Публикации

S.I. Nikolenko. Machine Learning: The Basics. Piter, 2025. Available at Piter Publishing House.

A. Farseev, S.I. Nikolenko, Q. Yang, D. You, Y. Chu-Farseeva, I. Gossoudarev, M. Ongpin. SOEX: Explainable AI for Competitor Communications Analytics. International World Wide Web Conference 2025 (WWW 2025), ACM, pp. 2823—2826, 2025.

N. Sorokin, A. Tikhonov, D. Abulkhanov, I. Piontkovskaya, I. Sedykh, S.I. Nikolenko, V. Malykh. CCT-Code: Cross-Consistency Training for Multilingual Clone Detection and Code Search. Proceedings of the 2025 Conference of the Nations of the Americas Chapter of the Association for Computational Linguistics: Human Language Technologies (NAACL 2025), ACM, 2025 (arXiv:2305.11626 [cs.SE]) (ACL Anthology).

J. Graf, V. Demianiuk, P. Chuprikov, Y. Feiran, S.I. Nikolenko, P. Eugster. CGFE: Efficient Range Encoding for TCAMs. IEEE International Conference on Computer Communications (INFOCOM 2025), 2025 (IEEExplore).

E. Shemetova, I. Shenbin, I. Smirnov, A. Alekseev, A. Rukhovich, S.I. Nikolenko, V. Lomshakov, I. Piontkovskaya. LAMeD: LLM-generated Annotations for Memory Leak Detection. 2025 International Conference on Evaluation and Assessment in Software Engineering (EASE 2025), 2025 (arXiv:https://arxiv.org/abs/2505.02376).

G. Polyakov, D. Abulkhanov, I. Sedykh, A. Bout, S.I. Nikolenko, I. Piontkovskaya. ToolReflection: Improving Large Language Models for Real-World API Calls with Self-Generated Data. 1st Workshop for Research on Agent Language Models (REALM 2025), pp. 184—199, 2025 (ACL Anthology).

T. Turatali, A. Alekseev, G. Jumalieva, G. Kabaeva, S.I. Nikolenko. Human-Annotated NER Dataset for the Kyrgyz Language. 10th International Conference on Computer Science and Engineering (IEEE UBMK 2025), pp. 1607—1612, 2025 (arXiv:arXiv:2509.19109) (IEEExplore).

A. Farseev, Q. Yang, M. Ongpin, I. Gossoudarev, Y. Chu-Farseeva, S.I. Nikolenko. MindFuse: Towards GenAI Explainability in Marketing Strategy Co-Creation. 33rd ACM International Conference on Multimedia (ACM MM 2025), ACM, pp. 12409—12418, 2025 (arXiv:2512.04112).

P. Zhang, T. Gao, J. Guo, J. Duan, S.I. Nikolenko. Early Warning Prediction with Automatic Labelling in Epilepsy Patients. The ANZIAM Journal, pp. 1—16, 2025.

Q. Yang, A. Farseev, M. Ongpin, A. Huang, Y. Chu-Farseeva, D. You, K. Lepikhin, S.I. Nikolenko. Fusing Predictive and Large Language Models for Actionable Recommendations In Creative Marketing. ACM Transactions on Information Systems, pp. 1—16, 2025.

A. Farseev, M. Ongpin, Q. Yang, A. Huang, S.I. Nikolenko, K. Lepikhin, Y. Chu-Farseeva. Automated actionable insights and content generation based upon large language models, multi-view machine learning, and generative models. Patent no. US20250045802A1 (Google Patents).

I. Sedykh, N. Sorokin, D. Abulkhanov, S.I. Nikolenko, V. Malykh. Searching by Code: a New SearchBySnippet Dataset and SnippeR Retrieval Model for Searching by Code Snippets. Proceedings of the 2024 Joint International Conference on Computational Linguistics, Language Resources and Evaluation (LREC-COLING 2024), pp. 14472—14477, 2024 (arXiv:2305.11625 [cs.CL]).

I. Shenbin, S.I. Nikolenko. ImplicitSLIM and How it Improves Embedding-based Collaborative Filtering. Proceedings of the 12th International Conference on Learning Representations (ICLR 2024), 2024.

M. Shirokikh, I. Shenbin, A. Alekseev, A. Volodkevich, A. Vasilev, A. Savchenko, S.I. Nikolenko. Neural Click Models for Recommender Systems. Proceedings of the 47th International ACM SIGIR Conference on Research and Development in Information Retrieval (SIGIR 2024), pp. 2553—2558, 2024.

L. Kushnareva, T. Gaintseva, D. Abulkhanov, K. Kuznetsov, G. Magai, E. Tulchinskii, S. Barannikov, S.I. Nikolenko, I. Piontkovskaya. AI-generated text boundary detection with RoFT. Proceedings of the 2024 Conference on Language Modeling (COLM 2024), 2024 (arXiv:2311.08349 [cs.CL]).

A. Shabanov, A. Tarasov, S.I. Nikolenko. STIR: Siamese Transformer for Image Retrieval Postprocessing. Proceedings of the 33rd ACM International Conference on Information and Knowledge Management (CIKM 2024), 2024 (arXiv:2304.13393 [cs.IR]).

K. Yakovlev, S.I. Nikolenko, A. Bout. Toolken+: Improving LLM Tool Usage with Reranking and a Reject Option. Proceedings of the 2024 Conference on Empirical Methods in Natural Language Processing (EMNLP 2024), 2024.

V. Lomshakov, A. Podivilov, S. Savin, O. Baryshnikov, A. Lisevych, S.I. Nikolenko. ProConSuL: Project Context for Code Summarization with LLMs. Proceedings of the 2024 Conference on Empirical Methods in Natural Language Processing (EMNLP 2024), 2024.

K. Kuznetsov, E. Tulchinskii, L. Kushnareva, G. Magai, S. Barannikov, S.I. Nikolenko, I. Piontkovskaya. Robust AI-Generated Text Detection by Restricted Embeddings. Proceedings of the 2024 Conference on Empirical Methods in Natural Language Processing (EMNLP 2024), 2024.

K. Khrabrov, A. Ber, A. Tsypin, K. Ushenin, E. Rumiantsev, A. Telepov, D. Protasov, I. Shenbin, A. Alekseev, M. Shirokikh, S.I. Nikolenko, E. Tutubalina, A. Kadurin. ∇²DFT: A Universal Quantum Chemistry Dataset of Drug-Like Molecules and a Benchmark for Neural Network Potentials. Proceedings of the 38th Annual Conference on Neural Information Processing Systems (NeurIPS 2024), 2024 (arXiv:2406.14347 [physics.chem-ph]). Available at openreview.

A. Alekseev, A. Tillabaeva, G. Kabaeva, S.I. Nikolenko. Syntactic Transfer to Kyrgyz Using the Treebank Translation Method. Zapiski nauchnyh seminarov POMI, pp. 252—275, 2024 (arXiv:arXiv:2412.13146 [cs.CL]). Available at Zapiski PDMI.

V. Lomshakov, S.I. Nikolenko. Large Language Models for Source Code Generation and Editing. Zapiski nauchnyh seminarov POMI, pp. 276—350, 2024. Available at Zapiski PDMI.

A. Farseev, Q. Yang, M. Ongpin, I. Gossoudarev, Y. Chu-Farseeva, S.I. Nikolenko. SOMONITOR: Explainable Marketing Data Processing and Analysis with Large Language Models. arXiv:2407.13117 [cs.CY], 2024.

A. Huang, Q. Yang, S.I. Nikolenko, M. Ongpin, I. Gossoudarev, N.Y. Duong, K. Lepikhin, S. Vishnyakov, Y. Chu-Farseeva, A. Farseev. SoCraft: Advertiser-level Predictive Scoring for Creative Performance on Meta. Proceedings of the Sixteenth ACM International Conference on Web Search and Data Mining (WSDM 2023), pp. 1132—1135, 2023.

Q. Yang, C. Tzelepis, S.I. Nikolenko, I. Patras, A. Farseev. "Just To See You Smile": SMILEY, a Voice-Guided GAN. Proceedings of the Sixteenth ACM International Conference on Web Search and Data Mining (WSDM 2023), pp. 1196—1199, 2023.

A. Alekseev, S.I. Nikolenko, G. Kabaeva. Benchmarking Multi-Label Topic Classification in Kyrgyz Language. Proceedings of the 11th International Conference on Analysis of Images, Social Networks and Texts (AIST 2023), 2023 (arXiv:2308.15952 [cs.CL]).

V. Lomshakov, S. Kovalchuk, M. Omelchenko, S.I. Nikolenko, A. Aliev. Fine-Tuning Large Language Models for Answering Programming Questions with Code Snippets. Proceedings of the International Conference on Computational Science 2023 (ICCS 2023), pp. 171—179, 2023 (springerlink).

K. Yakovlev, A. Podolskiy, A. Bout, S.I. Nikolenko, I. Piontkovskaya. GEC-DePenD: Non-Autoregressive Grammatical Error Correction with Decoupled Permutation and Decoding. Proceedings of the 61st Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers) (ACL 2023), pp. 1546—1558, 2023 (arXiv:2311.08191 [cs.CL]).

D. Abulkhanov, N. Sorokin, S.I. Nikolenko, V. Malykh. LAPCA: Language-Agnostic Pretraining with Cross-Lingual Alignment. Proceedings of the 46th International ACM SIGIR Conference on Research and Development in Information Retrieval (SIGIR 2023), pp. 2098—2102, 2023.

K. Yakovlev, G. Polyakov, I.S. Alimova, A. Podolskiy, A. Bout, S.I. Nikolenko, I. Piontkovskaya. Sinkhorn Transformations for Single-Query Postprocessing in Text-Video Retrieval. Proceedings of the 46th International ACM SIGIR Conference on Research and Development in Information Retrieval (SIGIR 2023), pp. 2394—2398, 2023 (arXiv:2311.08143 [cs.CL]).

E. Tulchinskii, K. Kuznetsov, L. Kushnareva, D. Cherniavskii, S. Barannikov, I. Piontkovskaya, S.I. Nikolenko, E. Burnaev. Topological Data Analysis for Speech Processing. Proceedings of the 24th INTERSPEECH (INTERSPEECH 2023), pp. 311—315, 2023 (arXiv:2211.17223 [cs.SD]).

Q. Yang, M. Ongpin, S.I. Nikolenko, A. Huang, A. Farseev. Against Opacity: Explainable AI and Large Language Models for Effective Digital Advertising. Proceedings of the 31st ACM International Conference on Multimedia (MM 2023), pp. 9299—9305, 2023.

A. Bout, A. Podolskiy, S.I. Nikolenko, I. Piontkovskaya. Efficient Grammatical Error Correction Via Multi-Task Training and Optimized Training Schedule. Proceedings of the 2023 Conference on Empirical Methods in Natural Language Processing (EMNLP 2023), pp. 5800—5816, 2023 (arXiv:2311.11813 [cs.CL]).

E. Tulchinskii, K. Kuznetsov, L. Kushnareva, D. Cherniavskii, S.I. Nikolenko, I. Piontkovskaya, S. Barannikov, E. Burnaev. Intrinsic Dimension Estimation for Robust Detection of AI-Generated Texts. 37th Conference on Neural Information Processing Systems (NeurIPS 2023), 2023 (arXiv:2306.04723 [cs.CL]).

A. Alekseev, A. Savchenko, E. Tutubalina, E. Myasnikov, S.I. Nikolenko. Blending of Predictions Boosts Understanding for Multimodal Advertisements. Zapiski nauchnyh seminarov POMI, pp. 176—198, 2023. Available at Zapiski PDMI.

M. Shirokikh, I. Shenbin, A. Alekseev, A. Volodkevich, A. Vasilev, S.I. Nikolenko. User Response Modeling in Recommender Systems: A Survey. Zapiski nauchnyh seminarov POMI, pp. 141—190, 2023. Available at Zapiski PDMI.

I. Sedykh, D. Abulkhanov, N. Sorokin, S.I. Nikolenko, V. Malykh. Searching by Code: a New SearchBySnippet Dataset and SnippeR Retrieval Model for Searching by Code Snippets. arXiv:2305.11625 [cs.SE], 2023.

M. Shirokikh, I. Shenbin, A. Alekseev, S.I. Nikolenko. Machine Learning for SAT: Restricted Heuristics and New Graph Representations. arXiv:2307.09141 [cs.AI], 2023.

A. Alekseev, Z. Miftakhutdinov, E. Tutubalina, A. Shelmanov, V. Ivanov, V. Kokh, A. Nesterov, M. Avetisian, A. Chertok, S.I. Nikolenko. Medical Crossing: a Cross-lingual Evaluation of Clinical Entity Linking. Proceedings of the Thirteenth Language Resources and Evaluation Conference (LREC 2022), pp. 4212—4220, 2022.

A. Nesterov, G. Zubkova, Z. Miftakhutdinov, V. Kokh, E. Tutubalina, A. Shelmanov, A. Alekseev, M. Avetisian, A. Chertok, S.I. Nikolenko. RuCCoN: Clinical Concept Normalization in Russian. Findings of the Association for Computational Linguistics: ACL 2022 (ACL Findings 2022), pp. 239—245, 2022.

Q. Yang, S.I. Nikolenko, A. Huang, A. Farseev. Personality-Driven Social Multimedia Content Recommendation. Proceedings of the 30th ACM International Conference on Multimedia (MM 2022), pp. 7290—7299, 2022 (arXiv:2207.12236 [cs.IR]).

M. Vasilkovsky, A. Alekseev, V. Malykh, I. Shenbin, E. Tutubalina, D. Salikhov, M. Stepnov, A. Chertok, S.I. Nikolenko. DetIE: Multilingual Open Information Extraction Inspired by Object Detection. Proceedings of the 36th AAAI Conference on Artificial Intelligence (AAAI-22), 2022 (arXiv:2206.12514 [cs.CL]). Available at open access.

I. Makarov, M. Bakhanova, S.I. Nikolenko, O. Gerasimova. Self-supervised recurrent depth estimation with attention mechanisms. PeerJ Computer Science, 2022. Available at PeerJ.

A. Sokolova, A. Savchenko, S.I. Nikolenko. Open-set face identification with automatic detection of out-of-distribution images. Computer Optics, pp. 801—807, 2022. Available at Computer Optics.

Q. Yang, A. Farseev, S.I. Nikolenko, A. Filchenkov. Do we behave differently on Twitter and Facebook: Multi-view social network user personality profiling for content recommendation. Frontiers in Big Data, 2022. Available at Frontiers Open Access.

K. Khrabrov, I. Shenbin, A. Ryabov, A. Tsypin, A. Telepov, A. Alekseev, A. Grishin, P. Strashnov, P. Zhilyaev, S.I. Nikolenko, A. Kadurin. nablaDFT: Large-Scale Conformational Energy and Hamiltonian Prediction benchmark and dataset. Physical Chemistry Chemical Physics, pp. 25853—25863, 2022.

E. Tutubalina, S.I. Nikolenko. Topic models with sentiment priors based on distributed representations. Patent no. US11379668B2 (Google Patents).

S.I. Nikolenko. Algorithms for networking problems and their theoretical analysis. 2022.

S.I. Nikolenko. Synthetic Data for Deep Learning. Springer, 2021. Available at Springer.

A. Davydow, S.I. Nikolenko, V. Demianiuk, P. Chuprikov, K. Kogan. SRPT-based Congestion Control for Flows with Unknown Sizes. 2021 IFIP Networking Conference (IFIP Networking) (IFIP Networking), pp. 1—10, 2021 (IEEExplore).

A. Alekseev, E. Tutubalina, S. Kwon, S.I. Nikolenko. Near-Zero-Shot Suggestion Mining with a Little Help from WordNet. Proceedings of the 10th International Conference on Analysis of Images, Social Networks and Texts (AIST 2021), Springer, pp. 23—36, 2021 (arXiv:2111.12956 [cs.CL]) (springerlink).

E. Tutubalina, I.S. Alimova, Z. Miftakhutdinov, A. Sakhovskiy, V. Malykh, S.I. Nikolenko. The Russian Drug Reaction Corpus and neural models for drug reactions and effectiveness detection in user reviews.. Bioinformatics, pp. 243—249, 2021 (arXiv:2004.03659 [cs.CL]).

E. Tutubalina, S.I. Nikolenko. Topic Models with Sentiment Priors Based on Distributed Representations. Zapiski nauchnyh seminarov POMI, pp. 284—301, 2021.

V. Demianiuk, S. Gorinsky, S.I. Nikolenko, K. Kogan. Robust Distributed Monitoring of Traffic Flows. IEEE Transactions on Networking, pp. 275—288, 2021 (IEEExplore).

E. Arkhangelskaya, S.I. Nikolenko. Deep Learning for Natural Language Processing: A Survey. Zapiski nauchnyh seminarov POMI, pp. 137—205, 2021.

A. Alekseev, S.I. Nikolenko. Recovering Word Forms by Context for Morphologically Rich Languages. Zapiski nauchnyh seminarov POMI, pp. 129—136, 2021.

R. Galinsky, A. Alekseev, S.I. Nikolenko. Word-based Russian text augmentation for character-level models. Zapiski nauchnyh seminarov POMI, pp. 206—221, 2021.

P. Chuprikov, A. Davydow, K. Kogan, S.I. Nikolenko, A.V. Sirotkin. Formalization and taxonomy of compute-aggregate problems for cloud computing applications. Computer Networks, 2021 (sciencedirect).

A. Davydow, P. Chuprikov, S.I. Nikolenko, K. Kogan. Competitive buffer management for packets with latency constraints. Computer Networks, 2021 (sciencedirect).

V. Demianiuk, K. Kogan, S.I. Nikolenko. Approximate Packet Classifiers With Controlled Accuracy. IEEE Transactions on Networking, pp. 1141—1154, 2021 (IEEExplore).

A. Yakubovich, A. Odinokov, S.I. Nikolenko, Y. Jung, H. Choi. Computational Discovery of TTF Molecules with Deep Generative Models. Frontiers in Chemistry, 2021. Available at Frontiers Open Access.

I.S. Alimova, E. Tutubalina, S.I. Nikolenko. Cross-Domain Limitations of Neural Models on Biomedical Relation Classification. IEEE Access, pp. 1432—1439, 2021 (IEEExplore).

M. Romanov, N. Patatkin, A. Vorontsova, S.I. Nikolenko, A. Konushin, D. Senyushkin. Towards General Purpose Geometry-Preserving Single-View Depth Estimation. arXiv:2009.12419 [cs.CV], 2021.

A. Savchenko, A. Alekseev, S. Kwon, E. Tutubalina, E. Myasnikov, S.I. Nikolenko. Ad Lingua: Text Classification Improves Symbolism Prediction in Image Advertisements. 28th International Conference on Computational Linguistics (COLING 2020), pp. 1886—1892, 2020.

I. Shenbin, A. Alekseev, E. Tutubalina, V. Malykh, S.I. Nikolenko. RecVAE: A New Variational Autoencoder for Top-N Recommendations with Implicit Feedback. 13th International Conference on Web Search and Data Mining (WSDM 2020), pp. 528—536, 2020 (arXiv:1912.11160 [cs.IR]).

I. Anokhin, P. Solovev, D. Korzhenkov, A. Kharlamov, T. Khakhulin, A. Silvestrov, S.I. Nikolenko, V. Lempitsky, G. Sterkin. High-Resolution Daytime Translation Without Domain Labels. 2020 IEEE Conference on Computer Vision and Pattern Recognition (CVPR 2020), pp. 7488—7497, 2020 (arXiv:2003.08791 [cs.CV]).

A. Alekseev, S.I. Nikolenko. Recognizing Preferred Grammatical Gender in Russian Anonymous Online Confessions. 23rd International Conference on Text, Speech, and Dialogue (TSD 2020), pp. 222—230, 2020 (springerlink).

R. Shayakhmetov, M. Kuznetsov, A. Zhebrak, A. Kadurin, I. Baskov, S.I. Nikolenko, A. Aliper, D. Polykovskiy. Molecular Generation for Desired Transcriptome Changes with Adversarial Autoencoders. Frontiers in Pharmacology, 2020.

K. Ovchinnikova, A. Rakhlin, L. Stuart, S.I. Nikolenko, T. Alexandrov. ColocML: Machine learning quantifies co-localization between mass spectrometry images. Bioinformatics, 2020.

V. Demianiuk, S.I. Nikolenko, P. Chuprikov, K. Kogan. New Alternatives to Optimize Policy Classifiers. IEEE Transactions on Networking, pp. 1088—1101, 2020 (IEEExplore).

P. Chuprikov, S.I. Nikolenko, K. Kogan. Towards Declarative Self-Adapting Buffer Management. ACM SIGCOMM Computer Communication Review, pp. 30—37, 2020.

L. Rappez, A. Rakhlin, A. Rigopoulos, S.I. Nikolenko, T. Alexandrov. DeepCycle reconstructs a cyclic cell cycle trajectory from unsegmented cell images using convolutional neural networks. Molecular Systems Biology, 2020.

K. Kogan, D. Menikkumbura, G. Petri, Y. Noh, S.I. Nikolenko, A.V. Sirotkin, P. Eugster. Towards Software-Defined Buffer Management. IEEE Transactions on Networking, pp. 2337—2349, 2020 (IEEExplore).

D. Polykovskiy, A. Zhebrak, B. Sanchez-Lengeling, S. Golovanov, O. Tatanov, S. Belyaev, R. Kurbanov, A. Artamonov, V. Aladinsky, M. Veselov, A. Kadurin, S.I. Nikolenko, A. Aspuru-Guzlik, A. Zhavoronkov. Molecular Sets (MOSES): A Benchmarking Platform for Molecular Generation Models. Frontiers in Pharmacology, 2020 (arXiv:1811.12823 [cs.CV]).

P. Ostyakov, R. Suvorov, E. Logacheva, O. Khomenko, S.I. Nikolenko. Joint unsupervised object segmentation and inpainting. Patent no. WO2020101246A1 (Google Patents).

G. Sterkin, I. Anokhin, T. Khakhulin, A. Kharlamov, D. Korzhenkov, V. Lempitsky, S.I. Nikolenko, A. Silvestrov, P. Solovev. Plausible dayscale timelapse generation method and computing device. Patent no. WO2021096191A1 (Google Patents).

S.I. Nikolenko, Y. Behzadi. System and method for adaptive generation using feedback from a trained model. Patent no. US20200320351A1 (Google Patents).

S.I. Nikolenko, Y. Behzadi. System and method for generating training data for computer vision systems based on image segmentation. Patent no. US20200320346A1 (Google Patents).

S.I. Nikolenko, Y. Behzadi. System and method for visual recognition using synthetic training data. Patent no. US20200320345A1 (Google Patents).

S.I. Nikolenko, Y. Behzadi. System and method for domain adaptation using synthetic data. Patent no. US20200320347A1 (Google Patents).

A.L. Tulupyev, S.I. Nikolenko, A.V. Sirotkin. Foundations of the Bayesian Networks Theory. SPSU Press, St. Petersburg, 2019. Available at ozon.ru.

V. Malykh, A. Alekseev, S.I. Nikolenko, E. Tutubalina, I. Shenbin. Wear the Right Head: Comparing Strategies for Encoding Sentences for Aspects Extraction. Accepted to 8th International Conference on Analysis of Images, Social networks and Texts (AIST 2019), 2019.

V. Demianiuk, K. Kogan, S.I. Nikolenko. Approximate Classifiers with Controlled Accuracy. 38th IEEE International Conference on Computer Communications (INFOCOM 2019), pp. 2044—2052, 2019 (IEEExplore).

A. Alekseev, S.I. Nikolenko, E. Tutubalina, I. Shenbin, V. Malykh. AspeRa: Aspect-Based Rating Prediction Model. 41st European Conference on Information Retrieval (ECIR 2019), pp. 163—171, 2019 (arXiv:1901.07829 [cs.CL]) (springerlink).

S. Golovanov, A. Tselousov, R. Kurbanov, S.I. Nikolenko. Lost in Conversation: A Conversational Agent Based on the Transformer and Transfer Learning. The NeurIPS '18 Competition, pp. 295—315, 2019 (springerlink).

J. Atwood, Y. Halpern, P. Baljekar, E. Breck, D. Sculley, P. Ostyakov, S.I. Nikolenko, I. Ivanov, R. Solovyev, W. Wang, M. Skalic. The Inclusive Images Competition. The NeurIPS '18 Competition, pp. 155—186, 2019 (springerlink).

S. Golovanov, R. Kurbanov, S.I. Nikolenko, K. Truskovskyi, A. Tselousov, T. Wolf. Large-Scale Transfer Learning for Natural Language Generation. 57th Annual Meeting of the Association for Computational Linguistics (ACL 2019), pp. 6053—6058, 2019.

V. Demianiuk, S. Gorinsky, S.I. Nikolenko, K. Kogan. Robust Distributed Monitoring of Traffic Flows. 27th IEEE International Conference on Network Protocols (ICNP 2019), pp. 1—11, 2019 (IEEExplore).

A. Alekseev, E. Tutubalina, V. Malykh, S.I. Nikolenko. Improving unsupervised neural aspect extraction for online discussions using out-of-domain classification. 7th International Symposium on Language and Knowledge Engineering (LKE 2019), 2019 (arXiv:2006.09766 [cs.CL]).

D. Nikulin, A. Ianina, A. Aliev, S.I. Nikolenko. Free-Lunch Saliency via Attention in Atari Agents. ICCV 2019 Workshop «Interpreting and Explaining Visual Artificial Intelligence Models» (ICCVW 2019), 2019 (arXiv:1908.02511 [cs.LG]).

A. Rakhlin, A.A. Shvets, A.A. Kalinin, A. Tiulpin, V.I. Iglovikov, S.I. Nikolenko. Breast Tumor Cellularity Assessment using Deep Neural Networks. ICCV 2019 Workshop «Visual Recognition for Medical Images» (ICCVW 2019), 2019 (arXiv:1905.01743 [cs.CV]).

M. Panin, S.I. Nikolenko. Rendering Atmospheric Clouds with Latent Space Light Probes. 12th ACM SIGGRAPH Conference and Exhibition on Computer Graphics & Interactive Techniques in Asia (SIGGRAPH ASIA 2019), pp. 21—24, 2019.

P. Ostyakov, S.I. Nikolenko. Adapting Convolutional Neural Networks for Geographical Domain Shift. arXiv:1901.06345 [cs.CV], 2019.

I. Bochkov, A. Davydow, N. Gaevoy, S.I. Nikolenko. New Competitiveness Bounds for the Shared Memory Switch. arXiv:1907.04399 [cs.NI], 2019.

S.I. Nikolenko, E. Tutubalina, Z. Miftakhutdinov, E. Beloded. CommentsRadar: Dive into Unique Data on All Comments on the Web. arXiv:1908.07069 [cs.IR], 2019.

S.I. Nikolenko. Synthetic Data for Deep Learning. arXiv:1909.11512 [cs.LG], 2019.

L.N. Tuzova, D.V. Tuzoff, S.I. Nikolenko, A.S. Krasnov. Teeth and Landmarks Detection and Classification Based on Deep Neural Networks. Computational Techniques for Dental Image Analysis, IGI Global, pp. 129—150, 2019.

K. Kogan, S.I. Nikolenko, V. Demianiuk, P. Chuprikov, A. Davydow. Personal Insights on Three Research Directions in Networked Systems. Proc. 10^th International Conference on Communication Systems and Networks (COMSNETS 2018), IEEE, pp. 1—8, 2018 (IEEExplore).

P. Chuprikov, K. Kogan, S.I. Nikolenko. How to implement complex policies on existing network infrastructure. Proc. 4^th Symposium on SDN Research (SOSR 2018), ACM, pp. 1—8, 2018.

P. Chuprikov, A. Davydow, K. Kogan, S.I. Nikolenko, A.V. Sirotkin. Formalizing Compute-Aggregate Problems in Cloud Computing. 25th International Colloquium on Structural Information and Communication Complexity (SIROCCO 2018), pp. 377—391, 2018 (springerlink).

V. Demianiuk, S. Gorinsky, S.I. Nikolenko, K. Kogan. Distributed Counting along Lossy Paths Without Feedback. 25th International Colloquium on Structural Information and Communication Complexity (SIROCCO 2018), pp. 30—33, 2018 (springerlink).

S. Golovanov, R. Kurbanov, A. Artamonov, A. Davydow, S.I. Nikolenko. Building Detection From Satellite Imagery Using a Composite Loss Function. Proc. IEEE Conference on Computer Vision and Pattern Recognition 2018 Workshops (CVPR 2018 Workshops), pp. 229—232, 2018.

A. Davydow, S.I. Nikolenko. Land Cover Classification With Superpixels and Jaccard Index Post-Optimization. Proc. IEEE Conference on Computer Vision and Pattern Recognition 2018 Workshops (CVPR 2018 Workshops), pp. 280—284, 2018.

A. Rakhlin, A. Davydow, S.I. Nikolenko. Land Cover Classification From Satellite Imagery With U-Net and Lovasz-Softmax Loss. Proc. IEEE Conference on Computer Vision and Pattern Recognition 2018 Workshops (CVPR 2018 Workshops), pp. 262—266, 2018.

V. Demianiuk, S.I. Nikolenko, P. Chuprikov, K. Kogan. New Alternatives to Optimize Policy Classifiers. 26th IEEE International Conference on Network Protocols (ICNP 2018), pp. 121—131, 2018 (IEEExplore).

D. Polykovskiy, D. Soloviev, S.I. Nikolenko. Concorde: Morphological Agreement in Conversational Models. 10th Asian Conference on Machine Learning (ACML 2018), pp. 407—421, 2018.

R.I. Nugmanov, E. Tutubalina, Z. Miftakhutdinov, T.I. Madzhidov, S.I. Nikolenko, I.S. Alimova, A.E. Tropsha. Exploring semantic analysis of biomedical texts for identification of drugs with similar therapeutic effects. European Journal of Clinical Investigation, 2018.

D. Kuzminykh, D. Polykovskiy, A. Kadurin, A. Zhebrak, I. Baskov, S.I. Nikolenko, R. Shayakhmetov, A. Zhavoronkov. 3D Molecular Representations Based on the Wave Transform for Convolutional Neural Networks. Molecular Pharmaceutics, pp. 4378—4385, 2018.

E. Tutubalina, S.I. Nikolenko. Exploring convolutional neural networks and topic models for user profiling from drug reviews. Multimedia Tools and Applications, pp. 4791—4809, 2018 (springerlink).

E. Tutubalina, Z. Miftakhutdinov, S.I. Nikolenko, V. Malykh. Medical Concept Normalization in Social Media Posts with Recurrent Neural Networks. Journal of Biomedical Informatics, 2018 (sciencedirect).

E. Tutubalina, Z. Miftakhutdinov, S.I. Nikolenko, V. Malykh. Sequence Learning with RNNs for Medical Concept Normalization in User-Generated Texts. Journal of Biomedical Informatics, pp. 93—102, 2018 (arXiv:1811.11523 [cs.CV]).

P. Eugster, A. Kesselman, K. Kogan, S.I. Nikolenko, A.V. Sirotkin. Admission Control in Shared Memory Switches. Journal of Scheduling, pp. 533—543, 2018 (springerlink).

P. Chuprikov, S.I. Nikolenko, K. Kogan, A. Davydow. Priority Queueing for Packets with Two Characteristics. IEEE Transactions on Networking, pp. 342—355, 2018 (IEEExplore).

P. Ostyakov, E. Logacheva, R. Suvorov, A. Aliev, G. Sterkin, O. Khomenko, S.I. Nikolenko. Label Denoising with Large Ensembles of Heterogeneous Neural Networks. arXiv:1809.04403 [cs.CV], 2018.

P. Ostyakov, R. Suvorov, E. Logacheva, O. Khomenko, S.I. Nikolenko. SEIGAN: Towards Compositional Image Generation by Simultaneously Learning to Segment, Enhance, and Inpaint. arXiv:1811.07630 [cs.CV], 2018.

P. Solovev, A. Aliev, P. Ostyakov, G. Sterkin, E. Logacheva, S. Troeshestov, R. Suvorov, A. Mashikhin, O. Khomenko, S.I. Nikolenko. Learning State Representations in Complex Systems with Multimodal Data. arXiv:1811.11067 [cs.CV], 2018.

S.I. Nikolenko, A. Kadurin, E. Arkhangelskaya. Deep Learning. Piter, 2017. Available at Piter Publishing House.

P. Chuprikov, K. Kogan, S.I. Nikolenko. General Ternary Bit Strings on Commodity Longest-Prefix-Match Infrastructures. 25th IEEE International Conference on Network Protocols (ICNP 2017), 2017 (IEEExplore).

P. Chuprikov, A. Davydow, K. Kogan, S.I. Nikolenko, A.V. Sirotkin. Planning in Compute-Aggregate Problems as Optimization Problems on Graphs. 25th IEEE International Conference on Network Protocols (ICNP 2017), 2017 (IEEExplore).

K. Kogan, D. Menikkumbura, G. Petri, Y. Noh, S.I. Nikolenko, A.V. Sirotkin, P. Eugster. A Programmable Buffer Management Platform. 25th IEEE International Conference on Network Protocols (ICNP 2017), 2017 (IEEExplore).

S.I. Nikolenko, K. Kogan, A. Fernàndez Anta. Network Simplification Preserving Bandwidth and Routing Capabilities. 2017 IEEE International Conference on Computer Communications (INFOCOM 2017), 2017 (IEEExplore).

A. Davydow, P. Chuprikov, S.I. Nikolenko, K. Kogan. Throughput Optimization with Latency Constraints. 2017 IEEE International Conference on Computer Communications (INFOCOM 2017), 2017 (IEEExplore).

E. Tutubalina, S.I. Nikolenko. Combination of Deep Recurrent Neural Networks and Conditional Random Fields for Extracting Adverse Drug Reactions from User Reviews. Journal of Healthcare Engineering, 2017.

A. Alekseev, S.I. Nikolenko. Word Embeddings of User Profiling in Online Social Networks. Computación y Sistemas, pp. 203—226, 2017.

E. Tutubalina, S.I. Nikolenko. Demographic Prediction based on User Reviews about Medications. Computación y Sistemas, pp. 227—241, 2017.

S.I. Nikolenko, O. Koltsova, S. Koltsov. Topic Modelling for Qualitative Studies. Journal of Information Science, pp. 88—102, 2017.

S. Bodrunova, O. Koltsova, S. Koltsov, S.I. Nikolenko. Who’s Bad? Attitudes Toward Resettlers From the Post-Soviet South Versus Other Nations in the Russian Blogosphere. International Journal of Communication, pp. 3242—3264, 2017.

A. Kadurin, S.I. Nikolenko, K. Khrabrov, A. Aliper, A. Zhavoronkov. druGAN: An Advanced Generative Adversarial Autoencoder Model for de Novo Generation of New Molecules with Desired Molecular Properties in Silico. Molecular Pharmaceutics, pp. 3098—3104, 2017.

K. Kogan, A. Lòpez-Ortiz, S.I. Nikolenko, A.V. Sirotkin. The Impact of Processing Order on Performance: A Taxonomy of Semi-FIFO Policies. Journal of Computer and System Sciences, pp. 220—235, 2017 (sciencedirect).

E. Tutubalina, Z. Miftakhutdinov, R.I. Nugmanov, T.I. Madzhidov, S.I. Nikolenko, I.S. Alimova, A.E. Tropsha. Using Semantic Analysis of Texts for the Identification of Drugs with Similar Therapeutic Effects. Russian Chemical Bulletin, pp. 2180—2189, 2017 (springerlink).

K. Kogan, S.I. Nikolenko, P. Eugster, A. Shalimov, O. Rottenstreich. Efficient FIB Representations on Distributed Platforms. IEEE Transactions on Networking, pp. 3309—3322, 2017 (IEEExplore).

A. Palmer, P. Phapale, I. Chernyavsky, R. Lavigne, D. Fay, A. Tarasov, V. Kovalev, J. Fuchser, S.I. Nikolenko, C. Pineau, M. Becker, T. Alexandrov. FDR-controlled metabolite annotation for high-resolution imaging mass spectrometry. Nature Methods, pp. 57—60, 2017.

P. Eugster, K. Kogan, S.I. Nikolenko, A.V. Sirotkin. Heterogeneous Packet Processing in Shared Memory Buffers. Journal of Parallel and Distributed Computing, pp. 1—12, 2017 (sciencedirect).

S. Koltsov, S.I. Nikolenko, O. Koltsova, S. Bodrunova. Stable Topic Modeling for Web Science: Granulated LDA. Proc. 8th ACM Conference on Web Science (WebSci '16), ACM, pp. 342—343, 2016.

S.I. Nikolenko. ARTM vs. LDA: an SVD Extension Case Study. Proc. 5th International Conference on Analysis of Images, Social Networks, and Texts (AIST 2016), pp. 276—282, 2016. Available at https://ceur-ws.org/Vol-1710/paper27.pdf.

S.I. Nikolenko, A. Alekseev. User Profiling in Text-Based Recommender Systems Based on Distributed Word Representations. Proc. 5th International Conference on Analysis of Images, Social Networks, and Texts (AIST 2016), pp. 196—207, 2016 (springerlink).

E. Tutubalina, S.I. Nikolenko. Constructing Aspect-Based Sentiment Lexicons with Topic Modeling. Proc. 5th International Conference on Analysis of Images, Social Networks, and Texts (AIST 2016), pp. 208—220, 2016 (springerlink).

S. Koltsov, S.I. Nikolenko, O. Koltsova, V. Filipov, S. Bodrunova. Stable Topic Modeling with Local Density Regularization. Proc. 3rd international conference on Internet Science (INSCI 2016), Springer, pp. 176—188, 2016 (springerlink).

M. Apishev, S. Koltsov, O. Koltsova, S.I. Nikolenko, K. Vorontsov. Additive Regularization for Topic Modeling in Sociological Studies of User-Generated Texts. Proc. 15th Mexican International Conference on Artificial Intelligence (MICAI 2016), pp. 169—184, 2016 (springerlink).

N. Semenov, I. Zakhlebin, A. Tolmach, S.I. Nikolenko. Pseudo-Bimodal Community Detection in Twitter-Based Networks. Proc. 8th International Congress on Ultra Modern Telecommunications and Control Systems (ICUMT 2016), IEEE, pp. 336—341, 2016 (IEEExplore).

E. Tutubalina, S.I. Nikolenko. Automated Prediction of Demographic Information from Medical User Reviews. Accepted to Proc. 4th International Conference on Mining Intelligence and Knowledge Exploration (MIKE 2016), 2016.

A. Alekseev, S.I. Nikolenko. Predicting the Age of Social Network Users from User-Generated Texts with Word Embeddings. Proc. 5th conference on Artificial Intelligence and Natural Language (AINL 2016), pp. 3—13, 2016.

R. Galinsky, A. Alekseev, S.I. Nikolenko. Improving Neural Network Models for Natural Language Processing in Russian with Synonyms. Proc. 5th conference on Artificial Intelligence and Natural Language (AINL 2016), pp. 45—51, 2016.

P. Chuprikov, S.I. Nikolenko, K. Kogan. On Demand Elastic Capacity Planning for Service Auto-scaling. 2016 IEEE International Conference on Computer Communications (INFOCOM 2016), pp. 1—9, 2016 (IEEExplore).

K. Kogan, S.I. Nikolenko, P. Eugster, A. Shalimov, O. Rottenstreich. FIB Efficiency in Distributed Platforms. 24th IEEE International Conference on Network Protocols (ICNP 2016), pp. 1—10, 2016 (IEEExplore).

S.I. Nikolenko, K. Kogan, G. Retvari, E.R. Berczi-Kovacs, A. Shalimov. How to Represent IPv6 Forwarding Tables on IPv4 or MPLS Dataplanes. Proc. 2016 IEEE Conference on Computer Communications Workshops (INFOCOM WKSHPS): GI 2016: 9th IEEE Global Internet Symposium (IEEE GI 2016), 2016 (IEEExplore).

S.I. Nikolenko. Topic Quality Metrics Based on Distributed Word Representations. Proc. 39th International ACM SIGIR Conference on Research and Development in Information Retrieval (SIGIR 2016), pp. 1029—1032, 2016.

K. Kogan, D. Menikkumbura, G. Petri, Y. Noh, S.I. Nikolenko, P. Eugster. BASEL (Buffering Architecture SpEcification Language). 12^th ACM/IEEE Symposium on Architectures for Networking and Communications Systems (ANCS 2016), pp. 69—74, 2016.

S. Koltsov, S.I. Nikolenko, O. Koltsova. Gibbs sampler optimization for analysis of a granulated medium. Technical Physics Letters, Springer, pp. 837—839, 2016 (springerlink).

D. Ignatov, S.I. Nikolenko, T. Abaev, J. Poelmans. Online Recommender System for Radio Station Hosting Based on Information Fusion and Adaptive Tag-Aware Profiling. Expert Systems with Applications, pp. 546—558, 2016 (sciencedirect).

M. Apishev, S. Koltsov, O. Koltsova, S.I. Nikolenko, K. Vorontsov. Mining Ethnic Content Online with Additively Regularized Topic Models. Computación y Sistemas, pp. 387—403, 2016.

K. Kogan, A. Lòpez-Ortiz, S.I. Nikolenko, G. Scalosub, M. Segal. Large profits or fast gains: A dilemma in maximizing throughput with applications to network processors. Journal of Network and Computer Applications, pp. 31—43, 2016 (sciencedirect).

K. Kogan, S.I. Nikolenko, O. Rottenstreich, W. Culhane, P. Eugster. Exploiting Order Independence for Scalable and Expressive Packet Classification. IEEE Transactions on Networking, pp. 1251—1264, 2016 (IEEExplore).

O. Koltsova, S. Koltsov, S.I. Nikolenko. Communities of co-commenting in the Russian LiveJournal and their topical coherence. Internet Research, pp. 710—732, 2016.

K. Kogan, A. Lòpez-Ortiz, S.I. Nikolenko, A.V. Sirotkin. Online Scheduling FIFO Policies with Admission and Push-Out. Theory of Computing Systems, pp. 322—344, 2016 (springerlink).

S.I. Nikolenko. A Probabilistic Rating System for Team Competitions with Individual Contributions. Proc. 4th International Conference on Analysis of Images, Social Networks, and Texts (AIST 2015), Springer, pp. 3—13, 2015 (springerlink).

A. Semenov, A. Natekin, S.I. Nikolenko, P. Upravitelev, M. Trofimov, M. Kharchenko. Discerning Depression Propensity Among Participants of Suicide and Depression-Related Groups of Vk.com. Proc. 4th International Conference on Analysis of Images, Social Networks, and Texts (AIST 2015), Springer, pp. 24—35, 2015 (springerlink).

I. Zakhlebin, A. Semenov, A. Tolmach, S.I. Nikolenko. Detecting Opinion Polarisation on Twitter by Constructing Pseudo-Bimodal Networks of Mentions and Retweets. Proc. 9th Russian Summer School in Information Retrieval (RUSSIR 2015), Springer, pp. 169—178, 2015 (springerlink).

S.I. Nikolenko. SVD-LDA: Topic Modeling for Full-Text Recommender Systems. Proc. 14th Mexican International Conference on Artificial Intelligence (MICAI 2015), Springer, pp. 67—79, 2015 (springerlink).

E. Tutubalina, S.I. Nikolenko. Inferring Sentiment-Based Priors in Topic Models. Proc. 14th Mexican International Conference on Artificial Intelligence (MICAI 2015), Springer, pp. 92—104, 2015 (springerlink).

P. Eugster, A. Kesselman, K. Kogan, S.I. Nikolenko, A.V. Sirotkin. Essential Traffic Parameters for Shared Memory Switch Performance. 22nd International Colloquium on Structural Information and Communication Complexity (SIROCCO 2015), Springer, pp. 61—75, 2015 (springerlink).

P. Chuprikov, S.I. Nikolenko, K. Kogan. Priority Queueing with Multiple Packet Characteristics. 2015 IEEE International Conference on Computer Communications (INFOCOM 2015), pp. 1418—1426, 2015 (IEEExplore).

R. Leon-Zayas, M. Novotny, S. Podell, C. Shepard, E. Berkenpas, S.I. Nikolenko, P.A. Pevzner, E. Lasken, D. Bartlett. Single Cells within the Puerto Rico Trench Suggest Hadal Adaptation of Microbial Lineages. Applied and Environmental Microbiology, pp. 8265—8276, 2015.

K. Kogan, D. Menikkumbura, G. Petri, Y. Noh, S.I. Nikolenko, P. Eugster. BASEL (Buffering Architecture SpEcification Language). arXiv:1510.04235 [cs.NI], 2015.

D. Ignatov, S.I. Nikolenko, T. Abaev, N. Konstantinova. Online recommender system for radio station hosting: experimental results revisited. Proceedings of 2014 IEEE/WIC/ACM International Joint Conferences on Web Intelligence (WI) and Intelligent Agent Technologies (IAT) (WIC 2014), pp. 229—236, 2014.

K. Kogan, A. Lòpez-Ortiz, S.I. Nikolenko, G. Scalosub. Balancing Work and Size with Bounded Buffers. Proc. 6^th International Conference on Communication Systems and Networks (COMSNETS 2014), IEEE Press, pp. 1—8, 2014 (arXiv:1202.5755 [cs.NI]) (IEEExplore).

S.I. Nikolenko, S. Koltsov, O. Koltsova. Measuring Topic Quality in Latent Dirichlet Allocation. Proc. Philosophy, Mathematics, Linguistics: Aspects of Interaction (PhML-2014), pp. 149—157, 2014.

S. Bodrunova, O. Koltsova, S.I. Nikolenko, S. Koltsov, S. Alekseeva. Political Actor or Ritualised Other? Mapping Ethnic Attitudes in the Russian Blogosphere by Methods of Big Data Research. ECPR General Conference (ECPR 2014), 2014.

K. Kogan, S.I. Nikolenko, P. Eugster, E. Ruan. Strategies for Mitigating TCAM Space Bottlenecks. 22nd IEEE Annual Symposium on High-Performance Interconnects (HOTI 2014), IEEE, pp. 25—32, 2014 (IEEExplore).

S. Koltsov, O. Koltsova, S.I. Nikolenko. Latent Dirichlet Allocation: Stability and Applications to Studies of User-Generated content. Proceedings of the 2014 ACM Conference on Web Science (WebSci 2014), pp. 161—165, 2014.

K. Kogan, S.I. Nikolenko, O. Rottenstreich, W. Culhane, P. Eugster. SAX-PAC (Scalable And eXpressive PAcket Classification). Proceedings of the 2014 ACM conference on SIGCOMM (SIGCOMM 2014), ACM Press, pp. 15—26, 2014.

P. Eugster, K. Kogan, S.I. Nikolenko, A.V. Sirotkin. Shared-Memory Buffer Management for Heterogeneous Packet Processing. Proceedings of the 34^th International Conference on Distributed Computing Systems (ICDCS 2014), IEEE Press, pp. 471—480, 2014 (IEEExplore).

T. Alexandrov, I. Chernyavsky, M. Becker, F. von Eggeling, S.I. Nikolenko. Analysis and Interpretation of Imaging Mass Spectrometry Data by Clustering Mass-to-Charge Images According to Their Spatial Similarity. Analytical Chemistry, pp. 11189—11195, 2014.

D. Ignatov, S.I. Nikolenko, T. Abaev, J. Poelmans. Improving Quality Of Service For Radio Station Hosting: An Online Recommender System Based On Information Fusion. 2014.

S.I. Nikolenko, K. Kogan. Single and Multiple Buffer Processing. Encyclopaedia of Algorithms, Springer, pp. 1—9, 2014 (springerlink).

S. Bodrunova, S. Koltsov, O. Koltsova, S.I. Nikolenko, A. Shimorina. Interval Semi-Supervised LDA: Classifying Needles in a Haystack. Proc. 12th Mexican International Conference on Artificial Intelligence (MICAI 2013), Springer, pp. 265—274, 2013 (springerlink).

V.A. Leksin, S.I. Nikolenko. Semi-Supervised Tag Extraction in a Web Recommender System. Proc. 6^th International Conference on Similarity Search and Applications (SISAP 2013), Springer, pp. 206—212, 2013 (springerlink).

K. Kogan, A. Lòpez-Ortiz, S.I. Nikolenko, A.V. Sirotkin. Multi-Queued Network Processors for Packets with Heterogeneous Processing Requirements. Proc. 5^th International Conference on Communication Systems and Networks (COMSNETS 2013), IEEE Press, pp. 1—8, 2013 (IEEExplore).

K. Kogan, S.I. Nikolenko, S. Keshav, A. Lòpez-Ortiz. Efficient demand assignment in multi-connected microgrids. Proc. 4^th Energy-Efficient Computing and Networking (e-Energy 2013), pp. 277—278, 2013.

K. Kogan, S.I. Nikolenko, W. Culhane, P. Eugster, E. Ruan. Towards efficient implementation of packet classifiers in SDN/OpenFlow. Proc. 2^nd ACM SIGCOMM Workshop on Hot Topics in Software Defined Networking (HotSDN 2013), pp. 153—154, 2013.

K. Kogan, S.I. Nikolenko, S. Keshav, A. Lòpez-Ortiz. Efficient Demand Assignment in Multi-Connected Microgrids with a Shared Central Grid. Proc. 3^rd IFIP Conference on Sustainable Internet and ICT for Sustainability 2013 (SustainIT 2013), 2013 (IEEExplore).

E.A. Hirsch, S.I. Nikolenko. Feebly Secure Cryptographic Primitives. Journal of Mathematical Sciences, pp. 17—34, 2013 (springerlink).

S.I. Nikolenko, A. Korobeynikov, M. Alekseyev. BayesHammer: Bayesian clustering for error correction in single-cell sequencing. BMC Genomics, 2013 (arXiv:1211.2756 [qbio.QM]). Available at open access.

A. Davydow, S.I. Nikolenko. Circuit Complexity of Linear Functions: Gate Elimination and Feeble Security. Journal of Mathematical Sciences, pp. 35—43, 2013 (springerlink).

S.I. Nikolenko, D. Tugaryov. A Complete One-Way Function based on a Finite Rank Free -module. Journal of Mathematical Sciences, pp. 307—315, 2013 (springerlink).

O. Koltsova, S. Koltsov, S.I. Nikolenko. Comment-Based Discussion Communities in the Russian LiveJournal and Their Topical Coherence. 2013.

A. Fishkov, S.I. Nikolenko. A New Click Model for Relevance Prediction in Web Search. Proceedings of EEML 2012, an ICFCA 2012 workshop (EEML 2012), pp. 45—54, 2012.

S.I. Nikolenko. A New Recommender System for the Interactive Radio Network FMhost. Proceedings of EEML 2012, an ICFCA 2012 workshop (EEML 2012), pp. 72—85, 2012.

K. Kogan, A. Lòpez-Ortiz, S.I. Nikolenko, A.V. Sirotkin, D. Tugaryov. FIFO Queueing Policies for Packets with Heterogeneous Processing. Proc. 1^st Mediterranean Conference on Algorithms (MedAlg 2012), Springer, pp. 248—260, 2012 (arXiv:1204.5443 [cs.NI]) (springerlink).

K. Kogan, A. Lòpez-Ortiz, S.I. Nikolenko, A.V. Sirotkin. A Taxonomy of Semi-FIFO Policies. Proc. 31^st IEEE International Performance Computing and Communications Conference (IPCCC 2012), IEEE Press, pp. 295—304, 2012 (IEEExplore).

D. Ignatov, A. Konstantinov, S.I. Nikolenko, J. Poelmans, V. Zaharchuk. Online Recommender System for Radio Station Hosting. Proceedings of BIR 2012, Springer, pp. 1—12, 2012 (springerlink).

I. Chernyavsky, T. Alexandrov, P. Maass, S.I. Nikolenko. A Two-Step Soft Segmentation Procedure for MALDI Imaging Mass Spectrometry Data. Proceedings of the 18^th German Conference in Bioinformatics (GCB-2012), pp. 39—48, 2012.

D. Grigoriev, S.I. Nikolenko. Continuous hard-to-invert functions and biometric authentication. Groups – Complexity – Cryptology, pp. 19—32, 2012.

A. Fishkov, S.I. Nikolenko. SCM: a new user behaviour model for web search. SPIIRAS Proceedings, pp. 72—100, 2012. Available at Proc. SPIIRAS.

A. Fishkov, S.I. Nikolenko. A survey of user behaviour models for search results ranking. SPIIRAS Proceedings, pp. 139—175, 2012. Available at Proc. SPIIRAS.

I. Chernyavsky, T. Alexandrov, S.I. Nikolenko. Segmentation of MALDI imaging results based on graphical models. SPIIRAS Proceedings, pp. 120—142, 2012. Available at Proc. SPIIRAS.

S.I. Nikolenko, D.V. Serdyuk, A.V. Sirotkin. Bayesian rating systems with additional information on tournament results. SPIIRAS Proceedings, pp. 189—204, 2012. Available at Proc. SPIIRAS.

A. Bankevich, S. Nurk, D. Antipov, A. Gurevich, M. Dvorkin, A.S. Kulikov, V.M. Lesin, S.I. Nikolenko, S. Pham, A.D. Prjibelski, A. Pyshkin, A.V. Sirotkin, N. Vyahhi, G. Tesler, M. Alekseyev, P.A. Pevzner. SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing. Journal of Computational Biology, pp. 455—477, 2012.

S.I. Nikolenko. Provably Secure Cryptographic Constructions. Cryptography and Security in Computing, InTech, pp. 3—22, 2012. Available at electronic edition.

S.I. Nikolenko. The Markov School in the 21^st Century. Logic in Central and Eastern Europe: History, Science and Discourse, University Press of America, pp. 388—427, 2012. Available at publisher's web site.

G.E. Mints, S.I. Nikolenko. History of the Leningrad (St. Petersburg) School of Constructive Mathematics and Proof Theory. Logic in Central and Eastern Europe: History, Science and Discourse, University Press of America, pp. 380—387, 2012. Available at publisher's web site.

S.I. Nikolenko. Provably Secure Constructions in Cryptography. Lambert Academic Publishing, 2011. Available at morebooks.de.

S.I. Nikolenko, M. Alekseyev. New Formulations for the Genome Assembly Problem. Proceedings of the 5^th International Moscow Conference on Computational Molecular Biology (MCCMB 2011), pp. 251—252, 2011. Available at abstract book.

A. Davydow, S.I. Nikolenko. Gate Elimination for Linear Functions and New Feebly Secure Constructions. Proceedings of the 6^th Computer Science Symposium in Russia (CSR 2011), pp. 148—161, 2011 (springerlink).

S.I. Nikolenko, A.V. Sirotkin. A New Bayesian Rating System for Team Competitions. Proceedings of the 28^th International Conference on Machine Learning (ICML 2011), pp. 601—608, 2011.

I. Baltiysky, S.I. Nikolenko. A Probabilistic Graphical Model for the Music Harmony Similarity Problem. SPIIRAS Proceedings, pp. 136—163, 2011. Available at Proc. SPIIRAS.

I. Baltiysky, S.I. Nikolenko. Probabilistic Graphical Models of Harmony in Automated Music Analysis: a Survey. SPIIRAS Proceedings, pp. 174—196, 2011. Available at Proc. SPIIRAS.

M. Churakov, S.I. Nikolenko, Y. Porozov. Predicting DNA Replication Origins with Machine Learning Techniques. ISMB/ECCB 2011, 2011.

S.I. Nikolenko, M. Alekseyev, P.A. Pevzner. Bayesian Evaluation of de novo Genome Assembly. ISMB/ECCB 2011, 2011.

A. Krass, S.I. Nikolenko, E. Stepanov, Y. Porozov. Protein conformational movements modeling based on the average action principle. ISMB/ECCB 2011, 2011.

I. Gnilomedov, S.I. Nikolenko. Agent-Based Economic Modeling with Finite State Machines. Proceedings of the 36^th Annual Convention of the Society for the Study of Artificial Intelligence and Simulation of Behaviour (AISB 2010), 2010.

I. Gnilomedov, S.I. Nikolenko. Fuzzy computing via multiagent negotiations. Proceedings of the 9^th International Conference on Applications of Fuzzy Systems and Soft Computing (ICAFS 2010), pp. 210—220, 2010.

S.I. Nikolenko, A.V. Sirotkin. Extensions of the TrueSkill^TM rating system. Proceedings of the 9^th International Conference on Applications of Fuzzy Systems and Soft Computing (ICAFS 2010), pp. 151—160, 2010.

A.L. Tulupyev, A.V. Sirotkin, S.I. Nikolenko. Bayesian belief networks: probabilistic logic inference on directed acyclic graphs. SPSU Press, St. Petersburg, 2009.

S.I. Nikolenko. Mechanism design theory. Intuit, Moscow, 2009. Available at ozon.ru.

S.I. Nikolenko, A.L. Tulupyev. Learning Systems. MCCME Press, Moscow, 2009. Available at mccme.ru.

E.A. Hirsch, S.I. Nikolenko. A feebly secure trapdoor function. Proceedings of the 4^th Computer Science Symposium in Russia (CSR 2009), pp. 129—142, 2009.

S.I. Nikolenko, A.V. Sirotkin. Bayesian Inference in Rating Systems: a Survey. Proc. SoftComp 2009, pp. 29—48, 2009.

C.A. Pshenichny, S.I. Nikolenko, A.V. Yakovlev. The event bush formalism for knowledge representation and probabilistic inference in geological hazard evaluation. Geoinformatics, pp. 62—71, 2009.

A. Kojevnikov, S.I. Nikolenko. On Complete One-Way Functions. Problems of Information Transmission, pp. 101—118, 2009.

N.A. Vavilov, S.I. Nikolenko. A₂-proof of structure theorems for Chevalley groups of type F₄. St. Petersburg Mathematical Journal, pp. 527—551, 2009.

S.I. Nikolenko, N. Semenov, K. Zainoulline. Motivic decomposition of anisotropic varieties of type F₄ into generalized Rost motives. Journal of K-Theory, pp. 85—102, 2009.

C.A. Pshenichny, S.I. Nikolenko, R. Carniel, P.A. Vaganov, Z.V. Khrabrykh, V.P. Moukhachov, V.L. Akimova-Shterkhun, A.A. Rezyapkin. The Event Bush as a Semantic-based Numerical Approach to Natural Hazard Assessment (Exemplified by Volcanology). Computers and Geosciences, pp. 1017—1034, 2009.

S.I. Nikolenko. New constructions of cryptographic primitives based on semigroups, groups, and linear algebra. 2009.

C.A. Pshenichny, S.I. Nikolenko, R. Carniel, A. Sobissevich, P.A. Vaganov, Z.V. Khrabrykh, V.P. Moukhachov, V.L. Shterkhun, A.A. Rezyapkin, A.V. Yakovlev, R.A. Fedukov, E.A. Gusev. The Event Bush as a Potential Complex Methodology of Conceptual Modeling in Geosciences. Proceedings of iEMSs'08: International Congress on Environmental Modelling and Software, 2008.

S.I. Nikolenko, C.A. Pshenichny, R. Carniel. Learning Conditional Probabilities in Event Bushes with Temporal Labels. Proceedings of iEMSs'08: International Congress on Environmental Modelling and Software, 2008.

A. Kojevnikov, S.I. Nikolenko. New Combinatorial Complete One-Way Functions. Proceedings of the 25^th International Symposium on Theoretical Aspects of Computer Science, Bordeaux, France (STACS 2008), pp. 457—466, 2008 (arXiv:0802.2863 [cs.CC]).

S.I. Nikolenko, C.A. Pshenichny, A. Sobissevich, A.V. Yakovlev. Spatial Volcanic Hazard Assessment by the Event Bush Method. XXIV IUGG General Assembly, Perugia, Italy, 2008.

D. Grigoriev, A. Kojevnikov, S.I. Nikolenko. Algebraic Cryptography: New Constructions and Their Security against Provable Break. St. Petersburg Mathematical Journal, pp. 119—147, 2008.

E.A. Hirsch, A. Kojevnikov, A.S. Kulikov, S.I. Nikolenko. Complexity of Semialgebraic Proofs with Restricted Degree of Falsity. Journal of Satisfiability, pp. 53—69, 2008.

E.A. Hirsch, S.I. Nikolenko. A feebly secure trapdoor function. 2008.

S.I. Nikolenko, C.A. Pshenichny. Temporal Assessment by Means of an Event Bush. Geophysical Research Abstracts, 2007.

M. Gavrilovich, S.I. Nikolenko, N.A. Vavilov. Structure of Chevalley Groups: the Proof from the Book. Journal of Mathematical Sciences, pp. 626—645, 2007 (springerlink).

D. Grigoriev, A. Kojevnikov, S.I. Nikolenko. Invariant-Based Cryptosystems and Their Security Against Provable Worst-Case Break. 2007.

A.L. Tulupyev, S.I. Nikolenko, A.V. Sirotkin. Bayesian Networks: A Probabilistic Logic Approach. St.-Petersburg, Nauka, 2006. Available at ozon.ru.

A.L. Tulupyev, A.V. Sirotkin, S.I. Nikolenko. Coordinated estimates of probabilities of statements in intellectual informational systems. Priborostroenie, pp. 20—26, 2006.

A.L. Tulupyev, S.I. Nikolenko, D.A. Nikitin, A.V. Sirotkin. A posteriori estimates of statement probabilities in intellectual informational systems: deterministic case. Priborostroenie, pp. 35—39, 2006.

A.L. Tulupyev, S.I. Nikolenko, A.V. Sirotkin. A posteriori probability estimates with probabilistic evidence in intellectual informational systems with interval probabilities. Priborostroenie, pp. 39—44, 2006.

S.I. Nikolenko, N. Semenov. Chow ring structure made simple. arXiv:math/0606335 [math.AG], 2006.

E.A. Hirsch, S.I. Nikolenko. Simulating Cutting Planes proofs with restricted degree of falsity by Resolution. Proceedings of SAT'05, Springer, pp. 135—142, 2005 (springerlink). Available at ECCC TR05-006.

A.L. Tulupyev, S.I. Nikolenko. Directed Cycles in Bayesian Belief Networks: Probabilistic Semantics and Consistency Checking Complexity. Proceedings of the 4th Mexican International Conference on Artificial Intelligence (MICAI-2005), pp. 214—223, 2005.

S.I. Nikolenko, N. Semenov, K. Zainoulline. Motivic decomposition of anisotropic varieties of type F₄ and generalized Rost motives. arXiv:math/0502382 [math.AG], 2005.

S.I. Nikolenko. A₂-proof of structure theorems for Chevalley groups of type F₄. 2005.

S. Fedin, A. Kojevnikov, B. Konev, A.S. Kulikov, S.I. Nikolenko, V.P. Orevkov. First report on the semialgebraic prover. 2004.

S.I. Nikolenko, A.V. Sirotkin. Worst-case upper bounds for SAT: automated proof. Student Session Proceedings, 15th European Summer School in Logic, Language, and Information, Vienna, Austria (ESSLLI 2003), pp. 225—232, 2003.

S.I. Nikolenko. Hard satisfiable instances for DPLL-type algorithms. Journal of Mathematical Sciences, pp. 139—149, 2003 (arXiv:0301012 [cs.CC]) (springerlink).