• Journal of KIISE:Computing Practices and Letters
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• v.16 no.10
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• pp.980-984
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• 2010

Exploring microRNA (miRNA) and mRNA regulatory interactions may give new insights into diverse biological phenomena. Recently, miRNAs have been discovered as important regulators that play a major role in various cellular processes. Therefore, it is essential to identify functional interactions between miRNAs and mRNAs for understanding the context- dependent activities of miRNAs in complex biological systems. While elucidating complex miRNA-mRNA interactions has been studied with experimental and computational approaches, it is still difficult to infer miRNA-mRNA regulatory modules. Here we present a novel method, termed layered hypernetworks (LHNs), for identifying functional miRNA-mRNA interactions from heterogeneous expression data. In experiments, we apply the LHN model to miRNA and mRNA expression profiles on multiple cancers. The proposed method identifies cancer-specific miRNA-mRNA interactions. We show the biological significance of the discovered miRNA- mRNA interactions.

• KIISE Transactions on Computing Practices
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• v.22 no.11
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• pp.583-590
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• 2016

Recently, the rapidly increasing interest in IoT in almost all areas of casual human life has led to wide acceptance of speech recognition as a means of HCI. Simultaneously, the demand for speech recognition systems for mobile environments is increasing rapidly. The server-based speech recognition systems are typically fast and show high recognition rates; however, an internet connection is necessary, and complicated server computation is required since a voice is recognized by units of words that are stored in server databases. In this paper, we present a novel method for recognizing the Korean vowel 'ㅗ', as a part of a phoneme based Korean speech recognition system. The proposed method involves analyses of waveform patterns in the time domain instead of the frequency domain, with consequent reduction in computational cost. Elementary algorithms for detecting typical waveform patterns of 'ㅗ' are presented and combined to make final decisions. The experimental results show that the proposed method can achieve 89.9% recognition accuracy.

• KIISE Transactions on Computing Practices
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• v.22 no.11
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• pp.591-600
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• 2016

Computing technologies are increasingly applied to most casual human environment networks, as computing technologies are further developed. In addition, the rapidly increasing interest in IoT has led to the wide acceptance of speech recognition as a means of HCI. In this study, we present a novel method for recognizing the Korean vowel 'ㅜ', as a part of a phoneme based Korean speech recognition system. The proposed method involves analyses of bulk indicators calculated in the time domain instead of analysis in the frequency domain, with consequent reduction in the computational cost. Four elementary algorithms for detecting typical waveform patterns of 'ㅜ' using bulk indicators are presented and combined to make final decisions. The experimental results show that the proposed method can achieve 90.1% recognition accuracy, and recognition speed of 0.68 msec per syllable.

• Journal of KIISE:Computing Practices and Letters
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• v.16 no.4
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• pp.482-486
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• 2010

Recently, gesture recognition methods based on dynamic time warping (DTW) have been actively investigated as more mobile devices have equipped the accelerometer. DTW has no additional training step since it uses given samples as the matching templates. However, it is difficult to apply the DTW on mobile environments because of its computational complexity of matching step where the input pattern has to be compared with every templates. In order to address the problem, this paper proposes a gesture recognition method based on DTW that uses localized subset of templates. Here, the k-means clustering algorithm is used to divide each class into subclasses in which the most centered sample in each subclass is employed as the localized template. It increases the recognition speed by reducing the number of matches while it minimizes the errors by preserving the diversities of the training patterns. Experimental results showed that the proposed method was about five times faster than the DTW with all training samples, and more stable than the randomly selected templates.

• Journal of KIISE:Computing Practices and Letters
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• v.16 no.11
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• pp.1106-1110
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• 2010

This paper proposes a method of optimizing a stacking strategy for an automated container terminal using multi-objective evolutionary algorithms (MOEAs). Since the yard productivities of seaside and landside are conflicting objectives to be optimized, it is impossible to maximize them simultaneously. Therefore, we derive a Pareto optimal set instead of a single best solution using an MOEA. Preliminary experiments showed that the population is frequently stuck in local optima because of the difficulty of the given problem depending on the yard occupancy rate. To cope with this problem, we propose another method of simultaneously optimizing two problems with different difficulties so that diverse solutions can be preserved in the population. Experimental results showed the proposed method can derive better stacking policies than the compared method solving a single problem given the same computational costs.

• Journal of KIISE:Computing Practices and Letters
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• v.15 no.4
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• pp.284-288
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• 2009

With explosively growing PPI databases, the computational approach for a prediction and configuration of PPI network has been a big stream in the bioinformatics area. Recent researches gradually consider physicochemical properties of proteins and support high resolution results with integration of experimental results. With regard to current research trend, it is very close future to complete a PPI network configuration of each organism. However, direct applying the PPI network to real field is complicated problem because PPI network is only a set of co-expressive proteins or gene products, and its network link means simple physical binding rather than in-depth knowledge of biological process. In this paper, we suggest a protein functional flow model which is a directed network based on a protein functions' relation of signaling transduction pathway. The vertex of the suggested model is a molecular function annotated by gene ontology, and the relations among the vertex are considered as edges. Thus, it is easy to trace a specific function's transition, and it can be a constraint to extract a meaningful sub-path from whole PPI network. To evaluate the model, 11 functional flow models of Homo sapiens were built from KEGG, and Cronbach's alpha values were measured (alpha=0.67). Among 1023 functional flows, 765 functional flows showed 0.6 or higher alpha values.

• KIISE Transactions on Computing Practices
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• v.21 no.11
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• pp.681-688
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• 2015

The k nearest neighbor (k-NN) graph construction is an important operation with many web-related applications, including collaborative filtering, similarity search, and many others in data mining and machine learning. Despite its many elegant properties, the brute force k-NN graph construction method has a computational complexity of $O(n^2)$, which is prohibitive for large scale data sets. Thus, (Key, Value)-based distributed framework, MapReduce, is gaining increasingly widespread use in Locality Sensitive Hashing which is efficient for high-dimension and sparse data. Based on the two-stage strategy, we engage the locality sensitive hashing technique to divide users into small subsets, and then calculate similarity between pairs in the small subsets using a brute force method on MapReduce. Specifically, generating a candidate group stage is important since brute-force calculation is performed in the following step. However, existing methods do not prevent large candidate groups. In this paper, we proposed an efficient algorithm for approximate k-NN graph construction by regrouping candidate groups. Experimental results show that our approach is more effective than existing methods in terms of graph accuracy and scan rate.