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Causal Discovery from a Mixture of Experimental and Observational Data
Gregory F. Cooper,Changwon Yoo
Computer Science , 2013,
Abstract: This paper describes a Bayesian method for combining an arbitrary mixture of observational and experimental data in order to learn causal Bayesian networks. Observational data are passively observed. Experimental data, such as that produced by randomized controlled trials, result from the experimenter manipulating one or more variables (typically randomly) and observing the states of other variables. The paper presents a Bayesian method for learning the causal structure and parameters of the underlying causal process that is generating the data, given that (1) the data contains a mixture of observational and experimental case records, and (2) the causal process is modeled as a causal Bayesian network. This learning method was applied using as input various mixtures of experimental and observational data that were generated from the ALARM causal Bayesian network. In these experiments, the absolute and relative quantities of experimental and observational data were varied systematically. For each of these training datasets, the learning method was applied to predict the causal structure and to estimate the causal parameters that exist among randomly selected pairs of nodes in ALARM that are not confounded. The paper reports how these structure predictions and parameter estimates compare with the true causal structures and parameters as given by the ALARM network.
Reverse Engineering of Modified Genes by Bayesian Network Analysis Defines Molecular Determinants Critical to the Development of Glioblastoma
Brian W. Kunkle, Changwon Yoo, Deodutta Roy
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0064140
Abstract: In this study we have identified key genes that are critical in development of astrocytic tumors. Meta-analysis of microarray studies which compared normal tissue to astrocytoma revealed a set of 646 differentially expressed genes in the majority of astrocytoma. Reverse engineering of these 646 genes using Bayesian network analysis produced a gene network for each grade of astrocytoma (Grade I–IV), and ‘key genes’ within each grade were identified. Genes found to be most influential to development of the highest grade of astrocytoma, Glioblastoma multiforme were: COL4A1, EGFR, BTF3, MPP2, RAB31, CDK4, CD99, ANXA2, TOP2A, and SERBP1. All of these genes were up-regulated, except MPP2 (down regulated). These 10 genes were able to predict tumor status with 96–100% confidence when using logistic regression, cross validation, and the support vector machine analysis. Markov genes interact with NFkβ, ERK, MAPK, VEGF, growth hormone and collagen to produce a network whose top biological functions are cancer, neurological disease, and cellular movement. Three of the 10 genes - EGFR, COL4A1, and CDK4, in particular, seemed to be potential ‘hubs of activity’. Modified expression of these 10 Markov Blanket genes increases lifetime risk of developing glioblastoma compared to the normal population. The glioblastoma risk estimates were dramatically increased with joint effects of 4 or more than 4 Markov Blanket genes. Joint interaction effects of 4, 5, 6, 7, 8, 9 or 10 Markov Blanket genes produced 9, 13, 20.9, 26.7, 52.8, 53.2, 78.1 or 85.9%, respectively, increase in lifetime risk of developing glioblastoma compared to normal population. In summary, it appears that modified expression of several ‘key genes’ may be required for the development of glioblastoma. Further studies are needed to validate these ‘key genes’ as useful tools for early detection and novel therapeutic options for these tumors.
Interlayer coupling enhancement in graphene/hexagonal boron nitride heterostructures by intercalated defects and vacancies
Sohee Park,Changwon Park,Gunn Kim
Physics , 2014, DOI: 10.1063/1.4870097
Abstract: Among two-dimensional atomic crystals, hexagonal boron nitride (hBN) is one of the most remarkable materials to fabricate heterostructures revealing unusual properties. We perform first-principles calculations to determine whether intercalated metal atoms and vacancies can mediate interfacial coupling and influence the structural and electronic properties of the graphene/hBN heterostructure. Metal impurity atoms (Li, K, Cr, Mn, Co, and Cu) as extrinsic defects between the graphene and hBN sheets produce $n$-doped graphene. We also consider intrinsic vacancy defects and find that a boron monovacancy in hBN act as a magnetic dopant for graphene whereas a nitrogen monovacancy in hBN serves as a nonmagnetic dopant for graphene. In contrast, smallest triangular vacancy defects in hBN are unlikely to result in significant changes in the electronic transport of graphene. Our findings reveal that the hBN layer with some vacancies or metal impurities enhance the interlayer coupling in the graphene/hBN heterostructure with respect to charge doping and electron scattering.
Decay behavior of localized states at reconstructed armchair graphene edges
Changwon Park,Jisoon Ihm,Gunn Kim
Physics , 2013, DOI: 10.1103/PhysRevB.88.045403
Abstract: Density functional theory calculations are used to investigate the electronic structures of localized states at reconstructed armchair graphene edges. We consider graphene nanoribbons with two different edge types and obtain the energy band structures and charge densities of the edge states. By examining the imaginary part of the wavevector in the forbidden energy region, we reveal the decay behavior of the wavefunctions in graphene. The complex band structures of graphene in the armchair and zigzag directions are presented in both tight-binding and first-principles frameworks.
Edge Adaptive Color Demosaicking Based on the Spatial Correlation of the Bayer Color Difference
Oh HyunMook,Kim ChangWon,Han YoungSeok,Kang MoonGi
EURASIP Journal on Image and Video Processing , 2010,
Abstract: An edge adaptive color demosaicking algorithm that classifies the region types and estimates the edge direction on the Bayer color filter array (CFA) samples is proposed. In the proposed method, the optimal edge direction is estimated based on the spatial correlation on the Bayer color difference plane, which adopts the local directional correlation of an edge region of the Bayer CFA samples. To improve the image quality with the consistent edge direction, we classify the region of an image into three different types, such as edge, edge pattern, and flat regions. Based on the region types, the proposed method estimates the edge direction adaptive to the regions. As a result, the proposed method reconstructs clear edges with reduced visual distortions in the edge and the edge pattern regions. Experimental results show that the proposed method outperforms conventional edge-directed methods on objective and subjective criteria.
Region Adaptive Color Demosaicing Algorithm Using Color Constancy
Kim ChangWon,Oh HyunMook,Yoo DuSic,Kang MoonGi
EURASIP Journal on Advances in Signal Processing , 2010,
Abstract: This paper proposes a novel way of combining color demosaicing and the auto white balance (AWB) method, which are important parts of image processing. Performance of the AWB is generally affected by demosaicing results because most AWB algorithms are performed posterior to color demosaicing. In this paper, in order to increase the performance and efficiency of the AWB algorithm, the color constancy problem is examined during the color demosaicing step. Initial estimates of the directional luminance and chrominance values are defined for estimating edge direction and calculating the AWB gain. In order to prevent color failure in conventional edge-based AWB methods, we propose a modified edge-based AWB method that used a predefined achromatic region. The estimation of edge direction is performed region adaptively by using the local statistics of the initial estimates of the luminance and chrominance information. Simulated and real Bayer color filter array (CFA) data are used to evaluate the performance of the proposed method. When compared to conventional methods, the proposed method shows significant improvements in terms of visual and numerical criteria.
Relative Codon Adaptation Index, a Sensitive Measure of Codon Usage Bias
Soohyun Lee,Seyeon Weon,Sooncheol Lee,Changwon Kang
Evolutionary Bioinformatics , 2010,
Abstract: We propose a simple, sensitive measure of synonymous codon usage bias, the Relative Codon Adaptation Index (rCAI), as a way to discriminate better between highly biased and unbiased regions, compared with the widely used Codon Adaptation Index (CAI). CAI is a geometric mean of the relative usage of codons in a gene, and is calculated using the codon usage table trained with a set of highly expressed genes. In contrast, rCAI is computed by subtracting the background codon usage trained with two noncoding frames of highly expressed genes from the codon usage in the coding frame. rCAI has higher signal-to-noise ratio than CAI, considering that non-coding frames would not show codon bias. Translation efficiency and protein abundance correlates comparably or better with rCAI than CAI or other measures such as ‘effective number of codons’ and ‘SCUMBLE offsets’. Within overlapping coding regions, one of the two coding frames dominates in codon usage bias according to rCAI. Presumably, rCAI could substitute CAI in diverse applications.
Factors Affecting De Novo Urinary Retention after Holmium Laser Enucleation of the Prostate
Sung Han Kim, Changwon Yoo, Minsoo Choo, Jae-Seung Paick, Seung-June Oh
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0084938
Abstract: Objective Patients can experience urinary retention (UR) after Holmium laser enucleation of the prostate (HoLEP) that requires bladder distension during the procedure. The aim of this retrospective study is to identify factors affecting the UR after HoLEP. Materials and Methods 336 patients, which underwent HoLEP for a symptomatic benign prostatic hyperplasia between July 2008 and March 2012, were included in this study. Urethral catheters were routinely removed one or two days after surgery. UR was defined as the need for an indwelling catheter placement following a failure to void after catheter removal. Demographic and clinical parameters were compared between the UR (n = 37) and the non-urinary retention (non-UR; n = 299) groups. Results The mean age of patients was 68.3 (±6.5) years and the mean operative time was 75.3 (±37.4) min. Thirty seven patients (11.0%) experienced a postoperative UR. UR patients voided catheter free an average of 1.9 (±1.7) days after UR. With regard to the causes of UR, 24 (7.1%) and 13 (3.9%) patients experienced a blood clot-related UR and a non-clot related UR respectively. Using multivariate analysis (p<0.05), we found significant differences between the UR and the non-UR groups with regard to a morcellation efficiency (OR 0.701, 95% CI 0.498–0.988) and a bleeding-related complication, such as, a reoperation for bleeding (OR 0.039, 95% CI 0.004–0.383) or a transfusion (OR 0.144, 95% CI 0.027–0.877). Age, history of diabetes, prostate volume, pre-operative post-void residual, bladder contractility index, learning curve, and operative time were not significantly associated with the UR (p>0.05). Conclusions De novo UR after HoLEP was found to be self-limited and it was not related to learning curve, patient age, diabetes, or operative time. Efficient morcellation and careful control of bleeding, which reduces clot formation, decrease the risk of UR after HoLEP.
Controlling Half-Metallicity of Graphene Nanoribbons by Using a Ferroelectric Polymer
Yea-Lee Lee,Seungchul Kim,Changwon Park,Jisoon Ihm,Young-Woo Son
Physics , 2010, DOI: 10.1021/nn9019064
Abstract: On the basis of first-principles computational approaches, we present a new method to drive zigzag graphene nanoribons (ZGNRs) into the half-metallic state using a ferroelectric material, poly(vinylidene fluoride) (PVDF). Owing to strong dipole moments of PVDFs, the ground state of the ZGNR becomes half-metallic when a critical coverage of PVDFs is achieved on the ZGNR. Since ferroelectric polymers are physisorbed, the direction of the dipole field in PVDFs can be rotated by relatively small external electric fields, and the switching between half-metallic and insulating states may be achieved. Our results suggest that, without excessively large external gate electric fields, half-metallic states of ZGNRs are realizable through the deposition of ferroelectric polymers and their electronic and magnetic properties are controllable via noninvasive mutual interactions.
Analysis of the near-resonant fluorescence spectra of a single rubidium atom localized in a three-dimensional optical lattice
Wookrae Kim,Changwon Park,Jung-Ryul Kim,Yea-Lee Lee,Jisoon Ihm,Kyungwon An
Physics , 2010,
Abstract: Supplementary information is presented on the recent work by W. Kim et al. on the matter-wave-tunneling-induced broadening in the near-resonant spectra of a single rubidium atom localized in a three-dimensional optical lattice in a strong Lamb-Dicke regime.
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