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A Novel model for Predicting LncRNA-disease Associations Based on the LncRNA-MiRNA-disease Interactive Network

CURRENT BIOINFORMATICS 2019年第3期14卷 269-278页

作者： Wang, Lei Xuan, Zhanwei Zhou, Shunxian Kuang, Linai Pei, Tingrui Xiangtan Univ Coll Informat Engn Xiangtan 411105 Peoples R China Xiangnan Univ Coll Software & Commun Engn Xiangtan 423000 Peoples R China

Background: Accumulating experimental studies have manifested that long-non-coding RNAs (IncRNAs) play an important part in various biological process. It has been shown that their alterations and dysrcgulations are closely related to many critical complex diseases. Objective: It is of great importance to develop effective computational models for predicting potential lncRNA-disease associations. Method: Based on the hypothesis that there would be potential associations between a lncRNA and a disease if both of them have associations with the same group of microRNAs, and similar diseases tend to be in close association with functionally similar IneRNAs. A novel method for calculating similarities of both lncRNAs and diseases is proposed, and then a novel prediction model LDLMD for inferring potential IncRNA-disease associations is proposed. Results: LDLMD can achieve an AUC of 0.8925 in the Leave-One-Out Cross Validation (LOOCV), which demonstrated that the newly proposed model LDLMD significantly outperforms previous state-of-the-art methods and could be a great addition to the biomedical research field. Conclusion: Here, we present a new method for predicting IncRNA-disease associations, moreover, the method of our present decrease the time and cost of biological experiments.

关键词： Similarity computing model prediction lncRNA-disease associations LncRNA-MiRNA-disease interactive network

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A Computer Simulation model for Design of Variable Buoyancy System for Autonomous Underwater Vehicles/Gliders

A Computer Simulation Model for Design of Variable Buoyancy ...

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OCEANS Conference

作者： Tiwari, B. K. Sharma, R. Asokan, T. IIT Madras Dept Ocean Engn Design & Simulat Lab Madras 600036 Tamil Nadu India IIT Madras Dept Engn Design Madras 600036 Tamil Nadu India

ISBN: (纸本)9781467397247

The efficient control of buoyancy with low power is critically important in the design of new age 'Autonomous Underwater Vehicles/Gliders (AUVs/Gs)'. This paper presents a 'Computer Simulation model (CSM)' for the primary design of 'Variable Buoyancy System (VBS)' for AUVs/AUGs to efficient control buoyancy and the simulation model is built in the environment of integration, modular architecture and specific range of applicability. The CSM for design of VBS is integrated in the overall design process of AUVs/AUGs. Finally, we present design example of the VBS for a AUVhaving two ballast tanks (each of a buoyancy capacity of +/- B = 10kg), maximum rate of change of buoyancy = 9 kg/minute;and our presented results show that the proposed CSM for the design of VBS for AUVs/AUGs simulates the design process efficiently and leads to an efficient and economic design with the desired and specific range of applications.

关键词： Variable buoyancy system Underwater vehicle computing model System dynamics Non-linear programming

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Mutual Comparison of Two Pavement computing models

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Procedia Engineering 2017年 190卷 547-553页

作者： Veronika Valašková Gabriela Lajčáková University of Žilina Univerzitná 8215/1 010 26 Žilina Slovak Republic

Moving load effect on pavements is actual engineering problem. For the numerical simulation of moving load effect on pavements the various computing models were created. In the proposed paper two computing models of pavement are described and mutually compared. One computing model is created in the sense of the beam on elastic foundation and the second in the sense of Finite Element method. The plane computing model of vehicle is adopted.

关键词： Moving load pavement computing model vehicle beam on elastic foundation Finite Element Methods

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A Novel Approach Based on Bipartite Network to Predict Human Microbe-Disease Associations

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CURRENT BIOINFORMATICS 2018年第2期13卷 141-148页

作者： Wang, Lei Ping, Pengyao Kuang, Linai Ye, Songtao Lqbal, Faisal Muhammad Buland Pei, Tingrui Xiangtan Univ Coll Informat Engn Xiangtan Peoples R China Xiangtan Univ Key Lab Intelligent Comp & Informat Proc Xiangtan Peoples R China

Background: Accumulating studies have indicated that the human microbiome plays critical roles in human health and disease. It is significantly important to analyze the relationships between microbe and disease, which is helpful for the understanding of disease mechanism, diagnosis and therapy. Predicting potential microbe-disease associations would not only boost understanding of the disease mechanism but also it will help to find biomarkers for disease diagnosis and prognosis. However, systems understanding of microbe-disease relationships is mostly undefined. Objective: It is important to analyze the relationships between microbe and disease, for this, we proposed a new method to predict potential microbe-disease associations. Method: In this article, we constructed a gene-disease bipartite network and a microbe-disease bipartite network based on known human gene-disease associations and microbe-disease interactions, respectively. Then, a model for predicting potential microbe-disease associations was designed based on the two bipartite networks. In order to evaluate the prediction performance of our proposed method, Leave-One-Out Cross Validation (LOOCV) and K-fold Cross Validation procedures were implemented. Results: Simulation results show that our method can achieve a reliable performance with AUC of 0.8993 based on microbe-disease associations downloaded from HMDAD database and human genedisease relationships downloaded from DisGeNET database. Furthermore, it also can reach to a sound performance with AUC of 0.8640 only based on the known microbe-disease associations in the framework of LOOCV, which is clearly better than the performance of state of the art KATZHMDA model with AUC of 0.8382. Conclusion: It is anticipated that our proposed model could be used to predict more potential microbedisease associations, which is helpful for the understanding of disease mechanism, diagnosis and prognosis.

关键词： Bipartite network similarity computing model prediction microbe-disease associations

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Universal resources for quantum computing

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Communications in Theoretical Physics 2023年第12期75卷 57-74页

作者： Dong-Sheng Wang CAS Key Laboratory of Theoretical Physics Institute of Theoretical PhysicsChinese Academy of SciencesBeijing 100190China

Unravelling the source of quantum computing power has been a major goal in the field of quantum information *** recent years,the quantum resource theory(QRT)has been established to characterize various quantum resources,yet their roles in quantum computing tasks still require *** so-called universal quantum computing model(UQCM),*** circuit model,has been the main framework to guide the design of quantum algorithms,creation of real quantum computers *** this work,we combine the study of UQCM together with *** find,on one hand,using QRT can provide a resource-theoretic characterization of a UQCM,the relation among models and inspire new ones,and on the other hand,using UQCM offers a framework to apply resources,study relation among these resources and classify *** develop the theory of universal resources in the setting of UQCM,and find a rich spectrum of UQCMs and the corresponding universal *** on a hierarchical structure of resource theories,we find models can be classified into *** this work,we study three natural families of UQCMs in detail:the amplitude family,the quasi-probability family,and the Hamiltonian *** include some well known models,like the measurement-based model and adiabatic model,and also inspire new models such as the contextual model that we *** family contains at least a triplet of models,and such a succinct structure of families of UQCMs offers a unifying picture to investigate resources and design *** also provides a rigorous framework to resolve puzzles,such as the role of entanglement versus interference,and unravel resource-theoretic features of quantum algorithms.

关键词： quantum resource computing model quantum algorithm

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Survey of external memory large-scale graph processing on a multi-core system

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JOURNAL OF SUPERcomputing 2020年第1期76卷 549-579页

作者： Huang, Jianqiang Qin, Wei Wang, Xiaoying Chen, Wenguang Tsinghua Univ Dept Comp Sci & Technol Beijing 100084 Peoples R China Qinghai Univ Dept Comp Technol & Applicat Xining 810016 Qinghai Peoples R China

The fast development of big data computing contributes to the fact that large-scale graph processing has become a basic computing model in both academic and industrial communities, and it has been applied in many actual big data computing works, such as social network analysis, Web search, and product promotion. These computing works include large-scale graphs of billions of vertices and trillions of edges. Such scale has brought many challenges to large-scale graph processing. This paper mainly introduces the essential features and challenges of large-scale graph processing and how we can handle billions of edges on a multi-core machine, for which we represent out-of-core processing system and semi-external memory processing systems. This paper also summarizes the key technologies in graph processing systems and forecasts the future development of large-scale graph processing systems.

关键词： Graph data processing Parallel computing computing model Graph algorithms

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Verification and Application of computing models of Genglubu in the South China Sea

Verification and Application of Computing Models of Genglubu...

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第四届材料科学应用与能源材料国际研讨会

作者： Bing Yuan Wenhua Li School of Computer Science and Cyberspace Security Hainan University

Starting from the four key elements of Genglu, this paper, with evidence from Genglubu itself and relevant documents, presents a discussion on reliability of range computing model and deviation estimation model in Genglubu research. These two digital models are established with mathematical method, and their establishment is based on the four key elements of Genglubu and involve the disciplines of geography, nautical navigation and toponymy. This discussion shows that these two models are scientific and reliable and can be applied to examine the genglus in doubt and clarify doubts in different versions of Genglubu. This research is of significance in promoting multidisciplinary research on Genglubu.

关键词： Genglubu computing model Verification Application

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Dynamic Placement Optimization for Bio-Inspired Self-Repairing Hardware

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IEEE ACCESS 2020年 8卷 11007-11018页

作者： Liu Xiubin Qian Yanling Feng Xiangli Zhuo Qingqi Li Yue Natl Univ Def Technol Sci & Technol Integrated Logist Support Lab Changsha 410073 Peoples R China Tsinghua Univ Sch Aerosp Engn Beijing 100084 Peoples R China

Bio-inspired self-repairing hardware is a distributed self-adaptive system, characterized by powerful fault-tolerant ability and environment adaptivity. However, it suffers from some difficulties such as large resource consumption and degraded circuit performances. From the viewpoint of cybernetics and computer science, the cellular differentiation and substitution process of bio-inspired self-repairing hardware can be converted into dynamic placement problems on a reconfigurable system. Current systems can only generate some predefined fault-free placements from a finite number of initial placements. The aim of this paper was to achieve high-quality placements from arbitrary initial placements. Based on P systems, an analysis has been made on the limitations of current systems and an improved computing system has been developed to achieve the ergodic property. Its computational power has been verified by a constructive proof. Moreover, centering on the problem how to improve the placement quality on a distributed platform, the optimization model, task allocation, optimization strategy, and membrane optimization algorithm have been designed and developed. The optimization performances were verified and the calculation amount was exhibited by experiments. Finally, it indicated by comparison that the proposed approach would reduce the resource consumption and maintain good circuit performances.

关键词： Bio-inspired self-repairing hardware dynamic placement optimization P systems computing model membrane optimization algorithms

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Decoder Design Based on Spiking Neural P Systems

IEEE TRANSACTIONS ON NANOBIOSCIENCE

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IEEE TRANSACTIONS ON NANOBIOSCIENCE 2016年第7期15卷 639-644页

作者： Li, Jun Huang, Yourui Xu, Jiachang Anhui Univ Sci & Technol Sch Elect & Informat Engn Huainan 232001 Anhui Peoples R China

The spiking neural P systems (SN P systems, for short) refer to the parallel-distributed biocomputing models, which have currently become research hotspots in the biocomputing field. In computing systems, logical operations and arithmetic operations are the most important parts, while the decoders composed of logical circuits are their indispensable parts. In this paper, considering the characteristics of SN P systems, a computing model for the general single-input single-output n-2n decoder is proposed. The decoding results of the n-bit input binary sequence can be derived on the MeCoSim platform. The computing steps of a 3-8 decoder and its simulations on the MeCoSim platform are also described in detail. Simulation results show the effectiveness of the proposed computing model for decoders.

关键词： computing model decoder MeCoSim spiking neural P system

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INTERCONNECTION-FREE BIOMOLECULAR computing

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COMPUTER 1992年第11期25卷 41-50页

作者： AOKI, T KAMEYAMA, M HIGUCHI, T TOHOKU UNIV DEPT INFORMAT ENGNSENDAIMIYAGI 980JAPAN

The basic concept of interconnection-free biomolecular computing and its realization in a computing model based on the massive, natural parallelism between enzymes and their substrates are described. An approach to implementing the model is presented. The approach involves two primitive switching functions: detecting specific substrates in solution using enzyme-based biosensors and producing specific substrates in response to the electric signal from the biodevice's selection function. The major challenges involved in implementing the computational model are reviewed

关键词： biodevice's selection function biomolecular electronics biosensors computational model computing model electric signal enzymes interconnection-free biomolecular computing natural parallelism primitive switching functions proteins substrates

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