Global and time-resolved monitoring of crop photosynthesis with chlorophyll fluorescence.

Photosynthesis is the process by which plants harvest sunlight to produce sugars from carbon dioxide and water. It is the primary source of energy for all life on Earth; hence it is important to understand how this process responds to climate change and human impact. However, model-based estimates of gross primary production (GPP, output from photosynthesis) are highly uncertain, in particular over heavily managed agricultural areas. Recent advances in spectroscopy enable the space-based monitoring of sun-induced chlorophyll fluorescence (SIF) from terrestrial plants. Here we demonstrate that spaceborne SIF retrievals provide a direct measure of the GPP of cropland and grassland ecosystems. Such a strong link with crop photosynthesis is not evident for traditional remotely sensed vegetation indices, nor for more complex carbon cycle models. We use SIF observations to provide a global perspective on agricultural productivity. Our SIF-based crop GPP estimates are 50-75% higher than results from state-of-the-art carbon cycle models over, for example, the US Corn Belt and the Indo-Gangetic Plain, implying that current models severely underestimate the role of management. Our results indicate that SIF data can help us improve our global models for more accurate projections of agricultural productivity and climate impact on crop yields. Extension of our approach to other ecosystems, along with increased observational capabilities for SIF in the near future, holds the prospect of reducing uncertainties in the modeling of the current and future carbon cycle.

Nonlinearities and adaptation of color vision from sequential principal curves analysis.

Mechanisms of human color vision are characterized by two phenomenological aspects: the system is nonlinear and adaptive to changing environments. Conventional attempts to derive these features from statistics use separate arguments for each aspect. The few statistical explanations that do consider both phenomena simultaneously follow parametric formulations based on empirical models. Therefore, it may be argued that the behavior does not come directly from the color statistics but from the convenient functional form adopted. In addition, many times the whole statistical analysis is based on simplified databases that disregard relevant physical effects in the input signal, as, for instance, by assuming flat Lambertian surfaces. In this work, we address the simultaneous statistical explanation of the nonlinear behavior of achromatic and chromatic mechanisms in a fixed adaptation state and the change of such behavior (i.e., adaptation) under the change of observation conditions. Both phenomena emerge directly from the samples through a single data-driven method: the sequential principal curves analysis (SPCA) with local metric. SPCA is a new manifold learning technique to derive a set of sensors adapted to the manifold using different optimality criteria. Here sequential refers to the fact that sensors (curvilinear dimensions) are designed one after the other, and not to the particular (eventually iterative) method to draw a single principal curve. Moreover, in order to reproduce the empirical adaptation reported under D65 and A illuminations, a new database of colorimetrically calibrated images of natural objects under these illuminants was gathered, thus overcoming the limitations of available databases. The results obtained by applying SPCA show that the psychophysical behavior on color discrimination thresholds, discount of the illuminant, and corresponding pairs in asymmetric color matching emerge directly from realistic data regularities, assuming no a priori functional form. These results provide stronger evidence for the hypothesis of a statistically driven organization of color sensors. Moreover, the obtained results suggest that the nonuniform resolution of color sensors at this low abstraction level may be guided by an error-minimization strategy rather than by an information-maximization goal.

Iterative Gaussianization: from ICA to random rotations.

Most signal processing problems involve the challenging task of multidimensional probability density function (PDF) estimation. In this paper, we propose a solution to this problem by using a family of rotation-based iterative Gaussianization (RBIG) transforms. The general framework consists of the sequential application of a univariate marginal Gaussianization transform followed by an orthonormal transform. The proposed procedure looks for differentiable transforms to a known PDF so that the unknown PDF can be estimated at any point of the original domain. In particular, we aim at a zero-mean unit-covariance Gaussian for convenience. RBIG is formally similar to classical iterative projection pursuit algorithms. However, we show that, unlike in PP methods, the particular class of rotations used has no special qualitative relevance in this context, since looking for interestingness is not a critical issue for PDF estimation. The key difference is that our approach focuses on the univariate part (marginal Gaussianization) of the problem rather than on the multivariate part (rotation). This difference implies that one may select the most convenient rotation suited to each practical application. The differentiability, invertibility, and convergence of RBIG are theoretically and experimentally analyzed. Relation to other methods, such as radial Gaussianization, one-class support vector domain description, and deep neural networks is also pointed out. The practical performance of RBIG is successfully illustrated in a number of multidimensional problems such as image synthesis, classification, denoising, and multi-information estimation.

Correction of systematic spatial noise in push-broom hyperspectral sensors: application to CHRIS/PROBA images.

Hyperspectral remote sensing images are affected by different types of noise. In addition to typical random noise, nonperiodic partially deterministic disturbance patterns generally appear in the data. These patterns, which are intrinsic to the image formation process, are characterized by a high degree of spatial and spectral coherence. We present a new technique that faces the problem of removing the spatially coherent noise known as vertical striping, usually found in images acquired by push-broom sensors. The developed methodology is tested on data acquired by the Compact High Resolution Imaging Spectrometer (CHRIS) onboard the Project for On-board Autonomy (PROBA) orbital platform, which is a typical example of a push-broom instrument exhibiting a relatively high noise component. The proposed correction method is based on the hypothesis that the vertical disturbance presents higher spatial frequencies than the surface radiance. A technique to exclude the contribution of the spatial high frequencies of the surface from the destriping process is introduced. First, the performance of the proposed algorithm is tested on a set of realistic synthetic images with added modeled noise in order to quantify the noise reduction and the noise estimation accuracy. Then, algorithm robustness is tested on more than 350 real CHRIS images from different sites, several acquisition modes (different spatial and spectral resolutions), and covering the full range of possible sensor temperatures. The proposed algorithm is benchmarked against the CHRIS reference algorithm. Results show excellent rejection of the noise pattern with respect to the original CHRIS images, especially improving the removal in those scenes with a natural high contrast. However, some low-frequency components still remain. In addition, the developed correction model captures and corrects the dependency of the noise patterns on sensor temperature, which confirms the robustness of the presented approach.

Upport vector machines for nonlinear kernel ARMA system identification.

Nonlinear system identification based on support vector machines (SVM) has been usually addressed by means of the standard SVM regression (SVR), which can be seen as an implicit nonlinear autoregressive and moving average (ARMA) model in some reproducing kernel Hilbert space (RKHS). The proposal of this letter is twofold. First, the explicit consideration of an ARMA model in an RKHS (SVM-ARMA2K) is proposed. We show that stating the ARMA equations in an RKHS leads to solving the regularized normal equations in that RKHS, in terms of the autocorrelation and cross correlation of the (nonlinearly) transformed input and output discrete time processes. Second, a general class of SVM-based system identification nonlinear models is presented, based on the use of composite Mercer's kernels. This general class can improve model flexibility by emphasizing the input-output cross information (SVM-ARMA4K), which leads to straightforward and natural combinations of implicit and explicit ARMA models (SVR-ARMA2K and SVR-ARMA4K). Capabilities of these different SVM-based system identification schemes are illustrated with two benchmark problems.

Perceptual adaptive insensitivity for support vector machine image coding.

Support vector machine (SVM) learning has been recently proposed for image compression in the frequency domain using a constant epsilon-insensitivity zone by Robinson and Kecman. However, according to the statistical properties of natural images and the properties of human perception, a constant insensitivity makes sense in the spatial domain but it is certainly not a good option in a frequency domain. In fact, in their approach, they made a fixed low-pass assumption as the number of discrete cosine transform (DCT) coefficients to be used in the training was limited. This paper extends the work of Robinson and Kecman by proposing the use of adaptive insensitivity SVMs [2] for image coding using an appropriate distortion criterion [3], [4] based on a simple visual cortex model. Training the SVM by using an accurate perception model avoids any a priori assumption and improves the rate-distortion performance of the original approach.

Profiled support vector machines for antisense oligonucleotide efficacy prediction.

BACKGROUND: This paper presents the use of Support Vector Machines (SVMs) for prediction and analysis of antisense oligonucleotide (AO) efficacy. The collected database comprises 315 AO molecules including 68 features each, inducing a problem well-suited to SVMs. The task of feature selection is crucial given the presence of noisy or redundant features, and the well-known problem of the curse of dimensionality. We propose a two-stage strategy to develop an optimal model: (1) feature selection using correlation analysis, mutual information, and SVM-based recursive feature elimination (SVM-RFE), and (2) AO prediction using standard and profiled SVM formulations. A profiled SVM gives different weights to different parts of the training data to focus the training on the most important regions. RESULTS: In the first stage, the SVM-RFE technique was most efficient and robust in the presence of low number of samples and high input space dimension. This method yielded an optimal subset of 14 representative features, which were all related to energy and sequence motifs. The second stage evaluated the performance of the predictors (overall correlation coefficient between observed and predicted efficacy, r; mean error, ME; and root-mean-square-error, RMSE) using 8-fold and minus-one-RNA cross-validation methods. The profiled SVM produced the best results (r = 0.44, ME = 0.022, and RMSE= 0.278) and predicted high (>75% inhibition of gene expression) and low efficacy (<25%) AOs with a success rate of 83.3% and 82.9%, respectively, which is better than by previous approaches. A web server for AO prediction is available online at http://aosvm.cgb.ki.se/. CONCLUSIONS: The SVM approach is well suited to the AO prediction problem, and yields a prediction accuracy superior to previous methods. The profiled SVM was found to perform better than the standard SVM, suggesting that it could lead to improvements in other prediction problems as well.

Foetal ECG recovery using dynamic neural networks.

Non-invasive electrocardiography has proven to be a very interesting method for obtaining information about the foetus state and thus to assure its well-being during pregnancy. One of the main applications in this field is foetal electrocardiogram (ECG) recovery by means of automatic methods. Evident problems found in the literature are the limited number of available registers, the lack of performance indicators, and the limited use of non-linear adaptive methods. In order to circumvent these problems, we first introduce the generation of synthetic registers and discuss the influence of different kinds of noise to the modelling. Second, a method which is based on numerical (correlation coefficient) and statistical (analysis of variance, ANOVA) measures allows us to select the best recovery model. Finally, finite impulse response (FIR) and gamma neural networks are included in the adaptive noise cancellation (ANC) scheme in order to provide highly non-linear, dynamic capabilities to the recovery model. Neural networks are benchmarked with classical adaptive methods such as the least mean squares (LMS) and the normalized LMS (NLMS) algorithms in simulated and real registers and some conclusions are drawn. For synthetic registers, the most determinant factor in the identification of the models is the foetal-maternal signal-to-noise ratio (SNR). In addition, as the electromyogram contribution becomes more relevant, neural networks clearly outperform the LMS-based algorithm. From the ANOVA test, we found statistical differences between LMS-based models and neural models when complex situations (high foetal-maternal and foetal-noise SNRs) were present. These conclusions were confirmed after doing robustness tests on synthetic registers, visual inspection of the recovered signals and calculation of the recognition rates of foetal R-peaks for real situations. Finally, the best compromise between model complexity and outcomes was provided by the FIR neural network. Both the methodology for selecting a model and the introduction of advanced neural models are the main contributions of this paper.

Dosage individualization of erythropoietin using a profile-dependent support vector regression.

The external administration of recombinant human erythropoietin is the chosen treatment for those patients with secondary anemia due to chronic renal failure in periodic hemodialysis. The objective of this paper is to carry out an individualized prediction of the EPO dosage to be administered to those patients. The high cost of this medication, its side-effects and the phenomenon of potential resistance which some individuals suffer all justify the need for a model which is capable of optimizing dosage individualization. A group of 110 patients and several patient factors were used to develop the models. The support vector regressor (SVR) is benchmarked with the classical multilayer perceptron (MLP) and the Autoregressive Conditional Heteroskedasticity (ARCH) model. We introduce a priori knowledge by relaxing or tightening the epsilon-insensitive region and the penalization parameter depending on the time period of the patients' follow-up. The so-called profile-dependent SVR (PD-SVR) improves results of the standard SVR method and the MLP. We perform sensitivity analysis on the MLP and inspect the distribution of the support vectors in the input and feature spaces in order to gain knowledge about the problem.

Prediction of cyclosporine dosage in patients after kidney transplantation using neural networks.

This paper proposes the use of neural networks for individualizing the dosage of cyclosporine A (CyA) in patients who have undergone kidney transplantation. Since the dosing of CyA usually requires intensive therapeutic drug monitoring, the accurate prediction of CyA blood concentrations would decrease the monitoring frequency and, thus, improve clinical outcomes. Thirty-two patients and different factors were studied to obtain the models. Three kinds of networks (multilayer perceptron, finite impulse response (FIR) network, and Elman recurrent network) and the formation of neural-network ensembles are used in a scheme of two chained models where the blood concentration predicted by the first model constitutes an input to the dosage prediction model. This approach is designed to aid in the process of clinical decision making. The FIR network, yielding root-mean-square errors (RMSEs) of 52.80 ng/mL and mean errors (MEs) of 0.18 ng/mL in validation (10 patients) showed the best blood concentration predictions and a committee of trained networks improved the results (RMSE = 46.97 ng/mL, ME = 0.091 ng/mL). The Elman network was the selected model for dosage prediction (RMSE = 0.27 mg/Kg/d, ME = 0.07 mg/Kg/d). However, in both cases, no statistical differences on the accuracy of neural methods were found. The models' robustness is also analyzed by evaluating their performance when noise is introduced at input nodes, and it results in a helpful test for models' selection. We conclude that neural networks can be used to predict both dose and blood concentrations of cyclosporine in steady-state. This novel approach has produced accurate and validated models to be used as decision-aid tools.