• Biotechnology and Bioprocess Engineering:BBE
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• 제9권3호
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• pp.156-165
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• 2004

Concentrations of substrates, glucose, and ammionia in biological processes have been on-line monitored by using glucose-flow injection (FIA) and ammonia-FIA systems. Based on the on-line monitored data the concentrations of substrates have been controlled by an on-off controller, a PID controller, and a neural network (NN) based controller. A simulation program has been developed to test the control quality of each controller and to estimate the control parameters. The on-off controller often produced high oscillations at the set point due to its low robustness. The control quality of a PID controller could have been improved by a high analysis frequency and by a short residence time of sample in a FIA system. A NN-based controller with 3 layers has been developed, and a 3(input)-2(hidden)-1(output) network structure has been found to be optimal for the NN-based controller. The performance of the three controllers has been tested in a simulated process as well as in a cultivation process of Saccharomyces cerevisiae, and the performance has also been compared to simulation results. The NN-based controller with the 3-2-1 network structure was robust and stable against some disturbances, such as a sudden injection of distilled water into a biological process.

• 제어로봇시스템학회:학술대회논문집
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• 제어로봇시스템학회 1998년도 제13차 학술회의논문집
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• pp.356-361
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• 1998

Neural Networks, modeled succinctly from the real nervous system of a living body, can be categorized into two folds; artificial neural network(ANN) and biological neural network(BNN). While the former has been developed to solve practical problems using function approximation capability, pattern classification) clustering algorithm, etc, the latter has been focused on verifying the information processing capability to which brain research gives an impetus, by mimicking real biological systems. However, BNN suffers Iron severe nonlinearities dealt with. A bridge between two neural networks is chaotic neural network(CNN), which simply delineate the real nor-vous system and comprises almost all the ANN structures by selecting parameters. Main research theme of this area is to develop an explanation tool to clarify the information processing mechanism in biological systems and its extension to engineering applications. The CNN has a Gaussian-shaped refractory function with hysteresis effect and the chaotic responses of it have been observed fur a wide range of parameter space. Through the examination of the coupling effects of excitatory and inhibitory connections, the secrets of information processing and memory structure will appear.

• Genomics & Informatics
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• 제19권1호
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• pp.4.1-4.9
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• 2021

Lip and oral cavity cancer, which can occur in any part of the mouth, is the 11th most common type of cancer worldwide. The major obstacles to patients' survival are the poor prognosis, lack of specific biomarkers, and expensive therapeutic alternatives. This study aimed to identify the main genes and pathways associated with lip and oral cavity carcinoma using network analysis and to analyze its molecular mechanism and prognostic significance further. In this study, 472 genes causing lip and oral cavity carcinoma were retrieved from the DisGeNET database. A protein-protein interaction network was developed for network analysis using the STRING database. VEGFA, IL6, MAPK3, INS, TNF, MAPK8, MMP9, CXCL8, EGF, and PTGS2 were recognized as network hub genes using the maximum clique centrality algorithm available in cytoHubba, and nine potential drug candidates (ranibizumab, siltuximab, sulindac, pomalidomide, dexrazoxane, endostatin, pamidronic acid, cetuximab, and apricoxib) for lip and oral cavity cancer were identified from the DGIdb database. Gene enrichment analysis was also performed to identify the gene ontology categorization of cellular components, biological processes, molecular functions, and biological pathways. The genes identified in this study could furnish a new understanding of the underlying molecular mechanisms of carcinogenesis and provide more reliable biomarkers for early diagnosis, prognostication, and treatment of lip and oral cavity cancer.

• Molecules and Cells
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• 제42권8호
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• pp.579-588
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• 2019

Gene set enrichment analysis (GSEA) is a popular tool to identify underlying biological processes in clinical samples using their gene expression phenotypes. GSEA measures the enrichment of annotated gene sets that represent biological processes for differentially expressed genes (DEGs) in clinical samples. GSEA may be suboptimal for functional gene sets; however, because DEGs from the expression dataset may not be functional genes per se but dysregulated genes perturbed by bona fide functional genes. To overcome this shortcoming, we developed network-based GSEA (NGSEA), which measures the enrichment score of functional gene sets using the expression difference of not only individual genes but also their neighbors in the functional network. We found that NGSEA outperformed GSEA in identifying pathway gene sets for matched gene expression phenotypes. We also observed that NGSEA substantially improved the ability to retrieve known anti-cancer drugs from patient-derived gene expression data using drug-target gene sets compared with another method, Connectivity Map. We also repurposed FDA-approved drugs using NGSEA and experimentally validated budesonide as a chemical with anti-cancer effects for colorectal cancer. We, therefore, expect that NGSEA will facilitate both pathway interpretation of gene expression phenotypes and anti-cancer drug repositioning. NGSEA is freely available at www.inetbio.org/ngsea.

• 한국정보과학회논문지:시스템및이론
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• 제37권3호
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• pp.138-146
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• 2010

생체네트워크는 여러 종류의 환경 변화에 매우 강건하다고 알려져 있지만 그 메커니즘은 아직 밝혀지지 않고 있다. 본 논문에서는 랜덤 네트워크에 비해 생체네트워크에 되먹임 루프가 매우 많이 존재한다는 구조적 특징을 발견하고 그것이 네트워크의 강건성에 어떤 영향을 미치는지를 살펴보았다. 이를 위해 불리언 네트워크 모델을 이용하여 네트워크 강건성을 적절하게 측정하는 방법을 정의하고 많은 불리언 네트워크에 대해서 시뮬레이션하였다. 그 결과, 불리언 네트워크에서 되먹임 루프의 개수가 증가하면 고정점 끌개의 개수는 거의 변화가 없지만 유한순환 끌개의 개수는 크게 줄어든다는 사실을 밝혔다. 또한, 되먹임 루프의 개수가 증가함에 따라 고정점 끌개로 수렴하는 거대한 끌개 영역이 생성됨을 보였다. 이러한 사실들은 매우 많은 수의 되먹임 루프가 네트워크의 강건성을 높이는 데 중요한 요인임을 설명한다.

• Asian Pacific Journal of Cancer Prevention
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• 제15권7호
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• pp.3145-3149
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• 2014

Gene expression profiling facilitates the understanding of biological characteristics of gliomas. Previous studies mainly used regression/variance analysis without considering various background biological and environmental factors. The aim of this study was to investigate gene expression differences between grade III and IV gliomas through partial least squares (PLS) based analysis. The expression data set was from the Gene Expression Omnibus database. PLS based analysis was performed with the R statistical software. A total of 1,378 differentially expressed genes were identified. Survival analysis identified four pathways, including Prion diseases, colorectal cancer, CAMs, and PI3K-Akt signaling, which may be related with the prognosis of the patients. Network analysis identified two hub genes, ELAVL1 and FN1, which have been reported to be related with glioma previously. Our results provide new understanding of glioma pathogenesis and prognosis with the hope to offer theoretical support for future therapeutic studies.

• Genomics & Informatics
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• 제9권4호
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• pp.173-180
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• 2011

Recent trends in generating multiple, large-scale datasets provide new challenges to manipulating the relationship of different types of components, such as gene expression and drug response data. Integrative analysis of compound response and gene expression datasets generates an opportunity to capture the possible mechanism of compounds by using signature genes on diverse types of cancer cell lines. Here, we integrated datasets of compound response and gene expression profiles on NCI60 cell lines and constructed a network, revealing the relationship for 801 compounds and 341 gene probes. As examples, obtusol, which shows an exclusive sensitivity on a small number of colon cell lines, is related to a set of gene probes that have unique overexpression in colon cell lines. We also found that the SLC7A11 gene, a direct target of miR-26b, might be a key element in understanding the action of many diverse classes of anticancer compounds. We demonstrated that this network might be useful for studying the mechanisms of varied compound response on diverse cancer cell lines.

• 한국지능시스템학회논문지
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• 제25권6호
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• pp.529-535
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• 2015

지금까지 생체 네트워크 분석 연구는 정적(static)인 개념으로만 다루어졌다. 그러나 실제 생명현상이 발생하는 세포 내에서는 세포의 상태 및 외부 환경에 따라 일부 단백질과 그 상호작용만이 선택적으로 활성화된다. 따라서 생체 네트워크의 구조가 시간의 흐름에 따라 변화하는 동적(dynamic)인 개념이 적용되어야 하며, 이런 개념은 질병의 진행 추이를 분석하는데 효율적이다. 본 논문에서는 동적인 네트워크 방법을 알츠하이머 질병에 적용하여 질병이 진행되는 단계에 따라 변화하는 단백질 상호작용 네트워크의 구조적, 기능적 특징에 대하여 분석하고자 한다. 우선, 유전자 발현데이터를 기반으로 각 질병의 진행 상태에 따른 부분 네트워크(정상, 초기, 중기, 말기)를 구축하였다. 이를 기반으로, 네트워크의 구조적 특성 분석을 수행하였다. 또한 기능적 특성 분석을 위해 유전자 군집(module)을 탐색하고, 군집별 유전자 기능(Gene Ontology) 분석을 수행했다. 그 결과, 네트워크의 특성들은 각 질병의 단계와 잘 대응되며, 동적 네트워크 분석법이 중요한 생물학적 이벤트를 설명하는데 이용될 수 있음을 보였다. 결론적으로 제안된 연구 방법을 통하여 그동안 알려지지 않았던 질병유발에 관련된 주요 네트워크 변화를 관측할 수 있고, 질병에 관여하는 복잡한 분자 수준의 발생 기작과 진행 과정을 이해하는데 중요한 정보를 획득할 수 있다.

• 대한의용생체공학회:의공학회지
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• 제11권2호
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• pp.249-256
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• 1990

In this study, LPC cepstrum coefficients are used as feature vector extracted from AR model of EMG signal, and a reduced-connection network whlch has reduced connection between nodes is constructed to classify and recognize EMG functional classes. The proposed network reduces learning time and improves system stability Therefore it is Ehown that the proposed network is appropriate in recognizing function of EMG signal.

• 대한의용생체공학회:의공학회지
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• 제12권3호
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• pp.191-202
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• 1991

This paper describes ECG data compression algorithm using neural network. As a learning method, we use back error propagation algorithm. ECG data compression is performed using learning ability of neural network. CSE database, which is sampled 12bit digitized at 500samp1e/sec, is selected as a input signal. In order to reduce unit number of input layer, we modify sampling ratio 250samples/sec in QRS complex, 125samples/sec in P & T wave respectively. hs a input pattern of neural network, from 35 points backward to 45 points forward sample Points of R peak are used.