• Title/Summary/Keyword: random vectors

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A Combination Strategy for Construction of Peptide-β2m-H-2Kb Single Chain with Overlap Extension PCR and One-Step Cloning

  • Xu, Tao;Li, Xiaoe;Wu, You;Shahzad, Khawar Ali;Wang, Wei;Zhang, Lei;Shen, Chuanlai
    • Journal of Microbiology and Biotechnology
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    • v.26 no.12
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    • pp.2184-2191
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    • 2016
  • The time-consuming and high-cost preparation of soluble peptide-major histocompatibility complexes (pMHC) currently limits their wide uses in monitoring antigen-specific T cells. The single-chain trimer (SCT) of peptide-${\beta}2m$-MHC class I heavy chain was developed as an alternative strategy, but its gene fusion is hindered in many cases owing to the incompatibility between the multiple restriction enzymes and the restriction endonuclease sites of plasmid vectors. In this study, overlap extension PCR and one-step cloning were adopted to overcome this restriction. The SCT gene of the $OVA_{257-264}$ peptide-$(GS_4)_3-{\beta}2m-(GS_4)_4-H-2K^b$ heavy chain was constructed and inserted into plasmid pET28a by overlap extension PCR and one-step cloning, without the requirement of restriction enzymes. The SCT protein was expressed in Escherichia coli, and then purified and refolded. The resulting $H-2K^b/OVA_{257-264}$ complex showed the correct structural conformation and capability to bind with $OVA_{257-264}$-specific T-cell receptor. The overlap extension PCR and one-step cloning ensure the construction of single-chain MHC class I molecules associated with random epitopes, and will facilitate the preparation of soluble pMHC multimers.

Bivariate ROC Curve (이변량 ROC곡선)

  • Hong, C.S.;Kim, G.C.;Jeong, J.A.
    • Communications for Statistical Applications and Methods
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    • v.19 no.2
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    • pp.277-286
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    • 2012
  • For credit assessment models, the ROC curves evaluate the classification performance using two univariate cumulative distribution functions of the false positive rate and true positive rate. In this paper, it is extended to two bivariate normal distribution functions of default and non-default borrowers; in addition, the bivariate ROC curves are proposed to represent the joint cumulative distribution functions by making use of the linear function that passes though the mean vectors of two score random variables. We explore the classification performance based on these ROC curves obtained from various bivariate normal distributions, and analyze with the corresponding AUROC. The optimal threshold could be derived from the bivariate ROC curve using many well known classification criteria and it is possible to establish an optimal cut-off criteria of bivariate mixture distribution functions.

Genetic Diversity and Population Structure of Chimaphila japonica in Southern Part of Korea (한국 남부지역의 매화노루발의 유전적 다양성과 집단구조)

  • Joo-Soo Choi;Man-Kyu Huh
    • Journal of Life Science
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    • v.8 no.6
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    • pp.687-694
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    • 1998
  • Enzyme electrophoresis was used to estimate genetic diversity and population structure of Chimaphila japonica Miq. in Korea. The percent of polymorphic loci within the enzymes was 48.7%. Genetic diversity at the species level and at the population level was high (Hes=0.278 ; Hep=0.222, respectively), whereas the extent of the population divergence was relatively low ( $G_{ST}$ =0.079). $F_{IS}$ , a measure of the deviation from random mating within the 7 populations, was 0.355. An indirect estimate of the number of migrants per generation (Nm=2.61) indicates that gene flow is high among Korean populations of the species. In addition, analysis of fixation indices revealed a substantial heterozygosity deficiency in some populations and at some loci. Factors contributing to the high levels of genetic dive-rsity found in the entire species of C. japonica include wide distribution, long-lived perennials, ability to regenerate due to rhizomatous spread, outcrossing induced by animal vectors, and occasional pollen dispersal by wind.

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Undecided inference using logistic regression for credit evaluation (신용평가에서 로지스틱 회귀를 이용한 미결정자 추론)

  • Hong, Chong-Sun;Jung, Min-Sub
    • Journal of the Korean Data and Information Science Society
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    • v.22 no.2
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    • pp.149-157
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    • 2011
  • Undecided inference could be regarded as a missing data problem such as MARand MNAR. Under the assumption of MAR, undecided inference make use of logistic regression model. The probability of default for the undecided group is obtained with regression coefficient vectors for the decided group and compare with the probability of default for the decided group. And under the assumption of MNAR, undecide dinference make use of logistic regression model with additional feature random vector. Simulation results based on two kinds of real data are obtained and compared. It is found that the misclassification rates are not much different from the rate of rawdata under the assumption of MAR. However the misclassification rates under the assumption of MNAR are less than those under the assumption of MAR, and as the ratio of the undecided group is increasing, the misclassification rates is decreasing.

MCMC Algorithm for Dirichlet Distribution over Gridded Simplex (그리드 단체 위의 디리슐레 분포에서 마르코프 연쇄 몬테 칼로 표집)

  • Sin, Bong-Kee
    • KIISE Transactions on Computing Practices
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    • v.21 no.1
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    • pp.94-99
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    • 2015
  • With the recent machine learning paradigm of using nonparametric Bayesian statistics and statistical inference based on random sampling, the Dirichlet distribution finds many uses in a variety of graphical models. It is a multivariate generalization of the gamma distribution and is defined on a continuous (K-1)-simplex. This paper presents a sampling method for a Dirichlet distribution for the problem of dividing an integer X into a sequence of K integers which sum to X. The target samples in our problem are all positive integer vectors when multiplied by a given X. They must be sampled from the correspondingly gridded simplex. In this paper we develop a Markov Chain Monte Carlo (MCMC) proposal distribution for the neighborhood grid points on the simplex and then present the complete algorithm based on the Metropolis-Hastings algorithm. The proposed algorithm can be used for the Markov model, HMM, and Semi-Markov model for accurate state-duration modeling. It can also be used for the Gamma-Dirichlet HMM to model q the global-local duration distributions.

Detection of Depression Trends in Literary Cyber Writers Using Sentiment Analysis and Machine Learning

  • Faiza Nasir;Haseeb Ahmad;CM Nadeem Faisal;Qaisar Abbas;Mubarak Albathan;Ayyaz Hussain
    • International Journal of Computer Science & Network Security
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    • v.23 no.3
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    • pp.67-80
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    • 2023
  • Rice is an important food crop for most of the population in Nowadays, psychologists consider social media an important tool to examine mental disorders. Among these disorders, depression is one of the most common yet least cured disease Since abundant of writers having extensive followers express their feelings on social media and depression is significantly increasing, thus, exploring the literary text shared on social media may provide multidimensional features of depressive behaviors: (1) Background: Several studies observed that depressive data contains certain language styles and self-expressing pronouns, but current study provides the evidence that posts appearing with self-expressing pronouns and depressive language styles contain high emotional temperatures. Therefore, the main objective of this study is to examine the literary cyber writers' posts for discovering the symptomatic signs of depression. For this purpose, our research emphases on extracting the data from writers' public social media pages, blogs, and communities; (3) Results: To examine the emotional temperatures and sentences usage between depressive and not depressive groups, we employed the SentiStrength algorithm as a psycholinguistic method, TF-IDF and N-Gram for ranked phrases extraction, and Latent Dirichlet Allocation for topic modelling of the extracted phrases. The results unearth the strong connection between depression and negative emotional temperatures in writer's posts. Moreover, we used Naïve Bayes, Support Vector Machines, Random Forest, and Decision Tree algorithms to validate the classification of depressive and not depressive in terms of sentences, phrases and topics. The results reveal that comparing with others, Support Vectors Machines algorithm validates the classification while attaining highest 79% f-score; (4) Conclusions: Experimental results show that the proposed system outperformed for detection of depression trends in literary cyber writers using sentiment analysis.

Separations and Feature Extractions for Image Signals Using Independent Component Analysis Based on Neural Networks of Efficient Learning Rule (효율적인 학습규칙의 신경망 기반 독립성분분석을 이용한 영상신호의 분리 및 특징추출)

  • Cho, Yong-Hyun
    • Journal of the Korean Institute of Intelligent Systems
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    • v.13 no.2
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    • pp.200-208
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    • 2003
  • This paper proposes a separation and feature extraction of image signals using the independent component analysis(ICA) based on neural networks of efficient learning rule. The proposed learning rule is a hybrid fixed-point(FP) algorithm based on secant method and momentum. Secant method is applied to improve the performance by simplifying the 1st-order derivative computation for optimizing the objective function, which is to minimize the mutual informations of the independent components. The momentum is applied for high-speed convergence by restraining the oscillation in the process of converging to the optimal solution. The proposed algorithm has been applied to the composite images generated by random mixing matrix from the 10 images of $512\times512$-pixel. The simulation results show that the proposed algorithm has better performances of the separation speed and rate than those using the FP algorithm based on Newton and secant method. The proposed algorithm has been also applied to extract the features using a 3 set of 10,000 image patches from the 10 fingerprints of $256\times256$-pixel and the front and the rear paper money of $480\times225$-pixel, respectively, The simulation results show that the proposed algorithm has also better extraction speed than those using the another methods. Especially, the 160 basis vectors(features) of $16\times16$-pixel show the local features which have the characteristics of spatial frequency and oriented edges in the images.

Floating Point Unit Design for the IEEE754-2008 (IEEE754-2008을 위한 고속 부동소수점 연산기 설계)

  • Hwang, Jin-Ha;Kim, Hyun-Pil;Park, Sang-Su;Lee, Yong-Surk
    • Journal of the Institute of Electronics Engineers of Korea SD
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    • v.48 no.10
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    • pp.82-90
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    • 2011
  • Because of the development of Smart phone devices, the demands of high performance FPU(Floating-point Unit) becomes increasing. Therefore, we propose the high-speed single-/double-precision FPU design that includes an elementary add/sub unit and improved multiplier and compare and convert units. The most commonly used add/sub unit is optimized by the parallel rounding unit. The matrix operation is used in complex calculation something like a graphic calculation. We designed the Multiply-Add Fused(MAF) instead of multiplier to calculate the matrix more quickly. The branch instruction that is decided by the compare operation is very frequently used in various programs. We bypassed the result of the compare operation before all the pipeline processes ended to decrease the total execution time. And we included additional convert operations that are added in IEEE754-2008 standard. To verify our RTL designs, we chose four hundred thousand test vectors by weighted random method and simulated each unit. The FPU that was synthesized by Samsung's 45-nm low-power process satisfied the 600-MHz operation frequency. And we confirm a reduction in area by comparing the improved FPU with the existing FPU.

Human Visual Perception-Based Quantization For Efficiency HEVC Encoder (HEVC 부호화기 고효율 압축을 위한 인지시각 특징기반 양자화 방법)

  • Kim, Young-Woong;Ahn, Yong-Jo;Sim, Donggyu
    • Journal of Broadcast Engineering
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    • v.22 no.1
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    • pp.28-41
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    • 2017
  • In this paper, the fast encoding algorithm in High Efficiency Video Coding (HEVC) encoder was studied. For the encoding efficiency, the current HEVC reference software is divided the input image into Coding Tree Unit (CTU). then, it should be re-divided into CU up to maximum depth in form of quad-tree for RDO (Rate-Distortion Optimization) in encoding precess. But, it is one of the reason why complexity is high in the encoding precess. In this paper, to reduce the high complexity in the encoding process, it proposed the method by determining the maximum depth of the CU using a hierarchical clustering at the pre-processing. The hierarchical clustering results represented an average combination of motion vectors (MV) on neighboring blocks. Experimental results showed that the proposed method could achieve an average of 16% time saving with minimal BD-rate loss at 1080p video resolution. When combined the previous fast algorithm, the proposed method could achieve an average 45.13% time saving with 1.84% BD-rate loss.

Ensemble Learning with Support Vector Machines for Bond Rating (회사채 신용등급 예측을 위한 SVM 앙상블학습)

  • Kim, Myoung-Jong
    • Journal of Intelligence and Information Systems
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    • v.18 no.2
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    • pp.29-45
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    • 2012
  • Bond rating is regarded as an important event for measuring financial risk of companies and for determining the investment returns of investors. As a result, it has been a popular research topic for researchers to predict companies' credit ratings by applying statistical and machine learning techniques. The statistical techniques, including multiple regression, multiple discriminant analysis (MDA), logistic models (LOGIT), and probit analysis, have been traditionally used in bond rating. However, one major drawback is that it should be based on strict assumptions. Such strict assumptions include linearity, normality, independence among predictor variables and pre-existing functional forms relating the criterion variablesand the predictor variables. Those strict assumptions of traditional statistics have limited their application to the real world. Machine learning techniques also used in bond rating prediction models include decision trees (DT), neural networks (NN), and Support Vector Machine (SVM). Especially, SVM is recognized as a new and promising classification and regression analysis method. SVM learns a separating hyperplane that can maximize the margin between two categories. SVM is simple enough to be analyzed mathematical, and leads to high performance in practical applications. SVM implements the structuralrisk minimization principle and searches to minimize an upper bound of the generalization error. In addition, the solution of SVM may be a global optimum and thus, overfitting is unlikely to occur with SVM. In addition, SVM does not require too many data sample for training since it builds prediction models by only using some representative sample near the boundaries called support vectors. A number of experimental researches have indicated that SVM has been successfully applied in a variety of pattern recognition fields. However, there are three major drawbacks that can be potential causes for degrading SVM's performance. First, SVM is originally proposed for solving binary-class classification problems. Methods for combining SVMs for multi-class classification such as One-Against-One, One-Against-All have been proposed, but they do not improve the performance in multi-class classification problem as much as SVM for binary-class classification. Second, approximation algorithms (e.g. decomposition methods, sequential minimal optimization algorithm) could be used for effective multi-class computation to reduce computation time, but it could deteriorate classification performance. Third, the difficulty in multi-class prediction problems is in data imbalance problem that can occur when the number of instances in one class greatly outnumbers the number of instances in the other class. Such data sets often cause a default classifier to be built due to skewed boundary and thus the reduction in the classification accuracy of such a classifier. SVM ensemble learning is one of machine learning methods to cope with the above drawbacks. Ensemble learning is a method for improving the performance of classification and prediction algorithms. AdaBoost is one of the widely used ensemble learning techniques. It constructs a composite classifier by sequentially training classifiers while increasing weight on the misclassified observations through iterations. The observations that are incorrectly predicted by previous classifiers are chosen more often than examples that are correctly predicted. Thus Boosting attempts to produce new classifiers that are better able to predict examples for which the current ensemble's performance is poor. In this way, it can reinforce the training of the misclassified observations of the minority class. This paper proposes a multiclass Geometric Mean-based Boosting (MGM-Boost) to resolve multiclass prediction problem. Since MGM-Boost introduces the notion of geometric mean into AdaBoost, it can perform learning process considering the geometric mean-based accuracy and errors of multiclass. This study applies MGM-Boost to the real-world bond rating case for Korean companies to examine the feasibility of MGM-Boost. 10-fold cross validations for threetimes with different random seeds are performed in order to ensure that the comparison among three different classifiers does not happen by chance. For each of 10-fold cross validation, the entire data set is first partitioned into tenequal-sized sets, and then each set is in turn used as the test set while the classifier trains on the other nine sets. That is, cross-validated folds have been tested independently of each algorithm. Through these steps, we have obtained the results for classifiers on each of the 30 experiments. In the comparison of arithmetic mean-based prediction accuracy between individual classifiers, MGM-Boost (52.95%) shows higher prediction accuracy than both AdaBoost (51.69%) and SVM (49.47%). MGM-Boost (28.12%) also shows the higher prediction accuracy than AdaBoost (24.65%) and SVM (15.42%)in terms of geometric mean-based prediction accuracy. T-test is used to examine whether the performance of each classifiers for 30 folds is significantly different. The results indicate that performance of MGM-Boost is significantly different from AdaBoost and SVM classifiers at 1% level. These results mean that MGM-Boost can provide robust and stable solutions to multi-classproblems such as bond rating.