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BayesHammer: Bayesian clustering for error correction in single-cell sequencing
BMC Genomics. 2013. Vol. 14. No. Suppl. 1. P. S7.
Error correction of sequenced reads remains a difficult task, especially in single-cell sequencing projects with extremely non-uniform coverage. While existing error correction tools designed for standard (multi-cell) sequencing data usually come up short in single-cell sequencing projects, algorithms actually used for single-cell error correction have been so far very simplistic.
We introduce several novel algorithms based on Hamming graphs and Bayesian subclustering in our new error correction tool BAYESHAMMER. While BAYESHAMMER was designed for single-cell sequencing, we demonstrate that it also improves on existing error correction tools for multi-cell sequencing data while working much faster on real-life datasets. We benchmark BAYESHAMMER on both k-mer counts and actual assembly results with the SPADES genome assembler.
Priority areas:
IT and mathematics
Language:
English
Avdoshin S.M., Patrushev K. A., Proceedings of the Institute for System Programming of the RAS 2026 No. 4 часть 2 P. 245–256
The cardinality-constrained Markowitz problem is NP-hard and traditionally solved with commercial MIQP solvers. Following the 2022 export restrictions that rendered both commercial MIQP software and cloud quantum platforms (IBM Quantum, D-Wave Leap) inaccessible from the Russian Federation, practitioners require open-source alternatives. This paper systematically compares three solver families for the discrete mean-variance problem: two open-source ...
Added: August 27, 2026
Zaikin A., Vlasenko D., Zakharov D. et al., Diagnostics 2026 Vol. 16 No. 17 P. 1–15
Background/Objectives: Synolitic graphs (SGs) were developed for task-based fMRI, where
edge weights encode the discriminative power of pairwise regional features; whether similar
information can be recovered from resting-state data was untested. We benchmarked
SGs for autism spectrum disorder (ASD) classification using the multisite ABIDE-I dataset
(871 subjects: 403 subjects with ASD, 468 typical controls; 17 sites; CC200 atlas). Methods:
Using ...
Added: August 27, 2026
Тула: Тульский государственный педагогический университет им. Л.Н. Толстого, 2025.
Сборник содержит материалы, представленные на XXIV Международной конференции «Алгебра, теория чисел, дискретная геометрия и многомасштабное моделирование: современные проблемы, приложения и проблемы истории», посвящённой 110-летию со дня рождения академика Юрия Владимировича Линника и 110-летию со дня рождения профессора Андрея Борисовича Шидловского и 80-летию со дня рождения профессора Геннадия Ивановича Архипова. Материалы конференции будут полезны научным работникам, ...
Added: August 27, 2026
Eduard Sopin, Nazarin A., Begishev V. et al., IEEE Transactions on Vehicular Technology 2026 Vol. 75 No. 6 P. 10995–11007
Aimed at rate-greedy applications having extreme requirements for the data rate at the air interface, 5G New Radio (NR) systems may experience problems when the number of user equipment (UE) in the coverage of the cell increases due to limited capacity of the physical downlink control channel (PDCCH).The aim of this study is to explore ...
Added: August 26, 2026
Джонов А. Т., Avdoshin S. M., Информационные технологии 2026 Т. 32 № 8 С. 421–427
This systematic review presents an analysis of the "Vibe Coding" methodology — a contemporary approach to the iterative software development process using Large Language Models (LLMs). Code generation tools are transforming software development by enabling programmers to formulate tasks and describe the desired behavior of software in natural language, while LLMs generate source code corresponding ...
Added: August 25, 2026
Melman A., Evsyutin O., Journal of the Franklin Institute 2026 Vol. 363 No. 15 Article 109005
Open access to images creates opportunities for violation of the authors' rights. Digital watermarks can be used to securely publish images online. They are invisibly added into the images before publication and can be extracted at any time to verify ownership. However, achieving a balance between embedding imperceptibility and robustness to image processing operations is ...
Added: August 25, 2026
IEEE, 2026.
It is with great pleasure that we welcome all the participants of the 12th Conference on Control, Decision and Information Technologies (CoDIT 2026) at the Polytechnic University of Bari – Orabona Street 4, 70125 Bari, Italy, July 13-16, 2026. CoDIT has grown to become one of the largest conferences organized in Europe and in the ...
Added: August 24, 2026
Кубкин Я. В., Российский кардиологический журнал 2026 Т. 31 № 8S
Goal. To assess the contribution of polygenic risk scores to the short‑term mortality prediction model in patients with dilated cardiomyopathy (DCM).
Materials and methods. The study included 137 patients with DCM. The mean age was 56.8 ± 13.5 years; there were 115 men (83.9 %). The median follow‑up period was 17 [13; 22] months. During the follow‑up period, 26 ...
Added: August 24, 2026
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
Лукьяненко Д. В., Ragimova A., Мухорина А. et al., European Physical Journal: Special Topics 2026 P. 1–24
Electronic health records (EHRs) contain vast volumes of clinical information that encode complex relationships between diseases. Traditional approaches to the analysis of interrelated or co-occurring diseases have focused on pairwise associations between diagnoses, missing the higher-order structures that characterise multimorbid patients. The present paper offers a narrative review of existing statistical, machine-learning, and artificial intelligence ...
Added: August 20, 2026
CEUR-WS.org, 2026.
The second edition of the Generative Code Intelligence Workshop (GeCoIn 2026) was held in conjunction with the 35th International Joint Conference on Artificial Intelligence (IJCAI-ECAI 2026), in Bremen, Germany, August 16, 2026. The workshop arose from the desire to bring together a research community that has, in recent years, witnessed rapid progress in the application ...
Added: August 20, 2026
Ryumina E., Aksenov A., Koryakovskaya D. et al., IEEE Access 2026 Vol. 14 P. 124759–124778
Psychological characteristic estimation from multimodal in-the-wild behavior is usually studied using separate corpora, each annotated for a single target task. Such annotation fragmentation limits cross-task learning and cross-domain generalization across affective, dispositional, and interactional phenomena. To address this problem, we use emotion, apparent personality trait, and ambivalence recognition as representative tasks and introduce MM-PSYCHE, a ...
Added: August 20, 2026
Association for Computational Linguistics, 2026.
19th Conference of the European Chapter of the Association for Computational Linguistics, Workshop on Linguistic Analysis for Health (2026) ...
Added: August 19, 2026
Gorbacheva A., Krenke A., Puzachenko M. et al., Geoderma Regional 2026 Vol. 46 Article e01124
Legacy soil maps remain essential for national land-use planning. However, their thematic accuracy and spatial resolution are often insufficient for contemporary applications requiring reliable estimates. This study presents a digital soil-mapping approach to update legacy soil information without extensive field sampling, demonstrated for arable lands in the Republic of Tatarstan (4.5 million ha). The proposed ...
Added: August 18, 2026
Vlasenko D., Saranskaia I., Zakharov D., European Physical Journal: Special Topics 2026 P. 1–16
Hypergraphs provide a natural framework for representing neurophysiological interactions distributed across sets of sensors. A key methodological question is how hyperedges should be defined from frequency-resolved electroencephalography/magnetoencephalography (EEG/MEG) data. We demonstrate a construction strategy in which hyperedges are obtained from canonical coherence (caCOH), an extension of coherence that estimates coupling between multidimensional signal spaces. To ...
Added: August 18, 2026
Moshkin A., Fedorov M., Arlazarov V. et al., Algorithms 2026 Vol. 19 No. 7 Article 523
Artificial intelligence (AI) technologies, which are being actively developed in modern medicine today, increase the speed and quality of patient care. This article mainly seeks to demonstrate the use of various options of computer analysis of clinical images to solve practical problems of increasing the efficiency of routine diagnostics using retrospective analysis, as well as ...
Added: August 17, 2026
Springer, 2026.
The Smart Innovation, Systems and Technologies book series encompasses the topics of knowledge, intelligence, innovation and sustainability. The aim of the series is to make available a platform for the publication of books on all aspects of single and multi-disciplinary research on these themes in order to make the latest results available in a readily-accessible ...
Added: August 16, 2026
Khorunzheva K., Postnikov E., Zakharov D., Chaos, Solitons and Fractals 2026 Vol. 212 No. 2 P. 1–12
Identification of coherent states of spiking neural networks is a fundamental problem of
synchronization theory but conventional methods are computationally expensive. We apply
the crystallographic ideas of processing periodic structures to the analysis of various
states of spiking neuronal networks. In particular, the introduced approach is based on
the application of two-dimensional Fourier transform to rasterplots. By the position ...
Added: August 13, 2026
Yu Z., Wang J., Wang Z. et al., Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 2026 Vol. 384 P. 1–16
The integration of data-driven and knowledge-driven approaches in generative geospatial modelling (GGM) is often hindered by their mathematical incompatibilities. Here, we propose a geometric algebra (GA)-based framework that employs a unified multi-vector representation to fuse heterogeneous data and diverse knowledge. The framework facilitates structured reasoning and hypothesis generation through a task-adaptable, five-stage cycle: representation, reasoning, ...
Added: August 13, 2026
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
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
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
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