MMX-Accelerated Real-Time Hand Tracking System

We describe a system for tracking real-time hand gestures captured by a cheap web camera and a standard Intel Pentium based personal computer with no specialized image processing hardware. To attain the necessary processing speed, the system exploits the Multi-Media Instruction set(MMX) extensions of the Intel Pentium chip family through software including. the Microsoft DirectX SDK and the Intel Image Processing and Open Source Computer Vision (OpenCV) libraries. The system is based on the Camshift algorithm (from OpenCV) and the compound constant acceleration Kalman filter algorithms. Tracking is robust and efficient and can track hand motion at 30 fps

Reducing Bias of Allele Frequency Estimates by Modeling SNP Genotype Data with Informative Missingness

The presence of missing single-nucleotide polymorphism (SNP) genotypes is common in genetic studies. For studies with low-density SNPs, the most commonly used approach to dealing with genotype missingness is to simply remove the observations with missing genotypes from the analyses. This naïve method is straightforward but is valid only when the missingness is random. However, a given assay often has a different capability in genotyping heterozygotes and homozygotes, causing the phenomenon of “differential dropout” in the sense that the missing rates of heterozygotes and homozygotes are different. In practice, differential dropout among genotypes exists in even carefully designed studies, such as the data from the HapMap project and the Wellcome Trust Case Control Consortium. Under the assumption of Hardy–Weinberg equilibrium and no genotyping error, we here propose a statistical method to model the differential dropout among different genotypes. Compared with the naïve method, our method provides more accurate allele frequency estimates when the differential dropout is present. To demonstrate its practical use, we further apply our method to the HapMap data and a scleroderma data set

Hand gesture extraction by active shape models

The paper applied active statistical model for hand gesture extraction and recognition. After the hand contours are found out by a real-time segmenting and tracking system, a set of feature points (Landmarks) are marked out automatically and manually along the contour. A set of feature vectors will be normalized and aligned and then trained by Principal Component Analysis (PCA). Mean shape, eigenvalues and eigenvectors are computed out and composed of active shape model. When the model parameter is adjusted continually, various shape contours are generated to match the hand edges extracted from the original images. The gesture is finally recognized after well matching

PSMIX: an R package for population structure inference via maximum likelihood method

BACKGROUND: Inference of population stratification and individual admixture from genetic markers is an integrative part of a study in diverse situations, such as association mapping and evolutionary studies. Bayesian methods have been proposed for population stratification and admixture inference using multilocus genotypes and widely used in practice. However, these Bayesian methods demand intensive computation resources and may run into convergence problem in Markov Chain Monte Carlo based posterior samplings. RESULTS: We have developed PSMIX, an R package based on maximum likelihood method using expectation-maximization algorithm, for inference of population stratification and individual admixture. CONCLUSION: Compared with software based on Bayesian methods (e.g., STRUCTURE), PSMIX has similar accuracy, but more efficient computations. PSMIX and its supplemental documents are freely available at

Interactive Lossy Compression for Images and Video

Abstract—In any given scene, a human observer is typically more interested in some objects than others, and will pay more at-tention to those objects they are interested in. This paper aims to capture this attention focusing behavior by selectively merging a fine-scale oversegmentation of a frame so that interesting regions are segmented into smaller regions than uninteresting regions. This results in a new type of image partitioning which reflects in the image the amount of attention we pay to a particular image region. This is done using a novel, interactive method for learning merging rules for images and videos based on defining a weighted distance metric between adjacent oversegments. We present as an example application of this technique a new lossy image and video stream compression method which attempts to minimize the loss in areas of interest. I

Rare Variant Association Testing by Adaptive Combination of P-values

With the development of next-generation sequencing technology, there is a great demand for powerful statistical methods to detect rare variants (minor allele frequencies (MAFs)-MidPmethod (Cheung et al., 2012, Genet Epidemiol 36: 675–685) and propose an approach (named ‘adaptive combination of P-values for rare variant association testing’, abbreviated as ‘ADA’) that adaptively combines per-site P-values with the weights based on MAFs. Before combining P-values, we first imposed a truncation threshold upon the per-site P-values, to guard against the noise caused by the inclusion of neutral variants. ThisADA method is shown to outperform popular burden tests and non-burden tests under many scenarios. ADA is recommended for next-generation sequencing data analysis where many neutral variants may be included in a functional region

A hidden markov model for haplotype inference for present-absent data of clustered genes using identified haplotypes and haplotype patterns

The majority of killer cell immunoglobin-like receptor (KIR) genes are detected as either present or absent using locus-specific genotyping technology. Ambiguity arises from the presence of a specific KIR gene since the exact copy number (one or two) of that gene is unknown. Therefore, haplotype inference for these genes is becoming more challenging due to such large portion of missing information. Meantime, many haplotypes and partial haplotype patterns have been previously identified due to tight linkage disequilibrium (LD) among these clustered genes thus can be incorporated to facilitate haplotype inference. In this paper, we developed a hidden Markov model (HMM) based method that can incorporate identified haplotypes or partial haplotype patterns for haplotype inference from present-absent data of clustered genes (e.g., KIR genes). We compared its performance with an expectation maximization (EM) based method previously developed in terms of haplotype assignments and haplotype frequency estimation through extensive simulations for KIR genes. The simulation results showed that the new HMM based method outperformed the previous method when some incorrect haplotypes were included as identified haplotypes and/or the standard deviation of haplotype frequencies were small. We also compared the performance of our method with two methods that do not use previously identified haplotypes and haplotype patterns, including an EM based method, HPALORE, and a HMM based method, MaCH. Our simulation results showed that the incorporation of identified haplotypes and partial haplotype patterns can improve accuracy for haplotype inference. The new software package HaploHMM is available and can be downloaded at http://www.soph.uab.edu/ssg/files/People/KZhang/HaploHMM/haplohmm-index.html

Application of imputation methods to the analysis of rheumatoid arthritis data in genome-wide association studies

Most genetic association studies only genotype a small proportion of cataloged single-nucleotide polymorphisms (SNPs) in regions of interest. With the catalogs of high-density SNP data available (e.g., HapMap) to researchers today, it has become possible to impute genotypes at untyped SNPs. This in turn allows us to test those untyped SNPs, the motivation being to increase power in association studies. Several imputation methods and corresponding software packages have been developed for this purpose. The objective of our study is to apply three widely used imputation methods and corresponding software packages to a data from a genome-wide association study of rheumatoid arthritis from the North American Rheumatoid Arthritis Consortium in Genetic Analysis Workshop 16, to compare the performances of the three methods, to evaluate their strengths and weaknesses, and to identify additional susceptibility loci underlying rheumatoid arthritis. The software packages used in this paper included a program for Bayesian imputation-based association mapping (BIMBAM), a program for imputing unobserved genotypes in case-control association studies (IMPUTE), and a program for testing untyped alleles (TUNA). We found some untyped SNP that showed significant association with rheumatoid arthritis. Among them, a few of these were not located near any typed SNP that was found to be significant and thus may be worth further investigation

Effect of Initial HMM Choices in Multiple Sequence Training for Gesture Recognition

We present several ways to initialize and train Hidden Markov Models (HMMs) for gesture recognition. These include using a single initial model for training (reestimation), multiple random initial models, and initial models directly computed from physical considerations. Each of the initial models is trained on multiple observation sequences using both Baum-Welch and the Viterbi Path Counting algorithm on three different model structures: Fully Connected (or ergodic), Left-Right, and Left-Right Banded. After performing many recognition trials on our video database of 780 letter gestures, results show that a) the simpler the structure is, the less the effect of the initial model, b) the direct computation method for designing the initial model is effective and provides insight into HMM learning, and c) Viterbi Path Counting performs best overall and depends much less on the initial model than does Baum-Welch training