Proceedings of 11th Moscow Conference on Computational Molecular Biology MCCMB'23

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Proceedings of 11th Moscow Conference on Computational Molecular Biology MCCMB'23

IITP RAS, 2023.

Regulatory potential of flipons revealed by deep learning.

Poptsova M., Умеренков Д., Fedorov A. et al., , in: Proceedings of 11th Moscow Conference on Computational Molecular Biology MCCMB'23.: IITP RAS, 2023.

Flipons – non-B DNA conformations – have been shown to play an important role in various genomic processes. Flipons identification and localization is difficult due to their dynamic nature. We developed deep learning approaches to identify non-B DNA secondary structures using available information from thousands of omics data sets. We created DeepZ models based on CNN and RNN, and ...

Added: November 30, 2023

Консервативные Z-флипоны и ассоциированные с ними омиксные факторы, в геномах мыши и человека.

Konovalov D., Beknazarov N., Герберт А. et al., В кн.: Proceedings of 11th Moscow Conference on Computational Molecular Biology MCCMB'23.: IITP RAS, 2023.

Разработанный нами ранее подход DeepZ [1], основанный на глубинных нейронных сетях и использующий как данные о последовательности, так и омиксные данные, был использован для генерации полногеномных аннотаций генома мыши и человека участками Z-ДНК. В данной работе мы использовали подход DeepZ для изучения консервативных Z-флипонов и консервативных транскрипционных факторов и гистоновых меток, которые обогащены Z-флипонами в обоих геномах. Мы отобрали более 500 ...

Added: December 1, 2023

Unsupervised domain adaptation methods for cross-species transfer of regulatory code signals

Pavel Latyshev, Fedor Pavlov, Herbert A. et al., , in: Proceedings of 11th Moscow Conference on Computational Molecular Biology MCCMB'23.: IITP RAS, 2023.

Added: December 1, 2023

Analysis of Cell Interactions between Tumour and Microenvironment

Mikhailova A., Poptsova M., Herbert A., , in: Proceedings of 11th Moscow Conference on Computational Molecular Biology MCCMB'23.: IITP RAS, 2023.

Added: December 1, 2023

Association of Z-RNA with QTL variants

Glimanova D., , in: Proceedings of 11th Moscow Conference on Computational Molecular Biology MCCMB'23.: IITP RAS, 2023.

Z-DNA and Z-RNA, or Z-flipons, have been shown to play an important role in many cellular processes. Recently the whole-genome map of Z-DNA was generated with Z-DNABERT based on transformer algorithm and trained on the experimental permanganate/S1 nuclease dataset [1]. It was demonstrated how predicted Z-flipons containing single nucleotide variants may affect Z-RNA formation and ...

Added: December 1, 2023

Глубинное обучение для выявления ассоциаций между функциональными геномными элементами

Цветкова А., В кн.: Proceedings of 11th Moscow Conference on Computational Molecular Biology MCCMB'23.: IITP RAS, 2023.

Архитектура глубинного обучения, трансформер, отличается механизмом внимания, который позволяет проинтерпретировать вывод моделей. DNABERT – одна из таких моделей, она обучена на геноме человека, то есть в ней уже заложена информация о некоторых взаимосвязях в ДНК. Модель можно настроить для других задач путем дообучения на небольшом датасете. В ходе работы была поставлена цель – проинтерпретировать мотивы, выявленные при ...

Added: December 1, 2023

Полигенная оценка риска с помощью моделей глубинного обучения

Perelygin V., Poptsova M., Камелин А. В. et al., В кн.: Proceedings of 11th Moscow Conference on Computational Molecular Biology MCCMB'23.: IITP RAS, 2023.

В данной работы было показано, что использование нелинейных моделей, в частности методов глубинного обучения, может заметно улучшить полигенную оценку риска некоторых видов заболеваний, в первую очередь высоко ассоциированных с эпистазом. ...

Added: December 1, 2023

High-throughput computational design of protein binders for complex targets using deep learning models

Alekseev K., Poptsova M., Shaitan A., , in: Proceedings of 11th Moscow Conference on Computational Molecular Biology MCCMB'23.: IITP RAS, 2023.

Computational protein design methods has transformed structural bioinformatics by overcom- ing many experimental limitations. Previously, experimental methods such as directed evo- lution were utilized to create protein binders. Many advancements in computational protein design have made it possible to generate de novo binders solely based on target structure and sequence information. However, despite recent progress, designing de novo protein ...

Added: December 1, 2023

Detection of non-coding variants in regulatory elements in patients with early atherosclerosis based on whole genome sequencing data

Okhrimenko G., Malko D., Zateyshchikov D. et al., , in: Proceedings of 11th Moscow Conference on Computational Molecular Biology MCCMB'23.: IITP RAS, 2023.

Added: December 1, 2023

Программный комплекс для предсказания функциональных элементов генома методами глубинного обучения с использованием омиксных данных

Voytetsky A., Fedorov A., Боровков П. В. et al., В кн.: Proceedings of 11th Moscow Conference on Computational Molecular Biology MCCMB'23.: IITP RAS, 2023.

Одной из важных задач геномики и молекулярной биологии состоит в предсказании расположения геномных функциональных элементов (ГФЭ), которые играют важную роль в работе и регуляции геномных и клеточных процессов, но для которых экспериментальные данных либо неполные, либо отсутствуют. Данная задача в настоящее время наиболее эффективно решается методами глубинного обучения на основе информации из доступных полногеномных экспериментов ...

Added: December 1, 2023

Biomarkers study to improve Machine Learning prediction of long-term risk of myocardial infarction, stroke, and cardiac death

K.M. Burkin, A.V. Kirdeev, Nikolaev K. Y. et al., , in: Proceedings of 11th Moscow Conference on Computational Molecular Biology MCCMB'23.: IITP RAS, 2023.

Added: December 1, 2023

Research target: Biology Computer Science Medical and Health Sciences

Language: English

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Proceedings of 11th Moscow Conference on Computational Molecular Biology MCCMB'23

Functional Brain Connectivity and Musical Training: Insights from EEG Phase Synchronization during Music Perception

Radygina A., Kulikova S., Herald of the Russian Academy of Sciences 2025 Vol. 95 No. 6 P. 963–970

Musical training has a significant impact on brain organization, leading to functional and structural adaptations that enhance auditory, visual, motor, and cognitive processes. This study investigates how extensive musical training shapes functional brain connectivity by comparing professional musicians and non-musicians. Using EEG phase-locking value (PLV) analysis, we examined neural synchronization across alpha, beta, and gamma frequency ranges during music ...

Added: August 5, 2026

WWW '23 Companion: Companion Proceedings of the ACM Web Conference 2023

Фирсанова В. И., ACM, 2026.

The inclusion of autistic people can be augmented by a mobile app that provides information without a human mediator making information perception more liberating for people in the spectrum. This paper is an overview of a doctoral work dedicated to the development of a web-based mobile tool for supporting the inclusion of people on the ...

Added: August 4, 2026

Joint Proceedings of the ESWC 2025 Workshops and Tutorials co-located with 22nd Extended Semantic Web Conference (ESWC 2025), Portorož, Slovenia, June 1-2, 2025.

Фирсанова В. И., Хлусова Я. К., CEUR Workshop Proceedings, 2025.

Knowledge graphs are widely used in Retrieval Augmented Generation (RAG) and Explainable AI (XAI), since they can illustrate semantic relationships generated by Large Language Models (LLMs). Recent studies focus on generating knowledge graphs from unstructured data to improve RAG performance; however, they do not explain the underlying graph structure. The analysis of synthetic graphs behind ...

Added: August 4, 2026

Mathematical methods of reinforcement learning

Belomestny D., Gasnikov A., Gladin E. et al., Russian Mathematical Surveys 2026 Vol. 81 No. 4(490) P. 3–90

Reinforcement learning (RL) is increasingly grounded in tools from probability, optimization, and operator theory. This survey organizes the mathematical structures that underpin the design and analysis of modern algorithms in RL. We begin from Markov decision processes (MDPs) and the Bellman operators, emphasizing contraction mappings, monotonicity, and fixed-point theory that yield convergence guarantees and rates ...

Added: August 3, 2026

Чеповский А.М. Анализ корпусов текстов на естественных языках. Математические методы. Учебное пособие – М.: Мастерская Печати Идей, 2026. – 274 с.: илл.

Chepovskiy A., Мастерская Печати Идей, 2026.

The textbook presents methods and algoгithms for automatic analysis of соrроrа of texts in natural languages. It is intended fоr sfudenБ of methods of processing texts in паtчrаl languages and creating training arays of texts. Fоr students, graduate students and researchers studying methods of computational linguistics and word processing. ...

Added: August 1, 2026

Three Algorithms for Merging Hierarchical Navigable Small World Graphs

Ponomarenko A., / Series Computer Science "arxiv.org". 2025.

This paper addresses the challenge of merging hierarchical navigable small world (HNSW) graphs, a critical operation for distributed systems, incremental indexing, and database compaction. We propose three algorithms for this task: Naive Graph Merge (NGM), Intra Graph Traversal Merge (IGTM), and Cross Graph Traversal Merge (CGTM). These algorithms differ in their approach to vertex selection ...

Added: July 30, 2026

Профессиональная верификация: Руководство по продвинутой функциональной верификации

Уилкокс П., Romanov A., М.: ДМК Пресс, 2025.

Книга, которую вы держите в руках, продолжает серию «Книжная полка истового инженера», которая издается при поддержке компании YADRO. Данная книга представляет собой учебник по теоретическим основам продвинутой функциональной верификации и содержит лучшие практики, используемые в настоящее время. В ней подробно описана унифицированная методология верификации (UVM) и раскрыты такие темы, как функциональный виртуальный прототип, функциональное покрытие, утверждения, формальная верификация, тестбенчи, косимуляция, эмуляция, аппаратное ...

Added: July 30, 2026

EEG evidence for reproducible neural states during Buddhist Highest Yoga Tantra meditation

Mikhaylets E. V., Razorenova A. М., Chernyshev V. L. et al., Scientific Reports 2026 Vol. 16 Article 23560

Meditation offers a naturalistic paradigm for studying introspection, yet the neural dynamics of advanced tantric practices remain largely unexplored. Buddhist Highest Yoga Tantra (BHYT) comprises a sequence of eight dissolution stages culminating in the “clear light” state. We recorded EEG during eyes-closed BHYT meditation performed in monasteries and hermitages (51 sessions from 36 male practitioners; ...

Added: July 29, 2026

Machine Learning-based Adaptive Reconstruction of Video Stream Fragments Taking into Account Scene Dynamics. Proceedings of the Institute for System Programming of the RAS

Думкин Н. А., Alexandrov D., Прозорский М. А., Труды Института системного программирования РАН 2026 Т. 38 № 1 С. 255–274

A theoretically sound approach to adaptive client-side video fragment restoration is proposed using machine learning and scene analysis methods. The method includes a formal problem statement, a finite-state machine model for decision making, a restoration cost function, and a new stage in video preparation: scene dynamics assessment followed by recording a feature in an HLS playlist. This feature ...

Added: July 27, 2026

Automated Reasoning: 13th International Joint Conference, IJCAR 2026, Lisbon, Portugal, July 26–29, 2026, Proceedings, Part II. (LNCS, volume 16689)

Cham: Springer, 2026.

This open access set, LNAI 16688-16689, constitutes the proceedings of the 13th International Joint Conference, IJCAR 2026, held in Lisbon, Portugal, during July 26–29, 2026. The 41 full research papers and 8 short papers included in these two volumes were carefully reviewed and selected from 112 submissions. The papers cover the following topical sections: Part I: Theorem ...

Added: July 26, 2026

Local Fault-Tolerant Routing in 3D Mesh NoCs using Single-Hop Rollback

Edward R. Rzaev, Aleksandr Y. Romanov, Andrey M. Sukhov, IEEE Access 2026 Vol. 14 P. 2169–3536

This work presents a hierarchy of strictly local fault-tolerant routing algorithms for 3D mesh networks-on-chip, culminating in an algorithm that combines a live-neighbor selection rule with a bounded single-hop rollback mechanism. The proposed algorithms operate exclusively on immediate neighbor information, maintain O(1) per hop complexity, and require no global topology knowledge, additional virtual channels, or ...

Added: July 23, 2026

Библиометрия фольклора: русские пословицы в научных журналах

Pislyakov V., Вестник Томского государственного университета. Филология 2026 № 101 С. 175–192

This article examines the use of proverbs in academic texts—specifically, articles published in Russian research journals. For the experiment, ten proverbs were selected as the intersection of two fundamentally different paremiological surveys aimed at compiling lists of popular or common Russian proverbs. One of these surveys was conducted by the classic of paremiology, G.L. Permyakov, ...

Added: July 22, 2026

SIGIR '26: Proceedings of the 49th International ACM SIGIR Conference on Research and Development in Information Retrieval

Association for Computing Machinery (ACM), 2026.

Wominjeka, and welcome to the 49th International ACM SIGIR Conference on Research and Development in Information Retrieval (SIGIR 2026), held in Melbourne | Naarm, Australia, from 20–24 July 2026. SIGIR 2026 takes place on the unceded lands of the Woi Wurrung and Boon Wurrung language groups of the eastern Kulin nation, and we pay our ...

Added: July 22, 2026

Long-range machine-learning potentials with environment-dependent charges enable predicting LO-TO splitting and dielectric constants

Korogod D., Shapeev A., Ivan S. Novikov, Physical Review B: Condensed Matter and Materials Physics 2026 Vol. 114 No. 2 Article 024104

We present two models with explicit long-range electrostatics in the form of Coulomb interactions. Both models include point charges depending on their local atomic environments, and the second model also conserves a total charge of an atomic system. We combine the proposed long-range models with the local moment tensor potential (MTP) and demonstrate that they ...

Added: July 22, 2026

Global optimization of atomic clusters via physically constrained tensor train decomposition

Sozykin K., Rybin N., Chertkov A. et al., Physical Review B: Condensed Matter and Materials Physics 2026 Vol. 113 No. 22 Article 224111

The global optimization of atomic clusters represents a fundamental challenge in computational chemistry and materials science due to the exponential growth of local minima with system size (i.e., the curse of dimensionality). We introduce a framework that overcomes this limitation by exploiting the low-rank structure of potential energy surfaces through tensor train (TT) decomposition. Our ...

Added: July 22, 2026

WSI-GT: Pseudo-Label Guided Graph Transformer for Whole-Slide Histology

Михайлов И. А., Machine Learning and Knowledge Extraction 2026 Vol. 8 No. 1 Article 8

Whole-slide histology images (WSIs) can exceed 100 k × 100 k pixels, making direct pixel-level segmentation infeasible and requiring patch-level classification as a practical alternative for downstream WSI segmentation. However, most approaches either treat patches independently, ignoring spatial and biological context, or rely on deep graph models prone to oversmoothing and loss of local tissue ...

Added: July 16, 2026

On the construction of Barnes–Wall lattices and their application in cryptography

Kuninets A., Malygina E., Leevik A. G. et al., Journal of Computer Virology and Hacking Techniques 2026 No. 22 Article 62

In this work, we investigate the application of Barnes–Wall lattices in post-quantum cryptographic schemes. We survey and analyze several constructions of Barnes–Wall lattices, including subgroup chains, the generalized k-ing construction, and connections with Reed-Muller codes, highlighting their equivalence over both Z[i] and Z. Building on these structural insights, we introduce a new algorithm for efficient ...

Added: July 16, 2026

Tencent и Open Source. Как относится к открытому ПО самый дорогой бренд Китая?

Silakov D., Системный администратор 2026 № 5 С. 46–51

В предыдущей статье про Open Source в КНР [1] мы рассказали про Alibaba – крупную корпорацию, занимающую тридцатое место в рейтинге самых значимых мировых брэндов за 2025 год [2]. Место почетное, но не первое среди китайских компаний – на тринадцатом месте расположилась Tencent, разработчик WeChat и ряда других продуктов, широко используемых нашими восточными соседями. Tencent ...

Added: July 14, 2026

2026 IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR)

IEEE, 2026.

Added: July 13, 2026

Neural-molecular signatures of insomnia: Insights from signed differential mapping and gene expression analysis

Wang R., He Y., Myachykov A. et al., Neuroimage 2026 Vol. 332 Article 121926

Insomnia disorder (ID) exhibits considerable heterogeneity in neuroimaging findings across studies, and whether functional brain alterations are consistent across resting and task states remains unclear. This study aimed to identify neural dysfunction across states in ID and explore its transcriptomic correlates. ...

Added: July 13, 2026

Kolmogorov–Arnold networks for genomic tasks

Cherednichenko O., Poptsova M., Briefings in Bioinformatics 2025 Vol. 26 No. 2 Article bbaf129

Kolmogorov–Arnold networks (KANs) emerged as a promising alternative for multilayer perceptrons (MLPs) in dense fully connected networks. Multiple attempts have been made to integrate KANs into various deep learning architectures in the domains of computer vision and natural language processing. Integrating KANs into deep learning models for genomic tasks has not been explored. Here, we ...

Added: June 19, 2026

Optimizing Computational Infrastructure for Large Language Models in Bioinformatics: A Case Study

Beknazarov N., , in: Parallel Computational Technologies, 19th International Conference, PCT 2025, Moscow, Russia, April 8–10, 2025, Revised Selected Papers. (CCIS, volume 2891)Vol. 2891.: Springer, 2026. P. 3–16.

This paper addresses the challenge of efficiently training Large Language Models (LLMs) on large-scale, sparse omics datasets in high-performance computing (HPC) environments. Using over 1000 BED tracks as a representative data source, we propose a method combining interval-based chunked storage, sparse matrix transformation, and parallel data loading, integrated within a PyTorch Lightning training framework. Our ...

Added: May 19, 2026

Multimodal graph, surface, and language-based model for protein protein interaction prediction

Arteaga Moreano B. D., Chervov N., Poptsova M., Scientific Reports 2026 Vol. 16 No. 1 Article 4772

Accurate prediction of protein-protein interactions (PPIs) is fundamental to understanding biological processes and disease mechanisms. While deep learning offers a powerful alternative to costly experimental methods, existing approaches often overlook critical protein-surface information and rely on simplistic feature fusion techniques, thereby limiting performance. To address this, we introduce GSMFormer-PPI, a novel multimodal framework that integrates ...

Added: February 4, 2026

Prediction of protein-protein interactions using point transformer and spherical Convex Hull graphs

David Arteaga, Poptsova M., Computational and Structural Biotechnology Journal 2026 Vol. 31 P. 82–93

Accurate predictions and large-scale identification of protein-protein interactions (PPIs) are crucial for understanding their inherent biological mechanisms and protein functions in virtually all biological processes. Nowadays, graph-based deep learning models have made significant contributions in modeling proteins with physicochemical and geometric features. However, most of these models rely on conventional graph construction methods, such as ...

Added: December 22, 2025