• The Journal of the Korea Contents Association
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• v.9 no.5
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• pp.332-336
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• 2009

Functional prediction of unannotated proteins is one of the most important tasks in yeast genomics. Analysis of a protein-protein interaction network leads to a better understanding of the functions of unannotated proteins. A number of researches have been performed for the functional prediction of unannotated proteins from a protein-protein interaction network. A chi-square method is one of the existing methods for the functional prediction of unannotated proteins from a protein-protein interaction network. But, the method does not consider the topology of network. In this paper, we propose a novel method that is able to predict specific molecular functions for unannotated proteins from a protein-protein interaction network. To do this, we investigated all protein interaction DBs of yeast in the public sites such as MIPS, DIP, and SGD. For the prediction of unannotated proteins, we employed a modified chi-square measure based on neighborhood counting and we assess the prediction accuracy of protein function from a protein-protein interaction network.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2000.11a
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• pp.28-31
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• 2000

We describe a hidden Markov model, HMMTIR, for general protein sequence based on the I-sites library of sequence-structure motifs. Unlike the linear HMMs used to model individual protein families, HMMSTR has a highly branched topology and captures recurrent local features of protein sequences and structures that transcend protein family boundaries. The model extends the I-sites library by describing the adjacencies of different sequence-structure motifs as observed in the database, and achieves a great reduction in parameters by representing overlapping motifs in a much more compact form. The HMM attributes a considerably higher probability to coding sequence than does an equivalent dipeptide model, predicts secondary structure with an accuracy of 74.6% and backbone torsion angles better than any previously reported method, and predicts the structural context of beta strands and turns with an accuracy that should be useful for tertiary structure prediction. HMMSTR has been incorporated into a public, fully-automated protein structure prediction server.

• Journal of Institute of Control, Robotics and Systems
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• v.15 no.9
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• pp.929-938
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• 2009

This paper presents a novel control methodology for communication network based nonlinear systems with time delay nature. We construct a nominal nonlinear control law for representing a linear model and a reset control system which is aimed for corrective control strategy to compensate system error due to uncertain time delay through wireless communication network. Next, online neural control approach is proposed for overcoming nonstationary statistical nature in the network topology. Additionally, DBN (Dynamic Bayesian Network) technique is accomplished for modeling of its dynamics in terms of casuality, which is then utilized for estimating prediction of system output. We evaluate superiority and reliability of the proposed control approach through numerical simulation example in which a nonlinear inverted pendulum model is employed as a networked control system.

• Computers and Concrete
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• v.31 no.4
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• pp.315-325
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• 2023

Calcium leaching is one of the main deterioration factors in concrete structures contact with water, such as dams, water treatment structures, and radioactive waste structures. It causes a porous microstructure and may be coupled with various harmful factors resulting in mechanical degradation of concrete. Several numerical modeling studies focused on the calcium leaching depth prediction. However, these required a lot of cost and time for many experiments and analyses. This study presents an artificial neural network (ANN) approach to predict the leaching depth quickly and accurately. Totally 132 experimental data are collected for model training and validation. An optimal ANN model was proposed by ANN topology. Results indicate that the model can be applied to estimate the calcium leaching depth, showing the determination coefficient of 0.91. It might be used as a simulation tool for engineering problems focused on durability.

• BMB Reports
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• v.46 no.1
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• pp.41-46
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• 2013

Identifying genes indispensable for an organism's life and their characteristics is one of the central questions in current biological research, and hence it would be helpful to develop computational approaches towards the prediction of essential genes. The performance of a predictor is usually measured by the area under the receiver operating characteristic curve (AUC). We propose a novel method by implementing genetic algorithms to maximize the partial AUC that is restricted to a specific interval of lower false positive rate (FPR), the region relevant to follow-up experimental validation. Our predictor uses various features based on sequence information, protein-protein interaction network topology, and gene expression profiles. A feature selection wrapper was developed to alleviate the over-fitting problem and to weigh each feature's relevance to prediction. We evaluated our method using the proteome of budding yeast. Our implementation of genetic algorithms maximizing the partial AUC below 0.05 or 0.10 of FPR outperformed other popular classification methods.

• KSII Transactions on Internet and Information Systems (TIIS)
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• v.14 no.8
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• pp.3399-3419
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• 2020

In the Vehicular Ad-hoc Network (VANET), the data transmission of time-sensitive applications requires low latency, such as accident warnings, driving guidance, etc. However, frequent changes of topology in VANET will result in data transmission failures. In order to improve the efficiency of VANETs data transmission and increase the timeliness of data, this paper proposes a relay scheme based on Recurrent Neural Network (RNN) trajectory prediction, which can be used to select the optimal relay vehicle to transmit data. The proposed scheme learns vehicle trajectory in a distributed manner and calculates the predicted trajectory, and then the optimal vehicle can be selected to complete the data transmission, which ensures the timeliness of the data. Finally, we carry out a set of simulations to demonstrate the performance of the algorithm. Simulation results show that the proposed scheme enhances the timeliness of the data and the accuracy of the predicted driving trajectory.

• KSII Transactions on Internet and Information Systems (TIIS)
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• v.17 no.8
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• pp.2030-2052
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• 2023

Analysis of a bipartite (two-mode) network is a significant research area to understand the formation of social communities, economic systems, drug side effect topology, etc. in complex information systems. Most of the previous works talk about a projection-based model or latent feature model, which predicts the link based on singular similarity. The projection-based models suffer from the loss of structural information in the projected network and the latent feature is hardly present. This work proposes a novel method for link prediction in the bipartite network based on an ensemble of composite similarities, overcoming the issues of model-based and latent feature models. The proposed method analyzes the structure, neighborhood nodes as well as latent attributes between the nodes to predict the link in the network. To illustrate the proposed method, experiments are performed with five real-world data sets and compared with various state-of-art link prediction methods and it is inferred that this method outperforms with ~3% to ~9% higher using area under the precision-recall curve (AUC-PR) measure. This work holds great significance in the study of biological networks, e-commerce networks, complex web-based systems, networks of drug binding, enzyme protein, and other related networks in understanding the formation of such complex networks. Further, this study helps in link prediction and its usability for different purposes ranging from building intelligent systems to providing services in big data and web-based systems.

• Journal of the Korean Magnetic Resonance Society
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• v.17 no.1
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• pp.59-66
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• 2013

BldD, a developmental transcription factor from Streptomyces coelicolor, is a homodimeric, DNA-binding protein with 167 amino acids in each subunit. Each monomer consists of two structurally distinct domains, the N-terminal domain (BldD-NTD) responsible for DNA-binding and dimerization and the C-terminal domain (BldD-CTD). In contrast to the BldD-NTD, of which crystal structure has been solved, the BldD-CTD has been characterized neither in structure nor in function. Thus, in terms of structural genomics, structural study of the BldD-CTD has been conducted in solution, and in the present work, mainchain NMR assignments of the recombinant BldD-CTD (residues 80-167 of BldD) could be achieved by a series of heteronuclear multidimensional NMR experiments on a [$^{13}C/^{15}N$]-enriched protein sample. Finally, the secondary structure prediction by CSI and TALOS+ analysis using the assigned chemical shifts data identified a ${\beta}-{\alpha}-{\alpha}-{\beta}-{\alpha}-{\alpha}-{\alpha}$ topology of the domain. The results will provide the most fundamental data for more detailed approach to the atomic structure of the BldD-CTD, which would be essential for entire understanding of the molecular function of BldD.

• The Journal of Korean Institute of Communications and Information Sciences
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• v.34 no.7B
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• pp.659-667
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• 2009

Mobile Ad-hoc Network consists of mobile nodes without immobile base station. In mobile ad-hoc network, network cutting has occurred frequently in node because of energy restriction and frequent transfer of node. Therefore, it requires research for certain techniques that react softly in topology alteration in order to improve reliability of transmission path. This paper proposes path selection techniques to consider mobility of node that respond when search path using AOMDV routing protocol. As applying proposed techniques, We can improve reliability and reduce re-searching number of times caused by path cutting.

• KIPS Transactions on Computer and Communication Systems
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• v.9 no.11
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• pp.256-264
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• 2020

Industrial Wireless Sensor Networks (IWSNs) is exploited to achieve various objectives such as improving productivity and reducing cost in the diversity of industrial application, and it has requirements such as low-delay and high reliability packet transmission. To accomplish the requirement, the network manager performs graph construction and resource allocation about network topology, and determines the transmission cycle and path of each node in advance. However, this network management scheme cannot treat mobile devices that cause continuous topology changes because graph reconstruction and resource reallocation should be performed as network topology changes. That is, despite the growing need of mobile devices in many industries, existing scheme cannot adequately respond to path failure caused by movement of mobile device and packet loss in the process of path recovery. To solve this problem, a network management scheme is required to prevent packet loss caused by mobile devices. Thus, we analyse the location and movement cycle of mobile devices over time using machine learning for predicting the mobility pattern. In the proposed scheme, the network manager could prevent the problems caused by mobile devices through performing graph construction and resource allocation for the predicted network topology based on the movement pattern. Performance evaluation results show a prediction rate of about 86% compared with actual movement pattern, and a higher packet delivery ratio and a lower resource share compared to existing scheme.