?
Label-Free Quantification in the Crux Toolkit
Journal of Proteome Research. 2026. Vol. 25. No. 7. P. 3764–3768.
Ultimately, most tandem mass spectrometry (MS/MS) proteomics experiments aim to not just detect but also quantify the proteins in a given complex sample. Here, we describe an extension to the Crux MS/MS analysis toolkit to enable label-free quantification of peptides. We demonstrate that Crux’s new quantification command, which is modeled after the algorithms implemented in the widely used FlashLFQ software, is both efficient and accurate. In particular, we achieve a 1.9-fold speedup while reducing the memory usage by 26%. The new crux-lfq command is available in Crux v5.0.
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
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
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
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
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
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
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
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
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
Aly Ismailov, Poptsova M., Plos One 2026 Vol. 21 No. 9 Article e0355902
Added: October 2, 2026
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
International Joint Conferences on Artificial Intelligence, 2026.
Added: October 1, 2026
Ryumina E., Aksenov A., Сысоев Д. С. et al., IEEE Computer Society, 2026.
Ambivalence/hesitancy recognition in unconstrained videos is a challenging problem due to the subtle, multimodal, and context-dependent nature of this behavioral state. In this paper, a multimodal approach for video-level ambivalence/hesitancy recognition is presented for the 10th ABAW Competition. The proposed approach integrates four complementary modalities: scene, face, audio, and text. Scene dynamics are captured with ...
Added: September 30, 2026
Ivanov F., Kotov F., IEEE Access 2026 Vol. 14 P. 104662–104679
U-UV codes, based on the Plotkin (U, U + V) construction, provide a unified framework that includes polar and Reed–Muller codes and enables flexible design through the choice of component codes. While modern capacity-approaching codes achieve excellent performance at large block lengths, their efficiency at short and moderate lengths remains limited, especially under low-latency constraints. ...
Added: September 30, 2026
Djambong Tenkeu H., Institute for System Programming of the RAS, 2026.
Added: September 29, 2026
Ivanashev Y., Доклады Российской академии наук. Математика, информатика, процессы управления (ранее - Доклады Академии Наук. Математика) 2026 Т. 529 С. 93–101
Язык L является нижним для релятивизируемого сложностного класса C, если CL=C. Для классов #P, GapP и SpanP известны точные нижние классы языков: Low(#P) = UP ∩ coUP, Low(GapP) = SPP и Low(SpanP) = NP ∩ coNP. В этой статье мы доказываем, что Low(TotP) = P, и приводим характеризации нижних классов функций для #P, GapP, TotP ...
Added: September 28, 2026
Piliugin L., Antropov A., Lobashev E. et al., Journal of Nuclear Materials 2026 Vol. 632 Article 156876
The effects of dislocations on the mobility of gas nanobubbles pinned to them are considered as novel unex- plored mechanisms of accelerated fission gas release and investigated using classical molecular dynamics of helium bubbles in FCC aluminum. Non-equilibrium methods are developed to calculate the mobility of a pinned bubble both along and across the dislocation ...
Added: September 28, 2026
Kashpurovich I., Oleynichenko A., Stegailov V., Supercomputing Frontiers and Innovations 2026 Vol. 13 No. 1 P. 52–73
We report a high-performance implementation of the resolution-of-the-identity Hartree–Fock method that fully exploits the permutational symmetry of three-center electron repulsion integrals (ERI). The present implementation adopts a hybrid MPI+OpenMP parallelization strategy. Two different algorithmic approaches (with and without the pre-transformation of ERIs) are compared. A custom data layout introduced previously is employed. Designed to efficiently ...
Added: September 28, 2026
Bhimani K. R., Peresadina A., Burmak K. et al., 2026 Vol. 519 Article 117532
Database-searching based precursor ion identification in tandem mass spectrometry data analysis is limited to the search space. Once a single amino acid variation (SAAV) or a modification is not included to the search space, then its observed spectra will not be annotated correctly. Several methods have been developed to identify and localize post-translational modifications (PTMs); ...
Added: October 2, 2025
Kertesz-Farkas A., Acquaye F. L., Ostapenko V. et al., Journal of Proteome Research 2025 Vol. 24 No. 9 P. 4831–4837
Over the past 30 years, software for searching tandem mass spectrometry data against a protein database has improved dramatically in speed and statistical power. However, existing tools can still struggle to analyze truly massive data sets when either the number of spectra or the number of proteins being analyzed grows too large. Here, we describe ...
Added: September 11, 2025
Acquaye F. L., Kertesz-Farkas A., Stafford Noble W., Journal of Proteome Research 2023 Vol. 22 No. 2 P. 577–584
The first step in the analysis of protein tandem mass spectrometry data typically involves searching the observed spectra against a protein database. During database search, the search engine must digest the proteins in the database into peptides, subject to digestion rules that are under user control. The choice of these digestion parameters, as well as ...
Added: December 2, 2022
Kertesz-Farkas A., Acquaye F. L., Kishankumar Bhimani et al., Journal of Proteome Research 2023 Vol. 22 No. 2 P. 561–569
The Crux tandem mass spectrometry data analysis toolkit provides a collection of algorithms for analyzing bottom-up proteomics tandem mass spectrometry data. Many publications have described various individual components of Crux, but a comprehensive summary has not been published since 2014. The goal of this work is to summarize the functionality of Crux, focusing on developments ...
Added: December 2, 2022
Kudriavtseva P., Kashkinov M., Kertész-Farkas A., Journal of Proteome Research 2021 Vol. 20 No. 10 P. 4708–4717
Spectrum annotation is a challenging task due to the presence of unexpected peptide fragmentation ions as well as the inaccuracy of the detectors of the spectrometers. We present a deep convolutional neural network, called Slider, which learns an optimal feature extraction in its kernels for scoring mass spectrometry (MS)/MS spectra to increase the number of ...
Added: August 30, 2021