ALBERT

Description: Postdisaster search and rescue is an important application of ultrawideband (UWB) radar systems, which mainly detect trapped victims by their respiratory-motion response. The development of a respiratory-motion detection (RMD) algorithm that can eliminate nonstationary clutter and noise is a challenging task for the application. A new algorithm is proposed to deal with the task in this letter. It uses the multichannel singular spectrum analysis (MSSA) technique to reconstruct the respiratory-motion response detected by a UWB radar. During the reconstruction, the periodicity and range interrelation characteristics of the response are exploited to adaptively identify signal subspaces. The performance of the algorithm is verified both by simulated and real data. The results show its improved performance over the reference algorithms, e.g., a singular-value-decomposition-based algorithm. The adaptive-MSSA-based RMD algorithm has great promise not only in practical use but also for future research of UWB-radar-based human being remote sensing.

Description: Land–sea contamination observed in Soil Moisture and Ocean Salinity (SMOS) brightness temperature images is found to have two main contributions: the floor error inherent of image reconstruction and a multiplicative error either in the antenna temperature or in the visibility samples measured by the correlator. The origin of this last one is traced down to SMOS calibration parameters to yield a simple correction scheme, which is validated against several geophysical scenarios. Autoconsistency rules in interferometric synthesis together with redundant and complementary calibration procedures provide a robust SMOS calibration scheme.

Description: This letter proposes a novel algorithm, which is based on the generalized method of moments (GMM), for the estimation and correction of phase errors induced in synthetic aperture radar (SAR) imagery. The GMM algorithm is used to replace the original phase-estimation kernel in the basic structure of the phase-gradient-autofocus algorithm. Since this novel algorithm does not require the observed signal to be a certain distribution model, it is able to estimate arbitrary phase errors. The GMM algorithm has the ability of estimating range-dependent phase errors, which makes it an efficient estimator. As a result, higher accuracy of the estimated phase errors and a better focused image can be achieved. Excellent results have been obtained in autofocusing and imaging experiments on real SAR data.

Description: Strong clutter reflections of terrain and marine surfaces obscure the contrast between the target-of-interest and clutter (terrain and marine surface reflections) in synthetic aperture radar (SAR) images and consequently hinder the efficiency of image interpretation and analysis. To overcome this problem, this letter proposes an efficient clutter suppression method in SAR images, which is named shedding irrelevant patterns (SIP). The essence is to construct a regression function that can suppress clutter and preserve the target patterns concurrently. We assume that the clutter is irrelevant to the target-of-interest and distinguishable in patterns in terms of image-pixel distribution and intensity (spatial information). Experimental results show the efficiency of the proposed method in both clutter suppression and target pattern preservation.

Description: A concern in hyperspectral image classification is the high number of required training samples. When traditional classifiers are applied, feature reduction (FR) techniques are the most common approaches to deal with this problem. Subspace-based classifiers, which are developed based on high-dimensional space characteristics, are another way to handle the high dimension of hyperspectral images. In this letter, a novel subspace-based classification approach is proposed and compared with basic and improved subspace-based classifiers. The proposed classifier is also compared with traditional classifiers that are accompanied by an FR technique and the well-known support vector machine classifier. Experimental results prove the efficiency of the proposed method, especially when a limited number of training samples are available. Furthermore, the proposed method has a very high level of automation and simplicity, as it has no parameters to be set.

Description: To improve the spatial density of measurement points of persistent-scatterer interferometry, distributed scatterer (DS) should be considered and processed. An important procedure in DS interferometry is the phase triangulation (PT). This letter introduces two modified PT algorithms (i.e., equal-weighted PT and coherence-weighted PT) and analyzes the mathematical relations between different published PT methods (i.e., the maximum-likelihood phase estimator, least squares estimator, and eigendecomposition-based phase estimators). The analysis shows that the above five PT methods share very similar mathematical forms with different weight values in the estimation procedure.

Description: Sparse representation-based classifier and its variants have been widely adopted for hyperspectral image (HSI) classification recently. However, sparse representation is unstable so that similar features might obtain significantly different sparse codes. Despite the instability, we find that the sparse codes follow a class-dependent distribution under the structured dictionary consisting of training samples from all classes. Based on this observation, a novel discriminative feature, sparse code histogram (SCH), is developed for HSI classification. By counting the SCH of each sample from the sparse codes of its spatial neighbors, we can statistically obtain the distribution pattern of sparse codes of the class to which the sample belongs, and then treat the SCH as a new feature for classification. To reduce the possible outliers among the neighbors, a shape-adaptive neighborhood extractor is also employed to enhance the stability of the histogram feature. Experimental results demonstrate that SCH enjoys a strong discriminative power, which can achieve notably better performance than several state-of-the-art methods for HSI classification with limited training samples.

Description: Several detection statistics have been proposed for detecting fine ground disturbances between two synthetic aperture radar (SAR) images, such as vehicle tracks. The standard method involves estimating a local correlation coefficient between images. Other methods have been proposed using various statistical hypothesis tests. One of these alternative methods is a generalized likelihood ratio test (GLRT), which compares a full-correlation image model to a no-correlation image model. In this letter, we expand the GLRT to polarimetric SAR data and derive the appropriate GLRT detection statistics. Additionally, we explore relaxing the equal variance/equal polarimetric covariance assumptions used in previous results and find improved performance on macroscopic scene changes.

Description: For downward-looking linear array 3-D synthetic aperture radar, the resolution in cross-track direction is much lower than the ones in range and azimuth. Hence, superresolution reconstruction algorithms are desired. Since the cross-track signal to be reconstructed is sparse in the object domain, compressive sensing algorithm has been used. However, the imaging processing on the 3-D scene brings large computational loads, which renders challenges in both data acquisition and processing. To cover this shortage, truncated singular value decomposition is utilized to reconstruct a reduced-redundancy spatial measurement matrix. The proposed algorithm provides advantages in terms of computational time while maintaining the quality of the scene reconstructions. Moreover, our results on uniform linear array are generally applicable to sparse nonuniform linear array. Superresolution properties and reconstruction accuracies are demonstrated using simulations under the noise and clutter scenarios.

Description: This letter proposes a signal processing method of passive bistatic radar (PBR) exploiting an uncooperative radar as an illuminator. Compared with other opportunity illuminators, the transmitting signal of a radar usually has a better ambiguity function, which leads to a higher range resolution. Two channels are needed in PBR system. The reference channel is used to estimate radar signal parameters and reconstruct directly propagated signal. The surveillance channel is used to receive scattered wave. An array antenna and a simultaneous multibeam algorithm are necessary in the surveillance channel due to the flexible beam scanning of the uncooperative radar. The procedure of the proposed method is explained in detail, which is then followed by a field experiment. Preliminary results from the field experiment show that the proposed method can be applied to target angle and bistatic range measurement successfully.

Description: In order to achieve 3-D imaging with an airborne down-looking linear-array synthetic aperture radar (LASAR), a uniform virtual antenna array may be obtained by aperture synthesis of the cross-track sparse multiple-input–multiple-output array. However, the actual 3-D imaging quality is unavoidably degraded by errors in the virtual element position. In this letter, we investigate the effects of these errors on the forms and the degrees of image quality degradation by decomposing the error-related stochastic processes via an orthogonal transform based on discrete Legendre polynomials. It should be noted that these analyses are helpful for designing a LASAR system and providing a reference for specifying the requisite precision of measurement devices and calibration methods. Finally, we briefly consider the use of calibration methods to eliminate the effects of errors.

Description: In problems where labeled data are scarce, semisupervised learning (SSL) techniques are an attractive framework that can exploit both labeled and unlabeled data. These approaches typically rely on a smoothness assumption such that examples that are similar in input space should also be similar in label space. In many domains, such as remotely sensed hyperspectral image (HSI) classification, the data violate this assumption. In response, we propose a general method by which a neighborhood graph used in SSL is learned using binary classifiers that are trained to predict whether a pair of pixels shares the same label. Working within the framework of semisupervised neural networks (SSNNs), we show that our approach improves on the performance of the SSNN on two HSI data sets.

Description: In this letter, new models for the spatial correlation of sea clutter texture and intensity are proposed as improved versions of current power law models or exponential decay model. The models for texture have three unknown parameters, and thus can be called triparametric models. The structure of the models is a weighted sum of two components, which can describe the decaying process of the correlation coefficient with spatial lags, as well as the periodic behavior due to the existence of transient coherent structures in sea clutter. Unknown parameters are optimized by the nonlinear least square fit method. Models for sea clutter intensity can be obtained through a linear transform for uncorrelated speckle based on the compound-Gaussian representation of sea clutter. The proposed models are validated and compared with current models using S- and C-band measured sea clutter data. Analysis results indicate the effectiveness of the proposed models in that they can describe the behavior of spatial correlation coefficients with higher accuracy.

Description: Terrestrial laser scanning (TLS) has become a popular tool for acquiring source data points which can be used to construct digital elevation models (DEMs) for a wide number of applications. A TLS point cloud often has a very fine spatial resolution, which can represent well the spatial variation of a terrain surface. However, the uncertainty in DEMs created from this relatively new type of source data is not well understood, which forms the focus of this letter. TLS survey data representing four terrain surfaces of different characteristics were used to explore the effects of surface complexity and typical TLS data density (in terms of data point spacing) on DEM accuracy. The spatial variation in TLS data can be decomposed into parts corresponding to the signal of spatial variation (of terrain surfaces) and noise due to measurement error. We found a linear relation between the DEM error and the typical TLS data spacings considered (30–100 mm) which arises as a function of the interpolation error, and a constant contribution from the propagated data noise. This letter quantifies these components for each of the four surfaces considered and shows that, for the interpolation method considered here, higher density sampling would not be beneficial.

Description: A novel way to estimate the live fuel moisture content (LFMC) was explored from the ratio of canopy water content (CWC) and foliage dry biomass (FDB). The CWC was estimated using the PROSAIL (PROSPECT + SAIL) radiative transfer model from the Landsat 8 product. A weak constraint 4-D variational data assimilation method was employed to assimilate the temporally estimated leaf area index into a soil-water-atmosphere-plant (SWAP) model for optimizing the model control variables. Then, the SWAP model was reinitialized with this optimum set of control variables, and better prediction of FDB was obtained. Results showed that a high accuracy level was achieved for the estimated CWC ( $R^{2}=0.91$ , $mbox{RMSE}=84.74 mbox{g/m}^2$ ) and FDB ( $R^2=0.88$ , $mbox{RMSE}=48.54 mbox{g/m} ^2$ ) when compared with in situ measured values. However, the accuracy level of estimated LFMC was poor ( $R^2=0.59$ , $mbox{RMSE} =30.85%$ ) . Further analyses find that the estimated LFMC is reliable for low LFMC but challenged for high LFMC, which indicates that the presented method still makes sense to the assessment of wildfire risk since the wildfire generally occurs when the vegetation is in low LFMC condition.

Description: In this letter, we present the use of experimental human micro-Doppler signature data gathered by a multistatic radar system to discriminate between unarmed and potentially armed personnel walking along different trajectories. Different ways of extracting suitable features from the spectrograms of the micro-Doppler signatures are discussed, particularly empirical features such as Doppler bandwidth, periodicity, and others, and features extracted from singular value decomposition (SVD) vectors. High classification accuracy of armed versus unarmed personnel (between 90% and 97% depending on the walking trajectory of the people) can be achieved with a single SVD-based feature, in comparison with using four empirical features. The impact on classification performance of different aspect angles and the benefit of combining multistatic information is also evaluated in this letter.

Description: Automatic urban area detection in remote sensing images is an important application in the field of earth observation. Most of the existing methods employ feature classifiers and thereby contain a data training process. Moreover, some methods cannot detect urban areas in complex scenes accurately. This letter proposes an automatic urban area detection method that uses multiple features that have different resolutions. First, a downsampled low-resolution image is used to segment the candidate area. After the corner points of the urban area are extracted, a weighted Gaussian voting matrix technique is employed to integrate the corner points into the candidate area. Then, the edge features and homogeneous region are extracted by using the original high-resolution image. Using these results as the input, the processes of guided filtering and contrast enhancement can finally detect accurately the urban areas. This method combines multiple features, such as corner, edge, and regional characteristics, to detect the urban areas. The experimental results show that the proposed method has better detection accuracy for urban areas than the existing algorithms.

Description: In marine sciences, time series are often nonlinear and nonstationary. Adequate and specific methods are needed to analyze such series. In this letter, an application of the empirical mode decomposition method (EMD) associated to the Hilbert spectral analysis (HSA) is presented. Furthermore, EMD-based time-dependent intrinsic correlation (TDIC) analysis is applied to consider the correlation between two nonstationary time series. Four temperature time series obtained from automatic measurements in nearshore waters of the Réunion island are considered, recorded every 10 min from July 2011 to January 2012. The application of the EMD on these series and the estimation of their power spectra using the HSA are illustrated. The authors identify low-frequency tidal waves and display the pattern of correlations at different scales and different locations. By TDIC analysis, it was concluded that the high-frequency modes have small correlation, whereas the trends are perfectly correlated.

Description: Detecting vehicles in aerial images provides important information for traffic management and urban planning. Detecting the cars in the images is challenging due to the relatively small size of the target objects and the complex background in man-made areas. It is particularly challenging if the goal is near-real-time detection, i.e., within few seconds, on large images without any additional information, e.g., road database and accurate target size. We present a method that can detect the vehicles on a 21-MPixel original frame image without accurate scale information within seconds on a laptop single threaded. In addition to the bounding box of the vehicles, we extract also orientation and type (car/truck) information. First, we apply a fast binary detector using integral channel features in a soft-cascade structure. In the next step, we apply a multiclass classifier on the output of the binary detector, which gives the orientation and type of the vehicles. We evaluate our method on a challenging data set of original aerial images over Munich and a data set captured from an unmanned aerial vehicle (UAV).

Description: We compare five slope correction methods developed by Walter et al. , Montes et al. , Schleppi et al. , España et al. , and Gonsamo et al. (referred to as WAL, MON, SCH, ESP, and GON, respectively) using artificial fisheye pictures simulated by graphics software and a lookup table (LUT) retrieval method. The LUT is built by simulating the directional gap fraction as a function of leaf area index (LAI) and average leaf inclination angle (ALIA) using the Poisson law. LAI and ALIA estimates correspond to the case of the LUT that provides the lowest root-mean-square error between the observed gap fractions after slope correction and the simulated ones. Three LAI values (1.5, 3.5, and 5.5), four ALIA values (26.8°, 45°, 57.5°, and 63.2°), and three slope angles (0°, 20°, and 50°) constituted 36 samples of random scenes. ESP is recommended because its results are accurate and independent on the leaf angle distribution (LAD), while GON only performs well for spherical LAD. The three other methods present less good performances with underestimation or overestimation of LAI and/or ALIA depending on the LAD, and the recommended order for them is MON, SCH, and WAL.

Description: In this letter, an improved phase correlation (PC) method based on 2-D plane fitting and the maximum kernel density estimator (MKDE) is proposed, which combines the idea of Stone's method and robust estimator MKDE. The proposed PC method first utilizes a vector filter to minimize the noise errors of the phase angle matrix and then unwraps the filtered phase angle matrix by the use of the minimum cost network flow unwrapping algorithm. Afterward, the unwrapped phase angle matrix is robustly fitted via MKDE, and the slope coefficients of the 2-D plane indicate the subpixel shifts between images. The experiments revealed that the improved method can effectively avoid the impact of outliers on the phase angle matrix during the plane fitting and is robust to aliasing and noise. The matching accuracy can reach 1/50th of a pixel using simulated data. The real image sequence tracking experiment was also undertaken to demonstrate the effectiveness of the proposed PC method with a registration accuracy of root-mean-square error better than 0.1 pixels.

Description: Accurately mapping forest carbon density by combining sample plots and remotely sensed images has become popular because this method provides spatially explicit estimates. However, mixed pixels often impede the improvement of the estimation. In this letter, regression modeling and spectral unmixing analysis were integrated to improve the estimation of forest carbon density for the You County of Hunan, China, using Landsat Thematic Mapper images. Linear spectral unmixing with and without a constraint (LSUWC and LSUWOC) and nonlinear spectral unmixing (NSU) were compared to derive the fractions of five endmembers, particularly forests. Stepwise regression, logistic regression, and polynomial regression (PR) with and without the forest fraction used as an independent variable and the product of the forest fraction image and the map from the best model without the forest fraction were compared. The models were developed using 56 sample plots, and their results were validated using 26 test plots. The decomposition of mixed pixels was assessed using higher spatial resolution SPOT images and a corresponding land cover map. The results showed that 1) LSUWC more accurately estimated the endmember fractions than LSUWOC and NSU, 2) PR had the greatest estimation accuracy of forest carbon, and 3) combining regression modeling and spectral unmixing increased the estimation accuracy by 31%–39%, and introducing the forest fraction into the regressions performed better than the product of forest fraction image and the results from PR without the fraction. This implied that the integrations provided great potential in reducing the impacts of mixed pixels in mapping forest carbon.

Description: This letter proposes a multiresolution technique to address the high computational cost in remote sensing image registration. The scale-invariant feature transform is applied to detect keypoints and descriptors, and then, global information combined with descriptors is utilized to establish keypoint mappings. Keypoints are first classified according to their octaves. Then, in the lowest resolution, the keypoints of the largest octave are mapped with descriptors and the global information, giving an initial affine transformation $T_0$ . In the next octave, the keypoints of the second largest octave are mapped by employing $T_0$ to narrow the space of matching keypoints. By this means, the process of establishing keypoint correspondences is conducted from one resolution (octave) to the next as the obtained transformation gets finer until we get to the highest resolution. Due to the high computational expense of computing global information, the proposed technique is important for aligning large-size remote sensing imagery. Experimental results show that the proposed method can achieve a comparable registration accuracy but with a less computational cost than directly building keypoint mappings on images of large size.

Description: Presents corrections to the paper, "Estimation of forest biomass from two-level model inversion of single-pass InSAR data" (Soja, M.J., et al.,Trans. Geosci. Remote Sens., vol. 53, no. 9, pp. 5083???5099, Sep. 2015).

Description: In this letter, we present an efficient parallel implementation of composite kernels in support vector machines (SVMs) for hyperspectral image (HSI) classification. Our implementation makes effective use of commodity graphics processing units (GPUs). Specifically, we port the calculation of composite kernels to GPUs, perform intensive computations based on NVidia's compute unified device architecture, and execute the rest of the operations related with control and small data calculations in the CPU. Our experimental results, conducted using real hyperspectral data sets and NVidia GPU platforms, indicate significant improvements in terms of computational effectiveness, achieving near-real-time performance of spatial–spectral HSI classification for the first time in the literature.

Description: Compared with airborne laser scanning, terrestrial laser scanning (TLS) offers ground-based point cloud data of trees and provides greater potential to accurately estimate tree and stand parameters. However, there is a lack of effective methods to accurately identify locations of individual trees from TLS point cloud data. It is also unknown whether the estimation accuracy of the parameters, including tree height (H), diameter at breast height (DBH), and so on, using TLS can meet the requirement of forest management and planning. In this letter, a novel method to effectively process point cloud data and further determine the locations of individual trees in a stand based on the central coordinates of point cloud data on a defined grid according to the largest DBH was developed. Moreover, a point-cloud-data-based convex hull algorithm and the cylinder method were, respectively, used to estimate DBH and H of individual trees. This study was conducted in a pure Chinese fir plantation of 45 trees located in Huang-Feng-Qiao forest farm, You County of Hunan, China. The comparison of the estimated and observed values showed that the obtained tree locations had errors of less than 20 cm, and the relative root mean square errors for the estimates of both DBH and H were less than 5%. This implies that TLS is very promising for the retrieval of tree and stand parameters in forest stands. For the applications of these methods to mixed forests with a structure of multilayer canopies, further examination is needed.

Description: In this letter, a novel algorithm for attitude measurement based on a 3-D electromagnetic model (3-D em-model) is proposed. The 3-D em-model is established offline based on the geometric structure of the target, and it can be used to predict the scattering features at different target attitudes. In order to measure the attitude of the air target, we design a bistatic step frequency radar system. The directions of the two radars' lines of sight (LOSs) relative to the target are acquired by matching the high-resolution range profiles (HRRPs) from the target echoes to the HRRPs generated from the 3-D em-model. Since the directions of two radars' LOSs relative to the Earth are already known, the absolute attitude of the target can be acquired. The innovative contributions of this letter are as follows: 1) A comprehensive theoretical analysis of air target attitude measurement based on its own 3-D em-model is proposed; 2) the method can be applied to different kinds of air targets such as aircraft, satellite, missile, etc.; 3) the proposed attitude measurement method does not require target motion model in advance; and 4) the proposed algorithm can be applied to any kind of step frequency waveforms. Experiments using both data predicted by a high-frequency electromagnetic code and data measured in the chamber verify the validity of the method.

Description: The Soil Moisture and Ocean Salinity (SMOS) and Soil Moisture Active Passive (SMAP) missions provide Level-1 brightness temperature (Tb) observations that are used for global soil moisture estimation. However, the nature of these Tb data differs: the SMOS Tb observations contain atmospheric and select reflected extraterrestrial (“Sky”) radiation, whereas the SMAP Tb data are corrected for these contributions, using auxiliary near-surface information. Furthermore, the SMOS Tb observations are multiangular, whereas the SMAP Tb is measured at 40° incidence angle only. This letter discusses how SMOS Tb, SMAP Tb, and radiative transfer modeling components can be aligned in order to enable a seamless exchange of SMOS and SMAP Tb data in soil moisture retrieval and assimilation systems. The aggregated contribution of the atmospheric and reflected Sky radiation is, on average, about 1 K for horizontally polarized Tb and 0.5 K for vertically polarized Tb at 40° incidence angle, but local and short-term values regularly exceed 5 K.

Description: The temporal variations (diurnal and annual) in arboreal $(varepsilon_mathrm{Tree})$ and bare soil $(varepsilon_mathrm{Soil})$ dielectric constants and their correlation with precipitation were examined for several trees in Japan. A significant (1 $sigma$ (standard deviation) and 2 $sigma$ ) $varepsilon_mathrm{Tree}$ increase is observed after rainfall at 89.8% and 90.5% probability. However, rainfall does not always induce significant $varepsilon_mathrm{Tree}$ increases. Rainfall of more than 5 mm/day can induce 1 $sigma$ $varepsilon_mathrm{Tree}$ Tree increase at a 59.6% probability. In order to examine whether the increase in $varepsilon_mathrm{Tree}$ affects the L-band $sigma^{0}$ variation in a forest, the four-year temporal variation of the L-band backscattering coefficient $(sigma^{0})$ was estimated from observations by the Advanced Land Observing Satellite Phased Array type L-band Synthetic Aperture Radar. Observed maximum absolute deviations from the mean over the forest area were 1.0 and 1.2 dB for $sigma_{mathrm{HH}}^{0}$ and $sigma_mathrm{HV}^{0}$ , respectively, and 4.0 and 3.0 dB over open land. $sigma^{0}$ and rainfall correlations show that $varepsilon_mathrm{Tree}$ and $sigma_mathrm{Forest}^{0}$ are proportional to precipitation integrated over seven or eight days; $varepsilon_mathrm{Soil}$ and $sigma_mathrm{Open land}^{0}$ are proportional to precipitation integrated over three days. This finding indicates that $varepsilon_mathrm{Tree}$ variations influence $sigma_{mathrm{Forest areas}}^{0}$ . A stronger correlation between $sigma_mathrm{HV}^{0}$ and precipitation is observed in several sites with low $sigma_mathrm{HV}^{0}$ , where less biomass is expected, and several sites with high $sigma_mathrm{HV}^{0}$ , where more biomass is expected. A weaker correlation between $sigma_mathrm{HV}^{0}$ and precipitation is observed for several sites with high $sigma_mathrm{HV}^{0}$ . These differences may be explained by the different contributions of double bounce scattering and potential transpiration, which is a measure of the ability of the atmosphere to remove water from the surface th

Description: The spectral and radiometric quality of airborne imaging spectrometer data is affected by the anisotropic reflectance behavior of the imaged surface. Illumination and observation angle-dependent patterns of surface reflected radiation propagate into products, hinder quantitative assessment of biophysical/biochemical parameters, and decrease the comparability of data from multiple flight lines. The Ross–Li model, originally developed for multiangular observations, can be inverted to estimate and correct for surface anisotropy effects. This requires land cover be stratified into distinct types of scattering behavior. When the observations subsumed in these classes cover a range of view angles, a pseudo multiangular view on the surface can be employed to invert the Ross–Li model. A discrete land cover classification, however, bears the risk of inappropriate scattering correction resulting in spatial artifacts in the corrected data, predominantly in transition regions of two land cover types (e.g., soil and sparse vegetation with varying fractions). We invert the Ross–Li model on continuous land cover fraction layers. We decompose land cover in dominating structural types using linear spectral unmixing. Ross–Li kernel weights and formulations are estimated for each type independently; the correction is then applied pixel-wise according to the fractional distribution. The corrected Airborne Prism EXperiment imaging spectrometer data show significant reduction of anisotropic reflectance effects of up to 90% (average 60% to 75%, $p=0.05$ ), measured in the overlapping regions of adjacent flight lines. No spatial artifacts or spectral irregularities are observed after correction.

Description: Most spaceborne sensors have a tradeoff between high spatial and high temporal resolutions. This tradeoff limits the use of remote sensing data in various applications that require images in both the high spatial and high temporal resolutions. In this paper, we propose a novel technique to create a fine spatial and high temporal resolution images at a ground-based data processing system. Resourcesat-2 is one of the Indian Space Research Organization missions, and it carries the Linear Imaging Self-Scanning sensors (LISS III and LISS IV) and an Advanced Wide-Field Sensor (AWiFS) onboard. The spatial resolution of LISS III is 23.5 m, and that of AWiFS is 56 m. The temporal resolution of LISS III is 24 days, and that of AWiFS is five days. The proposed method creates a synthetic LISS-III image at 23.5-m spatial and five-day temporal resolutions. It is based on the subpixel relationship between a single AWiFS–LISS-III image pair, which is acquired before or after the prediction date. In temporal data composition, spurious spatial discontinuities are inevitable for land-cover type changes. These discontinuities were identified with temporal edge primitives and were smoothed with a spatial-profile-averaging method. A synthetic LISS-III image for time $t_{k}$ is predicted from an AWiFS image at time $t_{k}$ and a single AWiFS–LISS-III image pair at time $t_{0}$ , where $t_{0}ne t_{k}$ . Experimental results demonstrated that the proposed method is superior in terms of the computational efficiency and prediction accuracy with the other existing methods.

Description: Glacier avalanches are natural hazards that could damage infrastructures and threaten lives in high-altitude mountainous terrains. On April 7, 2012, a massive ice avalanche struck a Pakistani base at Gayari sector, Saltoro Valley, and buried/killed 148 soldiers and civilians. Keeping in view the catastrophe, a study was designed with the objectives to: 1) model and simulate the Gayari sector glacier avalanche incident in terms of height, extent, velocity, pressure, and momentum; 2) generate hazard risk assessment of possible other glacier avalanches in the Saltoro Valley through modeling and simulation; and 3) suitability analysis of current camp sites and recommendation of new safe camps sites locations in the Saltoro valley. To simulate the Gayari sector glacier event and other Glacier possible avalanches, a physical process-based rapid mass movements (RAMMS) was used. The RAMMS has two main components, i.e., Voellmy–Salm (VS) model and random kinetic energy, which deals with variables such as avalanche height and the mean avalanche velocity during the course of simulation. The suitability analysis of current camp sites were achieved using weighted overlay analysis with different constraints in ArcGIS Spatial Analyst. The RAMMS model simulation of the Gayari avalanche event predicted a maximum velocity of 74 ms -1 , generating a pressure of 5074 kPa and attaining a height of 45 m, whereas the predicted debris volume on the ground was 3.8145 million m 3 . A good agreement was found between actual debris height and extent, as compared with the RAMMS model output. The RAMMS model simulated all the potential tributary glacier avalanches of Saltoro valley very well. The weighted overlay analyses in ArcGIS Spatial Analyst revealed that the existing camp sites are safe and were not threatened by the glacier avalanche hazard. However, it was recommended that the Gayari camp should not be constructed at the same location and should be relocated- to the proposed safe camp sites identified in this research study. The proposed methodology developed in the current study could be applied in the Siachen conflict zone for avalanche hazard/risk analysis of all the camp sites located in the valley.

Description: Object-oriented remote sensing image classification is becoming more and more popular because it can integrate spatial information from neighboring regions of different shapes and sizes into the classification procedure to improve the mapping accuracy. However, object identification itself is difficult and challenging. Superpixels, which are groups of spatially connected similar pixels, have the scale between the pixel level and the object level and can be generated from oversegmentation. In this paper, we establish a new classification framework using a superpixel-based graphical model. Superpixels instead of pixels are applied as the basic unit to the graphical model to capture the contextual information and the spatial dependence between the superpixels. The advantage of this treatment is that it makes the classification less sensitive to noise and segmentation scale. The contribution of this paper is the application of a graphical model to remote sensing image semantic segmentation. It is threefold. 1) Gradient fusion is applied to multispectral images before the watershed segmentation algorithm is used for superpixel generation. 2) A probabilistic fusion method is designed to derive node potential in the superpixel-based graphical model to address the problem of insufficient training samples at the superpixel level. 3) A boundary penalty between the superpixels is introduced in the edge potential evaluation. Experiments on three real data sets were conducted. The results show that the proposed method performs better than the related state-of-the-art methods tested.

Description: We introduce a practical and accurate model, referred to as “GO4,” to describe near-nadir microwave scattering from the sea surface, and at the same time, we address the issue of the filtered mean square slope (mss) conventionally used in the geometrical optics model. GO4 is a simple correction of this last model, taking into account the diffraction correction induced by the rough surface through what we call an effective mean square curvature (msc). We evaluate the effective msc as a function of the surface wavenumber spectrum and the radar frequency and show that GO4 reaches the same accuracy as the physical optics model in a wide range of incidence and frequency bands with the sole knowledge of the mss and msc parameters. The key point is that the mss entering in GO4 is not the filtered but the total slope. We provide estimation of the effective msc on the basis of classical sea spectrum models. We also evaluate the effective msc from near-nadir satellite data in various bands and show that it is consistent with model predictions. Non-Gaussian effects are discussed and shown to be incorporated in the effective msc. We give some applications of the method, namely, the estimation of the total sea surface mss and the recalibration of relative radar cross sections.

Description: This paper evaluates the radiometric accuracy of observations from the Advanced Technology Microwave Sounder (ATMS) onboard Suomi National Polar-orbiting Partnership and Sondeur Atmospherique du Profil d' Humidité Intropicale par Radiométrie (SAPHIR) onboard Megha-Tropiques through intercalibration and validation versus in situ radiosonde and Global Positioning System Radio Occultation (GPS-RO) observations. SAPHIR and ATMS water vapor channels operate at slightly different frequencies. We calculated the bias due to radiometric errors as the difference between the observed and simulated differences between the two instruments. This difference, which is often referred to as double difference, ranges between 0.3 and 0.7 K, which shows good consistency between the instruments. We used a radiative transfer model to simulate the satellite brightness temperatures (Tbs) using radiosonde and GPS-RO profiles and then compared simulated and observed Tbs. The difference between radiosonde and ATMS Tbs for the middle and upper tropospheric temperature sounding channels was less than 0.5 K at most stations, but the difference between radiosonde and ATMS/SAPHIR Tbs for water vapor channels was between 0.5 and 2.0 K. The larger bias for the water vapor channels is mainly due to several errors in radiosonde humidity observations. The mean differences between the ATMS observations and the Tbs simulated using GPS-RO profiles were 0.2, 0.3, 0.4, 0.2, and −0.2 K for channels 10–14, respectively; and the uncertainty increases from 0.02 K for channel 10 to 0.07 K for channel 14.

Description: This paper presents a completely automatic processing chain for orthorectification of optical pushbroom sensors. The procedure is robust and works without manual intervention from raw satellite image to orthoimage. It is modularly divided in four main steps: metadata extraction, automatic ground control point (GCP) extraction, geometric modeling, and orthorectification. The GCP extraction step uses georeferenced vector roads as a reference and produces a file with a list of points and their accuracy estimation. The physical geometric model is based on collinearity equations and works with sensor-corrected (level 1) optical satellite images. It models the sensor position and attitude with second-order piecewise polynomials depending on the acquisition time. The exterior orientation parameters are estimated in a least squares adjustment, employing random sample consensus and robust estimation algorithms for the removal of erroneous points and fine-tuning of the results. The images are finally orthorectified using a digital elevation model and positioned in a national coordinate system. The usability of the method is presented by testing three RapidEye images of regions with different terrain configurations. Several tests were carried out to verify the efficiency of the procedure and to make it more robust. Using the geometric model, subpixel accuracy on independent check points was achieved, and positional accuracy of orthoimages was around one pixel. The proposed procedure is general and can be easily adapted to various sensors.

Description: This paper presents a new ground moving target imaging (GMTIm) algorithm for airborne synthetic aperture radar (SAR) based on a novel time-frequency representation (TFR), Lv's distribution (LVD). We first analyze generic moving target signatures for a multichannel SAR and then derive the analytical spectrum of a point target moving at a constant velocity by a polar format algorithm for SAR image formation. SAR motion deviation from a predetermined flight track is considered to facilitate airborne SAR applications. LVD, as a recently developed TFR for the analysis of multicomponent linear-frequency-modulated signal, is adopted to represent the target kinematic spectrum in the Doppler centroid frequency and chirp rate domain. As a result, the proposed SAR-GMTIm algorithm is capable of imaging multiple moving targets even when they are located at the same range resolution cell. Some practical issues such as imaging maneuvering targets and small/weak targets are discussed to enhance the applicability of the proposed algorithm. Simulation results with isotropic point moving targets are presented to validate the effectiveness and superiority of the proposed algorithm. Raw data collected by an airborne multichannel SAR are also used to verify the performance improvement made by the proposed algorithm.

Description: Satellite soil moisture estimates have received increasing attention over the past decade. This paper examines the applicability of estimating soil moisture states and soil hydraulic parameters through two particle filter (PF) methods: The PF with commonly used sampling importance resampling (PF-SIR) and the PF with recently developed Markov chain Monte Carlo sampling (PF-MCMC) methods. In a synthetic experiment, the potential of assimilating remotely sensed near-surface soil moisture measurements into a 1-D mechanistic soil water model (HYDRUS-1D) using both the PF-SIR and PF-MCMC algorithms is analyzed. The effects of satellite temporal resolution and accuracy, soil type, and ensemble size on the assimilation of soil moisture are analyzed. In a real data experiment, we first validate the Advanced Microwave Scanning Radiometer--Earth Observing System (AMSR-E) soil moisture products in the Oklahoma Little Washita Watershed. Aside from rescaling the remotely sensed soil moisture, a bias correction algorithm is implemented to correct the deep soil moisture estimate. Both the ascending and descending AMSR-E soil moisture data are assimilated into the HYDRUS-1D model. The synthetic assimilation results indicated that, whereas both updating schemes showed the ability to correct the soil moisture state and estimate hydraulic parameters, the PF-MCMC scheme is consistently more accurate than PR-SIR. For real data case, the quality of remotely sensed soil moisture impacts the benefits of their assimilation into the model. The PF-MCMC scheme brought marginal gains than the open-loop simulation in RMSE at both surface and root-zone soil layer, whereas the PF-SIR scheme degraded the open-loop simulation.

Description: We propose a new deterministic approach for remote sensing retrieval, called modified total least squares (MTLS), built upon the total least squares (TLS) technique. MTLS implicitly determines the optimal regularization strength to be applied to the normal equation first-order Newtonian retrieval using all of the noise terms embedded in the residual vector. The TLS technique does not include any constraint to prevent noise enhancement in the state space parameters from the existing noise in measurement space for an inversion with an ill-conditioned Jacobian. To stabilize the noise propagation into parameter space, we introduce an additional empirically derived regularization proportional to the logarithm of the condition number of the Jacobian and inversely proportional to the L2-norm of the residual vector. The derivation, operational advantages and use of the MTLS method are demonstrated by retrieving sea surface temperature from GOES-13 satellite measurements. An analytic equation is derived for the total retrieval error, and is shown to agree well with the observed error. This can also serve as a quality indicator for pixel-level retrievals. We also introduce additional tests from the MTLS solutions to identify contaminated pixels due to residual clouds, error in the water vapor profile and aerosols. Comparison of the performances of our new and other methods, namely, optimal estimation and regression-based retrieval, is performed to understand the relative prospects and problems associated with these methods. This was done using operational match-ups for 42 months of data, and demonstrates a relatively superior temporally consistent performance of the MTLS technique.

Description: Radar-based remote sensing for measurement of ocean surface waves presents advantages over conventional point sensors such as wave buoys. As its use becomes more widespread, it is important to understand the sensitivity of the extracted wave parameters to the characteristics of the radar and the scatterers. To examine such issues, experiments were performed offshore of the Scripps Institution of Oceanography pier in July 2010. Radar measurements in low wind speeds were performed with a dual-polarized high-resolution X-band pulse-Doppler radar at low grazing angles along with two independent measurements of the surface waves using conventional sensors, a GPS-based buoy, and an ultrasonic array. Comparison between radar cross section (RCS) and Doppler modulations shows peak values occurring nearly in-phase, in contrast with tilt modulation theory. Spectral comparisons between Doppler-based and RCS-based spectra show that Doppler-based spectra demonstrate greater sensitivity to swell-induced modulations, whereas RCS-based spectra show greater sensitivity to small-scale modulations (or generally have more noise at high frequency), and they equally capture energy at the wind wave peak. Doppler estimates of peak period were consistent with the conventional sensors, whereas the RCS differed in assignment of peak period to wind seas rather than swell in a couple of cases. Higher order period statistics of both RCS and Doppler were consistent with the conventional sensors. Radar-based significant wave heights are lower than buoy-based values and contain nontrivial variability of ∼33%. Comparisons between HH and VV polarization data show that VV data more accurately represent the wave field, particularly as the wind speeds decrease.

Description: Polarimetric synthetic aperture radar satellite and ground-based Ku- and X-band scatterometer measurements are used to explore the scattering mechanism for ice in shallow Arctic lakes, wherein strong radiometric responses are seen for floating ice, and low returns are evident where the ice has grounded. Scatterometer measurements confirm that high backscatter is from the ice/water interface, whereas polarimetric decomposition suggests that the dominant scattering mechanism from that interface is single bounce. Using Fresnel equations, a simple model for surface bounce from the ice/water interface is proposed, and its predictions are supported by experimental parameters such as co-pol phase difference, co-pol ratio, and the results of rigorous numerical modeling. Despite early research suggesting double-bounce scattering from columnar air bubbles and the ice/water interface as the dominant scattering mechanism in shallow lakes, this paper strongly supports a single-bounce model.

Description: The on-orbit radiometric calibration of the reflective solar bands (RSBs) of the Visible Infrared Imaging Radiometer Suite (VIIRS) aboard the Suomi National Polar-orbiting Partnership satellite is carried out primarily through observations of a fully illuminated solar diffuser (SD) panel. Accurate knowledge of the solar spectral radiance scattered from the SD is available. The sensor aperture spectral radiance is assumed to be a quadratic polynomial function of a VIIRS detector's background-subtracted response in digital number. The coefficients of the polynomial were initially determined prelaunch. Once on orbit, we assume that these coefficients change uniformly by a common calibration factor, which is referred to as the $F$ -factor. The known solar spectral radiance scattered from a fully illuminated SD allows for the determination of these $F$ -factors. We describe the methodology and the associated algorithms used in the calculation of the RSB $F$ -factors. Our results show that the $F$ -factors change over time, with the largest change occurring at a wavelength of 862 nm (with a value of about 1.55 on day 950 after the satellite launch, relative to its value at the beginning of the launch) . In addition, we estimate the relative error standard deviations of the computed top-of-the-atmosphere reflectance at the detector pixel level. On day 950 of the mission, the relative error standard deviations are all less or equal to 0.016, except for the M11 band (band central wavelength of 2257 nm) , which has a relative error standard deviation of about 0.049 due to a very low signal-to-noise ratio.

Description: This study proposes a quantitative measurement of split of the second heart sound (S2) based on nonstationary signal decomposition to deal with overlaps and energy modeling of the subcomponents of S2. The second heart sound includes aortic (A2) and pulmonic (P2) closure sounds. However, the split detection is obscured due to A2-P2 overlap and low energy of P2. To identify such split, HVD method is used to decompose the S2 into a number of components while preserving the phase information. Further, A2s and P2s are localized using smoothed pseudo Wigner-Ville distribution followed by reassignment method. Finally, the split iscalculated by taking the differences between the means of time indices of A2s and P2s. Experiments on total 33 clips of S2 signals are performed for evaluation of the method. The mean ± standard deviation of the split is 34.7 ± 4.6 ms. The method measures the splitefficiently, even when A2-P2 overlap is ≤ 20 ms and the normalized peak temporal ratio of P2 to A2 is low (≥ 0.22). This proposed method thus, demonstrates its robustness by defining split detectability (SDT), the split detection aptness through detecting P2s, by measuring upto 96 percent. Such findings reveal the effectiveness of the method as competent against the other baselines, especially for A2-P2 overlaps and low energy P2.

Description: Post-acquisition denoising of magnetic resonance (MR) images is an important step to improve any quantitative measurement of the acquired data. In this paper, assuming a Rician noise model, a new filtering method based on the linear minimum mean square error (LMMSE) estimation is introduced, which employs the self-similarity property of the MR data to restore the noise-less signal. This method takes into account the structural characteristics of images and the Bayesian mean square error (Bmse) of the estimator to address the denoising problem. In general, a twofold data processing approach is developed; first, the noisy MR data is processed using a patch-based L 2 -norm similarity measure to provide the primary set of samples required for the estimation process. Afterwards, the Bmse of the estimator is derived as the optimization function to analyze the pre-selected samples and minimize the error between the estimated and the underlying signal. Compared to the LMMSE method and also its recently proposed SNR-adapted realization (SNLMMSE), the optimized way of choosing the samples together with the automatic adjustment of the filtering parameters lead to a more robust estimation performance with our approach. Experimental results show the competitive performance of the proposed method in comparison with related state-of-the-art methods.

Description: Large-scale ad hoc analytics of genomic data is popular using the R-programming language supported by over 700 software packages provided by Bioconductor. More recently, analytical jobs are benefitting from on-demand computing and storage, their scalability and their low maintenance cost, all of which are offered by the cloud. While biologists and bioinformaticists can take an analytical job and execute it on their personal workstations, it remains challenging to seamlessly execute the job on the cloud infrastructure without extensive knowledge of the cloud dashboard. How analytical jobs can not only with minimum effort be executed on the cloud, but also how both the resources and data required by the job can be managed is explored in this paper. An open-source light-weight framework for executing R-scripts using Bioconductor packages, referred to as ‘RBioCloud’, is designed and developed. RBioCloud offers a set of simple command-line tools for managing the cloud resources, the data and the execution of the job. Three biological test cases validate the feasibility of RBioCloud. The framework is available from http://www.rbiocloud.com .

Description: Of major interest to translational genomics is the intervention in gene regulatory networks (GRNs) to affect cell behavior; in particular, to alter pathological phenotypes. Owing to the complexity of GRNs, accurate network inference is practically challenging and GRN models often contain considerable amounts of uncertainty. Considering the cost and time required for conducting biological experiments, it is desirable to have a systematic method for prioritizing potential experiments so that an experiment can be chosen to optimally reduce network uncertainty. Moreover, from a translational perspective it is crucial that GRN uncertainty be quantified and reduced in a manner that pertains to the operational cost that it induces, such as the cost of network intervention. In this work, we utilize the concept of mean objective cost of uncertainty (MOCU) to propose a novel framework for optimal experimental design. In the proposed framework, potential experiments are prioritized based on the MOCU expected to remain after conducting the experiment. Based on this prioritization, one can select an optimal experiment with the largest potential to reduce the pertinent uncertainty present in the current network model. We demonstrate the effectiveness of the proposed method via extensive simulations based on synthetic and real gene regulatory networks.

Description: A novel approach to Contact Map Overlap (CMO) problem is proposed using the two dimensional clusters present in the contact maps. Each protein is represented as a set of the non-trivial clusters of contacts extracted from its contact map. The approach involves finding matching regions between the two contact maps using approximate 2D-pattern matching algorithm and dynamic programming technique. These matched pairs of small contact maps are submitted in parallel to a fast heuristic CMO algorithm. The approach facilitates parallelization at this level since all the pairs of contact maps can be submitted to the algorithm in parallel. Then, a merge algorithm is used in order to obtain the overall alignment. As a proof of concept, MSVNS, a heuristic CMO algorithm is used for global as well as local alignment. The divide and conquer approach is evaluated for two benchmark data sets that of Skolnick and Ding et al. It is interesting to note that along with achieving saving of time, better overlap is also obtained for certain protein folds.

Description: Canalizing genes possess broad regulatory power over a wide swath of regulatory processes. On the other hand, it has been hypothesized that the phenomenon of intrinsically multivariate prediction (IMP) is associated with canalization. However, applications have relied on user-selectable thresholds on the IMP score to decide on the presence of IMP. A methodology is developed here that avoids arbitrary thresholds, by providing a statistical test for the IMP score. In addition, the proposed procedure allows the incorporation of prior knowledge if available, which can alleviate the problem of loss of power due to small sample sizes. The issue of multiplicity of tests is addressed by family-wise error rate (FWER) and false discovery rate (FDR) controlling approaches. The proposed methodology is demonstrated by experiments using synthetic and real gene-expression data from studies on melanoma and ionizing radiation (IR) responsive genes. The results with the real data identified DUSP1 and p53, two well-known canalizing genes associated with melanoma and IR response, respectively, as the genes with a clear majority of IMP predictor pairs. This validates the potential of the proposed methodology as a tool for discovery of canalizing genes from binary gene-expression data. The procedure is made available through an R package.

Description: Programming languages like C and Ada combined with proprietary embedded operating systems have dominated the real-time application space for decades. The new C++11 standard includes native, language-level support for concurrency, a required feature for any nontrivial event-oriented real-time software. Threads, Locks, and Atomics now exist to provide the necessary tools to build the structures that make up the foundation of a complex real-time system. The National Spherical Torus Experiment Upgrade (NSTX-U) at the Princeton Plasma Physics Laboratory (PPPL) is breaking new ground with the language as applied to the needs of fusion devices. A new Digital Coil Protection System (DCPS) will serve as the main protection mechanism for the magnetic coils, and it is written entirely in C++11 running on Concurrent Computer Corporation’s real-time operating system, RedHawk Linux. It runs over 600 algorithms in a 5 kHz control loop that determine whether or not to shut down operations before physical damage occurs. To accomplish this, NSTX-U engineers developed software tools that do not currently exist elsewhere, including real-time atomic synchronization, real-time containers, and a real-time logging framework. Together with a recent (and carefully configured) version of the GCC compiler, these tools enable data acquisition, processing, and output using a conventional operating system to meet a hard real-time deadline (that is, missing one periodic is a failure) of 200 microseconds.

Description: We present simplified expressions for the cross-polarized backscatter of a randomly rough surface predicted by the second-order small-slope approximation (SSA2). The simplification is based on appropriate polynomial approximations of the SSA2 kernel function. We obtain numerically efficient expressions for the cross-polarized backscattering amplitude of a deterministic surface in the form of a single space integral involving only the surface elevation and the second (mixed) derivative of the surface elevation. The ensemble average normalized radar cross section is then derived under a Gaussian random process assumption for the surface. The resulting expression has the form of a Kirchhoff integral involving the roughness correlation function and its second- and fourth-order cross-derivatives. Further simplification is achieved for off-nadir observations using a high-frequency approximation; the result is an analytical formula involving only the resonant curvature and the radar-filtered mean square slope in the out-of-plane direction. A numerical validation of the simplified expressions is provided by comparison with exact SSA2 predictions in representative test cases. The dependence of cross-polarized backscattering on the incidence angle as well as wind speed and direction is then investigated for the case of a directional sea surface model. At near nadir incidence, a clear maximum in azimuth of the cross-polarized backscatter is observed for radar look directions 45 $^{circ}$ from the wind direction.

Description: Thallium-bromide (TlBr) is currently under investigation as an alternative room-temperature semiconductor gamma-ray spectrometer due to its favorable material properties (large bandgap, high atomic numbers, and high density). Previous work has shown that 5 mm thick pixelated TlBr detectors can achieve sub-1% FWHM energy resolution at 662 keV for single-pixel events. These results are limited to $ - 20{^ circ }{rm C}$ operation where detector performance is stable. During the first one to five days of applied bias at $ - 20{^ circ }{rm C}$ , many TlBr detectors undergo a conditioning phase, where the energy resolution improves and the depth-dependent electron drift velocity stabilizes. In this work, the spectroscopic performance, drift velocity, and freed electron concentrations of multiple 5 mm thick pixelated TlBr detectors are monitored throughout the conditioning phase. Additionally, conditioning is performed twice on the same detector at different times to show that improvement mechanisms relax when the detector is stored without bias. We conclude that the improved spectroscopy results from internal electric field stabilization and uniformity caused by fewer trapped electrons.

Description: Silicon Photomultipliers (SiPMs) are attractive candidates for light detectors for next generation liquid xenon double-beta decay experiments, like nEXO (next Enriched Xenon Observatory). In this paper we discuss the requirements that the SiPMs must satisfy in order to be suitable for nEXO and similar experiments, describe the two test setups operated by the nEXO collaboration, and present the results of characterization of SiPMs from several vendors. In particular, we find that the photon detection efficiency at the peak of xenon scintillation light emission (175-178 nm) approaches the nEXO requirements for tested FBK and Hamamatsu devices. Additionally, the nEXO collaboration performed radio-assay of several grams of bare FBK devices using neutron activation analysis, indicating levels of $^{40}{rm K}$ , $^{232}{rm Th}$ , and $^{238}{rm U}$ of the order of $ 〈 0.15$ , ( $ 6.9cdot 10^{ - 4} - 1.3 cdot 10^{ - 2}$ ), and $ 〈 0.11 ~hbox{mBq}/hbox{kg}$ , respectively.

Description: It is very important for plant operators to be informed of the departure from nucleate boiling ratio (DNBR) to prevent the fuel cladding from melting and a boiling crisis in a nuclear reactor. The reactor core monitoring and protection systems require a minimum DNBR value to monitor reactor coolant conditions. In this study, in order to estimate the minimum DNBR value, a cascaded fuzzy neural network (CFNN) method was used. The CFNN model can be used to estimate the minimum DNBR value through the process of adding fuzzy neural networks (FNNs) repeatedly. The proposed DNBR estimation algorithm was verified by applying the nuclear and thermal data acquired from many numerical simulations of the optimized power reactor 1000 (OPR1000). The CFNN model was compared to previously developed models and was found to be superior to them. Therefore, this model can be used to effectively monitor and predict the minimum DNBR in the reactor core.

Description: How to produce the difference data of the two temporal images is a crucial factor in image change detection. In this letter, we propose multicontextual mutual information data (MMID) based on the bivariate Gaussian distribution (BGD) for synthetic aperture radar (SAR) image change detection and illustrate their superiorities over the classical difference data. MMID, which are an improved form of image spatial mutual information, are constructed based on the quadrilateral Markov random field (QMRF) and can be factored into the linear combination of the entropies. Then to adapt MMID to the change detection, we construct the 2-D entropies based on the BGD. In this way, MMID are able to capture the intertemporal statistical dependence of the two temporal images and thus can be taken as the feature-level difference data rather than the pixel-level data. The maximum-likelihood method, the automatic threshold method, and the Markov random field method are performed on the MMID of the real two temporal SAR images for the change detection. Experimental results demonstrate the superiorities of MMID over the traditional difference data.

Description: Spectral unmixing has been a popular technique for analyzing remotely sensed hyperspectral images. The goal of unmixing is to find a collection of pure spectral constituents (called endmembers ) that can explain each (possibly mixed) pixel of the scene as a combination of endmembers, weighted by their coverage fractions in the pixel or abundances . Over the last years, many algorithms have been presented to address the three main parts of the spectral unmixing chain: 1) estimation of the number of endmembers; 2) identification of the endmember signatures; and 3) estimation of the per-pixel fractional abundances. However, to date, there is no standardized tool that integrates these algorithms in a unified framework. In this letter, we present HyperMix, an open-source tool for spectral unmixing that integrates different approaches for spectral unmixing and allows building unmixing chains in graphical fashion, so that the end-user can define one or several spectral unmixing chains in fully configurable mode. HyperMix provides efficient implementations of most of the algorithms used for spectral unmixing, so that the tool automatically recognizes if the computer has a graphics processing unit (GPU) available and optimizes the execution of these algorithms in the GPU. This allows for the execution of spectral unmixing chains on large hyperspectral scenes in computationally efficient fashion. The tool is available online from http://hypercomphypermix.blogspot.com.es and has been validated with real hyperspectral scenes, providing state-of-the-art unmixing results.

Description: Seismic signals are nonlinear, and the seismic state-space model can be described as a nonlinear system. The particle filter (PF) method, as an effective method for estimating the state of a nonlinear system, can be applied to deal with seismic random noise attenuation. However, PF suffers from sample impoverishment caused by resampling, which results in serious loss of valid seismic information and leads to inaccurate representation of the reflected signal. To address the impoverishment issue and to further improve the particle quality, we propose a novel method to suppress seismic random noise—the adaptive fission particle filter (AFPF). In AFPF, all the particles undergo a fission process and produce “offspring” particles to maintain particle diversity. To implement the adaptation and to monitor the degree of fission, we apply a fission factor, which takes into account weights that indicate the quality of the particles. This leads to significant improvements in the particle quality, i.e., the proportion of highly weighted particles is increased. The effective seismic information provided by the resulting particles reproduces the true signal more reliably, reducing the bias of PF. In addition, we establish a dynamic state-space model suitable for seismic signals. Experimental results on synthetic records and field data illustrate the superior performance of AFPF in noise attenuation and reflected signal preservation compared with the PF.

Description: The synoptic determination of ocean circulation using the data acquired from space, with a coherent depiction of its turbulent characteristics, remains a fundamental challenge in oceanography. This determination has the potential of revealing all aspects of the ocean dynamic variability on a wide range of spatiotemporal scales and will enhance our understanding of ocean–atmosphere exchanges at superresolution, as required in the present context of climate change. Here, we show a four-year time series of spatial superresolution (4 km) turbulent ocean dynamics generated from satellite data using emerging ideas in signal processing coming from nonlinear physics, low-resolution dynamics, and superresolution oceanic sea surface temperature data acquired from optical sensors. The method at its core consists in propagating across the scales the low-resolution dynamics in a multiresolution analysis computed on adimensional critical transition information.

Description: This paper presents the theory, algorithm, and results of a new bistatic interferometry synthetic aperture radar (InSAR) method. It employs the data acquired in an innovative bistatic configuration, which uses the orbital sensors as transmitters of opportunity and the stationary receivers on the ground, to generate a digital elevation model (DEM). In the bistatic spaceborne/stationary InSAR configuration, the interferometric phase only depends on the target-receiver range, which could not be obtained directly from the measured bistatic range. Therefore, the conventional transforming relationship between the interferometric phase and the topographic height is no longer practical. In order to solve the problem, we introduce a new conversion relationship between the interferometric phase and the topographic height, which is derived by the model of the ellipsoidal projection in the bistatic configuration. Meanwhile, the error analysis of the new conversion is carried out through a simulation. Both the simulated and measured data are used to test and verify the feasibility of the new bistatic InSAR method. In the spaceborne/stationary InSAR experiment, YaoGan-3 (an L-band spaceborne SAR system launched by China) was selected as the transmitter and two stationary receivers were mounted on the top of a tall building. The generated DEM of high quality shows that the presented method performs very well in the bistatic InSAR data process.

Description: We present a nonparametric Bayesian hierarchical model (HDP_IBPs) to classify very high resolution panchromatic satellite images in an unsupervised way, in which the hierarchical Dirichlet process (HDP) and Indian buffet process (IBP) are combined on multiple scenes. The main contribution of this paper is a novel application framework to solve the problems of traditional probabilistic topic models and achieve the effective unsupervised classification of very high resolution (VHR) panchromatic satellite images. In this framework, a VHR satellite image is first oversegmented into basic processing units and divided into a set of subimages. We use the Chinese restaurant franchise process as a construct method of the HDP to capture the latent semantic structures (i.e., classes) and the class proportion (i.e., co-occurrence of topics) for each subimage. Meanwhile, the subimages are grouped into different scenes based on the class proportion. Finally, the IBP is employed to select the most appropriate classes for each subimage from all of the classes based on different scenes in turn. The hierarchical structure of our model transmits the spatial information from the original image to the scene layer implicitly and provides useful cues of classification. The experimental results show that HDP_IBPs outperforms state-of-the-art models in terms of both qualitative and quantitative evaluations.

Description: This paper describes a linear-image-transform-based algorithm for reducing stripe noise, track line artifacts, and motion-induced errors in remote sensing data. Developed for multibeam bathymetry (MB), the method has also been used for removing scalloping in synthetic aperture radar images. The proposed image transform is the composition of an invertible edge detection operator and a fast discrete Radon transform (DRT) due to Götz, Druckmüller, and Brady. The inverse DRT is computed by using an iterative method and exploiting an approximate inverse algorithm due to Press. The edge operator is implemented by circular convolution with a Laplacian point spread function modified to render the operator invertible. In the transformed image, linear discontinuities appear as high-intensity spots, which may be reset to zero. In MB data, a second noise signature is linked to motion-induced errors. A Chebyshev approximation of the original image is subtracted before applying the transform, and added back to the denoised image; this is necessary to avoid boundary effects. It is possible to process data faster and suppress motion-induced noise further by filtering images in nonoverlapping blocks using a matrix representation for the inverse DRT. Processed test images from several MB data sets had less noise and distortion compared with those obtained with standard low-pass filters. Denoising also improved the accuracy in statistical classification of geomorphological type by 10–28% for two sets of invariant terrain features.

Description: Sparse graph embedding (SGE) is a promising technique useful for the nonlinear feature extraction (FE) of hyperspectral images (HSIs). However, such images exhibit spatial variability and spectral multimodality, presenting challenges to existing FE methods, including SGE. To address this issue, this paper presents two novel SGE methods for HSI classification. One method, which is termed simultaneous SGE (SSGE), is designed to consider the spatial variability of spectral signatures by using a simultaneous sparse representation (SSR) model integrated with a shape-adaptive neighborhood building approach. In addition, a sparse graph is constructed via matrix computation based on sparse codes. Then, low-dimensional features are produced by employing linear graph embedding (LGE) based on the constructed sparse graph. The other method, which is termed simultaneous sparse multimanifold learning (SSMML), is proposed to handle the multimodality of an HSI. In SSMML, multiple views are generated to represent different modalities. Then, multiview-oriented submanifolds are produced by adopting SSGE, and they are further integrated via coregularization. SSGE is capable of modeling both local and global data structures. Furthermore, SSMML serves as a prototype that can model multimodal data structures. The proposed methods are evaluated by using sparse multinomial logistic regression for HSI classification. Experimental results with two popular hyperspectral data sets validate the good performance of the two methods in producing more representative low-dimensional features and yielding superior classification results compared with other related approaches.

Description: We present a new algorithm that simultaneously retrieves aerosol properties and land surface bidirectional reflectance distribution function (BRDF) over Australian from Advanced Along-Track Scanning Radiometer images. Three key components are addressed: 1) an analytical radiative transfer formulation, based on Green's function, linking top-of-atmosphere (TOA) reflectance to the surface BRDF; 2) a novel approach to modeling BRDF using an extended compositing period; and 3) a set of representative aerosol models based on a published typology of Australian aerosols. Due to the generally low aerosol loadings and widespread bright surfaces over Australia, BRDF modeling is crucial. By using a 9-month compositing period, 90% of the Australian continent can be modeled with an error in the forward-to-nadir reflectance ratio of 2.5% or less. Comparison with suitably processed Moderate Resolution Imaging Spectroradiometer BRDF/albedo products demonstrates satisfactory agreement. For the studying period from 2002 to 2008, validation of aerosol optical depth (AOD) against eight sun photometers across Australia encompassing widely different atmospheric and surface regimes shows high accuracy, with a mean absolute error in AOD at 550 nm of 0.03 and a bias of 0.007. About 60% of the matchup points are within an absolute error of 0.03, 80% are within 0.05, and 96% are within 0.1. The algorithm selects for each cell an optimal aerosol type from a set of four predefined candidate models. Continental aerosol maps derived from the new method indicate broadscale agreement with known seasonal aerosol sources, while providing new insights into the spatial and temporal distributions of aerosol over the Australian continent.

Description: This investigation examines the phenomenology effects of the squint angle on the morphology of moving target smears in spotlight synthetic aperture radar (SAR). This analysis includes both the smears resulting from standard image formation applied to simulated radar measurements as well as the theoretical predictions for the central contours of the signatures. In particular, this paper generates the down-range and cross-range components of the predicted central 2-D contours of mover signatures, including the locations of the cross-range offsets. The analytics for squinted geometry include additional contributions in the signature contour equations that do not arise for the case of broadside imaging. These terms can affect the overall contour morphology, particularly in terms of shape and extent. Numerous examples are presented to demonstrate that the signature prediction equations yield excellent agreement with standard image formation with simulated radar data. Therefore, this analysis can provide an effective tool in predicting the shape, extent, and location of smears due to arbitrarily moving surface targets for squinted spotlight SAR.

Description: In this paper, we consider signal subspace estimation based on low-rank representation for hyperspectral imagery. It is often assumed that major signal sources occupy a low-rank subspace. Due to the mixed nature of hyperspectral remote sensing data, the underlying data structure may include multiple subspaces instead of a single subspace. Therefore, in this paper, we propose the use of low-rank subspace representation to estimate the number of subspaces in hyperspectral imagery. In particular, we develop simple estimation approaches without user-defined parameters because these parameters can be fixed as constants. Both real data experiments and computer simulations demonstrate excellent performance of the proposed approaches over those currently in the literature.

Description: The conventional spaced-receiver approach uses amplitude scintillations to estimate equatorial ionospheric irregularity drift velocities. This approach is less applicable at high latitudes where there is a lack of substantial amplitude scintillations. This paper presents a method to estimate ionosphere irregularity horizontal drift velocities based on GPS signal carrier phase measurements. Joint time–frequency analysis of the carrier phase measurements using an adaptive periodogram technique generates time-varying spectrograms of ionospheric irregularity-induced phase fluctuations. Cross correlation of the spectrograms between antenna pairs provides time lag information on propagating radio signals through the same ionospheric structure. The time lag information is combined with known positions of the receiver array, satellite orbits, and assumed irregularity altitude to infer ionospheric irregularity horizontal drift velocity. This paper presents the methodology and demonstrates its feasibility using data collected by a GPS receiver array at Gakona, Alaska. The potential error sources of this method are also analyzed.

Description: The Regression Network plugin for Cytoscape ( RegNetC ) implements the RegNet algorithm for the inference of transcriptional association network from gene expression profiles. This algorithm is a model tree-based method to detect the relationship between each gene and the remaining genes simultaneously instead of analyzing individually each pair of genes as correlation-based methods do. Model trees are a very useful technique to estimate the gene expression value by regression models and favours localized similarities over more global similarity, which is one of the major drawbacks of correlation-based methods. Here, we present an integrated software suite, named RegNetC , as a Cytoscape plugin that can operate on its own as well. RegNetC facilitates, according to user-defined parameters, the resulted transcriptional gene association network in .sif format for visualization, analysis and interoperates with other Cytoscape plugins, which can be exported for publication figures. In addition to the network, the RegNetC plugin also provides the quantitative relationships between genes expression values of those genes involved in the inferred network, i.e., those defined by the regression models.

Description: We introduce a new method for normalization of data acquired by liquid chromatography coupled with mass spectrometry (LC-MS) in label-free differential expression analysis. Normalization of LC-MS data is desired prior to subsequent statistical analysis to adjust variabilities in ion intensities that are not caused by biological differences but experimental bias. There are different sources of bias including variabilities during sample collection and sample storage, poor experimental design, noise, etc. In addition, instrument variability in experiments involving a large number of LC-MS runs leads to a significant drift in intensity measurements. Although various methods have been proposed for normalization of LC-MS data, there is no universally applicable approach. In this paper, we propose a Bayesian normalization model (BNM) that utilizes scan-level information from LC-MS data. Specifically, the proposed method uses peak shapes to model the scan-level data acquired from extracted ion chromatograms (EIC) with parameters considered as a linear mixed effects model. We extended the model into BNM with drift (BNMD) to compensate for the variability in intensity measurements due to long LC-MS runs. We evaluated the performance of our method using synthetic and experimental data. In comparison with several existing methods, the proposed BNM and BNMD yielded significant improvement.

Description: Performing clustering analysis is one of the important research topics in cancer discovery using gene expression profiles, which is crucial in facilitating the successful diagnosis and treatment of cancer. While there are quite a number of research works which perform tumor clustering, few of them considers how to incorporate fuzzy theory together with an optimization process into a consensus clustering framework to improve the performance of clustering analysis. In this paper, we first propose a random double clustering based cluster ensemble framework (RDCCE) to perform tumor clustering based on gene expression data. Specifically, RDCCE generates a set of representative features using a randomly selected clustering algorithm in the ensemble, and then assigns samples to their corresponding clusters based on the grouping results. In addition, we also introduce the random double clustering based fuzzy cluster ensemble framework (RDCFCE), which is designed to improve the performance of RDCCE by integrating the newly proposed fuzzy extension model into the ensemble framework. RDCFCE adopts the normalized cut algorithm as the consensus function to summarize the fuzzy matrices generated by the fuzzy extension models, partition the consensus matrix, and obtain the final result. Finally, adaptive RDCFCE (A-RDCFCE) is proposed to optimize RDCFCE and improve the performance of RDCFCE further by adopting a self-evolutionary process (SEPP) for the parameter set. Experiments on real cancer gene expression profiles indicate that RDCFCE and A-RDCFCE works well on these data sets, and outperform most of the state-of-the-art tumor clustering algorithms.

Description: Named-entity recognition (NER) plays an important role in the development of biomedical databases. However, the existing NER tools produce multifarious named-entities which may result in both curatable and non-curatable markers. To facilitate biocuration with a straightforward approach, classifying curatable named-entities is helpful with regard to accelerating the biocuration workflow. Co-occurrence Interaction Nexus with Named-entity Recognition (CoINNER) is a web-based tool that allows users to identify genes, chemicals, diseases, and action term mentions in the Comparative Toxicogenomic Database (CTD). To further discover interactions, CoINNER uses multiple advanced algorithms to recognize the mentions in the BioCreative IV CTD Track. CoINNER is developed based on a prototype system that annotated gene, chemical, and disease mentions in PubMed abstracts at BioCreative 2012 Track I (literature triage). We extended our previous system in developing CoINNER. The pre-tagging results of CoINNER were developed based on the state-of-the-art named entity recognition tools in BioCreative III. Next, a method based on conditional random fields (CRFs) is proposed to predict chemical and disease mentions in the articles. Finally, action term mentions were collected by latent Dirichlet allocation (LDA). At the BioCreative IV CTD Track, the best F-measures reached for gene/protein, chemical/drug and disease NER were 54 percent while CoINNER achieved a 61.5 percent F-measure. System URL: http://ikmbio.csie.ncku.edu.tw/coinner/introduction.htm.

Description: Next-generation short-read sequencing is widely utilized in genomic studies. Biological applications require an alignment step to map sequencing reads to the reference genome, before acquiring expected genomic information. This requirement makes alignment accuracy a key factor for effective biological interpretation. Normally, when accounting for measurement errors and single nucleotide polymorphisms, short read mappings with a few mismatches are generally considered acceptable. However, to further improve the efficiency of short-read sequencing alignment, we propose a method to retrieve additional reliably aligned reads (reads with more than a pre-defined number of mismatches), using a Bayesian-based approach. In this method, we first retrieve the sequence context around the mismatched nucleotides within the already aligned reads; these loci contain the genomic features where sequencing errors occur. Then, using the derived pattern, we evaluate the remaining (typically discarded) reads with more than the allowed number of mismatches, and calculate a score that represents the probability that a specific alignment is correct. This strategy allows the extraction of more reliably aligned reads, therefore improving alignment sensitivity. Implementation: The source code of our tool, ResSeq, can be downloaded from: https://github.com/hrbeubiocenter/Resseq.

Description: In genome assembly graphs, motifs such as tips, bubbles, and cross links are studied in order to find sequencing errors and to understand the nature of the genome. Superbubble, a complex generalization of bubbles, was recently proposed as an important subgraph class for analyzing assembly graphs. At present, a quadratic time algorithm is known. This paper gives an -time algorithm to solve this problem for a graph with $m$ edges.

Description: The papers in this special section focus on software and databases that are central in bioinformatics and computational biology.. These programs are playing more and more important roles in biology and medical research. These papers cover a broad range of topics, including computational genomics and transcriptomics, analysis of biological networks and interactions, drug design, biomedical signal/image analysis, biomedical text mining and ontologies, biological data mining, visualization and integration, and high performance computing application in bioinformatics.

Description: In the computational biology community, machine learning algorithms are key instruments for many applications, including the prediction of gene-functions based upon the available biomolecular annotations. Additionally, they may also be employed to compute similarity between genes or proteins. Here, we describe and discuss a software suite we developed to implement and make publicly available some of such prediction methods and a computational technique based upon Latent Semantic Indexing (LSI), which leverages both inferred and available annotations to search for semantically similar genes. The suite consists of three components. BioAnnotationPredictor is a computational software module to predict new gene-functions based upon Singular Value Decomposition of available annotations. SimilBio is a Web module that leverages annotations available or predicted by BioAnnotationPredictor to discover similarities between genes via LSI. The suite includes also SemSim , a new Web service built upon these modules to allow accessing them programmatically. We integrated SemSim in the Bio Search Computing framework (http://www.bioinformatics.deib.polimi.it/bio-seco/seco/), where users can exploit the Search Computing technology to run multi-topic complex queries on multiple integrated Web services. Accordingly, researchers may obtain ranked answers involving the computation of the functional similarity between genes in support of biomedical knowledge discovery.

Description: Identification of cancer subtypes plays an important role in revealing useful insights into disease pathogenesis and advancing personalized therapy. The recent development of high-throughput sequencing technologies has enabled the rapid collection of multi-platform genomic data (e.g., gene expression, miRNA expression, and DNA methylation) for the same set of tumor samples. Although numerous integrative clustering approaches have been developed to analyze cancer data, few of them are particularly designed to exploit both deep intrinsic statistical properties of each input modality and complex cross-modality correlations among multi-platform input data. In this paper, we propose a new machine learning model, called multimodal deep belief network (DBN), to cluster cancer patients from multi-platform observation data. In our integrative clustering framework, relationships among inherent features of each single modality are first encoded into multiple layers of hidden variables, and then a joint latent model is employed to fuse common features derived from multiple input modalities. A practical learning algorithm, called contrastive divergence (CD), is applied to infer the parameters of our multimodal DBN model in an unsupervised manner. Tests on two available cancer datasets show that our integrative data analysis approach can effectively extract a unified representation of latent features to capture both intra- and cross-modality correlations, and identify meaningful disease subtypes from multi-platform cancer data. In addition, our approach can identify key genes and miRNAs that may play distinct roles in the pathogenesis of different cancer subtypes. Among those key miRNAs, we found that the expression level of miR-29a is highly correlated with survival time in ovarian cancer patients. These results indicate that our multimodal DBN based data analysis approach may have practical applications in cancer pathogenesis studies and provide useful guidelines for personali- ed cancer therapy.

Description: The papers in this special issue contain extended versions of works that were originally presented at the Brazilian Symposium on Bioinformatics 2013 (BSB 2013), held in Recife, Brazil, November 3-6, 2013.

Description: Computational methods for predicting protein-protein interactions are important tools that can complement high-throughput technologies and guide biologists in designing new laboratory experiments. The proteins and the interactions between them can be described by a network which is characterized by several topological properties. Information about proteins and interactions between them, in combination with knowledge about topological properties of the network, can be used for developing computational methods that can accurately predict unknown protein-protein interactions. This paper presents a supervised learning framework based on Bayesian inference for combining two types of information: i) network topology information, and ii) information related to proteins and the interactions between them. The motivation of our model is that by combining these two types of information one can achieve a better accuracy in predicting protein-protein interactions, than by using models constructed from these two types of information independently.

Description: We develop a theory of algebraic operations over linear and context-free grammars that makes it possible to combine simple “atomic” grammars operating on single sequences into complex, multi-dimensional grammars. We demonstrate the utility of this framework by constructing the search spaces of complex alignment problems on multiple input sequences explicitly as algebraic expressions of very simple one-dimensional grammars. In particular, we provide a fully worked frameshift-aware, semiglobal DNA-protein alignment algorithm whose grammar is composed of products of small, atomic grammars. The compiler accompanying our theory makes it easy to experiment with the combination of multiple grammars and different operations. Composite grammars can be written out in $ {rm L}^AT_{E}X$ for documentation and as a guide to implementation of dynamic programming algorithms. An embedding in Haskell as a domain-specific language makes the theory directly accessible to writing and using grammar products without the detour of an external compiler. Software and supplemental files available here: http://www.bioinf.uni-leipzig.de/Software/gramprod/

Description: Recent advancements in genomics and proteomics provide a solid foundation for understanding the pathogenesis of diabetes. Proteomics of diabetes associated pathways help to identify the most potent target for the management of diabetes. The relevant datasets are scattered in various prominent sources which takes much time to select the therapeutic target for the clinical management of diabetes. However, additional information about target proteins is needed for validation. This lacuna may be resolved by linking diabetes associated genes, pathways and proteins and it will provide a strong base for the treatment and planning management strategies of diabetes. Thus, a web source “Diabetes Associated Proteins Database (DAPD)” has been developed to link the diabetes associated genes, pathways and proteins using PHP, MySQL. The current version of DAPD has been built with proteins associated with different types of diabetes. In addition, DAPD has been linked to external sources to gain the access to more participatory proteins and their pathway network. DAPD will reduce the time and it is expected to pave the way for the discovery of novel anti-diabetic leads using computational drug designing for diabetes management. DAPD is open accessed via following url www.mkarthikeyan.bioinfoau.org/dapd.

Description: Determining the glycan topology automatically from mass spectra represents a great challenge. Existing methods fall into approximate and exact ones. The former including greedy and heuristic ones can reduce the computational complexity, but suffer from information lost in the procedure of glycan interpretation. The latter including dynamic programming and exhaustive enumeration are much slower than the former. In the past years, nearly all emerging methods adopted a tree structure to represent a glycan. They share such problems as repetitive peak counting in reconstructing a candidate structure. Besides, tree-based glycan representation methods often have to give different computational formulas for binary and ternary glycans. We propose a new directed acyclic graph structure for glycan representation. Based on it, this work develops a de novo algorithm to accurately reconstruct the tree structure iteratively from mass spectra with logical constraints and some known biosynthesis rules, by a single computational formula. The experiments on multiple complex glycans extracted from human serum show that the proposed algorithm can achieve higher accuracy to determine a glycan topology than prior methods without increasing computational burden.

Description: A crucial step in understanding the architecture of cells and tissues from microscopy images, and consequently explain important biological events such as wound healing and cancer metastases, is the complete extraction and enumeration of individual filaments from the cellular cytoskeletal network. Current efforts at quantitative estimation of filament length distribution, architecture and orientation from microscopy images are predominantly limited to visual estimation and indirect experimental inference. Here we demonstrate the application of a new algorithm to reliably estimate centerlines of biological filament bundles and extract individual filaments from the centerlines by systematically disambiguating filament intersections. We utilize a filament enhancement step followed by reverse diffusion based filament localization and an integer programming based set combination to systematically extract accurate filaments automatically from microscopy images. Experiments on simulated and real confocal microscope images of flat cells (2D images) show efficacy of the new method.

Description: The Local/Global Alignment (Zemla, 2003), or LGA, is a popular method for the comparison of protein structures. One of the two components of LGA requires us to compute the longest common contiguous segments between two protein structures. That is, given two structures $A=(a_1, ldots , a_n)$ and $B=(b_1, ldots , b_n)$ where $a_k$ , $b_kin mathbb {R}^3$ , we are to find, among all the segments $f=(a_i,ldots ,a_j)$ and $g=(b_i,ldots ,b_j)$ that fulfill a certain criterion regarding their similarity, those of the maximum length. We consider the following criteria: (1) the root mean squared deviation (RMSD) between $f$ and $g$ is to be within a given $tin mathbb {R}$ ; (2) $f$ and $g$ can be superposed such that for each $k$ , $ile kle j$ , $Vert a_k-b_kVert le t$ for a given $tin mathbb {R}$ . We give an algorithm of $O(n;log; n+n{{boldsymbol l}})$ time complexity when the first requirement applies, where ${{boldsymbol l}}$ is the maximum length of the segments fulfilling the criterion. We show an FPTAS which, for any

Description: Noise can induce various dynamical behaviors in nonlinear systems. White noise perturbed systems have been extensively investigated during the last decades. In gene networks, experimentally observed extrinsic noise is colored. As an attempt, we investigate the genetic toggle switch systems perturbed by colored extrinsic noise and with kinetic parameters. Compared with white noise perturbed systems, we show there also exists optimal colored noise strength to induce the best stochastic switch behaviors in the single toggle switch, and the best synchronized switching in the networked systems, which demonstrate that noise-induced optimal switch behaviors are widely in existence. Moreover, under a wide range of system parameter regions, we find there exist wider ranges of white and colored noises strengths to induce good switch and synchronization behaviors, respectively; therefore, white noise is beneficial for switch and colored noise is beneficial for population synchronization. Our observations are very robust to extrinsic stimulus strength, cell density, and diffusion rate. Finally, based on the Waddington’s epigenetic landscape and the Wiener-Khintchine theorem, physical mechanisms underlying the observations are interpreted. Our investigations can provide guidelines for experimental design, and have potential clinical implications in gene therapy and synthetic biology.

Description: Revealing the underlying evolutionary mechanism plays an important role in understanding protein interaction networks in the cell. While many evolutionary models have been proposed, the problem about applying these models to real network data, especially for differentiating which model can better describe evolutionary process for the observed network remains a challenge. The traditional way is to use a model with presumed parameters to generate a network, and then evaluate the fitness by summary statistics, which however cannot capture the complete network structures information and estimate parameter distribution. In this work, we developed a novel method based on Approximate Bayesian Computation and modified Differential Evolution algorithm (ABC-DEP) that is capable of conducting model selection and parameter estimation simultaneously and detecting the underlying evolutionary mechanisms for PPI networks more accurately. We tested our method for its power in differentiating models and estimating parameters on simulated data and found significant improvement in performance benchmark, as compared with a previous method. We further applied our method to real data of protein interaction networks in human and yeast. Our results show duplication attachment model as the predominant evolutionary mechanism for human PPI networks and Scale-Free model as the predominant mechanism for yeast PPI networks.

Description: Single nucleotide polymorphisms, a dominant type of genetic variants, have been used successfully to identify defective genes causing human single gene diseases. However, most common human diseases are complex diseases and caused by gene-gene and gene-environment interactions. Many SNP-SNP interaction analysis methods have been introduced but they are not powerful enough to discover interactions more than three SNPs. The paper proposes a novel method that analyzes all SNPs simultaneously. Different from existing methods, the method regards an individual’s genotype data on a list of SNPs as a point with a unit of energy in a multi-dimensional space, and tries to find a new coordinate system where the energy distribution difference between cases and controls reaches the maximum. The method will find different multiple SNPs combinatorial patterns between cases and controls based on the new coordinate system. The experiment on simulated data shows that the method is efficient. The tests on the real data of age-related macular degeneration (AMD) disease show that it can find out more significant multi-SNP combinatorial patterns than existing methods.

Description: Disulfide connectivity is an important protein structural characteristic. Accurately predicting disulfide connectivity solely from protein sequence helps to improve the intrinsic understanding of protein structure and function, especially in the post-genome era where large volume of sequenced proteins without being functional annotated is quickly accumulated. In this study, a new feature extracted from the predicted protein 3D structural information is proposed and integrated with traditional features to form discriminative features. Based on the extracted features, a random forest regression model is performed to predict protein disulfide connectivity. We compare the proposed method with popular existing predictors by performing both cross-validation and independent validation tests on benchmark datasets. The experimental results demonstrate the superiority of the proposed method over existing predictors. We believe the superiority of the proposed method benefits from both the good discriminative capability of the newly developed features and the powerful modelling capability of the random forest. The web server implementation, called TargetDisulfide, and the benchmark datasets are freely available at: http://csbio.njust.edu.cn/bioinf/TargetDisulfide for academic use.

Description: Proteins are molecules that form the mass of living beings. These proteins exist in dissociated forms like amino-acids and carry out various biological functions, in fact, almost all body reactions occur with the participation of proteins. This is one of the reasons why the analysis of proteins has become a major issue in biology. In a more concrete way, the identification of conserved patterns in a set of related protein sequences can provide relevant biological information about these protein functions. In this paper, we present a novel algorithm based on teaching learning based optimization (TLBO) combined with a local search function specialized to predict common patterns in sets of protein sequences. This population-based evolutionary algorithm defines a group of individuals (solutions) that enhance their knowledge (quality) by means of different learning stages. Thus, if we correctly adapt it to the biological context of the mentioned problem, we can get an acceptable set of quality solutions. To evaluate the performance of the proposed technique, we have used six instances composed of different related protein sequences obtained from the PROSITE database. As we will see, the designed approach makes good predictions and improves the quality of the solutions found by other well-known biological tools.

Description: We introduce Supervised Variational Relevance Learning (Suvrel), a variational method to determine metric tensors to define distance based similarity in pattern classification, inspired in relevance learning. The variational method is applied to a cost function that penalizes large intraclass distances and favors small interclass distances. We find analytically the metric tensor that minimizes the cost function. Preprocessing the patterns by doing linear transformations using the metric tensor yields a dataset which can be more efficiently classified. We test our methods using publicly available datasets, for some standard classifiers. Among these datasets, two were tested by the MAQC-II project and, even without the use of further preprocessing, our results improve on their performance.

Description: Fractional vegetation cover (FVC) plays an important role in earth surface process simulations, climate modeling, and global change studies. Several global FVC products have been generated using medium spatial resolution satellite data. However, the validation results indicate inconsistencies, as well as spatial and temporal discontinuities of the current FVC products. The objective of this paper is to develop a reliable estimation algorithm to operationally produce a high-quality global FVC product from the Moderate Resolution Imaging Spectroradiometer (MODIS) surface reflectance. The high-spatial-resolution FVC data were first generated using Landsat TM/ETM+ data at the global sampling locations, and then, the general regression neural networks (GRNNs) were trained using the high-spatial-resolution FVC data and the reprocessed MODIS surface reflectance data. The direct validation using ground reference data from validation of land European Remote Sensing instruments sites indicated that the performance of the proposed method ( $mathbf{R}^{2}=0.809$ , $mathbf{RMSE} =0.157$ ) was comparable with that of the GEOV1 FVC product ( $mathbf{R}^{2}=0.775$ , $mathbf{RMSE} =0.166$ ) , which is currently considered to be the best global FVC product from SPOT VEGETATION data. Further comparison indicated that the spatial and temporal continuity of the estimates from the proposed method was superior to that of the GEOV1 FVC product.

Description: This paper proposes a region kernel to measure the region-to-region distance similarity for hyperspectral image (HSI) classification. The region kernel is designed to be a linear combination of multiscale box kernels, which can handle the HSI regions with arbitrary shape and size. Integrating labeled pixels and labeled regions, we further propose a region-kernel-based support vector machine (RKSVM) classification framework. In RKSVM, three different composite kernels are constructed to describe the joint spatial–spectral similarity. Particularly, we design a desirable stack composite kernel that consists of the point-based kernel, the region-based kernel, and the cross point-to-region kernel. The effectiveness of the proposed RKSVM is validated on three benchmark hyperspectral data sets. Experimental results show the superiority of our region kernel method over the classical point kernel methods.

Description: Atmospheric refraction in the troposphere causes the propagation speed of electromagnetic signals to be less than the light speed. This creates a difference between the actual propagation path delay and the distance of the geometrical straight-line path, i.e., a quantity known as the tropospheric delay. As classical imaging algorithms for spaceborne synthetic aperture radar (SAR) do not take the tropospheric delay into account, imaging filters are designed based on the assumption of rectilinear propagation with the light speed. Therefore, a residual phase exists in imaging results, which affects focusing quality under the condition of high resolution. In order to compensate for the impact of tropospheric delay on focusing performance, this paper modifies the spaceborne SAR echo model and then proposes an imaging compensation algorithm. The key to this algorithm is to fit a range delay coefficient based on the European Geostationary Navigation Overlay Service model of zenith delay and Niell mapping function, which projects the zenith delay onto the looking direction. After range compensation, classical imaging, and azimuth compensation, which compose the proposed algorithm, the processed results are well focused.

Description: Accurate correction of atmospheric effects on data captured by an infrared (IR) camera is crucial for several applications such as vegetation monitoring, temperature monitoring, satellite images, hyperspectral imaging, numerical model simulations, surface properties characterization, and IR measurement interpretation. Atmospheric effects depend on the temporal changes, i.e., year, season, day, hour, etc., and on the geometry between the camera and the measured scene, i.e., line of sight. The orientation and the optical depth of the camera significantly affect the variation of the geometry across the pixels. In this paper, we propose a method to estimate the range and zenith angle of each pixel using only the Global Positioning System (GPS) coordinates of the camera and a point of interest in the scene. The estimated geometry and measured meteorological data are used to obtain the spectral atmospheric transmittance and path radiance. Furthermore, we propose an atmospheric effects removal, i.e., atmospheric correction, method that considers the spectral characteristics of the detector, lens, and filter. The proposed atmospheric correction process is analyzed in detail with the simultaneous measurements of two IR cameras. In this process, an enhanced temperature calibration method is developed and it is shown that the temperature accuracy for the dynamic range of the IR camera is very close to the noise equivalent temperature difference (NETD) value of the camera.

Description: Multiple scattering within a mixed pixel results in a nonlinear effect on the measured spectra in remotely sensed imagery. This study provides a quantitative assessment of multiple scattering in the reflectance of semiarid shrublands and explores its relationship to the characteristics of shrubs (density and height) and imaging parameters (wavelength and viewing angles). Field measurements were conducted at the southern fringe of the Otindag Sandy Land in China. A Monte Carlo ray tracing model, the Forest LIGHT interaction model (FLIGHT), was applied to simulate the multiple scattering results. FLIGHT simulation results were first evaluated against field measurements and then compared with a Landsat-8 OLI image. Results show that: 1) the contribution of multiple scattering to the spectra of a scene increases linearly with the fractional cover of vegetation and crown height; 2) in general, multiple scattering has a stronger effect on the near-infrared (NIR) domain than on the visible bands; 3) shadows significantly strengthen the multiple scattering effect, specifically within the visible bands; and 4) 80 to 100% of the total multiple scattering is caused by the second-order scattering within the visible bands and 60% to 90% within the NIR band. This study helps to improve our understanding of the multiple scattering effect and to select between linear and nonlinear spectral unmixing models to solve the abundances of shrubs and soil in mixed pixels.

Description: The main objective of the Chinese Chang'E-3 (CE-3) lunar satellite is to achieve soft-landing and roving exploration on the lunar surface. A multibeam radar in the lunar lander is implemented to measure the echoes from the lunar rough surface during its descending and to derive the speed of the lander. In this paper, numerical simulation of multiangular radar echoes and speed inversions from Doppler frequency are presented. An area of the Lunar Sinus Iridum bay, as landing site, is specifically selected. The rough surface described with the real DTM data is first divided into triangular patches for numerical Kirchhoff approximation calculation. The radar echoes of multiangular radar beams of CE-3 during the landing are numerically simulated. The echo phase and the Doppler frequency are then derived to obtain the vertical speed.

Description: Light scattering models of snow are very important for the remote sensing of snow. Many previous models have used unrealistic assumptions about the snow particle shape and microstructure. In this paper, a new model is proposed, wherein a bicontinuous medium is used to simulate the snow microstructure, and geometric optics theory is used in combination with the Monte Carlo method to simulate the scattering properties of snow. Then, using the radiative transfer equation, the snow reflectance, including the polarized reflectance, can be simulated. Unlike other models that use Monte Carlo ray tracing, the new model is computationally efficient and can be used for massive simulations and practical applications. The simulation results of the new model are compared with the ground measurements and simulation results of a traditional model based on the Mie theory. Through validations and comparisons, the new model is shown to demonstrate a significantly improved capability in simulating the bidirectional reflectance of snow. The importance of the grain shape and microstructure modeling in the light scattering models of snow is confirmed by the comparison of the simulation results.

Description: In microwave radiometric remote sensing, undetected radio frequency interference (RFI) can adversely affect the accuracy of the science products. A method is presented to adaptively tune the parameters of an RFI detection algorithm which controls the equivalent brightness temperature of undetected RFI. The method is adaptive in the sense that it adjusts to variations in the RFI environment, e.g., from high RFI conditions near some population centers to low RFI conditions in the tropical Pacific Ocean. The RFI environment is characterized by inferring the distribution of low-level undetected RFI from that of high-level detected RFI using appropriate scaling arguments. The resulting tuned algorithm adjusts its detection threshold to equalize the brightness temperature calibration bias due to RFI at the expense of the now variable measurement precision (noise equivalent delta temperature). This tradeoff between calibration bias and measurement precision can be represented as a modified version of the classic receiver-operating-characteristic curve. The radiometer on the Aquarius/SAC-D mission is used as an example.

Description: Polarimetric technology has been one of the most important advances in microwave remote sensing during recent decades. H-alpha decomposition, which is a type of polarimetric analysis technique, has been common for terrain and land-use classification in polarimetric synthetic aperture radar. However, the technique has been less common in the ground penetrating radar (GPR) community. In this paper, we apply the H-alpha decomposition to analyze the surface GPR data to obtain polarimetric attributes for subsurface target classification. Also, by combining H-alpha decomposition and migration, we can obtain a subsurface H-alpha color-coded reconstructed target image, from which we can use both the polarimetric attributes and the geometrical features of the subsurface targets to enhance the ability of subsurface target classification of surface GPR. A 3-D full polarimetric GPR data set was acquired in a laboratory experiment, in which four targets, a scatterer with many branches, a ball, a plate, and a dihedral scatter, were buried in dry sand under flat ground surface, and used to test these techniques. As results, we obtained the subsurface H-alpha distribution and classified the subsurface targets. Also, we derived a subsurface H-alpha color-coded reconstructed target image and identified all four targets in the laboratory experiment.

Description: Snow microwave radiance assimilation (RA) or brightness temperature data assimilation (DA) has shown promise for improving snow water equivalent (SWE) estimation. A successful RA study requires, however, an analysis of the error characteristics of coupled land surface-radiative transfer models (LSM/RTMs). This paper focuses on the Community Land Model version 4 (CLM4) as the land-surface model and on the microwave emission model for layered snowpacks (MEMLS) and the dense media radiative transfer multilayer (DMRT-ML) model as RTMs. Using the National Aeronautics and Space Administration Cold Land Processes Field Experiment (CLPX) data sets and through synthetic experiments, the errors of the coupled CLM4/DMRT-ML and CLM4/MEMLS are characterized by: 1) evaluating the CLM4 snowpack state simulations; 2) assessing the performance of RTMs in simulating the brightness temperature $(T_{B} )$ ; and 3) analyzing the correlations between the SWE error $(varepsilon_text{SWE})$ and the $T_{B}$ error $(varepsilon_T_{B} ) $ from the RA perspective. The results using the CLPX data sets show that, given a large error of the snow grain radius $(varepsilon_r_{e} )$ under dry snowpack conditions (along with a small error of the snow temperature $(varepsilon_T_mathrm{snow})$ ), the correlations between $varepsilon_text{SWE}$ and $varepsilon_T_{B} $ are mainly determined by the relationship between $varepsilon_r_{e}$ and the snow depth error $(varepsilon_d_{mathrm{snow}})$ or the snow density error $(varepsilon_rho_{mathrm{snow}} ) $ . The synthetic experiments were carried out for the CLPX region (shallow snowpack conditions and the Rocky Mountains (deep snowpack conditions using the atmospheric ensemble reanalysis produced by the coupled DA Research Testbed/Community Atmospheric Model (CAM4. The synthetic experiments support the results from the CLPX data sets and show that the errors of soil (the water content and the temperature, snow wetness, and snow temperature mostly result in positive correlations between $varepsilon_text{SWE}$ and $varepsilon_T_{B} $ . CLM4/DMRT-ML and CLM4/MEMLS tend to produce varying RA performance, with more positive and negative correlations between $varepsilon_text{SWE}$ and $varepsilon_T_{B} $ , respectively. These results suggest the necessity of using multiple snowpack RTMs in RA to improve the SWE estimation at the continental scale. The results in this paper also show that the magnitude of $varepsilon_r_{e}$ and its relationship to $varepsilon_text{SWE} $ are important for the RA performance. Most of the SWE estimations in RA are improved when $varepsilon_text{SWE}$ and

Description: This paper addresses the important yet unresolved problem of estimating forest properties from polarimetric-interferometric radar images affected by temporal decorrelation. We approach the problem by formulating a physical model of the polarimetric-interferometric coherence that incorporates both volumetric and temporal decorrelation effects. The model is termed random-motion-over-ground (RMoG) model, as it combines the random-volume-over-ground (RVoG) model with a Gaussian-statistic motion model of the canopy elements. Key features of the RMoG model are: 1) temporal decorrelation depends on the vertical structure of forests; 2) volumetric and temporal coherences are not separable as simple multiplicative factors; and 3) temporal decorrelation is complex-valued and changes with wave polarization. This third feature is particularly important as it allows compensating for unknown levels of temporal decorrelation using multiple polarimetric channels. To estimate model parameters such as tree height and canopy motion, we propose an algorithm that minimizes the least square distance between model predictions and complex coherence observations. The algorithm was applied to L-band NASA's Uninhabited Aerial Vehicle Synthetic Aperture Radar data acquired over the Harvard Forest (Massachussetts, USA). We found that the RMS difference at stand level between estimated RMoG-model tree height and NASA's lidar Laser Vegetation and Ice Sensor tree height was within 12% of the lidar-derived height, which improved significantly the RMS difference of 37% obtained using the RVoG model and ignoring temporal decorrelation. This result contributes to our ability of estimating forest biomass using in-orbit and forthcoming polarimetric-interferometric radar missions.