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PubMed2005

Standardized shrinking LORETA-FOCUSS (SSLOFO): a new algorithm for spatio-temporal EEG source reconstruction.

This paper presents a new algorithm called Standardized Shrinking LORETA-FOCUSS (SSLOFO) for solving the electroencephalogram (EEG) inverse problem. Multiple techniques are combined in a single procedure to robustly reconstruct the underlying source distribution with high spatial resolution. This algorithm uses a recursive process which takes the smooth estimate of sLORETA as initialization and then employs the re-weighted minimum norm introduced by FOCUSS. An important technique called standardization is involved in the recursive process to enhance the localization ability. The algorithm is further improved by automatically adjusting the source space according to the estimate of the previous step, and by the inclusion of temporal information. Simulation studies are carried out on both spherical and realistic head models. The algorithm achieves very good localization ability on noise-free data. It is capable of recovering complex source configurations with arbitrary shapes and can produce high quality images of extended source distributions. We also characterized the performance with noisy data in a realistic head model. An important feature of this algorithm is that the temporal waveforms are clearly reconstructed, even for closely spaced sources. This provides a convenient way to estimate neural dynamics directly from the cortical sources.

Action Potentials↗

PubMed2006

An effective and efficient compression algorithm for ECG signals with irregular periods.

This paper presents an effective and efficient preprocessing algorithm for two-dimensional (2-D) electrocardiogram (ECG) compression to better compress irregular ECG signals by exploiting their inter- and intra-beat correlations. To better reveal the correlation structure, we first convert the ECG signal into a proper 2-D representation, or image. This involves a few steps including QRS detection and alignment, period sorting, and length equalization. The resulting 2-D ECG representation is then ready to be compressed by an appropriate image compression algorithm. We choose the state-of-the-art JPEG2000 for its high efficiency and flexibility. In this way, the proposed algorithm is shown to outperform some existing arts in the literature by simultaneously achieving high compression ratio (CR), low percent root mean squared difference (PRD), low maximum error (MaxErr), and low standard derivation of errors (StdErr). In particular, because the proposed period sorting method rearranges the detected heartbeats into a smoother image that is easier to compress, this algorithm is insensitive to irregular ECG periods. Thus either the irregular ECG signals or the QRS false-detection cases can be better compressed. This is a significant improvement over existing 2-D ECG compression methods. Moreover, this algorithm is not tied exclusively to JPEG2000. It can also be combined with other 2-D preprocessing methods or appropriate codecs to enhance the compression performance in irregular ECG cases.

Algorithms↗

PubMed2006

Efficient localization of synchronous EEG source activities using a modified RAP-MUSIC algorithm.

Synchronization across different brain regions is suggested to be a possible mechanism for functional integration. Noninvasive analysis of the synchronization among cortical areas is possible if the electrical sources can be estimated by solving the electroencephalography inverse problem. Among various inverse algorithms, spatio-temporal dipole fitting methods such as RAP-MUSIC and R-MUSIC have demonstrated superior ability in the localization of a restricted number of independent sources, and also have the ability to reliably reproduce temporal waveforms. However, these algorithms experience difficulty in reconstructing multiple correlated sources. Accurate reconstruction of correlated brain activities is critical in synchronization analysis. In this study, we modified the well-known inverse algorithm RAP-MUSIC to a multistage process which analyzes the correlation of candidate sources and searches for independent topographies (ITs) among precorrelated groups. Comparative studies were carried out on both simulated data and clinical seizure data. The results demonstrated superior performance with the modified algorithm compared to the original RAP-MUSIC in recovering synchronous sources and localizing the epileptiform activity. The modified RAP-MUSIC algorithm, thus, has potential in neurological applications involving significant synchronous brain activities.

Algorithms↗

PubMed2006

Detection of pseudosinusoidal epileptic seizure segments in the neonatal EEG by cascading a rule-based algorithm with a neural network.

This paper presents an approach to detect epileptic seizure segments in the neonatal electroencephalogram (EEG) by characterizing the spectral features of the EEG waveform using a rule-based algorithm cascaded with a neural network. A rule-based algorithm screens out short segments of pseudosinusoidal EEG patterns as epileptic based on features in the power spectrum. The output of the rule-based algorithm is used to train and compare the performance of conventional feedforward neural networks and quantum neural networks. The results indicate that the trained neural networks, cascaded with the rule-based algorithm, improved the performance of the rule-based algorithm acting by itself. The evaluation of the proposed cascaded scheme for the detection of pseudosinusoidal seizure segments reveals its potential as a building block of the automated seizure detection system under development.

Algorithms↗

PubMedDate not supplied

An efficient algorithm for the identification of structured motifs in DNA promoter sequences.

We propose a new algorithm for identifying cis-regulatory modules in genomic sequences. The proposed algorithm, named RISO, uses a new data structure, called box-link, to store the information about conserved regions that occur in a well-ordered and regularly spaced manner in the data set sequences. This type of conserved regions, called structured motifs, is extremely relevant in the research of gene regulatory mechanisms since it can effectively represent promoter models. The complexity analysis shows a time and space gain over the best known exact algorithms that is exponential in the spacings between binding sites. A full implementation of the algorithm was developed and made available online. Experimental results show that the algorithm is much faster than existing ones, sometimes by more than four orders of magnitude. The application of the method to biological data sets shows its ability to extract relevant consensi.

Algorithms↗

PubMed2004

An efficient re-indexing algorithm for color-mapped images.

The efficiency of lossless compression algorithms for fixed-palette images (indexed images) may change if a different indexing scheme is adopted. Many lossless compression algorithms adopt a differential-predictive approach. Hence, if the spatial distribution of the indexes over the image is smooth, greater compression ratios may be obtained. Because of this, finding an indexing scheme that realizes such a smooth distribution is a relevant issue. Obtaining an optimal re-indexing scheme is suspected to be a hard problem and only approximate solutions have been provided in literature. In this paper, we restate the re-indexing problem as a graph optimization problem: an optimal re-indexing corresponds to the heaviest Hamiltonian path in a weighted graph. It follows that any algorithm which finds a good approximate solution to this graph-theoretical problem also provides a good re-indexing. We propose a simple and easy-to-implement approximation algorithm to find such a path. The proposed technique compares favorably with most of the algorithms proposed in literature, both in terms of computational complexity and of compression ratio.

Algorithms↗

PubMed2004

A multiple-substream unequal error-protection and error-concealment algorithm for SPIHT-coded video bitstreams.

This paper presents a coordinated multiple-substream unequal error-protection and error-concealment algorithm for SPIHT-coded bitstreams transmitted over lossy channels. In the proposed scheme, we divide the video sequence corresponding to a group of pictures into two subsequences and independently encode each subsequence using a three-dimensional SPIHT algorithm. We use two different partitioning schemes to generate the substreams, each of which offers some advantages under the appropriate channel condition. Each substream is protected by an FEC-based unequal error-protection algorithm, which assigns unequal forward error correction codes to each bit plane. Any information that is lost during the transmission for any substream is estimated at the receiver by using the correlation between the substreams and the smoothness of the video signal. Simulation results show that the proposed multiple-substream UEP algorithm is simple, fast, and robust in hostile network conditions, and that the proposed error-concealment algorithm can achieve 2-3-dB PSNR gain over the case when error concealment is not used at high packet-loss rates.

Algorithms↗

PubMed2005

Automatic selection of parameters for vessel/neurite segmentation algorithms.

An automated method is presented for selecting optimal parameter settings for vessel/neurite segmentation algorithms using the minimum description length principle and a recursive random search algorithm. It trades off a probabilistic measure of image-content coverage against its conciseness. It enables nonexpert users to select parameter settings objectively, without knowledge of underlying algorithms, broadening the applicability of the segmentation algorithm, and delivering higher morphometric accuracy. It enables adaptation of parameters across batches of images. It simplifies the user interface to just one optional parameter and reduces the cost of technical support. Finally, the method is modular, extensible, and amenable to parallel computation. The method is applied to 223 images of human retinas and cultured neurons, from four different sources, using a single segmentation algorithm with eight parameters. Improvements in segmentation quality compared to default settings using 1000 iterations ranged from 4.7%-21%. Paired t-tests showed that improvements are statistically significant (p < 0.0005). Most of the improvement occurred in the first 44 iterations. Improvements in description lengths and agreement with the ground truth were strongly correlated (p = 0.78).

Algorithms↗

PubMed2006

Nonlinear approximation based image recovery using adaptive sparse reconstructions and iterated denoising--Part II: Adaptive algorithms.

We combine the main ideas introduced in Part I with adaptive techniques to arrive at a powerful algorithm that estimates missing data in nonstationary signals. The proposed approach operates automatically based on a chosen linear transform that is expected to provide sparse decompositions over missing regions such that a portion of the transform coefficients over missing regions are zero or close to zero. Unlike prevalent algorithms, our method does not necessitate any complex preconditioning, segmentation, or edge detection steps, and it can be written as a progression of denoising operations. We show that constructing estimates based on nonlinear approximants is fundamentally a nonconvex problem and we propose a progressive algorithm that is designed to deal with this issue directly. The algorithm is applied to images through an extensive set of simulation examples, primarily on missing regions containing textures, edges, and other image features that are not readily handled by established estimation and recovery methods. We discuss the properties required of good transforms, and in conjunction, show the types of regions over which well-known transforms provide good predictors. We further discuss extensions of the algorithm where the utilized transforms are also chosen adaptively, where unpredictable signal components in the progressions are identified and not predicted, and where the prediction scenario is more general.

Algorithms↗

PubMed2003

Median-based robust algorithms for tracing neurons from noisy confocal microscope images.

This paper presents a method to exploit rank statistics to improve fully automatic tracing of neurons from noisy digital confocal microscope images. Previously proposed exploratory tracing (vectorization) algorithms work by recursively following the neuronal topology, guided by responses of multiple directional correlation kernels. These algorithms were found to fail when the data was of lower quality (noisier, less contrast, weak signal, or more discontinuous structures). This type of data is commonly encountered in the study of neuronal growth on microfabricated surfaces. We show that by partitioning the correlation kernels in the tracing algorithm into multiple subkernels, and using the median of their responses as the guiding criterion improves the tracing precision from 41% to 89% for low-quality data, with a 5% improvement in recall. Improved handling was observed for artifacts such as discontinuities and/or hollowness of structures. The new algorithms require slightly higher amounts of computation, but are still acceptably fast, typically consuming less than 2 seconds on a personal computer (Pentium III, 500 MHz, 128 MB). They produce labeling for all somas present in the field, and a graph-theoretic representation of all dendritic/axonal structures that can be edited. Topological and size measurements such as area, length, and tortuosity are derived readily. The efficiency, accuracy, and fully-automated nature of the proposed method makes it attractive for large-scale applications such as high-throughput assays in the pharmaceutical industry, and study of neuron growth on nano/micro-fabricated structures. A careful quantitative validation of the proposed algorithms is provided against manually derived tracing, using a performance measure that combines the precision and recall metrics.

Algorithms↗

PubMed2003

Quantitative comparison of FBP, EM, and Bayesian reconstruction algorithms for the IndyPET scanner.

We quantitatively compare filtered backprojection (FBP), expectation-maximization (EM), and Bayesian reconstruction algorithms as applied to the IndyPET scanner--a dedicated research scanner which has been developed for small and intermediate field of view imaging applications. In contrast to previous approaches that rely on Monte Carlo simulations, a key feature of our investigation is the use of an empirical system kernel determined from scans of line source phantoms. This kernel is incorporated into the forward model of the EM and Bayesian algorithms to achieve resolution recovery. Three data sets are used, data collected on the IndyPET scanner using a bar phantom and a Hoffman three-dimensional brain phantom, and simulated data containing a hot lesion added to a uniform background. Reconstruction quality is analyzed quantitatively in terms of bias-variance measures (bar phantom) and mean square error (lesion phantom). We observe that without use of the empirical system kernel, the FBP, EM, and Bayesian algorithms give similar performance. However, with the inclusion of the empirical kernel, the iterative algorithms provide superior reconstructions compared with FBP, both in terms of visual quality and quantitative measures. Furthermore, Bayesian methods outperform EM. We conclude that significant improvements in reconstruction quality can be realized by combining accurate models of the system response with Bayesian reconstruction algorithms.

Algorithms↗

PubMed2003

An adaptive spatial fuzzy clustering algorithm for 3-D MR image segmentation.

An adaptive spatial fuzzy c-means clustering algorithm is presented in this paper for the segmentation of three-dimensional (3-D) magnetic resonance (MR) images. The input images may be corrupted by noise and intensity nonuniformity (INU) artifact. The proposed algorithm takes into account the spatial continuity constraints by using a dissimilarity index that allows spatial interactions between image voxels. The local spatial continuity constraint reduces the noise effect and the classification ambiguity. The INU artifact is formulated as a multiplicative bias field affecting the true MR imaging signal. By modeling the log bias field as a stack of smoothing B-spline surfaces, with continuity enforced across slices, the computation of the 3-D bias field reduces to that of finding the B-spline coefficients, which can be obtained using a computationally efficient two-stage algorithm. The efficacy of the proposed algorithm is demonstrated by extensive segmentation experiments using both simulated and real MR images and by comparison with other published algorithms.

Algorithms↗

PubMed2004

Object dependency of resolution in reconstruction algorithms with interiteration filtering applied to PET data.

In this paper, we study the resolution properties of those algorithms where a filtering step is applied after every iteration. As concrete examples we take filtered preconditioned gradient descent algorithms for the Poisson log likelihood for PET emission data. For nonlinear estimators, resolution can be characterized in terms of the linearized local impulse response (LLIR). We provide analytic approximations for the LLIR for the class of algorithms mentioned above. Our expressions clearly show that when interiteration filtering (with linear filters) is used, the resolution properties are, in most cases, spatially varying, object dependent and asymmetric. These nonuniformities are solely due to the interaction between the filtering step and the Poisson noise model. This situation is similar to penalized likelihood reconstructions as studied previously in the literature. In contrast, nonregularized and postfiltered maximum-likelihood expectation maximization (MLEM) produce images with nearly "perfect" uniform resolution when convergence is reached. We use the analytic expressions for the LLIR to propose three different approaches to obtain nearly object independent and uniform resolution. Two of them are based on calculating filter coefficients on a pixel basis, whereas the third one chooses an appropriate preconditioner. These three approaches are tested on simulated data for the filtered MLEM algorithm or the filtered separable paraboloidal surrogates algorithm. The evaluation confirms that images obtained using our proposed regularization methods have nearly object independent and uniform resolution.

Algorithms↗

PubMed2004

Electrical conductivity imaging using gradient B, decomposition algorithm in magnetic resonance electrical impedance tomography (MREIT).

In magnetic resonance electrical impedance tomography (MREIT), we try to visualize cross-sectional conductivity (or resistivity) images of a subject. We inject electrical currents into the subject through surface electrodes and measure the z component Bz of the induced internal magnetic flux density using an MRI scanner. Here, z is the direction of the main magnetic field of the MRI scanner. We formulate the conductivity image reconstruction problem in MREIT from a careful analysis of the relationship between the injection current and the induced magnetic flux density Bz. Based on the novel mathematical formulation, we propose the gradient Bz decomposition algorithm to reconstruct conductivity images. This new algorithm needs to differentiate Bz only once in contrast to the previously developed harmonic Bz algorithm where the numerical computation of (inverted delta)2Bz is required. The new algorithm, therefore, has the important advantage of much improved noise tolerance. Numerical simulations with added random noise of realistic amounts show the feasibility of the algorithm in practical applications and also its robustness against measurement noise.

Algorithms↗

PubMed2004

Advanced search algorithms for information-theoretic learning with kernel-based estimators.

Recent publications have proposed various information-theoretic learning (ITL) criteria based on Renyi's quadratic entropy with nonparametric kernel-based density estimation as alternative performance metrics for both supervised and unsupervised adaptive system training. These metrics, based on entropy and mutual information, take into account higher order statistics unlike the mean-square error (MSE) criterion. The drawback of these information-based metrics is the increased computational complexity, which underscores the importance of efficient training algorithms. In this paper, we examine familiar advanced-parameter search algorithms and propose modifications to allow training of systems with these ITL criteria. The well known algorithms tailored here for ITL include various improved gradient-descent methods, conjugate gradient approaches, and the Levenberg-Marquardt (LM) algorithm. Sample problems and metrics are presented to illustrate the computational efficiency attained by employing the proposed algorithms.

Algorithms↗

PubMed2006

A fast and accurate online sequential learning algorithm for feedforward networks.

In this paper, we develop an online sequential learning algorithm for single hidden layer feedforward networks (SLFNs) with additive or radial basis function (RBF) hidden nodes in a unified framework. The algorithm is referred to as online sequential extreme learning machine (OS-ELM) and can learn data one-by-one or chunk-by-chunk (a block of data) with fixed or varying chunk size. The activation functions for additive nodes in OS-ELM can be any bounded nonconstant piecewise continuous functions and the activation functions for RBF nodes can be any integrable piecewise continuous functions. In OS-ELM, the parameters of hidden nodes (the input weights and biases of additive nodes or the centers and impact factors of RBF nodes) are randomly selected and the output weights are analytically determined based on the sequentially arriving data. The algorithm uses the ideas of ELM of Huang et al. developed for batch learning which has been shown to be extremely fast with generalization performance better than other batch training methods. Apart from selecting the number of hidden nodes, no other control parameters have to be manually chosen. Detailed performance comparison of OS-ELM is done with other popular sequential learning algorithms on benchmark problems drawn from the regression, classification and time series prediction areas. The results show that the OS-ELM is faster than the other sequential algorithms and produces better generalization performance.

Algorithms↗

PubMed2006

A class of self-stabilizing MCA learning algorithms.

In this letter, we propose a class of self-stabilizing learning algorithms for minor component analysis (MCA), which includes a few well-known MCA learning algorithms. Self-stabilizing means that the sign of the weight vector length change is independent of the presented input vector. For these algorithms, rigorous global convergence proof is given and the convergence rate is also discussed. By combining the positive properties of these algorithms, a new learning algorithm is proposed which can improve the performance. Simulations are employed to confirm our theoretical results.

Algorithms↗

PubMed2006

O(log2 M) self-organizing map algorithm without learning of neighborhood vectors.

In this letter, a new self-organizing map (SOM) algorithm with computational cost O(log2 M) is proposed where M2 is the size of a feature map. The first SOM algorithm with O(M2) was originally proposed by Kohonen. The proposed algorithm is composed of the subdividing method and the binary search method. The proposed algorithm does not need the neighborhood functions so that it eliminates the computational cost in learning of neighborhood vectors and the labor of adjusting the parameters of neighborhood functions. The effectiveness of the proposed algorithm was examined by an analysis of codon frequencies of Escherichia coli (E. coli) K12 genes. These drastic computational reduction and accessible application that requires no adjusting of the neighborhood function will be able to contribute to many scientific areas.

Algorithms↗