ИНСТИТУТ БИОИНФОРМАТИКИ. СБОРНИК ТЕЗИСОВ 2020/21

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ИНСТИТУТ БИОИНФОРМАТИКИ. СБОРНИК ТЕЗИСОВ 2020/21

СПб. : Федеральное государственное автономное образовательное учреждение высшего образования "Санкт-Петербургский политехнический университет Петра Великого", 2021.

Bioinformatics Institute 2020/21. Project abstracts. Bioinformatics Summer School 2021. Abstracts.

IMPROVE CASUAL GENE PRIORITIZATION BY PATIENT,S PHENOTYPE. IDENTIFICATION AND PARSING OF RELEVANT MENDELIAN DISEASE ARTICLES

Konstantinovskiy N., Smirnov D., Holger P., , in: ИНСТИТУТ БИОИНФОРМАТИКИ. СБОРНИК ТЕЗИСОВ 2020/21.: St. Petersburg: Федеральное государственное автономное образовательное учреждение высшего образования "Санкт-Петербургский политехнический университет Петра Великого", 2021. P. 24–24.

Added: August 9, 2021

Konstantinovskiy N., Kirillova E., Cherniatchik R., , in: ИНСТИТУТ БИОИНФОРМАТИКИ. СБОРНИК ТЕЗИСОВ 2020/21.: St. Petersburg: Федеральное государственное автономное образовательное учреждение высшего образования "Санкт-Петербургский политехнический университет Петра Великого", 2021. P. 59–60.

Added: August 9, 2021

Research target: Biology Computer Science

Priority areas: IT and mathematics

Language: English

ИНСТИТУТ БИОИНФОРМАТИКИ. СБОРНИК ТЕЗИСОВ 2020/21

Effects of Elevation Changes and Multilevel Structures on Vehicular Signal Propagation

Stepanyants V., Andrey V. Fizulin, Chibirov A. et al., FUTURE TRANSPORTATION 2026 Vol. 6 No. 5 Article 225

Reliable Vehicle-to-Everything (V2X) evaluation requires propagation models that represent terrain and multilevel infrastructure. Most integrated vehicular simulators still rely on planar models, but the magnitude of the resulting bias is unclear. This study quantitatively compares flattened two-dimensional (2D) and terrain-aware three-dimensional (3D) variants of three scenarios using identical Sionna RT settings. The pipeline combines OpenStreetMap ...

Added: October 8, 2026

Автоматизированное построение математических теорий

Люксембург А. А., УРСС, 2005.

Изучается возможность автоматизированного построения математических теорий. Рассматривается дедуктивная система, основанная на языке логики предикатов первого порядка, объектами системы являются математические выражения или формулы, которые описывают математические объекты или их свойства. В дедуктивной системе выводятся математические определения и теоремы. Для доказательства теорем используются методы автоматического доказательства. Разработан алгоритм, выводящий часть формул системы. Для решения задачи используется аппарат математической ...

Added: October 7, 2026

Automated Ranking of Soybean Plots from Close-Range RGB Video via Depth Filtering and Point-Based Counting

Groshev Maksim, Rybakov Petr, Teterin N. et al., Sensors 2026 Article 6171

Manual assessment of soybean yield components, such as pod number, is laborious, time-consuming, and subjective. Existing computer-vision approaches based on object detection or instance segmentation perform poorly on close-range RGB imagery of soybean canopies due to severe occlusions, ambiguous plant boundaries, and the high cost of bounding-box annotation. To address these challenges, we propose a ...

Added: October 7, 2026

Новые информационные технологии в исследовании сложных структур. Материалы шестнадцатой международной конференции 21–25 Сентября 2026 г.

Томск: Издательство Томского государственного университета, 2026.

Материалы сборника Шестнадцатой Международной конференции «Новые информационные технологии в исследовании сложных структур» (Москва, 21–25 сентября 2026 г.) ориентированы на широкий круг специалистов, работающих на стыке теории информации, системного анализа и прикладных предметных областей. В издание вошли результаты исследований, посвящённые моделированию дискретных и стохастических структур управления и связи, разработке высокопроизводительных вычислительных и телекоммуникационных систем, а также вопросам цифровой трансформации образования, архитектурно-градостроительного проектирования, экологического ...

Added: October 6, 2026

Оптимизация энергопотребления предприятия с использованием методов многокритериальной оптимизации

Серебренников Д. А., Belov A. V., Информационные технологии и вычислительные системы 2026 № 3 С. 157–169

В условиях роста стоимости энергоресурсов и необходимости повышения энергоэффективности производственных процессов особую актуальность приобретает задача оптимизации энергопотребления промышленных предприятий. В данной работе рассматривается подход к управлению энергозатратами машиностроительного предприятия на основе методов многокритериальной оптимизации. Постановка задачи включает несколько целевых функций: минимизацию энергопотребления, минимизацию стоимости электроэнергии с учётом тарифных ограничений и максимизацию производственной эффективности. Для решения ...

Added: October 5, 2026

On Practical Aspects of Constructing Quasi-Cyclic Subfield Subcodes of Dual Elliptic Codes and Their Application in McEliece-type Cryptosystems

Kuninets A., IEEE Transactions on Information Theory 2026 P. 1–1

In this work we study the applicability of Quasi-Cyclic Subfield Subcodes of Dual Elliptic (QC-SSDE) codes for integration into code-based cryptographic schemes. Detailed algorithms are provided for constructing parity-check matrices as well as block-circulant parity-check matrices for this family of codes, accompanied by empirical results that enable the construction of QC-SSDE codes with predetermined dimensions. ...

Added: October 3, 2026

Инкрементальный метод обновления многомерного куба по неупорядоченному потоку событий журналов информационных систем

Zykov S. V., Уфимцев Г. А., Моделирование, оптимизация и информационные технологии 2026 Т. 14 № 8 С. 1–13

Информационные системы формируют большие объёмы событийных журналов, которые используются для анализа работы приложений и сервисов. При этом события могут поступать в аналитический контур позже момента их фактического возникновения и не в исходном порядке. Такая рассинхронизация приводит к ошибкам при построении агрегированных временных показателей, а регулярный полный пересчёт многомерного аналитического куба требует значительных вычислительных затрат. Целью ...

Added: October 2, 2026

Polarization of opinions in the group: a modeling algorithm considering the dynamics of social bonds

Chebotarev V., Andreyuk D., Elizarova Anastasiya et al., Procedia Computer Science 2022 Vol. 213 No. C P. 596–601

The dynamics of opinion in a group are of interest for a number of practical purposes. In particular, consensus helps and polarization of opinions hinders cohesive teamwork. Existing approaches for modeling opinion dynamics mostly do not take into account the dynamism of social relations in a group. This paper proposes an algorithm and a program ...

Added: October 2, 2026

Enhancing Boundary Stability in Decision Trees and Random Forests: A Weighted Sample Duplication Approach

Konstantinov A., Elizarova Anastasiya P., Utkin L., Computing, Telecommunications and Control 2026 Vol. 19 No. 1 P. 16–25

Decision trees and their ensemble extensions, such as random forests, are widely used as classification models due to their simplicity and interpretability. However, in many real-world tasks where class labels overlap in the feature space, standard decision trees rely on hard splits that create fragile decision boundaries. In these regions, small perturbations in the input ...

Added: October 2, 2026

HLA class I escape drives the evolution of SARS-CoV-2 in human populations

Ekaterina D. Riumina, Klink G. V., Alekseeva E. et al., PNAS, США 2026 Vol. 123 No. 35 P. 1–20

The role of escape from the cytotoxic T cell (CTL) response in SARS-CoV-2 evolution remains controversial. Here, we study the origin and spread of SARS-CoV-2 variants whose mutations reduce presentation by the HLA class I alleles common in human populations. We find that 35% of mutations that are characteristic of the variants of concern, and ...

Added: October 2, 2026

Bayesian Adaptive Sparse Copula

Prokhorov A., Burda M., Journal of Computational and Graphical Statistics 2026 P. 1–13

Bayesian nonparametric density estimation procedures are typically based on single-scale priors, such as Dirichlet process mixtures. Alternative multiscale density priors built on decision trees have many well-known advantages, including the ability to characterize abrupt local changes and to provide an estimate with a desired level of resolution. Despite their theoretical appeal, multiscale methods have typically ...

Added: October 2, 2026

Pericyte-derived cancer-associated fibroblasts correlate with poor survival and are enriched after chemoradiotherapy in glioblastoma

Aly Ismailov, Poptsova M., Plos One 2026 Vol. 21 No. 9 Article e0355902

Added: October 2, 2026

Консервативные энтропийно и энергетически корректные разностные методы для одномерных квазигазодинамических систем уравнений

Zlotnik A., Математические заметки 2026 Т. 120 № 6 С. 1005–1009

Численным методам решения систем газодинамических уравнений посвящена обширная литература. Ранее было разработано и успешно апробировано специальное семейство симметричных по пространству консервативных разностных методов, основанных на предварительной кинетической, точнее, квазигазодинамической (КГД), регуляризации этих уравнений. Актуальной задачей является построение численных методов, которые обладают не только свойством консервативности по массе, импульсу и полной энергии, но и удовлетворяют условиям энтропийной ...

Added: October 1, 2026

A Three-Party W-State Quantum Secret Sharing Protocol with X-Gate Encoding and Forbidden-Outcome Detection

Teregulov T., Loubenets E. R., / Series Quantum Physics "arXiv". 2026. No. 2609.31472.

We develop a new three-party quantum secret-sharing (QSS) protocol based on a three-qubit W state. This protocol encodes the secret-sequence bits using X gates and employs randomly selected Hadamard operations and measurement bases to generate information and security-test rounds. We evaluate the efficiency of the proposed protocol and analyze its security against an internal adversary ...

Added: September 28, 2026

On calibration of remote sensing retrievals of ecosystem respiration (Reco) with tower measurements over,Russian forests and wetlands

Shabanov N., Kuricheva O., Kurbatova J. et al., / Series Working Papers SSRN "Department of Economics Ca’ Foscari University of Venice". 2026.

The carbon balance of an ecosystem is the difference between Gross Primary Productivity (GPP) and Ecosystem Respiration (Reco) as expressed by Net Ecosystem Exchange (NEE). While remote sensing retrievals of GPP have reached maturity, Reco estimation remains underexplored and ultimately cast bias on NEE. Here we present an end-to-end multi-scale analysis of the mechanism of ...

Added: August 21, 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

Growth in noncommutative algebras and entropy in derived categories

Piontkovski D., / Series arXiv "math". 2026.

A noncommutative projective variety is defined, following Artin and Zhang, by a graded coherent algebra 𝐴. The category of coherent sheaves is then the quotient qgr(𝐴) of the category of finitely presented graded modules by the subcategory of torsion modules. We consider the categorical and polynomial entropies of the Serre twist, that is, of the ...

Added: June 23, 2026

Multilinear nilalgebras and the Jacobian theorem

Piontkovski D., / Series arXiv "math". 2025.

If a symmetric multilinear algebra is weakly nil, then it is Engel. This result may be regarded as an infinite-dimensional analogue of the well-known Jacobian theorem, which states that if a polynomial mapping has a polynomial inverse, then its Jacobian matrix is invertible. This refines a theorem of Gerstenhaber and partially answers a question posed ...

Added: June 23, 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

ML-based Fast Simulation of FARICH Responses

Shipilov F., Barnyakov A., Ivanov A. et al., / Series Physics "arxiv.org". 2026.

A fast simulation of the detector response is a vital task in high-energy physics (HEP). Traditional Monte-Carlo methods form the backbone of modern particle physics simulation software but are computationally expensive. We present a machine-learning-based approach to fast simulation of the Focusing Aerogel Ring Imaging Cherenkov (FARICH) detector response. Given a particle track and momentum, ...

Added: May 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

Natural hazard database from Internet publications: text mining with a large language model

Derkacheva A., Sakirkina M., Kraev G. et al., /. 2026.

Comprehensive data on natural hazards and their consequences are crucial for effective for risk assessment, adaptation planning, and emergency response. However, many countries face challenges with fragmented, inconsistent, and inaccessible data, particularly regarding local-scale events. To address this data gap in Russia, we developed an end-to-end processing pipeline that scrapes news from various online sources, ...

Added: April 28, 2026

Algorithmic overlaps as thermodynamic variables: from local to cluster Monte Carlo dynamics in critical phenomena

Pilé I., Deng Y., Shchur L., / Series arXiv "math". 2026. No. 2604.10254.

We investigate the spatial overlap of successive spin configurations in Markov chain Monte Carlo simulations using the local Metropolis algorithm and the Svendsen-Wang and Wolff cluster algorithms. We examine the dynamics of these algorithms for two models in different universality classes: the Ising model and the Potts model with three components. The overlap of two ...

Added: April 20, 2026

Using predefined vector systems to speed up neural network multimillion class classification

Gabdullin N., Androsov I., / Series Computer Science "arxiv.org". 2026.

Label prediction in neural networks (NNs) has O(n) complexity proportional to the number of classes. This holds true for classification using fully connected layers and cosine similarity with some set of class prototypes. In this paper we show that if NN latent space (LS) geometry is known and possesses specific properties, label prediction complexity can ...

Added: April 2, 2026