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Correction: Enhancing SNV identification in whole-genome sequencing data through the incorporation of known genetic variants into the minimap2 index

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BMC bioinformatics 2024年第1期25卷 268页

作者： Egor Guguchkin Artem Kasianov Maksim Belenikin Gaukhar Zobkova Ekaterina Kosova Vsevolod Makeev Evgeny Karpulevich Ivannikov Institute for System Programming Moscow Russia. guguchkin@ispras.ru. Institute for Information Transmission Problems Moscow Russia. Evogen LLC Moscow Russia. Vavilov Institute of General Genetics Moscow Russia. Institute of Biochemistry and Genetics of Ufa Scientific Centre Ufa Russia. Cancer Research UK National Biomarker Centre University of Manchester Manchester Manchester M20 4BX UK. Ivannikov Institute for System Programming Moscow Russia.

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Verifying cryptographic protocols by Tamarin Prover

Verifying cryptographic protocols by Tamarin Prover

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Ivannikov Memorial Workshop (IVMEM)

作者： Evgenii Vinarskii Alexey Demakov Alexander Kamkin Nina Yevtushenko Lomonosov Moscow State University Moscow Russia Ivannikov Institute for System Programming of the RAS Moscow Russia Ivannikov Institute for System Programming of the RAS Moscow Institute of Physics and Technology Higher School of Economics Moscow Russia Higher School of Economics Moscow Russia

ISBN: (数字)9781728190884

ISBN: (纸本)9781728190891

Cryptographic protocols are utilized for establishing a secure session between “honest” agents which communicate strictly according to the protocol rules as well as for ensuring the authenticated and confidential transmission of messages. The specification of a cryptographic protocol is usually presented as a set of requirements for the sequences of transmitted messages including the format of such messages. Note that protocol can describe several execution scenarios. All these requirements lead to a huge formal specification for a real cryptographic protocol and therefore, it is difficult to verify the security of the whole cryptographic protocol at once. In this paper, to overcome this problem, we suggest verifying the protocol security for its fragments. Namely, we verify the security properties for a special set of so-called traces of the cryptographic protocol. Intuitively, a trace of the cryptographic protocol is a sequence of computations, value checks, and transmissions on the sides of “honest” agents permitted by the protocol. In order to choose such set of traces, we introduce an Adversary model and the notion of a similarity relation for traces. We then verify the security properties of selected traces with Tamarin Prover. Experimental results for the EAP and Noise protocols clearly show that this approach can be promising for automatic verification of large protocols.

关键词： Planing Computational modeling Complexity theory Security Formal specifications Cryptography Cryptographic protocols

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Network Intrusion Detection Based on Feature Selection and Hybrid Metaheuristic Optimization

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Computers, Materials & Continua 2023年第2期74卷 2677-2693页

作者： Reem Alkanhel El-Sayed M.El-kenawy Abdelaziz A.Abdelhamid Abdelhameed Ibrahim Manal Abdullah Alohali Mostafa Abotaleb Doaa Sami Khafaga Department of Information Technology College of Computer and Information SciencesPrincess Nourah bint Abdulrahman UniversityP.O.Box 84428Riyadh11671Saudi Arabia Department of Communications and Electronics Delta Higher Institute of Engineering and TechnologyMansoura35111Egypt Department of Computer Science Faculty of Computer and Information SciencesAin Shams UniversityCairo11566Egypt Department of Computer Science College of Computing and Information TechnologyShaqra University11961Saudi Arabia Computer Engineering and Control Systems Department Faculty of EngineeringMansoura UniversityMansoura35516Egypt Information Systems Department College of Computer and Information SciencesPrincess Nourah bint Abdulrahman UniversityP.O.Box 84428Riyadh11671Saudi Arabia Department of System Programming South Ural State UniversityChelyabinsk454080Russia Department of Computer Sciences College of Computer and Information SciencesPrincess Nourah bint Abdulrahman UniversityP.O.Box 84428Riyadh11671Saudi Arabia

Applications of internet-of-things(IoT)are increasingly being used in many facets of our daily life,which results in an enormous volume of *** computing and fog computing,two of the most common technologies used in IoT applications,have led to major security *** are on the rise as a result of the usage of these technologies since present security measures are *** artificial intelligence(AI)based security solutions,such as intrusion detection systems(IDS),have been proposed in recent *** technologies that require data preprocessing and machine learning algorithm-performance augmentation require the use of feature selection(FS)techniques to increase classification accuracy by minimizing the number of features *** the other hand,metaheuristic optimization algorithms have been widely used in feature selection in recent *** this paper,we proposed a hybrid optimization algorithm for feature selection in *** proposed algorithm is based on grey wolf(GW),and dipper throated optimization(DTO)algorithms and is referred to as *** proposed algorithm has a better balance between the exploration and exploitation steps of the optimization process and thus could achieve better *** the employed IoT-IDS dataset,the performance of the proposed GWDTO algorithm was assessed using a set of evaluation metrics and compared to other optimization approaches in 2678 CMC,2023,vol.74,no.2 the literature to validate its *** addition,a statistical analysis is performed to assess the stability and effectiveness of the proposed *** results confirmed the superiority of the proposed approach in boosting the classification accuracy of the intrusion in IoT-based networks.

关键词： Feature selection grey wolf optimization dipper throated optimization intrusion detection internet-of-things(IoT)

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Decentralized Personalized Federated Learning for Min-Max Problems

arXiv

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arXiv 2021年

作者： Borodich, Ekaterina Beznosikov, Aleksandr Sadiev, Abdurakhmon Sushko, Vadim Savelyev, Nikolay Takac, Martin Gasnikov, Alexander Moscow Institute of Physics and Technology Moscow Russia Mohamed bin Zayed University of Artificial Intelligence Abu Dhabi United Arab Emirates Ivannikov Institute for System Programming RAS Moscow Russia Bosch Center for Artificial Intelligence Renningen Germany

Personalized Federated Learning (PFL) has witnessed remarkable advancements, enabling the development of innovative machine learning applications that preserve the privacy of training data. However, existing theoretical research in this field has primarily focused on distributed optimization for minimization problems. This paper is the first to study PFL for saddle point problems encompassing a broader range of optimization problems, that require more than just solving minimization problems. In this work, we consider a recently proposed PFL setting with the mixing objective function, an approach combining the learning of a global model together with locally distributed learners. Unlike most previous work, which considered only the centralized setting, we work in a more general and decentralized setup that allows us to design and analyze more practical and federated ways to connect devices to the network. We proposed new algorithms to address this problem and provide a theoretical analysis of the smooth (strongly) convex–(strongly) concave saddle point problems in stochastic and deterministic cases. Numerical experiments for bilinear problems and neural networks with adversarial noise demonstrate the effectiveness of the proposed methods. Copyright © 2021, The Authors. All rights reserved.

关键词： Numerical methods

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Sydr: Cutting edge dynamic symbolic execution

arXiv

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arXiv 2020年

作者： Vishnyakov, Alexey Fedotov, Andrey Kuts, Daniil Novikov, Alexander Parygina, Darya Kobrin, Eli Logunova, Vlada Belecky, Pavel Kurmangaleev, Shamil Ivannikov Institute for System Programming of the RAS Lomonosov Moscow State University Russia Moscow Institute of Physics and Technology Moscow Russia

The security development lifecycle (SDL) is becoming an industry standard. Dynamic symbolic execution (DSE) has enormous amount of applications in computer security (fuzzing, vulnerability discovery, reverse-engineering, etc.). We propose several performance and accuracy improvements for dynamic symbolic execution. Skipping non-symbolic instructions allows to build a path predicate 1.2–3.5 times faster. Symbolic engine simplifies formulas during symbolic execution. Path predicate slicing eliminates irrelevant conjuncts from solver queries. We handle each jump table (switch statement) as multiple branches and describe the method for symbolic execution of multi-threaded programs. The proposed solutions were implemented in Sydr tool. Sydr performs inversion of branches in path predicate. Sydr combines DynamoRIO dynamic binary instrumentation tool with Triton symbolic engine. We evaluated Sydr features on 64-bit Linux executables. © 2020, CC BY-NC-ND.

关键词： Life cycle

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Research on the wake of the ducted propeller with POD and DMD

Research on the wake of the ducted propeller with POD and DM...

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Ivannikov ISPRAS Open Conference (ISPRAS)

作者： Tianyuan Wang Hongda Shi Qin Zhang Bo Yang Xin Liu Kraposhin Matvey College of Engineering Ocean University of China Qingdao China Ivannikov Institute for System Programming of the RAS Moscow Russia

ISBN: (数字)9781665412919

ISBN: (纸本)9781665448215

The paper attempts to apply the Proper Orthogonal Decomposition (POD) and Dynamic Mode Decomposition (DMD) to the ducted propeller wake analysis. The ducted propeller produces a complex wake flow field with multifrequency vortex structure coupling under the influence between blades and nozzle. Traditional analysis methods such as time-averaged flow, phase-averaged flow are only displaying the coupling results. In contrast, data mining technologies such as POD and DMD can extract independent flow patterns from the massive data obtained from physical experiments and numerical simulations. The paper focuses on the influence of computational subdomain (based on the OpenFOAM), snapshot sampling interval and data coverage revolutions on the modal convergence in the data preprocessing before employing POD and DMD. Taking a single ducted propeller wake data with the advance coefficient of J=0.4 as an example, it is found that the sampling interval of snapshots are independent of modal convergence after reaching a certain level and only affect the frequency range of the captured modes. The scope of the computational subdomain and the revolutions of data covered by snapshot matrix are vital factors to affect the modal convergence. At last, under the premise of modal convergence, the paper reconstructs the ducted propeller wake flow field by POD and DMD respectively, where errors between the original data can be ignored.

关键词： Couplings Propellers Blades Data preprocessing Numerical simulation Data mining Convergence

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Using Ansible as Part of TOSCA Orchestrator

Using Ansible as Part of TOSCA Orchestrator

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Ivannikov ISPRAS Open Conference (ISPRAS)

作者： Valeriya Shvetcova Oleg Borisenko Maxim Polischuk Ivannikov Institute for System Programming of the RAS Moscow Russia Bauman Moscow State Technical University Moscow Russia

ISBN: (数字)9781665412919

ISBN: (纸本)9781665448215

Cloud computing is used in many areas and by many specialists to ease application distribution and deployment. Cloud providers basically aim at providing resources varying from others. So it becomes very difficult to deploy multicloud applications or move to the cloud from own hardware clusters. TOSCA standard offers cloud resources model that unifies many cloud providers. In this paper we propose TOSCA orchestrator Clouni. Clouni takes TOSCA templates from the user and generates Ansible playbooks. Ansible is then used as a configuration tool for deployment automation. Clouni makes it easy for cloud users to deploy complex topologies.

关键词： Cloud computing Automation Tools Topology Network function virtualization Software defined networking Standards

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Computationally secure threshold secret sharing scheme with minimal redundancy 2

Computationally secure threshold secret sharing scheme with ...

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2nd International Workshop on Information, Computation, and Control systems for Distributed Environments, ICCS-DE 2020

作者： Babenko, M. Tchernykh, A. Golimblevskaia, E. Hung, Nguyen Viet Chaurasiya, V.K. North-Caucasus Federal University Stavropol Russia CICESE Research Center Ensenada BC Mexico South Ural State University Chelyabinsk Russia Ivannikov Institute for System Programming Moscow Russia LeQuyDon Technical University Hanoi Viet Nam Indian Institute of Information Technology Allahabad India

When designing and using distributed storage systems with cloud technology, the security issues become crucial. One of the promising mechanisms is the computationally secure threshold secret sharing scheme. We propose a computationally secure secret sharing scheme based on the minimally redundant modular code. It reduces the computational complexity of data encoding and decoding and reduce data redundancy. We show that it is computationally secure and provides data redundancy equivalent to the redundancy of the Rabin system. We demonstrate that the minimally redundant modular code does not satisfy the criterion of compactness of a sequence, but it can be used as an asymptotically ideal secret sharing scheme. Copyright © 2020 for this paper by its authors. Use permitted under Creative Commons License Attribution 4.0 International (CC BY 4.0).

关键词： Redundancy

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Evaluation of interpretability methods for adversarial robustness on real-world datasets

Evaluation of interpretability methods for adversarial robus...

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Ivannikov Memorial Workshop (IVMEM)

作者： Anna Chistyakova Maria Cherepnina Konstantin Arkhipenko Sergey D. Kuznetsov Chang-Seok Oh Sebeom Park Lomonosov Moscow State University Moscow Russia Ivannikov Institute for System Programming of the RAS Moscow Russia Moscow Institute of Physics and Technology (State University) Moscow Russia Plekhanov Russian University of Economics Moscow Russia Samsung Research Seoul South Korea

ISBN: (纸本)9781665423281

Adversarial training is considered the most powerful approach for robustness against attacks on deep neural networks involving adversarial examples. However, recent works have shown that the similar robustness level can be achieved by other means, namely interpretability-based regularization. We evaluate these interpretability-based approaches on real-world ResNet models trained on CIFAR-10 and ImageNet datasets. Our results show that interpretability can marginally improve robustness when combined with adversarial training, however, they bring additional computational complexity making these approaches questionable for such models and datasets.

关键词： Training Deep learning Computational modeling Conferences Neural networks Robustness Computational complexity

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The multifractal analysis in Geophysical Flows. In memory of Prof. Jose Manuel Redondo Apraiz

The multifractal analysis in Geophysical Flows. In memory of...

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Ivannikov ISPRAS Open Conference (ISPRAS)

作者： Jackson Tellez-Alvarez Sergei V. Strijhak FLUMEN Research Institute Technical University of Catalonia Barcelona Spain Ivannikov Institute for System Programming of the Russian Academy of Sciences Moscow Russia

ISBN: (数字)9781665412919

ISBN: (纸本)9781665448215

This paper describes the multifractal methodology for analysis of different geophysical flows such as vertical plumes in water, wakes behind 3D Sparse grid turbulence generators in wind tunnel, wakes behind wind turbines and vortices in the Atmospheric Boundary Layer. A brief description of Kolmogorov K41, K62 theory of turbulence, the energy spectra, the structure function is given. The estimation of the fractal dimension was made using the ImaCalc Software for different cases with geophysical flows. The advantage of this method is that we can estimate the fractal dimension using the numerical results of different open source solvers in OpenFOAM library. The calculated spectra are presented from the ImaCalc program. Furthermore, this paper dedicates to the memory of Prof. Jose Manuel Redondo Apraiz (1956-2020) who worked in UPC, Barcelona, Spain and was a leader of the SIG 14 “Stably Stratified and Rotating Turbulence” in ERCOFTAC.

关键词： Three-dimensional displays Wind tunnels Fractals Libraries Software Generators Wind turbines

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