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A Local Outlier Factor-Based Detection of Copy Number Variations From NGS Data

IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021年第5期18卷 1811-1820页

作者： Yuan, Xiguo Li, Junping Bai, Jun Xi, Jianing Xidian Univ Sch Comp Sci & Technol Xian 710071 Peoples R China Shaanxi Prov Peoples Hosp Dept Med Oncol Xian 710068 Peoples R China Xidian Univ Sch Comp Sci & Technol Xian 710072 Peoples R China

Copy number variation (CNV) is a major type of genomic structural variations that play an important role in human disorders. Next generation sequencing (NGS) has fueled the advancement in algorithm design to detect CNVs at base-pair resolution. However, accurate detection of CNVs of low amplitudes remains a challenging task. This paper proposes a new computational method, CNV-LOF, to identify CNVs of full-range amplitudes from NGS data. CNV-LOF is distinctly different from traditional methods, which mainly consider aberrations from a global perspective and rely on some assumed distribution of NGS read depths. In contrast, CNV-LOF takes a local view on the read depths and assigns an outlier factor to each genome segment. With the outlier factor profile, CNV-LOF uses a boxplot procedure to declare CNVs without the reliance of any distribution assumptions. simulation experiments indicate that CNV-LOF outperforms five existing methods with respect to F1-measure, sensitivity, and precision. CNV-LOF is further validated on real sequencing samples, yielding highly consistent results with peer methods. CNV-LOF is able to detect CNVs of low and moderate amplitudes where the other existing methods fail, and it is expected to become a routine approach for the discovery of novel CNVs on whole sequencing genome.

关键词： Genomics Bioinformatics Sequential analysis Tumors computer science Computational modeling Next generation networking Copy number variation local outlier factor next generation sequencing boxplot procedure

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The new energy material with great potential positron 7

The new energy material with great potential positron

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2020 7th international conference on computer-Aided Design, Manufacturing, modeling and simulation, CDMMS 2020

作者： Wang, Yixiong Li, Jinxi Wang, Wenbing Chen, Peng State Key Laboratory of Intense Pulsed Irradiation Simulation and Effect Northwest Institute of Nuclear Technology Xi'an710024 China

Positron has attracted much attention in particle research for it was the first antiparticle discovered. Due to its extreme instability, positron is easy to annihilate with electron and release photons or form unstable positronium. Positron releases 1000 times more energy than nuclear fission of the same mass with no radioactive substance. As a new energy source, positron has more potential than other energy sources. With the rapid development of technology, the problem of how-to storage positron is solved gradually which makes a good foundation for annihilation of positron and electron beams. In this paper, the energy released by collision between electron and positron beams is deduced by theoretical analysis, based on the latest experimental results. The positron beam is the same energy of 10 MeV as the electron beam, which is adopt. After the pulses cross each other, the energy released is closed to 15mJ with current intensity 1020e+/ s . The energy difference of different radius of pulses is studied. This work has great potential value in further research. © 2021 Institute of Physics Publishing. All rights reserved.

关键词： Positrons

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Research on the Application of computer Virtual Reality Technology in Urban-Rural Integration of Rural Revitalization Strategy

Research on the Application of Computer Virtual Reality Tech...

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Networking, Communications and Information Technology (NetCIT), international conference on

作者： Wenjing Sun Weisong Wang Guangxi Science and Technology Normal University Laibin Guangxi China

Urban and rural planning under the rural revitalization plan is an important research topic at present. Based on computer virtual reality technology, this paper puts forward the system structure and technical route of establishing a simulation-based urban and rural planning information platform and auxiliary decision support system, and gives some key technical solutions. In this paper, after in-depth understanding of the data and application requirements required for urban and rural planning business, at the data level, for the 3D model data required for system application, the combination of airborne Lidar technology and oblique aerial photography technology is used to quickly realize urban and rural 3D real scenes Modelling, greatly improving the production efficiency of 3D models. On the basis of integrating the existing planning thematic data, using the three-dimensional GIS software platform Skyline, a real three-dimensional scene including terrain and landscape is established. According to the functions required for urban and rural planning, the API program interface and COM components provided by the platform are used to expand the API interface of COM components and flexibly encapsulate related functions to develop a three-dimensional planning auxiliary decision support system.

关键词： Decision support systems Photography Solid modeling Three-dimensional displays Atmospheric modeling Virtual reality Production

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Parallel hybrid Monte Carlo / Molecular Statics for simulation of Solute Segregation in Solids 4

Parallel hybrid Monte Carlo / Molecular Statics for Simulati...

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4th international conference on computer simulation in Physics and Beyond, CSP 2020

作者： Ganesan, Hariprasath Longsworth, Margarita Sutmann, Godehard Institute of Materials Research Materials Mechanics Helmholtz-Zentrum Geesthacht GeesthachtD-21502 Germany Universite Grenoble Alpes CNRS Grenoble INP SIMaP GrenobleF-38000 France Julich Supercomputing Centre Forschungszentrum Julich JulichD-52425 Germany Ruhr-University Bochum BochumD-44801 Germany

A parallel hybrid Monte Carlo/molecular statics method is presented for studying segregation of interstitial atoms in the solid state. The method is based on the efficient use of virtual atoms as placeholders to find energetically favorable sites for interstitials in a distorted environment. MC trial moves perform an exchange between a randomly chosen virtual atom with a carbon atom followed by a short energy minimization via MS to relax the lattice distortion. The proposed hybrid method is capable of modeling solute segregation in deformed crystalline metallic materials with a moderate MC efficiency. To improve sampling efficiency, the scheme is extended towards a biased MC approach, which takes into account the history of successful trial moves in the system. Parallelization of the hybrid MC/MS method is achieved by a Manager-Worker model which applies a speculative execution of trial moves, which are asynchronously executed on the cores. The technique is applied to an Fe-C system including a dislocation as a symmetry breaking perturbation in the system. © Published under licence by IOP Publishing Ltd.

关键词： Atoms

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FBM: A Fuzzy Brokering Model for Service Selection in Federated Cloud

FBM: A Fuzzy Brokering Model for Service Selection in Federa...

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3rd international conference on Machine Learning and Data Engineering, ICMLDE 2024

作者： Chauhan, Sameer Singh Dodiya, Aniruddhsinh Gamit, Pradeep Patel, Shreyas Chaudhari, Avinash Information Technology Department Government Engineering College Modasa Gujarat Arvalli383315 India Computer Engineering Department Government Engineering College Modasa Gujarat Arvalli383315 India

Federated Cloud is made of multiple integrated cloud platforms governed by different cloud providers. The federated environment is created between various cloud providers either through agreement or standardization or third parties such as cloud brokers. The federation comprises services with varying access patterns, different performance levels, similar characteristics, and varying costs of use. These features create a heterogeneous environment that leads to a challenging service selection task. Cloud broker works as an intermediary between service providers and users to select the best service. A repository is created by a Cloud broker to store characteristics and users' feedback on various parameters of services. A brokering model based on fuzzy logic has been proposed for ranking cloud services on both users' feedback and characteristics. Based on the given criteria the best service is selected. The users provide feedback on various QoS parameters of a service that is used by them in linguistic terms. A new user requesting a service gives QoS requirements in linguistic form. It also provides a preference of demand for those QoS parameters. The linguistic terms can not be used in computation directly. The proposed model contains modules that convert these linguistic terms into numerical form. The model contains a method that considers both the preference of users for QoS parameters and feedback provided by other users in finding the rank of services. The proposed method is evaluated through simulation. Results are compared with existing literature. They show that the method successfully applies fuzzy logic in QoS modeling. The obtained results are compared on various performance metrics and they outperform than existing literature. © 2024 The Authors. Published by ELSEVIER B.V.

关键词： Semantics

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RoboMamba: efficient vision-language-action model for robotic reasoning and manipulation 24

RoboMamba: efficient vision-language-action model for roboti...

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Proceedings of the 38th international conference on Neural Information Processing Systems

作者： Jiaming Liu Mengzhen Liu Zhenyu Wang Pengju An Xiaoqi Li Kaichen Zhou Senqiao Yang Renrui Zhang Yandong Guo Shanghang Zhang State Key Laboratory of Multimedia Information Processing School of Computer Science Peking University AI 2 Robotics State Key Laboratory of Multimedia Information Processing School of Computer Science Peking University and Beijing Academy of Artificial Intelligence (BAAI)

ISBN: (纸本)9798331314385

A fundamental objective in robot manipulation is to enable models to comprehend visual scenes and execute actions. Although existing Vision-Language-Action (VLA) models for robots can handle a range of basic tasks, they still face challenges in two areas: (1) insufficient reasoning ability to tackle complex tasks, and (2) high computational costs for VLA model fine-tuning and inference. The recently proposed state space model (SSM) known as Mamba demonstrates promising capabilities in non-trivial sequence modeling with linear inference complexity. Inspired by this, we introduce RoboMamba, an end-to-end robotic VLA model that leverages Mamba to deliver both robotic reasoning and action capabilities, while maintaining efficient fine-tuning and inference. Specifically, we first integrate the vision encoder with Mamba, aligning visual tokens with language embedding through co-training, empowering our model with visual common sense and robotic-related reasoning. To further equip RoboMamba with SE(3) pose prediction abilities, we explore an efficient fine-tuning strategy with a simple policy head. We find that once RoboMamba possesses sufficient reasoning capability, it can acquire manipulation skills with minimal fine-tuning parameters (0.1% of the model) and time. In experiments, RoboMamba demonstrates outstanding reasoning capabilities on general and robotic evaluation benchmarks. Meanwhile, our model showcases impressive pose prediction results in both simulation and real-world experiments, achieving inference speeds 3 times faster than existing VLA models. Our project web page: https://***/view/robomamba-web

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DRAMSys4.0: A Fast and Cycle-Accurate SystemC/TLM-Based DRAM Simulator 1

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20th international conference on Embedded computer Systems - Architectures, modeling, and simulation (SAMOS)

作者： Steiner, Lukas Jung, Matthias Prado, Felipe S. Bykov, Kirill Wehn, Norbert Tech Univ Kaiserslautern Kaiserslautern Germany Fraunhofer IESE Kaiserslautern Germany

ISBN: (数字)9783030609399

ISBN: (纸本)9783030609399;9783030609382

The simulation of DRAMs (Dynamic Random Access Memories) on system level requires highly accurate models due to their complex timing and power behavior. However, conventional cycle-accurate DRAM models often become the bottleneck for the overall simulation speed. A promising alternative are DRAM simulation models based on Transaction Level modeling, which can be fast and accurate at the same time. In this paper we present DRAMSys4.0, which is, to the best of our knowledge, the fastest cycle-accurate open-source DRAM simulator and has a large range of functionalities. DRAMSys4.0 includes a novel simulator architecture that enables a fast adaptation to new DRAM standards using a Domain Specific Language. We present optimization techniques to achieve a high simulation speed while maintaining full temporal accuracy. Finally, we provide a detailed survey and comparison of the most prominent cycle-accurate open-source DRAM simulators with regard to their supported features, analysis capabilities and simulation speed.

关键词： DRAM simulation SystemC TLM

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Research on Engine simulation and Assembly Based on computer Digital Twin 3

Research on Engine Simulation and Assembly Based on Computer...

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3rd international conference on Artificial Intelligence and Advanced Manufacture, AIAM 2021

作者： Lin, Mu He, Weidong Shan, Lijun Dalian Jiaotong University Liaoning Dalian China

ISBN: (纸本)9781450385046

The current digital engine model only considers the surface geometric errors generated during the part manufacturing process and does not include information such as feature registration constraints and physical properties. The virtual assembly simulation results based on this digital model will be quite different from the actual assembly. This paper proposes a digital twin assembly model expression method that integrates multi-level information. Based on the engine geometry layer model, the shape, pose, and physical characteristics of the engine parts that affect subsequent assembly are considered to generate a real physical engine. A digital twin with identical parts. First, collect feature point cloud, registration element, center of mass information and other information from real engine parts, divide them into geometric shape layer, pose constraint layer, and physical state layer to construct a hierarchical model of engine part features. Secondly, perform reverse modeling for different levels, including geometric shape models based on polynomial fitting and discrete cosine transformation, pose constraint models based on element feature registration, and physical state models based on contact deformation, so as to obtain engine parts containing real information Digital twin. Based on the digital twin of engine parts, the assembly twin frame is constructed by fusing assembly process information. Finally, the research on the engine assembly technology example driven by the digital twin is carried out. Through the interaction and integration of the physical process of engine assembly and the digital model, the intelligence, initiative and predictability of the engine assembly process are improved, and the assembly level is promoted. © 2021 ACM.

关键词： Geometry

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Intelligent Transport System using Cloud Computing & PSY Key Generation for V2V Communication

Intelligent Transport System using Cloud Computing & PSY Key...

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international conference on Cognitive Computing and Information Processing

作者： Prdeep Kumar K Salma Itagi Nagarathna C Ashwini S S Srinidhi N N IEEE Member-98464920 Department of Computer Science & Engineering (AIML) Dayanand Sagar University Kudlu Gate Bengaluru Department of Computer Science & Engineering Sai Vidya Institute of Technology VTU Rajanukunte Bengaluru Department of Information Science & Engineering Sai Vidya Institute of Technology VTU Rajanukunte Bengaluru Department of Computer Science & Engineering Manipal Institute of Technology Bengaluru Manipal Academy of Higher Education Manipal India

ISBN: (数字)9781665456487

ISBN: (纸本)9781665456494

The Internet of Things (IoT) connects many sensors to the internet so that it will provide services and applications for smart cities. Vehicles connected to the internet can communicate, sense, analyze and also make decision on their own. Vehicular Cloud (VC) is new idea proposed to enhance vehicular services through mobile cloud computing and networking. This proposed paper highlights an Intelligent Transportation System (ITS) which provides creative applications and services related to traffic management and also to access the information for various users. A model is developed taking picture of vehicles in detail, time of availability of vehicle in a given region. A new paradigm to collect the data for tracking the intelligent system in vehicular communication is considered. The simulation results are produced regarding involvement of vehicles in low percentage in dynamic VCN which provides data for intelligent system.

关键词： Cloud computing Smart cities simulation Computational modeling Transportation Information processing Internet of Things

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A Practical Tool-Chain for the Development of Coordination Scenarios Graphical Modeler, DSL, Code Generators and Automaton-Based Simulator 23rd

A Practical Tool-Chain for the Development of Coordination S...

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23rd international conference on Coordination Models and Language (COORDINATION)

作者： Kuehn, Eva Maria TU Wien Fac Informat Compilers & Languages Grp Vienna Austria

ISBN: (纸本)9783030781415;9783030781422

Coordination scenarios have high demands on concurrency and interaction. However, these are typical sources for flaws in both design and implementation. A modeling approach enables reasoning about distributed algorithms and finding deficiencies right from the beginning. The Peer Model has been introduced as a modeling tool for distribution, concurrency and blackboard-based collaboration and coordination, relying on known foundations like tuple spaces, Petri Nets and Actor Model. A runtime system exists that serves Java developers for prototyping, but still a feasible tool-chain was missing, like for most academic systems. This paper presents a practical new tool-chain for the Peer Model consisting of a graphical modelling tool, building on a drawing program that exports XML. A translator parses the XML and translates it into a newly developed domain specific language that is the basis for code generation. One target is a new, formal automaton-based runtime written in the Go programming language. It allows systematic simulation runs of user models. The demo shows a peer competition scenario, where several players play a game, a global state holds the players' scores, and in addition each peer maintains a decentralized state. Before taking a move in the game, a peer asserts its current local state to be the same like the global one. If this is the case, it carries out its action and distributes the information about it to all other players for further verification. The scenario captures core coordination mechanisms found in blockchain systems.

关键词： Peer Model tool-chain coordination modelling coordination simulation

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