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Regular version of the site

109028, Moscow,
11, Pokrovsky boulevard

Phone: +7 (495) 531-00-00 *27254

Email: computerscience@hse.ru


First Deputy Dean Tamara Voznesenskaya
Deputy Dean for Research and International Relations Sergei Obiedkov
Deputy Dean for Methodical and Educational Work Ilya Samonenko
Deputy Dean for Development, Finance and Administration Irina Plisetskaya
Convergence rates for empirical barycenters in metric spaces: curvature, convexity and extendable geodesics

Ahidar-Coutrix A., Le Gouic T., Paris Q.

Probability Theory and Related Fields. 2019.

Machine Learning on data with sPlot background subtraction

M. Borisyak, N. Kazeev.

Journal of Instrumentation. 2019. Vol. 14. No. 08. P. 1-8.

Book chapter
Subspace Inference for Bayesian Deep Learning

Vetrov D., Izmailov P., Maddox W. J. et al.

In bk.: Proceedings of the 35th Uncertainty in Artificial Intelligence Conference (UAI-2019). 2019. P. 1-11.

Book chapter
The logic of action lattices is undecidable

Kuznetsov S.

In bk.: 34th Annual ACM/IEEE Symposium on Logic in Computer Science (LICS 2019). IEEE, 2019. Ch. 36. P. 1-9.

Selected Publications of the Faculty


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


Subspace inference for Bayesian deep learning 
Izmailov P., Maddox W., Kirichenko P., Garipov T., Vetrov D., Wilson A.  
Conference on Uncertainty in Artificial Intelligence (UAI 2019):435

The logic of action lattices is undecidable 
Kuznetsov S.  
Symposium on Logic in Computer Science (LICS 2019)

On reproducing semi-dense depth map reconstruction using deep convolutional neural networks with perceptual loss 
Makarov I., Maslov D., Gerasimova O., Aliev V., Korinevskaya A. et al. 
ACM International Conference on Multimedia (MM 2019), 1080-1084

Numerical pattern mining through compression 
Makhalova T., Kuznetsov S., Napoli A. 
Data Compression Conference (DCC 2019), 112-121

ChronoSDB in action: Manage, process, and visualize big geospatial arrays in the cloud
Rodriges Zalipynis R.A.
International Conference on Management of Data (SIGMOD 2019), 1985-1988


Observation of CP violation in charm decays*
Aaij R., Derkach D., Kazeev N., Ratnikov F., Ustyuzhanin A. et al. (The LHCb collaboration) 
Physical Review Letters 122:211803

*and 32 other publications prepared within the framework of CERN collaborations

Multidimensional frontier visualization based on optimization methods using parallel computations
Afanasiev A., Krivonozhko V., Lychev A.,  Sukhoroslov O. 
Journal of Global Optimization. In press

Convergence rates for empirical barycenters in metric spaces: curvature, convexity and extendable geodesics
Ahidar-Coutrix A., Le Gouic T., Paris Q.  
Probability Theory and Related Fields. In press

Coloring hypergraphs with bounded cardinalities of edge intersections
Akhmejanova M., Shabanov D.
Discrete Mathematics. In press

Commutative algebraic monoid structures on affine spaces
Arzhantsev I., Bragin S., Zaitseva Y.
Communications in Contemporary Mathematics. In press

Infinite transitivity, finite generation, and Demazure roots 
Arzhantsev I., Kuyumzhiyan K., Zaidenberg M. 
Advances in Mathematics 351, 1-32

Branching rules related to spherical actions on flag varieties 
Avdeev R., Petukhov A. 
Algebras and Representation Theory. In press

Unconstrained and curvature-constrained shortest-path distances and their approximation
Arias-Castro E., Le Gouic T. 
Discrete and Computational Geometry 62,1-28

Sums of Kloosterman sums in the prime geodesic theorem
Balkanova O., Frolenkov D.
Quarterly Journal of Mathematics 70, 649-674

Sparse covariance matrix estimation in high-dimensional deconvolution
Belomestny D. , Trabs M., Tsybakov A.
Bernoulli 25, 1901-1938

Minimax theorems for American options without time-consistency 
Belomestny D.  et al. 
Finance and Stochastics 23, 209-238

Low-frequency estimation of continuous-time moving average Lévy processes 
Belomestny D., Panov V., Woerner J. 
Bernoulli 25, 902-931

Non-uniform bounds in the Poisson approximation with applications to informational distances I  
Bobkov S., Chistyakov G., Götze F.
IEEE Transactions on Information Theory 65, 5283-5293

Higher order concentration of measure 
Bobkov S., Götze F., Sambale H. 
Communications in Contemporary Mathematics 21:1850043

Khinchine's theorem and Edgeworth approximations for weighted sums
Bobkov S. 
Annals of Statistics 47, 1616-1633

Machine Learning on data with sPlot background subtraction 
Borisyak M., Kazeev N.  
Journal of Instrumentation 14:P08020

Sprague-Grundy function of symmetric hypergraphs
Boros E., Gurvich V. 
Journal of Combinatorial Theory, Series A 165, 176-186

Separable discrete functions: Recognition and sufficient conditions 
Boros E., Cepek O., Gurvich V. 
Discrete Mathematics 342, 1275-1292

Gene expression across mammalian organ development
Cardoso-Moreira, M., Mazin P. et al.
Nature 571, 505-509

Tissue-specific impact of stem-loops and quadruplexes on cancer breakpoints formation 
Cheloshkina K., Poptsova M. 
BMC Cancer 19:434

Ultra-performance liquid chromatography-mass spectrometry for precise fatty acid profiling of oilseed crops 
Chernova A., Mazin P. et al. 
PeerJ 7  :e6547

LINC00116 codes for a mitochondrial peptide linking respiration and lipid metabolism
Chugunova A., Mazin P. et al. 
Proceedings of the National Academy of Sciences of the United States of America 116, 4940-4945

Bias in false discovery rate estimation in mass-spectrometry-based peptide identification 
Danilova Y., Voronkova A., Sulimov P., Kertesz-Farkas A. 
Journal of Proteome Research 18, 2354-2358

Core clustering as a tool for tackling noise in cluster labels 
de Amorim R., Makarenkov V., Mirkin B. 
Journal of Classification. In press

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. In press

On the structure of Ammann A2 tilings 
Durand B., Shen A., Vereshchagin N. 
Discrete and Computational Geometry. In press

Adaptive nonparametric clustering
Efimov K., Adamyan L., Spokoiny V.
IEEE Transactions on Information Theory 65,4875-4892

Predictive models of protease specificity based on quantitative protease-activity profiling data
Fedonin G., Gelfand M.
Biochimica et Biophysica Acta - Proteins and Proteomics  1867:140253

On multistochastic Monge–Kantorovich problem, bitwise operations, and fractals 
Gladkov N., Kolesnikov A., Zimin A.  
Calculus of Variations and Partial Differential Equations 58:173

Local semicircle law under fourth momentcondition 
Götze F., Naumov A., Tikhomirov A. 
Journal of Theoretical Probability. In press

Compression of recurrent neural networks for efficient language modeling 
Grachev A., Ignatov D., Savchenko A. 
Applied Soft Computing Journal 79, 354-362

Accelerated regularized Newton methods for minimizing composite convex functions 
Grapiglia G., Nesterov Y. 
SIAM Journal on Optimization 29, 77-99

Tropical Combinatorial Nullstellensatz and sparse polynomials  
Grigoriev D., Podolskii V.  
Foundations of Computational Mathematics. In press 

Reduced vs. standard dose native E. coli-asparaginase therapy in childhood acute lymphoblastic leukemia: long-term results of the randomized trial Moscow–Berlin 2002
Karachunskiy A., Korepanova N., Kuznetsov S. 
Journal of Cancer Research and Clinical Oncology 145, 1001-1012

Axiomatization of provable n-provability
Kolmakov E., Beklemishev L.E.V.
Journal of Symbolic Logic 84, 849-869

Survival forests under test: Impact of the proportional hazards assumption on prognostic and predictive forests for amyotrophic lateral sclerosis survival
Korepanova N., Seibold H., Steffen V., Hothorn T.
Statistical Methods in Medical Research. In press

Panchromatic 3-colorings of random hypergraphs 
Kravstov D., Krokhmal N., Shabanov D. 
European Journal of Combinatorics 78, 28-43

Dual network embedding for representing research interests in the link prediction problem on co-authorship networks
Makarov I., Gerasimova O., Sulimov P., Zhukov L.
PeerJ Computer Science 5:e172

Distance and consensus for preference relations corresponding to ordered partitions 
Mirkin B., Fenner T. 
Journal of Classification. In press

How to make the Perron eigenvector simple 
Protasov V. 
Calcolo 56:17

Main effects and interactions in mixed and incomplete data frames
Robin G., Moulines E. et al.
Journal of the American Statistical Association. In press

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. In press

Recognition of 3′-end L1, Alu, processed pseudogenes, and mRNA stem-loops in the human genome using sequence-based and structure-based machine-learning models 
Shein A., Zaikin A., Poptsova M. 
Scientific Reports 9:7211

Micro-evolution of three Streptococcus species: selection, antigenic variation, and horizontal gene inflow 
Shelyakin P., Bochkareva O., Karan A., Gelfand M. 
BMC Evolutionary Biology 19:83

Chlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction
Sigalova O., Gelfand M. et al.
BMC Genomics, 20:710

Bootstrap tuning in Gaussian ordered model selection
Spokoiny V., Willrich, N. 
Annals of Statistics 47, 1351-1380

Comparative genomic analysis of the regulation of aromatic metabolism in Betaproteobacteria 
Suvorova I., Gelfand M. 
Frontiers in Microbiology 10:642

Nuclear lamina integrity is required for proper spatial organization of chromatin in Drosophila 
Ulianov S., Gelfand M. et al. 
Nature Communications 10:1176

Peptogrid—rescoring function for autodock vina to identify new bioactive molecules from short peptide libraries 
Zalevsky A., Golovin A.  et al. 
Molecules 24:277


Statistical model checking of distance fraud attacks on the Hancke-Kuhn family of protocols 
Alturki M., Kanovich M., Scedrov A. et al. 
ACM Conference on Computer and Communications Security (CCS 2018), 60-71

Two techniques that enhance the performance of multi-robot prioritized path planning 
Andreychuk A., Yakovlev K. 
International Joint Conference on Autonomous Agents and Multiagent Systems (AAMAS 2018), 2177-2179

Decomposing 1-sperner hypergraphs
Boros E., Gurvich V., Milanic M.
Electronic Journal of Combinatorics 26:18

Randomized block cubic Newton method
Doikov N., Richtarik P. 
International Conference on Machine Learning (ICML 2018), 1290-1298

Computational optimal transport: Complexity by accelerated gradient descent is better than by Sinkhorn's algorithm 
Dvurechensky P., Gasnikov A., Kroshnin A. 
International Conference on Machine Learning (ICML 2018), 2196-2220

Realistic post-processing of rendered 3D scenes 
Feygina A., Ignatov D., Makarov I. 
ACM SIG International Conference on Computer Graphics and Interactive Techniques (SIGGRAPH 2018), 42:1-42:2

Conditional generators of words definitions 
Gadetsky A., Yakubovskiy I., Vetrov D. Kroshnin A. 
Annual Meeting of the Association for Computational Linguistics (ACL 2018) 2, 266-271

Loss surfaces, mode connectivity, and fast ensembling of DNNs 
Garipov T., Podoprikhin D., Vetrov D.  et al. 
Advances in Neural Information Processing Systems (NeurIPS 2018), 8789-8798

Averaging weights leads to wider optima and better generalization
Izmailov P., Podoprikhin D., Vetrov D.  et al. 
Conference on Uncertainty in Artificial Intelligence 
(UAI 2018), 876-885

A logical framework with commutative and non-commutative subexponentials 
Kanovich M., Kuznetsov S., Scedrov A. 
International Joint Conference on Automated Reasoning (IJCAR 2018), 228-245

Fast depth map super-resolution using deep neural network 
Korinevskaya A., Makarov I. 
IEEE International Symposium on Mixed and Augmented Reality (ISMAR-Adjunct), 117-122

Recommending co-authorship via network embeddings and feature engineering: The case of National Research University Higher School of Economics 
Makarov I., Gerasimova O., Sulimov P., Zhukov L. 
ACM/IEEE Joint Conference on Digital Libraries (JCDL 2018), 365-366

Non-metric similarity graphs for maximum inner product search 
Morozov S., Babenko A. 
Advances in Neural Information Processing Systems (NeurIPS 2018), 4726-4735

ChronosDB: distributed, file Based, geospatial array DBMS 
Rodriges Zalipynis R.A. 
International Conference on Very Large Data Bases (VLDB 2018). Proceedings of the VLDB Endowment 11, 1247-1261

Marginal weighted maximum log-likelihood for efficient learning of perturb-and-map models 
Shpakova T., Bach F., Osokin A. 
Conference on Uncertainty in Artificial Intelligence (UAI 2018), 279-289

Quantifying learning guarantees for convex but inconsistent surrogates 
Struminsky K., Lacoste-Julien S., Osokin A. 
Advances in Neural Information Processing Systems (NeurIPS 2018), 667-675

First measurement of the CP-violating phase ϕs dd in s 0 → (K + π )(K π +) decays 
Aaij R., Ratnikov F. et al.  (The LHCb collaboration) 
Journal of High Energy Physics 2018:140

Evidence for the rare decay Σ+ →+μ- 
Aaij R., Ratnikov F. et al.  (The LHCb collaboration) 
Physical Review Letters 120:221803

Measurement of the CP asymmetry in B  →  D  s    D 0 and B   →  D  D 0 decays 
Aaij R., Ratnikov F. et al. (The LHCb collaboration) 
Journal of High Energy Physics 2018:160

Search for the rare decay Λc + →+μ- 
Aaij R., Ratnikov F.   et al. (The LHCb collaboration) 
Physical Review D 97:091101

Studies of the resonance structure in D0→ Kπ±π±πdecays 
Aaij R., Ratnikov F. et al. (The LHCb collaboration) 
European Physical Journal C 78:443

Final results of the OPERA experiment on ντ appearance in the CNGS neutrino beam
Agafonova N., Ustyuzhanin A. et al. (OPERA Collaboration) 
Physical Review Letters 120:211801

*and 33 other publications prepared within the framework of CERN collaborations

A fast scaling algorithm for the weighted triangle-free 2-matching problem 
Artamonov S., Babenko M. 
European Journal of Combinatorics 68, 3-23

Deviation of polynomials from their expectations and isoperimetry 
Arutyunyan L., Kosov E. 
Bernoulli 24, 2043-2063

New and old results on spherical varieties via moduli theory 
Avdeev R. Cupit-Foutou S. 
Advances in Mathematics 328, 1299-1352

On the irreducible components of moduli schemes for affine spherical varieties 
Avdeev R., Cupit-Foutou S. 
Transformation Groups 23, 299-327

Bounds for a spectral exponential sum 
Balkanova O., Frolenkov D. 
Journal of the London Mathematical Society 99, 249-272

The mean value of symmetric square L-functions 
Balkanova O., Frolenkov D. 
Algebra and Number Theory 12, 35-59

On the prediction loss of the lasso in the partially labeled setting 
Bellec P., Dalalyan A., Grappin E., Paris Q. 
Electronic Journal of Statistics 12, 3443-3472

Minimax theorems for American options without time-consistency 
Belomestny D., et al. 
Finance and Stochastics 23, 209-238

Regression-based complexity reduction of the nested Monte Carlo methods 
Belomestny D., Häfner S., Urusov M. 
SIAM Journal on Financial Mathematics 9, 665-689

Projected particle methods for solving McKean-Vlasov stochastic differential equations 
Belomestny D., Schoenmakers J. 
SIAM Journal on Numerical Analysis 56, 3169-3195

Low-rank diffusion matrix estimation for high-dimensional time-changed Lévy processes 
Belomestny D., Trabs M. 
Annales de l'Institut Henri Poincare, Probabilités et Statistiques 54, 1583-1621

Ontology-mediated queries: Combined complexity and succinctness of rewritings via circuit complexity 
Bienvenu M., Podolskii V., Zakharyaschev M. et al. 
Journal of the ACM 65:28

Berry-Esseen bounds for typical weighted sums 
Bobkov S., Chistyakov G., Götze F. 
Electronic Journal of Probability 23:92

Genome rearrangements and phylogeny reconstruction in Yersinia pestis 
Bochkareva O., Gelfand M. et al. 
PeerJ 6:e4545

Genome rearrangements and selection in multi-chromosome bacteria Burkholderia spp. 
Bochkareva O., Gelfand M. et al. 
BMC Genomics 19:965

A potential reduction algorithm for two-person zero-sum mean payoff stochastic games 
Boros E., Gurvich V. et al.
Dynamic Games and Applications 
8, 22-41

A pathwise approach to the extinction of branching processes with countably many types 
Braunsteins P., Decrouez G., Hautphenne S. et al.
Stochastic Processes and their Applications 
129, 713-739

Sparse selfreducible sets and nonuniform lower bounds 
Buhrman H., Torenvliet L., Unger F., Vereshchagin N. 
Algorithmica 81, 179-200

UPLC-MS triglyceride profiling in sunflower and rapeseed seeds 
Chernova A., Mazin P. et al. 
Biomolecules 9:9

Asymptotic estimate for the counting problems corresponding to the dynamical system on some decorated graphs 
Chernyshev V., Tolchennikov A.  
Ergodic Theory and Dynamical Systems 38, 1697-1708

Linear switched dynamical systems on graphs 
Cicone A., Guglielmi N., Protasov V.
Nonlinear Analysis: Hybrid Systems 29, 165-186 

Latent variable method for automatic adaptation to background states in motor imagery BCI 
Dagaev N., Volkova K., Ossadtchi A. 
Journal of Neural Engineering 15:016004

On the exponentially weighted aggregate with the Laplace prior 
Dalalyan A., Grappin E., Paris Q. 
Annals of Statistics 46, 2452-2478

Model-free offline change-point detection in multidimensional time series of arbitrary nature via ε-complexity: Simulations and applications 
Darkhovsky B., Piryatinska A. 
Applied Stochastic Models in Business and Industry 34, 633-644

Finite sample properties of the mean occupancy counts and probabilities 
Decrouez G., Grabchak, M., Paris Q.
Bernoulli 24, 1910-1941

Bias-corrected estimation in continuous sampling plans 
Decrouez G., Robinson A. 
Risk Analysis 38, 177-193 

Structure factors for tunneling ionization rates of molecules: General grid-based methodology and convergence studies 
Dnestryan A. et al. 
Journal of Chemical Physics 149:164107

Knockdown of L1CAM significantly reduces metastasis in a xenograft model of human melanoma: L1CAM is a potential target for anti-melanoma therapy 
Ernst A., Galatenko V. et al. 
PLoS ONE 13:e0192525

FUS(1-359) transgenic mice as a model of ALS: pathophysiological and molecular aspects of the proteinopathy 
Funikov S., Rezvykh A., Mazin P. et al. 
Neurogenetics 19, 189-204

Comparative genomic analysis of Holospora spp., intranuclear symbionts of Paramecia 
Garushyants S., Gelfand M. et al. 
Frontiers in Microbiology 9:738

On the local semicircular law for Wigner ensembles 
Götze F., Naumov A. et al. 
Bernoulli 24, 2358-2400

Tropical effective primary and dual Nullstellensätze 
Grigoriev D., Podolskii V.
Discrete and Computational Geometry 59, 507-552

On the closest stable/unstable nonnegative matrix and related stability radii 
Guglielmi N., Protasov Y.
SIAM Journal on Matrix Analysis and Applications 39, 1642-1669

Relations between counting functions on free groups and free monoids
Hartnick T., Talambutsa A. 
Groups, Geometry, and Dynamics 12, 1485-1521

Particle-identification techniques and performance at LHCb in Run 2 
Hushchyn M., Chekalina V. (on behalf of the LHCb collaboration) 
Nuclear Instruments and Methods in Physics Research, Section A: Accelerators, Spectrometers, Detectors and Associated Equipment 936, 568-569

An evolutionary mechanism for the generation of competing RNA structures associated with mutually exclusive exons 
Ivanov T., Pervouchine D. 
Genes 9:356

A conditional information inequality and its combinatorial applications 
Kaced T., Romashchenko A., Vereshchagin N. 
IEEE Transactions on Information Theory 64, 3610-3615

Ontology-based access to temporal data with Ontop: A framework proposal 
Kalayci E., Zakharyaschev M. et al. 
International Journal of Applied Mathematics and Computer Science 29, 17-30

The genes of the sulphoquinovose catabolism in Escherichia coli are also associated with a previously unknown pathway of lactose degradation 
Kaznadzey A., Gelfand M. et al.
Scientific Reports 

Extremal Kähler–Einstein metric for two-dimensional convex bodies 
Klartag B., Kolesnikov A. 
Journal of Geometric Analysis 29, 2347-2373

Poincaré and Brunn-Minkowski inequalities on the boundary of weighted Riemannian manifolds 
Kolesnikov A., Milman E. 
American Journal of Mathematics 140, 1147-1185

The KLS isoperimetric conjecture for generalized Orlicz balls 
Kolesnikov A., Milman E. 
Annals of Probability 46, 3578-3615

Testing the efforts model of simultaneous interpreting: An ERP study 
Koshkin R., Shtyrov Y., Myachykov A., Ossadtchi A. 
PLoS ONE, 10:e0206129

Fractional smoothness of images of logarithmically concave measures under polynomials 
Kosov E. 
Journal of Mathematical Analysis and Applications 462, 390-406

On panchromatic colourings of a random hypergraph 
Kravtsov D., Krokhmal N., Shabanov D. 
Russian Mathematical Surveys 73, 731-733

Structural Instability in single-crystal rare-earth scandium borates RESc3(BO3)4 
Kuz’micheva G., Podbel’sky V.Chuykin N.  et al. 
Crystal Growth and Design 18, 1571-1580

On interestingness measures of formal concepts 
Kuznetsov S.Makhalova T. 
Information Sciences 442-443, 202-219

Commentary: Injecting instructions into premotor cortex 
Lebedev M., Ossadtchi A. 
Frontiers in Cellular Neuroscience 12:65

Navigation patterns and scent marking: Underappreciated contributors to hippocampal and entorhinal spatial representations? 
Lebedev M., Pimashkin A., Ossadtchi A. 
Frontiers in Behavioral Neuroscience 12:98

A notion of stability for k-means clustering 
Le Gouic T., Paris Q. 
Electronic Journal of Statistics 12, 4239-4263

60S dynamic state of bacterial ribosome is fixed by yeast mitochondrial initiation factor 3 
Levitskii S., Golovin A.   et al. 
PeerJ 6:e5620

Proteogenomics of malignant melanoma cell lines: The effect of stringency of exome data filtering on variant peptide identification in shotgun proteomics 
Lobas A., Pyatnitskiy M. et al. 
Journal of Proteome Research 17, 1801-1811

Conservation, evolution, and regulation of splicing during prefrontal cortex development in humans, chimpanzees, and macaques 
Mazin P.Gelfand M. et al.
24, 585-596

Cooption of heat shock regulatory system for anhydrobiosis in the sleeping chironomid Polypedilum vanderplanki 
Mazin P.Gelfand M. et al. 
Proceedings of the National Academy of Sciences of the United States of America 115, E2477-E2486

Pangenomic definition of prokaryotic species and the phylogenetic structure of Prochlorococcus spp. 
Moldovan M., Gelfand M.
Frontiers in Microbiology 9:428 

Qualitative judgement of research impact: Domain taxonomy as a fundamental framework for judgement of the quality of research 
Murtagh F., Orlov M.Mirkin B.
Journal of Classification 

Bootstrap confidence sets for spectral projectors of sample covariance 
Naumov A., Spokoiny V., Ulyanov V. 
Probability Theory and Related Fields 174, 1091-1132

Dual subgradient method with averaging for optimal resource allocation 
Nesterov Y. Shikhman V.European Journal of Operational Research 270,   907-916

Phase shift invariant imaging of coherent sources (PSIICOS) from MEG data 
Ossadtchi A., Altukhov D., Jerbi K. 
NeuroImage 183, 950-971

PQ, a new program for phylogeny reconstruction 
Penzar D., Krivozubov M., Spirin S. 
BMC Bioinformatics 19:374

Towards long-range RNA structure prediction in eukaryotic genes 
Pervouchine D.  
Genes 9:302

Entangled conditional adversarial autoencoder for de novo drug discovery 
Polykovskiy D., Vetrov D.  et al. 
Molecular Pharmaceutics 15, 4398-4405

Avoidance of recognition sites of restriction-modification systems is a widespread but not universal anti-restriction strategy of prokaryotic viruses 
Rusinov I., Spirin S. et al. 
BMC Genomics 19:885

Unconstrained face identification using maximum likelihood of distances between deep off-the-shelf features 
Savchenko A., Belova N. 
Expert Systems with Applications 108, 170-182

Observational evidence in favor of scale-free evolution of sunspot groups 
Shapoval A. et al. 
Astronomy and Astrophysics 618:A183

Microbiomes of gall-inducing copepod crustaceans from the corals Stylophora pistillata (Scleractinia) and Gorgonia ventalina (Alcyonacea) 
Shelyakin P., Gelfand M.  et al. 
Scientific Reports 8:11563

Bayesian inference for spectral projectors of the covariance matrix 
Silin I., Spokoiny V. 
Electronic Journal of Statistics 12, 1948-1987

NFBLab-A versatile software for neurofeedback and brain-computer interface research 
Smetanin N., Ossadtchi A. et al. 
Frontiers in Neuroinformatics 12:100

Predictive model for bottomhole pressure based on machine learning 
Spesivtsev P., Umnov A.Yarullin R. Vetrov D.  et al. 
Journal of Petroleum Science and Engineering 166, 825-841 

Building web-based services for practical exercises in parallel and distributed computing 
Sukhoroslov O
Journal of Parallel and Distributed Computing 118, 177-188 

Functional status of neuronal calcium sensor-1 is modulated by zinc binding 
Tsvetkov P., Golovin A.  et al. 
Frontiers in Molecular Neuroscience 11:459 

Consolidated mathematical growth model of the primary tumor and secondary distant metastases of breast cancer (CoMPaS) 
Tyuryumina E., Neznanov A. 
PLoS ONE 13:e0200148


AnnArbor: Approximate nearest neighbors using arborescence coding 
Babenko A., Lempitsky V. 
IEEE International Conference on Computer Vision (ICCV 2017), 4895-4903

Product split trees 
Babenko A., Lempitsky V. 
IEEE Conference on Computer Vision and Pattern Recognition (CVPR 2017), 6316-6324

Mining convex polygon patterns with formal concept analysis 
Belfodil A., Kuznetsov S.et al. 
International Joint Conference on Artificial Intelligence (IJCAI 2017), 1425-1432

The complexity of ontology-based data access with OWL 2 QL and bounded treewidth queries 
Bienvenu M., Podolskii V. et al. 
ACM SIGACT-SIGMOD-SIGART Symposium on Principles of Database Systems (PODS 2017), 201-216

Efficient mining of subsample-stable graph patterns 
Buzmakov A., Kuznetsov S., Napoli A. 
IEEE International Conference on Data Mining (ICDM 2017)757-762

Spatially adaptive computation time for residual networks 
Figurnov M.Vetrov D. et al. 
IEEE Conference on Computer Vision and Pattern Recognition (CVPR 2017), 1790-1799

Semi-dense depth interpolation using deep convolutional neural networks 
Makarov I.Aliev V.Gerasimova O. 
ACM Multimedia Conference (MM 2017), 1407-1415

Variational dropout sparsifies deep neural networks 
Molchanov D., Ashukha A., Vetrov D. 
International Conference on Machine Learning (ICML 2017), 2498-2507

Structured Bayesian Pruning via Log-Normal Multiplicative Noise 
Neklyudov K., Molchanov D., Ashukha A., Vetrov D. 
Advances in Neural Information Processing Systems (NIPS 2017), 6775-6784

Composing tree graphical models with persistent homology features for clustering mixed-type data 
Ni X., Quadrianto N. et al. 
International Conference on Machine Learning (ICML 2017), 2622-2631

GANs for biological image synthesis 
Osokin A. et al. 
IEEE International Conference on Computer Vision (ICCV 2017), 2252-2261

On Structured Prediction Theory with Calibrated Convex Surrogate Losses 
Osokin A., Bach F., Lacoste-Julien S. 
Advances in Neural Information Processing Systems (NIPS 2017), 302-313

Recycling privileged learning and distribution matching for fairness 
Quadrianto N., Sharmanska V. 
Advances in Neural Information Processing Systems (NIPS 2017), 677-688

Any-angle pathfinding for multiple agents based on SIPP algorithm 
Yakovlev K., Andreychuk A. 
International Conference on Automated Planning and Scheduling (ICAPS 2017), 586-593         

The automorphism group of a rigid affine variety
Arzhantsev I.Gaifullin S. 
Mathematische Nachrichten 290, 662-671 

Additive actions on toric varieties 
Arzhantsev I., Romaskevich E.
Proceedings of the American Mathematical Society 145, 1865-1879 

Cohomology of toric origami manifolds with acyclic proper faces 
Ayzenberg A.et al. 
Journal of Symplectic Geometry 15, 645-685

Dualization in lattices given by ordered sets of irreducibles 
Babin M., Kuznetsov S. 
Theoretical Computer Science 658, 316-326

Sieve estimation of the minimal entropy martingale marginal density with application to pricing kernel estimation 
Belomestny D., Härdle W.K., Krymova E. 
International Journal of Theoretical and Applied Finance 20:1750041

A convex programming-based algorithm for mean payoff stochastic games with perfect information 
Boros E., Gurvich V. et al. 
Optimization Letters 11, 1499-1512

A nested family of k-total effective rewards for positional games 
Boros E., Gurvich V.et al. 
International Journal of Game Theory 46, 263-293

Approximation schemes for stochastic mean payoff games with perfect information and few random positions 
Boros E., Gurvich V.et al. 
Algorithmica 80, 3132-3157

Regularity of non-stationary subdivision: A matrix approach 
Charina M., Protasov Vet al. 
Numerische Mathematik 135, 639-678

The second term in the asymptotics for the number of points moving along a metric graph 
Chernyshev V., Tolchennikov A. 
Regular and Chaotic Dynamics 22, 937-948

The Minkowski central partition as a pointer to a suitable distance exponent and consensus partitioning 
Cordeiro de Amorim R., Shestakov A.Mirkin B.  et al.  
Pattern Recognition 67, 62-72

Regularized Newton methods for minimizing functions with Hölder continuous Hessians 
Grapiglia G.N., Nesterov Y
SIAM Journal on Optimization 27, 478-506

Sugar Lego: Gene composition of bacterial carbohydrate metabolism genomic loci 
Kaznadzey A., Shelyakin, P. Gelfand M. 
Biology Direct 12:28

Receptor Mincle promotes skin allergies and is capable of recognizing cholesterol sulfate 
Kostarnoy A., Riabenko E. et al. 
Proceedings of the National Academy of Sciences of the United States of America 114, E2758-E2765

Genomic analysis of Caldithrix abyssi, the thermophilic anaerobic bacterium of the novel bacterial phylum Calditrichaeota 
Kublanov I., Gelfand M. et al. 
Frontiers in Microbiology 8:195

The transcriptome of type i murine astrocytes under interferon-gamma exposure and remyelination stimulus 
Kudriaeva A., Galatenko V.et al. 
Molecules 22:808

Colourings of uniform hypergraphs with large girth and applications 
Kupavskii A., Shabanov D. 
Combinatorics Probability and Computing 27, 245-273

Generating event logs for high-level process models 
Mitsyuk A., Shugurov I.Kalenkova A. van der Aalst W.  
Simulation Modelling Practice and Theory 74, 1-16

Parameterized ceteris paribus preferences over atomic conjunctions under conservative semantics 
Obiedkov S. 
Theoretical Computer Science 658, 375-390

Neurofeedback learning modifies the incidence rate of alpha spindles, but not their duration and amplitude 
Ossadtchi A., Okorokova E., Moiseeva V. et al. 
Scientific Reports 7:3772

The euler binary partition function and subdivision schemes 
Protasov V. 
Mathematics of Computation 86, 1499-1524

Matrix semigroups with constant spectral radius 
Protasov V.Voynov A. 
Linear Algebra and Its Applications 513, 376-408

Genome analysis of E. coli isolated from Crohn's disease patients 
Rakitina D., Gelfand M. et al. 
BMC Genomics 18:544

Dynamics of sunspot series on time scales from days to years: Correlation of sunspot births, variable lifetimes, and evolution of the high-frequency spectral component 
Shapoval A. et al. 
Journal of Geophysical Research: Space Physics 122, 11874-11887

Penalized maximum likelihood estimation and effective dimension 
Spokoiny V. 
Annales de l'institut Henri Poincare (B) Probability and Statistics 53, 389-429

Activation of the alpha-globin gene expression correlates with dramatic upregulation of nearby non-globin genes and changes in local and large-scale chromatin spatial structure 
Ulianov S., Gelfand M. et al. 
Epigenetics and Chromatin 10:35

Source-space EEG neurofeedback links subjective experience with brain activity during effortless awareness meditation 
van Lutterveld R., Ossadtchi A. et al. 
NeuroImage 151, 117-127

MEG signatures of a perceived match or mismatch between individual and group opinions 
Zubarev I., Klucharev V., Ossadtchi A., Moiseeva V., Shestakova A. 
Frontiers in Neuroscience 11:10


Learning supervised pagerank with gradient-based and gradient-free optimization methods 
Bogolubsky L., Nesterov Y. et al. 
Advances in Neural Information Processing Systems (NIPS 2016), 4914-4922

Model checking for symbolic-heap separation logic with inductive predicates 
Brotherston J., Kanovich M. et al. 
ACM Symposium on Principles of Programming Languages (POPL 2016), 84-96

PerforatedCNNs: Acceleration through elimination of redundant convolutions 
Figurnov M.Vetrov D. et al. 
Advances in Neural Information Processing Systems (NIPS 2016), 955-963

First-person shooter game for virtual reality headset with advanced multi-agent intelligent system 
Makarov I.Tokmakov M.Polyakov P. Zyuzin P. Martynov M.Konoplya O. Kuznetsov G. Guschenko-Cheverda I.Uriev M. Mokeev I. Gerasimova O.Tokmakova L. Kosmachev A. 
ACM Multimedia Conference (MM 2016), 735-736

Defining usability problems 
Manakhov P., Ivanov V. 
Conference on Human Factors in Computing Systems (CHI 2016), 3144-3151

A superlinearly-convergent proximal Newton-type method for the optimization of finite sums 
Rodomanov A., Kropotov D. 
International Conference on Machine Learning (ICML 2016), 3827-3853

Meta-learning with memory-augmented neural networks 
Santoro A., Bartunov S. et al. 
International Conference on Machine Learning (ICML 2016), 2740-2751                


Convergence of an alternating maximization procedure 
Andresen A., Spokoiny V. 
Journal of Machine Learning Research 17, 2229-2281

Algorithms for hub label optimization 
Babenko M. et al. 
ACM Transactions on Algorithms 13:16

URS DataBase: Universe of RNA structures and their motifs 
Baulin E., Yacovlev V.Roytberg M.  et al.  
Database 2016:baw085

Stratified regression-based variance reduction approach for weak approximation schemes 
Belomestny D., Häfner S., Urusov M. 
Mathematics and Computers in Simulation 143, 125-137

Optimal stopping under model uncertainty: Randomized stopping times approach 
Belomestny D., Krätschmer V. 
Annals of Applied Probability 26, 1260-1295

Statistical inference for time-changed Lévy processes via Mellin transform approach 
Belomestny D., Schoenmakers J. 
Stochastic Processes and their Applications 126, 2092-2122

Tangent cones to Schubert varieties in types An, Bn and Cn 
Bochkarev M., Ignatyev M., Shevchenko A. 
Journal of Algebra 465, 259-286

A new proof of the Lagrange multiplier rule 
Brinkhuis J., Protasov V. 
Operations Research Letters 44, 400-402

Towards a reverse Newman’s theorem in interactive Iinformation complexity 
Brody J., Vereshchagin N. et al. 
Algorithmica 76, 749-781

On mining complex sequential data by means of FCA and pattern structures 
Buzmakov A., Kuznetsov S.  et al. 
International Journal of General Systems 42, 135-159

A-Wardpβ: Effective hierarchical clustering using the Minkowski metric and a fast k-means initialization 
Cordeiro de Amorim R., Makarenkov V. Mirkin B. 
Information Sciences 370-371, 343-354

Application of sorting and next generation sequencing to study 5'-UTR influence on translation efficiency in Escherichia coli 
Evfratov S., Gelfand M.  et al. 
Nucleic Acids Research 45, 3487-3502

Small open reading frames, non-coding RNAs and repetitive elements in Bradyrhizobium japonicum USDA 110 
Hahn J., Gelfand M. et al. Evguenieva-Hackenberg E. 
PLoS ONE 11:e0165429

Online recommender system for radio station hosting based on information fusion and adaptive tag-aware profiling 
Ignatov D., Nikolenko S., Abaev T.Poelmans J. 
Expert Systems with Applications 55, 546-558

On dynamics of lagrangian trajectories for Hamilton–Jacobi equations 
Khanin K., Sobolevski A. 
Archive for Rational Mechanics and Analysis 219, 861-885

A subgradient method for free material design 
Kǒcvara M., Nesterov Y., Xia Y. 
SIAM Journal on Optimization 26, 2314-2354

Corrigendum: A dynamical model improves reconstruction of handwriting from multichannel electromyographic recordings 
Okorokova E., Ossadtchi A. et al. 
Frontiers in Neuroscience 9:517

Linear switching systems with slow growth of trajectories 
Protasov V. 
Systems and Control Letters 90, 54-60

Novel biomarkers in cancer: The whole is greater than the sum of its parts 
Samatov T., Galatenko V.  et al. 
Seminars in Cancer Biology 45, 50-57

How secure is your radiology department? Mapping digital radiology adoption and security worldwide 
Stites M., Pianykh O. 
American Journal of Roentgenology 206, 797-804

Nitrogen fixation and molecular oxygen: Comparative genomic reconstruction of transcription regulation in Alphaproteobacteria 
Tsoy O., Gelfand M. et al. 
Frontiers in Microbiology 7:1343

On the nature of the phase "η-TiO2" 
Vasilyeva I., Podbel’skiy V. et al. 
New Journal of Chemistry 40, 151-161


Tree quantization for large-scale similarity search and classification 
Babenko A., Lempitsky V. 
IEEE Computer Society Conference on Computer Vision and Pattern Recognition (CVPR 2015), 4240-4248

Wavelet trees meet suffix trees 
Babenko M.Starikovskaya T. et al. 
ACM-SIAM Symposium on Discrete Algorithms (SODA 2015), 572-591

Tree-like queries in OWL 2 QL: Succinctness and complexity results 
Bienvenu M., Kikot S., Podolskii V. 
Symposium on Logic in Computer Science (LICS 2015), 317-328

An approach to the problem of annotation of research publications 
Chernyak E. 
ACM International Conference on Web Search and Data Mining (WSDM 2015), 429-433

Rhetoric map of an answer to compound queries 
Galitsky B., Ilvovsky D.Kuznetsov S. 
Annual Meeting of the Association for Computational Linguistics and International Joint Conference on Natural Language Processing of the Asian Federation of Natural Language Processing (ACL-IJCNLP 2015), 681-686

Joint optimization of segmentation and color clustering 
Lobacheva E., Veksler O., Boykov Y. 
IEEE International Conference on Computer Vision (ICCV 2015), 1626–1634

Tensorizing neural networks 
Novikov A., Vetrov D. et al. 
Advances in Neural Information Processing Systems (NIPS 2015), 442-450

Parallel corpus approach for name matching in record linkage 
Sukharev J., Zhukov L., Popescul A. 
IEEE International Conference on Data Mining (ICDM 2015), 995-1000            

Equivariant embeddings of commutative linear algebraic groups of corank one 
Arzhantsev I.Kotenkova P. 
Documenta Mathematica 20, 1039-1054

Strongly solvable spherical subgroups and their combinatorial invariants 
Avdeev R. 
Selecta Mathematica, New Series 21, 931-993

The inverted multi-index 
Babenko A., Lempitsky V. 
IEEE Transactions on Pattern Analysis and Machine Intelligence 37, 1247-1260

Computing minimal and maximal suffixes of a substring 
Babenko M. et al. 
Theoretical Computer Science 638, 112-121

Prefix and plain Kolmogorov complexity characterizations of 2-randomness: Simple proofs 
Bauwens B. 
Archive for Mathematical Logic 54, 615-629

Addendum to: Multilevel dual approach for pricing American style derivatives 
Belomestny D., Joshi M., Schoenmakers J. 
Finance and Stochastics 19, 681-684

Statistical inference for generalized Ornstein-Uhlenbeck processes 
Belomestny D.Panov V. 
Electronic Journal of Statistics 9, 1974-2006

The Hausdorff spectrum of a class of multifractal processes 
Decrouez G., Hambly B., Jones O.D. 
Processes and their Applications 125, 1541-1568

The Voronoi conjecture for parallelohedra with simply connected δ-surfaces 
Garber A., Gavrilyuk A., Magazinov A. 
Discrete and Computational Geometry 53, 245-260

Triadic formal concept analysis and triclustering: Searching for optimal patterns 
Ignatov D.Gnatyshak D.Kuznetsov S. Mirkin B.  
Machine Learning 101, 271-302

Bisecting K-means and 1D projection divisive clustering: A unified framework and experimental comparison 
Kovaleva E.Mirkin B. 
Journal of Classification 32, 414-442

GALA: Group analysis leads to accuracy, a novel approach for solving the inverse problem in exploratory analysis of group MEG recordings 
Kozunov V., Ossadtchi A. 
Frontiers in Neuroscience 9:107

Interactive error correction in implicative theories 
Kuznetsov S.Revenko A 
International Journal of Approximate Reasoning 63, 89-100

Discovering structural alerts for mutagenicity using stable emerging molecular patterns 
Métivier J.-P., Buzmakov A., Kuznetsov S.  et al.  
Journal of Chemical Information and Modeling 55, 925-940

A seed expanding cluster algorithm for deriving upwelling areas on sea surface temperature images 
Nascimento S., Casca S., Mirkin B. 
Computers and Geosciences 85, 74-85

A dynamical model improves reconstruction of handwriting from multichannel electromyographic recordings 
Okorokova E., Ossadtchi A. et al. 
Frontiers in Neuroscience 9:389

Submodular relaxation for inference in Markov random fields 
Osokin A., Vetrov D. 
IEEE Transactions on Pattern Analysis and Machine Intelligence 37, 1347-1359

Statistical testing of segment homogeneity in classification of piecewise-regular objects 
Savchenko A., Belova N. 
International Journal of Applied Mathematics and Computer Science 25, 915-925

Heating and ultraviolet light activate anti-stress gene functions in humans 
Semenkov V., Michalski A., Sapozhnikov A. 
Frontiers in Genetics 6:245

Stochastic description of the high-frequency content of daily sunspots and evidence for regime changes 
Shapoval A. et al. 
Astrophysical Journal 799:56

When daily sunspot births become positively correlated 
Shapoval A. et al. 
Solar Physics 290, 2709-2717

Bootstrap confidence sets under model misspecification 
Spokoiny V., Zhilova M. 
Annals of Statistics 43, 2653-2675