32462907
Alignment of Optical Maps
We introduce a new scoring method for calculation of alignments of optical maps. Missing cuts, false cuts, and sizing errors present in optical maps are addressed by our alignment score through calculation of corresponding likelihoods. The size error model is derived through the application of Central Limit Theorem and validated by residual plots collected from real data. Missing cuts and false cuts are modeled as Bernoulli and Poisson events, respectively, as suggested by previous studies. Likelihoods are used to derive an alignment score through calculation of likelihood ratios for a certain hypothesis test. This allows us to achieve maximal descriminative power for the alignment score. Our scoring method is naturally embedded within a well known DP framework for finding optimal alignments.
12935102
Whole-Genome Analysis of Gene Conversion Events
Gene conversion events are often overlooked in analyses of genome evolution. In a conversion event, an interval of DNA sequence (not necessarily containing a gene) overwrites a highly similar sequence. The event creates relationships among genomic intervals that can confound attempts to identify orthologs and to transfer functional annotation between genomes. Here we examine 1,112,202 paralogous pairs of human genomic intervals, and detect conversion events in about 13.5% of them. Properties of the putative gene conversions are analyzed, such as the lengths of the paralogous pairs and the spacing between their sources and targets. Our approach is illustrated using conversion events in the beta-globin gene cluster.
12263549
Tree-guided Bayesian inference of population structures
MOTIVATION
Inferring population structures using genetic data sampled from a group of individuals is a challenging task. Many methods either consider a fixed population number or ignore the correlation between populations. As a result, they can lose sensitivity and specificity in detecting subtle stratifications. In addition, when a large number of genetic markers are used, many existing algorithms perform rather inefficiently.


RESULT
We propose a new Bayesian method to infer population structures using multiple unlinked single nucleotide polymorphisms (SNPs). Our approach explicitly considers the population correlation through a tree hierarchy, and treat the population number as a random variable. Using both simulated and real datasets of worldwide samples, we demonstrate that an incorporated tree can consistently improve the power in detecting subtle population stratifications. A tree-based model often involves a large number of unknown parameters, and the corresponding estimation procedure can be highly inefficient. We further implement a partition method to analytically integrate out all nuisance parameters in the tree. As a result, our method can analyze large SNP datasets with significantly improved convergence rate.


AVAILABILITY
http://www.stat.psu.edu/~yuzhang/tips.tar.
2330317
Semi-Supervised Discriminant Analysis using robust path-based similarity
Linear discriminant analysis (LDA), which works by maximizing the within-class similarity and minimizing the between-class similarity simultaneously, is a popular dimensionality reduction technique in pattern recognition and machine learning. In real-world applications when labeled data are limited, LDA does not work well. Under many situations, however, it is easy to obtain unlabeled data in large quantities. In this paper, we propose a novel dimensionality reduction method, called semi-supervised discriminant analysis (SSDA), which can utilize both labeled and unlabeled data to perform dimensionality reduction in the semi-supervised setting. Our method uses a robust path-based similarity measure to capture the manifold structure of the data and then uses the obtained similarity to maximize the separability between different classes. A kernel extension of the proposed method for nonlinear dimensionality reduction in the semi-supervised setting is also presented. Experiments on face recognition demonstrate the effectiveness of the proposed method.
20139173
Muscle-driven modeling of wrinkles for 3D facial expressions
Facial expression animation considering wrinkle formation is an aspiring goal and a challenging task. This paper presents a new geometric wrinkle model that is defined according to facial muscle anatomy for efficient simulation of dynamic wrinkles within expressions. Our method is applied to an anatomy-based face model with a multi-layer structure of skin, muscles, and skull. The location and orientation of the wrinkles are automatically determined based on muscle contraction and its influence on the skin. Corresponding to two types of facial muscles, the geometric wrinkle model governs evolution of wrinkle amplitude in the local deformed face regions. It provides intuitive parameters for easy control over wrinkle characteristics by taking into account the properties of real wrinkles. Results show that this method enables realistic wrinkles synchronized with facial movements to be dynamically simulated and rendered at an interactive rate.
35510017
A Link-Based Rank of Postings in Newsgroup
Discussion systems such as Usenet, BBS, Forum are important resources for information sharing, view exchanging, problem solving and product feedback, etc. on Internet. The postings in newsgroups on Usenet represents the judgments and choices of participators. The structure of postings could provide helpful information for the users. In this paper, we present a method called PostRank to rank the postings based on the structure of newsgroup. Its results correspond to the eigenvectors of the transition probability matrix and the stationary vectors of the Markov chains. It could provide useful global information for the newsgroup and it can be used to help the users access information in it more effectively and efficiently. This method can be also applied on other discussion systems. Some experimental results and discussions on real data sets collected by us are also provided.
18262600
Parameters optimization of support vector regression based on immune particle swarm optimization algorithm
A novel Immune Particle Swarm Optimization (IPSO) for parameters optimization of Support Vector Regression (SVR) is proposed in this article. After introduced clonal copy and mutation process of Immune Algorithm (IA), the particle of PSO is considered as antibodies. Therefore, evaluated the fitness of particles by the Leave-One-Out Cross-Validation (LOOCV) standard, the best individual mutated particle for each cloned group will be selected to compose the next generation to get better parameters of SVR. It can construct high accuracy and generalization performance regression model rapidly by optimizing the combination of three SVR parameters at the same time. Under the datasets generated from sinx function with additive noise and spectra dataset, simulation results show that the new method can determine the parameters of SVR quickly and the gotten models have superior learning accuracy and generalization performance.
4846997
Semi-supervised Discriminant Analysis Via CCCP
Linear discriminant analysis (LDA) is commonly used for dimensionality reduction. In real-world applications where labeled data are scarce, LDA does not work very well. However, unlabeled data are often available in large quantities. We propose a novel semi-supervised discriminant analysis algorithm called SSDA$_{\mathit{CCCP}}$. We utilize unlabeled data to maximize an optimality criterion of LDA and use the constrained concave-convex procedure to solve the optimization problem. The optimization procedure leads to estimation of the class labels for the unlabeled data. We propose a novel confidence measure for selecting those unlabeled data points with high confidence. The selected unlabeled data can then be used to augment the original labeled data set for performing LDA. We also propose a variant of SSDA$_{\mathit{CCCP}}$, called M-SSDA$_{\mathit{CCCP}}$, which adopts the manifold assumption to utilize the unlabeled data. Extensive experiments on many benchmark data sets demonstrate the effectiveness of our proposed methods.