An Analysis on the Support System of Low-rise Residential Areas Regeneration

Seungyeoun Cho,Soyi Cheong 한국주거학회 2015 한국주거학회 국제학술대회논문집 Vol.2015 No.4

Gene–gene interaction analysis for the survival phenotype based on the Cox model

Lee, Seungyeoun,Kwon, Min-Seok,Oh, Jung Mi,Park, Taesung Oxford University Press 2012 Bioinformatics Vol.28 No.18

<P><B>Motivation:</B> For the past few decades, many statistical methods in genome-wide association studies (GWAS) have been developed to identify SNP–SNP interactions for case-control studies. However, there has been less work for prospective cohort studies, involving the survival time. Recently, Gui <I>et al.</I> (2011) proposed a novel method, called Surv-MDR, for detecting gene–gene interactions associated with survival time. Surv-MDR is an extension of the multifactor dimensionality reduction (MDR) method to the survival phenotype by using the log-rank test for defining a binary attribute. However, the Surv-MDR method has some drawbacks in the sense that it needs more intensive computations and does not allow for a covariate adjustment. In this article, we propose a new approach, called Cox-MDR, which is an extension of the generalized multifactor dimensionality reduction (GMDR) to the survival phenotype by using a martingale residual as a score to classify multi-level genotypes as high- and low-risk groups. The advantages of Cox-MDR over Surv-MDR are to allow for the effects of discrete and quantitative covariates in the frame of Cox regression model and to require less computation than Surv-MDR.</P><P><B>Results:</B> Through simulation studies, we compared the power of Cox-MDR with those of Surv-MDR and Cox regression model for various heritability and minor allele frequency combinations without and with adjusting for covariate. We found that Cox-MDR and Cox regression model perform better than Surv-MDR for low minor allele frequency of 0.2, but Surv-MDR has high power for minor allele frequency of 0.4. However, when the effect of covariate is adjusted for, Cox-MDR and Cox regression model perform much better than Surv-MDR. We also compared the performance of Cox-MDR and Surv-MDR for a real data of leukemia patients to detect the gene–gene interactions with the survival time.</P><P><B>Contact:</B>leesy@sejong.ac.kr; tspark@snu.ac.kr</P>

개발종료 채석장 부지를 활용한 해외 복합 개발 사례에 대한 고찰 : 영국과 호주 사례

조승연(Seungyeoun Cho),임길재(Gil-Jae Yim),이진영(Jin Young Lee),지상우(Sangwoo Ji) 대한자원환경지질학회 2021 자원환경지질 Vol.54 No.5

21세기 들어 영국, 호주 등 해외에서도 대도시권의 주택가격 상승문제가 나타나고 있다. 이들 정부는 대도시 인근에 위치한 개발종료 채석장 부지를 택지로 적극 활용하여 주택부족 문제를 해소하고자 하고 있다. 본 연구에서 검토한 영국의 Erith Hill Quarry (The Quarry)나 Plymstock Quarry, 호주의 Lilydale Quarry (Kinley)와 Bombo Quarry는 모두 도시 계획적 제도를 통해 개발이 종료된 채석장을 주택, 상업 등 복합용도로 개발한 사례이다. 영국은 도시계획제도의 틀 안에서 Section 106이라는 계획 허가 제도를 통해 지방정부가 개발종료 채석장 부지의 복합개발을 허가하는 대신 지역에 필요한 학교 등의 공공시설과 저렴한 주택을 공급하도록 하고 있다. 호주는 채석장의 토지이용을 산업에서 복합용도로 변경할 수 있도록 지방정부의 허가권한을 활용하고, 개발계획에 저렴한 주거 외에도 도시기반시설, 오픈 스페이스 등이 포함되도록 하고 있다. 특히, 호주의 사례에서 개발 계획을 사전에 수립하고, 단계적 개발방식을 통해 상부 표토 및 표석을 채굴적을 메우는 충전재로 활용한 것은 사업비를 절감하는 효과도 있는 것으로 보인다. 영국과 호주 모두 개발종료 채석장 부지를 택지로 공급하는 것이 신규 녹지를 훼손하는 것보다 미래세대를 위한 지속가능한 친환경적 개발이라는 관점에서 바라보고 있다는 점에서 다소 경직된 우리의 도시개발 제도에 정책적 시사점을 제공할 수 있을 것으로 보인다. Recently, housing prices in metropolitan areas is also increasing in the UK and Australia. Their governments are trying to solve this problem by the housing development in the quarry sites near cities. The cases reviewed in this study, Erith Hill Quarry (The Quarry), Plymstock Quarry, Lilydale Quarry (Kinley), and Bombo Quarry are the mixed-used development cases in the closed quarry sites through the urban planning system. In the UK, the local government uses the urban planning scheme such as the planning permit system, section 106. The local government permits the quarry site development on the condition that it provides necessary public facilities, such as schools and affordable housing for the local community. In Australia, local governments use up-zoning permission rights to convert land uses in quarries from industrial to mixed-use. Development plans have to include urban infrastructure and open space in addition to affordable housings. In the case of Australia, establishing a development plan in advance and filling the quarry pit with overburden through a phased development is expected to have the effect of reducing the project cost. Both countries think that developing brownfields, such as quarry sites, is a more sustainable and eco-friendly development from the perspective of future generations than developing new green fields. Such a perspective of the UK and Australia will be able to give policy implications for our slightly rigid urban development system.

유전체 자료분석을 위한 생존분석방법에 관한 고찰

이승연(Seungyeoun Lee) 한국데이터정보과학회 2018 한국데이터정보과학회지 Vol.29 No.6

관심의 대상이 되는 사건이 발생할 때까지 걸리는 생존시간을 다루는 생존분석의 가장 큰 특성은 생존시간이 완전하게 관측되지 않고 중도 절단 된다는 점이다. 이러한 중도절단자료의 특성을 고려하여 추정, 검정 및 모형적합에 대하여 고전적인 생존분석 방법들이 많이 개발되어져 왔으나, 마이크로 어레이자료를 시작으로 대용량의 유전체 자료가 수집되면서 유전적 정보와 생존시간과의 연관성 연구가 진행되면서 표본의 수에 비하여 엄청나게 많은 수의 유전정보 변수들을 다루는 새로운 통계적인 방법들이 생존자료에 확장되었다. 결과적으로 기존의 임상자료로만 구축된 통계예측모형에 유전체 정보가 추가적으로 고려됨으로써 생존함수에 대한 예측력이 향상되었고, 개인의 유전정보에 따라 더 적합한 치료방법이나 치료약을 개발해야 한다는 개인맞춤의학의 필요성이 부각되기 시작되었다. 다양한 첨단 생물학 기술을 통하여 서로 다른 형태의 대용량의 유전체 자료를 통합하는 방법론에 대한 연구들이 이루어지면서 기계학습 방법이 생존분석에 접목되어 많은 연구방법들이 개발되고 있다. 본 연구에서는 기존의 임상자료를 기반으로 분석하는 전통적인 생존분석 방법들을 소개하고, 고차원의 유전체 자료를 분석하기 위한 생존분석 방법들과 통합적인 유전체 자료분석을 위하여 생존분석에 접목된 기계학습방법들에 대하여 간략하게 살펴보고자 한다. Survival analysis focuses on the statistical inference for the time to event of interest, which cannot be often completely observed due to censoring. Considering the characteristics of these censored data, traditional survival analysis methods have been developed for estimation, testing, and model development to predict survival time for patients based on clinical data. However, large-scale data from high-throughput genomic technologies, especially microarrays, have been collected, which poses the challenging statistical issues in combining those with the survival time. Many statistical methods have been developed by additionally considering the high-dimensional genomic information in the statistical prediction model constructed only by the existing clinical data. Recently, there have been many studies on the methodology of integrating different types of genomic data through various advanced biologic techniques, which results in making an early prediction for the disease and developing personalized medicine. As well, there has been considerable interest in applying machine learning techniques to analyse these complex and huge amount of genomic data associated with the censored data. In this paper, we review the basic concepts in survival analysis, traditional statistical methods based on clinical data, more appropriate statistical methods dealing with genomic data, and machine learning methods extended to the survival analysis.

Review of statistical methods for survival analysis using genomic data

Lee, Seungyeoun,Lim, Heeju Korea Genome Organization 2019 Genomics & informatics Vol.17 No.4

Survival analysis mainly deals with the time to event, including death, onset of disease, and bankruptcy. The common characteristic of survival analysis is that it contains "censored" data, in which the time to event cannot be completely observed, but instead represents the lower bound of the time to event. Only the occurrence of either time to event or censoring time is observed. Many traditional statistical methods have been effectively used for analyzing survival data with censored observations. However, with the development of high-throughput technologies for producing "omics" data, more advanced statistical methods, such as regularization, should be required to construct the predictive survival model with high-dimensional genomic data. Furthermore, machine learning approaches have been adapted for survival analysis, to fit nonlinear and complex interaction effects between predictors, and achieve more accurate prediction of individual survival probability. Presently, since most clinicians and medical researchers can easily assess statistical programs for analyzing survival data, a review article is helpful for understanding statistical methods used in survival analysis. We review traditional survival methods and regularization methods, with various penalty functions, for the analysis of high-dimensional genomics, and describe machine learning techniques that have been adapted to survival analysis.

Gene-Gene Interaction Analysis for the Accelerated Failure Time Model Using a Unified Model-Based Multifactor Dimensionality Reduction Method

Lee, Seungyeoun,Son, Donghee,Yu, Wenbao,Park, Taesung Korea Genome Organization 2016 Genomics & informatics Vol.14 No.4

Although a large number of genetic variants have been identified to be associated with common diseases through genome-wide association studies, there still exits limitations in explaining the missing heritability. One approach to solving this missing heritability problem is to investigate gene-gene interactions, rather than a single-locus approach. For gene-gene interaction analysis, the multifactor dimensionality reduction (MDR) method has been widely applied, since the constructive induction algorithm of MDR efficiently reduces high-order dimensions into one dimension by classifying multi-level genotypes into high- and low-risk groups. The MDR method has been extended to various phenotypes and has been improved to provide a significance test for gene-gene interactions. In this paper, we propose a simple method, called accelerated failure time (AFT) UM-MDR, in which the idea of a unified model-based MDR is extended to the survival phenotype by incorporating AFT-MDR into the classification step. The proposed AFT UM-MDR method is compared with AFT-MDR through simulation studies, and a short discussion is given.

Estimation of Seroconversion Dates of HIV by Imputation Based on Regression Models

Lee, Seungyeoun The Korean Statistical Society 2001 Communications for statistical applications and me Vol.8 No.3

The aim of this study is to estimate the seroconversion date of the human immunodeficiency virus(HIV) infection for the HIV infected patients in Korea. Data are collected from two cohorts. The first cohort is a group of "seroprevalent" patients who were seropositive and AIDS-free at entry. The other is a group of "seroincident" patients who were initially seronegative but later converted to HIV antibody-positive. The seroconversion dates of the seroincident cohort are available while those of the seroprevalent cohort are not. Estimation of seroconversion date is important because it can be used to calculate the incubation period of AIDS which is defined as the elapsed time between the HIV infection and the development of AIDS. In this paper, a Weibull regression model Is fitted for the seroincident cohort using information about the elapsed time since seroconversion and the CD4$^{+}$ cell count.The seroconversion dates for the seroprevalent cohort are imputed on the basis of the marker of maturity of HIV infection percent of CD4$^{+}$cell count.unt.

기성시가지 정비를 위한 입체환지 수법에 관한 연구

조승연(Cho, Seungyeoun),김옥연(Kim, Ok-yeon) 한국도시설계학회 2008 도시설계 : 한국도시설계학회지 Vol.9 No.4

일본의 비도시지역 난개발 방지를 위한 개발허가제 분석

조승연(Cho Seungyeoun),서순탁(Suh Soon-Tak) 한국도시행정학회 2009 도시 행정 학보 Vol.22 No.1

A Study on the Development Permit System for Urban Sprawl Control of Non-Urban Area : Case Study of Kanagawa and Manazuru in Japan In Korea, the development permit system as a means of development control in nonurban area has recently attracted interest from policy-makers and academics. This interest raises a question about how Japanese development permit system work effectively within the Japanese context since the introduction of the development permit system. Japan has made an effort to prevent disordered development in both urban planning zones and quasi-urban planning zones since 1968. In this context, this study is aimed at analyzing Japanese development control system in Kanagawa and Manazuru, and suggesting policy implications. Four policy implications are drawn through a case analysis. Firstly, the object of development permit should be clarified. Secondly the dual system of development permit should be built. Japanese cases show that a preconsultation device by ordinances of local government make up for the limitation of planning law. Thirdly, the permit power of a wide-area local government should be consolidated. Finally, development permit criteria considered local context should be suggested.

Analysis of clustered RNA-seq data

Park, Hyunjin,Lee, Seungyeoun,Kim, Ye Jin,Choi, Myung Sook,Park, Taesung Inderscience Enterprises Ltd. 2017 International journal of data mining and bioinform Vol.19 No.1