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Integrating microarray data and gene regulatory networks: Survey and critical considerations

Integrating microarray data and gene regulatory networks: Su...

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international workshop on Biomedical Engineering

作者： L. Koumakis G. Potamias M. Zervakis V. Moustakis Department of Production and Management Engineering Technical University of Crete Chania Greece Institute of Computer Science Foundation for Research and Technology Hellas FORTH Heraklion Greece Foundation for Research and Technology Hellas FORTH Heraklion Greece Department of Electronic and Computer Engineering Chania Technical University of Crete Greece Department of Production and Management Engineering Management Systems Laboratory Chania Technical University of Crete Greece

Microarray gene expression and gene regulatory interactions are two of the most significant data sources in the areas of molecular biology and biotechnology. In this article we survey existing methods and tools supporting the integration of these two data sources. We start with gene regulatory network reconstruction methods focusing on the reconstruction using microarray experiments. then we discuss methods and tools for gene expression data analysis based on gene regulatory network knowledge and we review algorithms and tools for gene regulatory networks selection using microarray data. Finally we introduce a new methodology for the identification of differentially expressed functional paths or sub-paths within a gene regulatory network using microarray data analysis.

关键词： Gene expression Bioinformatics data analysis Biological system modeling data mining Cancer

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Altitude Zoning for UTM 10

Altitude Zoning for UTM

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10th SESAR Innovation Days, SIDs 2020

作者： Sedov, Leonid Polishchuk, Valentin Acuna, Virgilio Communications and Transport Systems ITN Linköping University Norrköping Sweden Electrical Engineering Florida International University Miami United States

We give algorithms for splitting a geographical region into"approximately flat" rectangular zones. Each zone is assigned a feasible flight altitude, providing simple flight level guidance for future operations of unmanned aerial systems in low-level airspace. We consider a rural scenario with uneven ground level and an urban setting featuring many tall structures. In both cases, our solutions adapt to the underlying terrain or city landscape. In the rural scenario, operating on a fixed altitude within a rectangle allows the drone to stay within the upper limit of 120m while not flying too close to the ground;our objective is to minimize the complexity of the airspace. In the urban case, we aim at minimizing the volume of airspace reserved for drone operations, while allowing overflight over tall buildings in the city. Experiments with real landscape and city skyline data demonstrate output of our solutions with various input parameters. © 2020 IADIS. All rights reserved.

关键词： Drones

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Scalable, structured data placement over P2P storage utilities

Scalable, structured data placement over P2P storage utiliti...

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IEEE workshop on Future Trends of Distributed Computing Systems

作者： Zheng Zhang M. Mahalingam Zhichen Xu Wenting Tang Microsoft Research Asia China VMware Inc. Hewlett Packard Laboratories UK

ISBN: (纸本)0769521185

P2P overlays offer a convenient way to host an infrastructure that can scale to the size of the Internet and yet be manageable. Current proposals, however, do not offer support for structuring data, other than assuming a distributed hash table. In reality, both applications and users typically organize data in a structured form. One such popular structure is the tree as employed in a file system, and a database. A naive approach such as hashing the pathname not only ignores locality in important operations such as file/directory lookup, but also results in uncontrollable, massive object relocations when rename on a path component occur. In this paper, we investigate policies and strategies that place a tree onto the flat storage space of P2P systems. We found that, in general, there exists a tradeoff between lookup performance and balanced storage utilization, and attempt to balance these two requirements calls for an intelligent placement decision.

关键词： File systems Internet Proposals databases Peer to peer computing Intelligent structures IP networks Indexing XML data structures

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Detecting anomalies in cluster system using hybrid deep learning model 10th

Detecting anomalies in cluster system using hybrid deep lear...

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10th international Symposium on Parallel Architectures, algorithms and Programming, PAAP 2019

作者： Xiao, Chuming Huang, Jiaming Wu, Weigang School of Data and Computer Science Sun Yat-sen University Guangzhou China

Anomaly detection is of great importance for data centers. It could help operations discover system failures and perform root cause analysis. In recent years, deep learning has achieved great results in many fields. therefore, people begin to pay attention to applying deep learning for automatic anomaly detection. Convolution Neural Network (CNN) and Long Short-Term Memory (LSTM) are two classical structures in deep learning, which could effectively detect anomalies from system logs. However, the existing CNN-based and LSTM-based models have their shortcomings. In this paper, we propose a novel hybrid model for detecting anomalies from system logs, which mainly consist of CNN and LSTM. Considering logs as natural language sequences, the hybrid model embeds logs first and extracts features from embedding vectors with a convolution layer. then LSTM is used to automatically learn temporal log patterns from normal execution. the proposed model compares the log patterns that occur in practice with the log patterns it has learned before and detects anomalies when practical log patterns deviate from the model trained from log data under normal execution. To evaluate the performance of our model, we conduct experiments over large log data. the experiment results show that the hybrid model combines the advantages of CNN and LSTM models, which is an unsupervised model, reduces the requirements of training data set, and achieves great result in anomaly detection. © Springer Nature Singapore Pte Ltd. 2020.

关键词： Anomaly detection

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the SIGNAL approach to the design of system architectures

The SIGNAL approach to the design of system architectures

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international Conference and workshop on Engineering of Computer-Based Systems

作者： A. Gamatie T. Gautier IRISA INRIA Rennes France

Modeling plays a central role in system engineering. It significantly reduces costs and efforts in the design by providing developers with means for cheaper and more relevant experimentations. So, design choices can be assessed earlier. the use of a formalism, such as the synchronous language SIGNAL which relies on solid mathematical foundations for the modeling, allows validation. this is the aim of the methodology defined for the design of embedded systems where emphasis is put on formal techniques for verification, analysis, and code generation. this paper mainly focuses on the modeling of architecture components using SIGNAL. For illustration, we consider the modeling of a bounded FIFO queue, which is intended to be used for communication protocols. We bring out the capabilities of SIGNAL to allow specifications in an elegant way, and we check few elementary properties on the resulting model for correctness.

关键词： Signal design Embedded system Unified modeling language Systems engineering and theory Costs Solid modeling Mathematical model Protocols data engineering data structures

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Cache Performance and Efficiency Factors of Parallel data structures

Cache Performance and Efficiency Factors of Parallel Data St...

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international Symposium on Parallel and Distributed Processing with Applications, ISPA

作者： Ákos Dud's Juh'sz S'ndor

Multi-core CPUs are very efficient at executing multiple threads at the same time without significant performance penalty; this capability, however, results in increasing demand for the memory and the caches, which not only have to serve multiple parallel requests but also have to endure the consequences of parallel programming. the performance of parallel applications is not only limited by the CPU and the internal level of parallelism that the algorithms and data structures allow, but is also restricted by their memory characteristics. Altering the data structure for example to work with machine word-sized pointers required by atomic operations incurs additional cache misses, while a lock protecting a critical section not only consumes memory, but could also be responsible for increased memory traffic for cache-line invalidations when acquired or released. We investigate these effects and analyze the behavior of different parallelization mechanisms, both blocking and lock-free solutions, through the example of a basic data structure: a hash table.

关键词： data structures Instruction sets Parallel processing Scalability Hardware Synchronization Containers

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A hybrid architecture for visualization and decision making in battlespace environments

A hybrid architecture for visualization and decision making ...

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international Conference and workshop on Engineering of Computer-Based Systems

作者： J. Peng J.W. Rozenblit L. Suantak Department of Electrical and Computer Engineering University of Arizona Tucson Tucson AZ USA

this article presents a hybrid software/hardware architecture for commander's decision support in tactical operations. the architecture builds on the symbolic, object-oriented visualization software called Advanced Tactical Architecture for Combat Knowledge System (ATACKS). the extension discussed here is the design of a real-time robot agent layer that interacts wirelessly with ATACKS. this layer enacts decisions made by software agents (wargamers), continuously relays the execution states back to ATACKS, and updates its actions as advocated by replanning algorithms. the software layer is briefly described followed by the specification of the real-time requirements for the robotic architecture. the design and implementation are given with a small example that illustrates the hybrid system's operation.

关键词： Decision making Computer architecture Military computing Displays Knowledge based systems Robots Java Intelligent systems data visualization Military standards

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On the Design and Analysis of a Resilient Transport Protocol

On the Design and Analysis of a Resilient Transport Protocol

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international workshop on Reliable Networks Design and Modeling (RNDM)

作者： Truc Anh N. Nguyen James P. G. Sterbenz Information and Telecommunication Technology Center The University of Kansas Lawrence KS USA

We present the design and simulation analysis of ResTP, a multipath-capable configurable and adaptive transport-layer protocol developed for Future Internet resilience and survivability. ResTP is distinct from the conventional transport protocols such as TCP, UDP, and MPTCP by the flexibility in its design so that it can satisfy the requirements of various traffic classes, application types, and taking into account the underlying network characteristics, and its emphasis on achieving resilience, an essential property that is unfortunately lacking in the current Internet system. In this paper, we perform a simulation evaluation of ResTP, with the focus on its single-path mode, in comparison with TCP and UDP under various network conditions to show that ResTP can be used in place of these standard protocols with no performance loss. In some scenarios, ResTP outperforms the standards due to its flexibility in adopting the appropriate set of algorithms for specific application needs and network conditions.

关键词： Resilience Transport protocols Internet data models Standards Error correction

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Some Structural and Security Properties of the Modular Secret Sharing

Some Structural and Security Properties of the Modular Secre...

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international Symposium on Symbolic and Numeric algorithms for Scientific Computing (SYNASC)

作者： Tatsiana Galibus Gennadii Matveev Nikolay Shenets Department of Mathematical Modelling and Data Analysis Belarusian State University Minsk Belarus Department of Higher Mathematics Belarusian State University Minsk Belarus

We mainly study the modular secret sharing over the ring of univariate polynomials over the Galois field. the proposed modular schemes over these rings achieve improvements both in security and applicability compared to classical schemes over the ring of integers. Our threshold schemes are perfect i.e. secure in the sense of information theory and ideal i.e. efficient in the terms of memory storage (the size of the secret is equal to the size of the shares). then we consider the modular secret sharing schemes with pairwise co-prime moduli over the ring of polynomials and the ring of integers. We give a complete description of the access structures that can be realized by such modular schemes.

关键词： Cryptography Polynomials Mathematical model data analysis Scientific computing data security Mathematics Galois fields Information security Information theory

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Programming language support for multicast communication in distributed systems

Programming language support for multicast communication in ...

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international Conference on Distributed Computing Systems

作者： E.C. Cooper School of Computer Science Carnegie Mellon University Pittsburgh PA USA

A spectrum of abstractions for multicast communications is introduced in increasing order of both desirability and semantic level: functional mapping, iterators, and streams. Examples of distributed algorithms from the literature are used to illustrate the expressive power of each mechanism. Streams, in particular, provide first-class status for multicast communication in progress and can be implemented efficiently in typical multicast communication architectures. Related work and the criteria for multicast support are discussed. the layers of a typical distributed system that are relevant to language support for multicast communication are discussed.< >

关键词： Computer languages Multicast communication Multicast protocols Distributed algorithms Internet Transport protocols Computer science Safety Communication system control data structures

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