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Reliability of immune receptor rearrangements as genetic markers for minimal residual disease monitoring
Bone Marrow Transplantation. 2016. Vol. 1. No. 3.
Nazarov V. I., Minervina A. A., Komkov A. Y., Pogorelyy M., Maschan M. A., Olshanskaya Y. V., Zvyagin I., Chudakov D., Lebedev Y. B., Mamedov I.
Detection of minimal residual disease (MRD) is a powerful prognostic tool in many hematological malignancies including ALL.1 Several groups of markers are widely used to monitor the concentration of a malignant clone including the detection of 'clonal B-cell (BCR) or T-cell (TCR) gene receptor rearrangements2 in ALL. Identification of a clonal rearrangement specific for the malignant clone, which usually constitutes from 20 to 90% in the initial bone marrow sample is a relatively straightforward task. Tracking this rearrangement after therapy is more tricky as the concentration of malignant cells in the sample can be very low.
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
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
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
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
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
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
Sorokin K., Beketov M., Онучин А. et al., / arxiv.org. Серия cs.SI "Social and Information Networks ". 2025.
Community detection in complex networks is a fundamental problem, open to new approaches in various scientific settings. We introduce a novel community detection method, based on Ricci flow on graphs. Our technique iteratively updates edge weights (their metric lengths) according to their (combinatorial) Foster version of Ricci curvature computed from effective resistance distance between the ...
Added: January 15, 2026
Petrovanov I., Sergeev A., / Series Computer Science "arxiv.org". 2025. No. 2512.18332.
Transport coding reduces message delay in packet-switched networks by introducing controlled redundancy at the transport layer: original packets are encoded into coded packets, and the message is reconstructed after the first successful deliveries, effectively shifting latency from the maximum packet delay to the -th order statistic. We present a concise, reproducible discrete-event implementation of transport coding in OMNeT++, including ...
Added: December 24, 2025
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
Hessian-based lightweight neural network for brain vessel segmentation on a minimal training dataset
Меньшиков И. А., Бернадотт А. К., Elvimov N. S., / Series arXie "Statistical mechanics". 2025.
Accurate segmentation of blood vessels in brain magnetic resonance angiography (MRA) is essential for successful surgical procedures, such as aneurysm repair or bypass surgery. Currently, annotation is primarily performed through manual segmentation or classical methods, such as the Frangi filter, which often lack sufficient accuracy. Neural networks have emerged as powerful tools for medical image ...
Added: December 1, 2025
Chernyshov D., Satanin A., Shchur L., / Series arXiv "math". 2025.
We investigate the boundary separating regular and chaotic dynamics in the generalized Chirikov map, an extension of the standard map with phase-shifted secondary kicks. Lyapunov maps were computed across the parameter space (K,K(α, τ)) and used to train a convolutional neural network (ResNet18) for binary classification of dynamical regimes. The model reproduces the known critical ...
Added: November 21, 2025
Rubchinskiy A., Chubarova D., / Series WP7 "Математические методы анализа решений в экономике, бизнесе и политике". 2025. No. WP7/2025/01.
The article examines one of the most famous examples of socio-economic systems, characterized by significant uncertainty – the S&P-500 stock market, where shares of 500 largest US companies are traded. No assumptions are made about the probabilistic characteristics of the stock market. A flexible algorithm for daily trading has been developed, based on both known fixed data ...
Added: November 9, 2025
Meshchaninov V., Strashnov, P., Shevtsov A. et al., / Cornell University. Серия CoRR, arXiv:2403.03726 "Computing Research Repository,". 2025.
Protein design requires a deep understanding of the inherent complexities of the protein universe. While many efforts lean towards conditional generation or focus on specific families of proteins, the foundational task of unconditional generation remains underexplored and undervalued. Here, we explore this pivotal domain, introducing DiMA, a model that leverages continuous diffusion on embeddings derived ...
Added: October 5, 2025
Shabalin A., Meshchaninov V., Vetrov D., / Series cs.CL, arXiv:2505.18853 "Computation and Language". 2025.
Diffusion models have achieved state-of-the-art performance in generating images, audio, and video, but their adaptation to text remains challenging due to its discrete nature. Prior approaches either apply Gaussian diffusion in continuous latent spaces, which inherits semantic structure but struggles with token decoding, or operate in categorical simplex space, which respect discreteness but disregard semantic ...
Added: October 5, 2025
Абрамов А. С., Chernyshev V. L., Mikhaylets E. et al., / Series Social Science Research Network "Social Science Research Network". 2025.
Computer vision is one of the most relevant modern research areas with broad practical applications. However, traditional solutions based on deep learning have signicant limitations and can be misleading. Topological data analysis, on the other hand, is a modern approach to solving similar problems using mathematically deterministic methods of algebraic topology that reduce the risk ...
Added: September 23, 2025
Budkina A., Korneenko E., Kotov I. et al., Viruses 2021 No. 10 P. 2006
According to various estimates, only a small percentage of existing viruses have been discovered, naturally much less being represented in the genomic databases. High-throughput sequencing technologies develop rapidly, empowering large-scale screening of various biological samples for the presence of pathogen-associated nucleotide sequences, but many organisms are yet to be attributed specific loci for identification. This ...
Added: September 19, 2025
Kochetkov Y., / Series arXiv.org e-print archive "arXiv.math". 2025. No. 07600.
We demonstrate in an elementary way how to construct a frieze pattern of width m-3 from a partition of a convex m-gon
by not intersecting diagonals. ...
Added: September 17, 2025
Kochetkov Y., / Series arXiv.org e-print archive "arXiv.math". 2025. No. 20584.
We give a new proof of the following statement: the Catalan number C_n is divisible
by n+2, if n is odd and n<> 3k+1. ...
Added: September 9, 2025
KUDRYAVTSEVA A., Cancers 2023
Liver metastasis is a significant factor contributing to mortality associated with colorectal cancer. Establishing the biological mechanisms of metastasis is crucial for refining diagnostics and identifying therapeutic windows for interventions. Currently, little is known of the processes that govern the development of liver metastases, the role of the tumor microenvironment, the role of epigenetics, and ...
Added: July 1, 2025
Аксенова А. Ю., Жук А. С., Степченкова Е. И. et al., Экологическая генетика 2025 Т. 23 № 2 С. 1–14
Биоинформатика — это быстро развивающаяся дисциплина на стыке биологии, информатики и математики. Научно-технический прогресс в области биологических и биомедицинских наук за последние годы привел к стремительному росту объемов данных. Для анализа и интерпретации больших данных нужны мощные вычислительные инструменты и специалисты с глубокими знаниями в различных областях, включая молекулярную биологию, генетику, программирование и математику. В ...
Added: May 20, 2025
Stefan Nikolić, Ignatov D. I., Khvorykh G. et al., PeerJ Computer Science 2024 Vol. 10 Article e2454
Despite the identification of several dozen genetic loci associated with ischemic stroke (IS), the genetic bases of this disease remain largely unexplored. In this research we present the results of genome-wide association studies (GWAS) based on classical statistical testing and machine learning algorithms (logistic regression, gradient boosting on decision trees, and tabular deep learning model ...
Added: December 11, 2024
[б.и.], 2023.
The Workshop will be held in the Meshcheryakov Laboratory of Information Technologies (MLIT) of the Joint Institute for Nuclear Research (JINR) on July 6-8, 2022.
The workshop primarily focuses on the use of machine learning in particle astrophysics and high energy physics, but is not limited to this area. Topics of interest are various applications of ...
Added: March 12, 2024
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
IITP RAS, 2023.
В сборнике представлены тезисы работ участников 11-ой Московской конференции по вычислительной молекулярной биологии MCCMB'23. Работы посвящены актуальным вопросам анализа аминокислотных и нуклеотидных последовательностей, структур биополимеров, молекулярной эволюции, методов высокопроизводительного секвенирования, системной биологии и биоалгоритмов. ...
Added: November 30, 2023