of Target Wake Time and 802.11ba Wake-Up Radio
Stepanova E., Bankov D. et al.
IEEE Access 8, 221061-221076

Tailor: A Nonparametric and Rapid Score Calibration Method for Database Search-Based Peptide Identification in Shotgun Proteomics
Sulimov P., Kertesz-Farkas A. 
Journal of Proteome Research 19, 1481-1490

Spherical and geodesic growth rates of right-angled Coxeter and Artin proups are Perron numbers 
Talambutsa A., Kolpakov A. 
Discrete Mathematics 343:3

A mathematical model to predict diagnostic periods for secondary distant metastases in patients with ER/PR/HER2/KI-67 subtypes of breast cancer
Tyuryumina E., Neznanov A., Turumin J.
Cancers 12:2344

Descriptive complexity of computable sequences revisited
Vereshchagin V. 
Theoretical Computer Science 809, 531-537

Universal Scaling of Thin Current Sheets
Zelenyi L., Malova H., Grigorenko E., Popov V.  et al. 
Geophysical Research Letters 47:e2020GL088422

From equivalence queries to PAC learning: the case of implication theories
Yarullin R., Obiedkov S.
BInternational Journal of Approximate Reasoning 127, 1-16

Публикации 2019

Публикации 2018

Публикации 2017

Публикации 2016

Публикации 2015