The aim of this study is to perform motion segmentation and three‐dimensional shape recovery of a dynamic human body from an image sequence. The authors note that human body motion generally consists of large articulations between different body parts and small local deformations within each body part. On the basis of this notion, they develop an integrated framework that combines articulated structure from motion and non‐rigid SFM to estimate human body motion and shape as an articulated deformable structure. Unlike existing approaches that apply a low‐rank subspace method for motion segmentation, they use a metric constraint for identifying rigid subsets, which is more robust and, therefore, allow a more relaxed error threshold to be set for fitting rigid subsets, catering for small deformations within individual rigid subsets. They provide an automated statistical procedure for setting the aforementioned error threshold. The rigid subsets are then linked into articulated kinematic chains by minimum spanning tree search in a graph of joint costs. Finally, the blend‐shape method is applied to model local deformations of each individual subset. Experimental results show that the proposed method provides better performance for human motion segmentation and shape recovery compared with existing methods.

This paper is aimed to predict pain perception from laser-evoked EEG oscillatory activities in the time-frequency domain with multivariate pattern analysis (MVPA). We first identify pre-/post-stimulus EEG oscillatory activities that are correlated with the intensity of laser-evoked pain perception using a multivariate linear regression (MVLR) model, which is solved by partial least-squares regression (PLSR). Further, we used the MVLR model to predict the intensity of pain perception from identified pain-correlated time-frequency EEG data for each subject. Our results showed that the proposed MVLR prediction model provided a qualitative prediction of pain (classification of low pain and high pain) with an accuracy of 78.53 ± 1.16% and a quantitative prediction of pain (on a continuous scale from 0 to 10) with a mean absolute error (MAE) of 1.45 ± 0.05, both of which are significantly better than the results of the conventional pain prediction based on single-trial detection of laser-evoked potentials. Besides, for the first time it was found that the pre-stimulus EEG oscillation could significantly contribute to the prediction, which extended our notion of the determinants of pain perception.

BACKGROUND: Subtypes are widely found in cancer. They are characterized with different behaviors in clinical and molecular profiles, such as survival rates, gene signature and copy number aberrations (CNAs). While cancer is generally believed to have been caused by genetic aberrations, the number of such events is tremendous in the cancer tissue and only a small subset of them may be tumorigenic. On the other hand, gene expression signature of a subtype represents residuals of the subtype-specific cancer mechanisms. Using high-throughput data to link these factors to define subtype boundaries and identify subtype-specific drivers, is a promising yet largely unexplored topic. RESULTS: We report a systematic method to automate the identification of cancer subtypes and candidate drivers. Specifically, we propose an iterative algorithm that alternates between gene expression clustering and gene signature selection. We applied the method to datasets of the pediatric cerebellar tumor medulloblastoma (MB). The subtyping algorithm consistently converges on multiple datasets of medulloblastoma, and the converged signatures and copy number landscapes are also found to be highly reproducible across the datasets. Based on the identified subtypes, we developed a PCA-based approach for subtype-specific identification of cancer drivers. The top-ranked driver candidates are found to be enriched with known pathways in certain subtypes of MB. This might reveal new understandings for these subtypes. CONCLUSIONS: Our study indicates that subtype-signature defines the subtype boundaries, characterizes the subtype-specific processes and can be used to prioritize signature-related drivers.

This paper investigates robust consensus for a class of uncertain multi-agent dynamical systems. Specifically, it is supposed that the system is described by a weighted adjacency matrix whose entries are polynomial functions of an uncertain vector constrained in a semi-algebraic set. For this uncertain topology, we provide necessary and sufficient conditions for ensuring robust first-order consensus and robust second-order consensus, in both cases of positive and non-positive weighted adjacency matrices. Moreover, we show how these conditions can be investigated through convex programming by using standard software. Some numerical examples illustrate the proposed results.

Cancer is a complex disease and within a cancer, subtypes of patients with distinct behaviors often exist. The subtypes might have been caused by different hits, such as copy number aberrations (CNAs) and point mutations, on different pathways/cells-of-origin in a common tissue/organ. Identifying the subtypes with subtype-specific drivers, i.e., hits, is key to the understanding of cancer and development of novel treatments. Here, we report the development of an integrative method to identify the subtypes of cancer. Specifically, we consider CNAs and their impact on gene expressions. Based on these relations, we propose an iterative approach that alternates between kernel based gene expression clustering and gene signature selection. We applied the method to datasets of the pediatric cancer medulloblastoma (MB). The consensus number of clusters quickly converges to three; and for each of these three subtypes, the signature detection also converges to a consistent set of a few hundred highly functionally related genes. For each of the subtypes, we correlate its signature with the set of within-subtype recurrent CNA-affected genes for identifying drivers. The top-ranked driver candidates are found to be enriched with known pathways in certain subtypes of MB as well as containing novel genes that might reveal new understandings for other subtypes.

In this paper, a new approach for matching and recognizing affine-distorted planar shapes is proposed, which allows for partial occlusions. In our approach, each shape is divided into a sequence of ordered affine-invariant segments based on the properties of curvature scale space (CSS) shape descriptor. Then Smith-Waterman algorithm is applied for matching the pair of affine-invariant segment sequences. Finally the point correspondences along the two shapes are obtained and the affine transform is estimated accordingly. Experiments show that our algorithm is effective for matching and recognizing shapes which are distorted by affine transforms, including translation, rotation, scaling, and shearing. Furthermore, it is capable of dealing with the case where one of the shapes or both shapes are partially occluded.

This paper proposes a new method for identification of time-varying autoregressive (TVAR) models based on local polynomial modeling (LPM) and applies it to investigate the dynamic spectral information of event-related electroencephalogram (EEG). The proposed method models the TVAR coefficients locally by polynomials and estimates those using least-squares estimation with a kernel having a certain bandwidth. A data-driven variable bandwidth selection method is developed to obtain the optimal bandwidth, which minimizes the mean squared error (MSE). Simulation results show that the LPM-based TVAR identification method outperforms conventional methods for different scenarios. The advantages of the LPM method make it a useful high-resolution time-frequency analysis (TFA) technique for nonstationary biomedical signals like EEG. Experimental results show that the LPM method can reveal more meaningful time-frequency characteristics than wavelet transform.

Filters and wrappers are two prevailing approaches for gene selection in microarray data analysis. Filters make use of statistical properties of each gene to represent its discriminating power between different classes. The computation is fast but the predictions are inaccurate. Wrappers make use of a chosen classifier to select genes by maximizing classification accuracy, but the computation burden is formidable. Filters and wrappers have been combined in previous studies to maximize the classification accuracy for a chosen classifier with respect to a filtered set of genes. The drawback of this single-filter-single-wrapper (SFSW) approach is that the classification accuracy is dependent on the choice of specific filter and wrapper. In this paper, a multiple-filter-multiple-wrapper (MFMW) approach is proposed that makes use of multiple filters and multiple wrappers to improve the accuracy and robustness of the classification, and to identify potential biomarker genes. Experiments based on six benchmark data sets show that the MFMW approach outperforms SFSW models (generated by all combinations of filters and wrappers used in the corresponding MFMW model) in all cases and for all six data sets. Some of MFMW-selected genes have been confirmed to be biomarkers or contribute to the development of particular cancers by other studies.

Network component analysis (NCA) has been established as a promising tool for reconstructing gene regulatory networks from microarray data. NCA is a method that can resolve the problem of blind source separation when the mixing matrix instead has a known sparse structure despite the correlation among the source signals. The original NCA algorithm relies on alternating least squares (ALS) and suffers from local convergence as well as slow convergence. In this paper, we develop new and more robust NCA algorithms by incorporating additional signal constraints. In particular, we introduce the biologically sound constraints that all nonzero entries in the connectivity network are positive. Our new approach formulates a convex optimization problem which can be solved efficiently and effectively by fast convex programming algorithms. We verify the effectiveness and robustness of our new approach using simulations and gene regulatory network reconstruction from experimental yeast cell cycle microarray data.

Using high throughput DNA binding data for transcription factors and DNA microarray time course data, we constructed four transcription regulatory networks and analysed them using a novel extension to the network component analysis (NCA) approach. We incorporated probe level uncertainties in gene expression measurements into the NCA analysis by the application of probabilistic principal component analysis (PPCA), and applied the method to data from yeast metabolic cycle. Analysis shows statistically significant enhancement to periodicity in a large fraction of the transcription factor activities inferred from the model. For several of these we found literature evidence of post-transcriptional regulation. Accounting for probe level uncertainty of microarray measurements leads to improved network component analysis. Transcription factor profiles showing greater periodicity at their activity levels, rather than at the corresponding mRNA levels, for over half the regulators in the networks points to extensive post-transcriptional regulations.

In this paper, an efficient greedy scheduler for zero-forcing dirty-paper coding (ZF-DPC), which can be incorporated in complex Householder QR factorization of the channel matrix, is proposed. The ratio of the complexity of the proposed scheduler to the complexity of the channel matrix factorization required by ZF-DPC is O(M-1), while such ratio for the original greedy scheduler is O(M), where M is the number of transmitters. Therefore, the new scheduler reduces the overhead of scheduling from being the bottleneck of ZF-DPC to being negligible.

MOTIVATION: Recently developed network component analysis (NCA) approach is promising for gene regulatory network reconstruction from microarray data. The existing NCA algorithm is an iterative method which has two potential limitations: computational instability and multiple local solutions. The subsequently developed NCA-r algorithm with Tikhonov regularization can help solve the first issue but cannot completely handle the second one. Here we develop a novel Fast Network Component Analysis (FastNCA) algorithm which has an analytical solution that is much faster and does not have the above limitations. RESULTS: Firstly FastNCA is compared to NCA and NCA-r using synthetic data. The reconstruction of FastNCA is more accurate than that of NCA-r and comparable to that of properly converged NCA. FastNCA is not sensitive to the correlation among the input signals, while its performance does degrade a little but not as dramatically as that of NCA. Like NCA, FastNCA is not very sensitive to small inaccuracies in a priori information on the network topology. FastNCA is about several tens times faster than NCA and several hundreds times faster than NCA-r. Then, the method is applied to real yeast cell-cycle microarray data. The activities of the estimated cell-cycle regulators by FastNCA and NCA-r are compared to the semi-quantitative results obtained independently by Lee et al. (2002). It is shown here that there is a greater agreement between the results of FastNCA and Lee's, which is represented by the ratio 23/33, than that between the results of NCA-r and Lee's, which is 14/33. AVAILABILITY: Software and supplementary materials are available from http://www.eee.hku.hk/~cqchang/FastNCA.htm

BACKGROUND: Currently, clustering with some form of correlation coefficient as the gene similarity metric has become a popular method for profiling genomic data. The Pearson correlation coefficient and the standard deviation (SD)-weighted correlation coefficient are the two most widely-used correlations as the similarity metrics in clustering microarray data. However, these two correlations are not optimal for analyzing replicated microarray data generated by most laboratories. An effective correlation coefficient is needed to provide statistically sufficient analysis of replicated microarray data. RESULTS: In this study, we describe a novel correlation coefficient, shrinkage correlation coefficient (SCC), that fully exploits the similarity between the replicated microarray experimental samples. The methodology considers both the number of replicates and the variance within each experimental group in clustering expression data, and provides a robust statistical estimation of the error of replicated microarray data. The value of SCC is revealed by its comparison with two other correlation coefficients that are currently the most widely-used (Pearson correlation coefficient and SD-weighted correlation coefficient) using statistical measures on both synthetic expression data as well as real gene expression data from Saccharomyces cerevisiae. Two leading clustering methods, hierarchical and k-means clustering were applied for the comparison. The comparison indicated that using SCC achieves better clustering performance. Applying SCC-based hierarchical clustering to the replicated microarray data obtained from germinating spores of the fern Ceratopteris richardii, we discovered two clusters of genes with shared expression patterns during spore germination. Functional analysis suggested that some of the genetic mechanisms that control germination in such diverse plant lineages as mosses and angiosperms are also conserved among ferns. CONCLUSION: This study shows that SCC is an alternative to the Pearson correlation coefficient and the SD-weighted correlation coefficient, and is particularly useful for clustering replicated microarray data. This computational approach should be generally useful for proteomic data or other high-throughput analysis methodology.

This paper presents a hierarchical approach for fast and robust ellipse extraction from images. At the lowest level, the image is described as a set of edge pixels, from which line segments are extracted. Then, line segments that are potential candidates of elliptic arcs are linked to form arc segments according to connectivity and curvature relations. After that, arc segments that belong to the same ellipse are grouped together. Finally, a robust statistical method, namely RANSAC, is applied to fit ellipses. This method does not need a high dimensional parameter space like Hough transform based algorithms, and so it reduces the computation and memory requirements. Experiments on both synthetic and real images demonstrate that the proposed method has excellent performance in handling occlusion and overlapping ellipses.

This paper considers the problem of realizing visual servoing taking into account constraints such as visibility and workspace constraints while minimizing a cost function such as spanned image area and trajectory length. A new path-planning scheme is proposed by, first, introducing a robust object reconstruction which allows one to obtain feasible image trajectories. Second, the rotation path is parameterized through a particular extension of the Euler parameters in order to obtain an equivalent expression of the rotation matrix as a quadratic function of unconstrained variables, hence largely simplified with respect to standard parameterizations which involve transcendental functions. Then, polynomials of arbitrary degree are used to complete the parametrization and formulate a general optimization where a number of constraints and costs can be considered. The optimal trajectory is followed by tracking the image trajectories with standard IBVS controllers.

The problem of evaluating worst-case camera positioning error induced by unknown-but-bounded (UBB) image noise for a given object-camera configuration is considered. Specifically, it is shown that upper bounds to the rotation and translation worst-case error for a certain image noise intensity can be obtained through convex optimizations. These upper bounds, contrary to lower bounds provided by standard optimization tools, allow one to design robust visual servo systems.

Visual servoing consists of steering a robot from an initial to a desired location by exploiting the information provided by visual sensors. This paper deals with the problem of realizing visual servoing for robot manipulators taking into account constraints such as visibility, workspace (that is obstacle avoidance), and joint constraints, while minimizing a cost function such as spanned image area, trajectory length, and curvature. To solve this problem, a new path-planning scheme is proposed. First, a robust object reconstruction is computed from visual measurements which allows one to obtain feasible image trajectories. Second, the rotation path is parameterized through an extension of the Euler parameters that yields an equivalent expression of the rotation matrix as a quadratic function of unconstrained variables, hence, largely simplifying standard parameterizations which involve transcendental functions. Then, polynomials of arbitrary degree are used to complete the parametrization and formulate the desired constraints and costs as a general optimization problem. The optimal trajectory is followed by tracking the image trajectory with an IBVS controller combined with repulsive potential fields in order to fulfill the constraints in real conditions.

Previous algorithms for recovering 3D geometry from uncalibrated circular motion image sequences of unknown rotation angles are mostly for constant intrinsic parameters. In this paper, a new and simple method for recovering circular motion geometry in spite of varying intrinsic parameters is proposed. It is shown that the movement of the camera forms two concentric circles on the motion plane. By identifying the concentric conic loci in 3D projective frame, the geometry of circular motion can be recovered. Compared with existing rotation angle recovery methods, the new method is (i) more flexible in that it allows the intrinsic parameters to vary from image to image; (ii) simpler by avoiding the calculation of the intersection points of two conics which is notoriously complicated. Experimental results for real images are provided to show the performance of the proposed method.

In this paper we propose a novel and fast nonlinear association measure based on order statistics and rearrangement inequality. We employ one episode of heart signal, one episode of EEG signal and 1000 white Gaussian noises in our study. Extensive statistical analysis are performed based on one linear model and one nonlinear model. Comparative studies with three other prominent methods are presented. Theoretical derivations and experimental results suggest that our new method has small biasedness, high sensitivity to changes in association, fast computational speed, and robustness under monotone nonlinear transformations.

A new practical method is developed for 3D reconstruction from an image sequence captured by a camera with constant intrinsic parameters undergoing circular motion. We introduce a method for enforcing the circular constraint in a factorization-based projective reconstruction. This is called a circular projective reconstruction. Given a turntable sequence, our method uses a hierarchical approach to reconstructing the objects and cameras, which first computes a circular projective reconstruction of a sub-sequence and then extends the reconstruction to the complete sequence. Camera matrix and the motion parameters, i.e. the rotation angles, are computed iteratively in a way that minimizes the 2D reprojection error. Thus, an optimal reconstruction is obtained upon convergence. The algorithm is evaluated using real image sequence. 1

The problem of depth-from-motion using a monocular image sequence is considered. A pixel-based model is developed for direct depth estimation within a Kalman filtering framework. A method is proposed for incorporating local surface structure into the Kalman filter. Experimental results are provided to illustrate the effect of structural information on depth estimation.

A robust hybrid control method for robot manipulators is proposed which integrates an H/sup /spl infin// controller and an adaptive controller. The H/sup /spl infin// controller is used to minimize the effect of parameter uncertainties of the robot model on the tracking performance, while the adaptive controller continuously adjusts the model parameters to reduce the model error. Simulations show that disturbances generated from the model error will be quickly compensated and so small tracking errors can be achieved.>

The concept of generalized block diagonal dominance is used to extend a number of recently developed robust stability results for multivariable systems to large-scale interconnected systems.