Local spatial structure of forest biomass and its consequences for remote sensing of carbon stocks

Advances in forest carbon mapping have the potential to greatly reduce uncertainties in the global carbon budget and to facilitate effective emissions mitigation strategies such as REDD+ (Reducing Emissions from Deforestation and Forest Degradation). Though broad-scale mapping is based primarily on remote sensing data, the accuracy of resulting forest carbon stock estimates depends critically on the quality of field measurements and calibration procedures. The mismatch in spatial scales between field inventory plots and larger pixels of current and planned remote sensing products for forest biomass mapping is of particular concern, as it has the potential to introduce errors, especially if forest biomass shows strong local spatial variation. Here, we used 30 large (8-50 ha) globally distributed permanent forest plots to quantify the spatial variability in aboveground biomass density (AGBD in Mgha(-1)) at spatial scales ranging from 5 to 250m (0.025-6.25 ha), and to evaluate the implications of this variability for calibrating remote sensing products using simulated remote sensing footprints. We found that local spatial variability in AGBD is large for standard plot sizes, averaging 46.3% for replicate 0.1 ha subplots within a single large plot, and 16.6% for 1 ha subplots. AGBD showed weak spatial autocorrelation at distances of 20-400 m, with autocorrelation higher in sites with higher topographic variability and statistically significant in half of the sites. We further show that when field calibration plots are smaller than the remote sensing pixels, the high local spatial variability in AGBD leads to a substantial ``dilution'' bias in calibration parameters, a bias that cannot be removed with standard statistical methods. Our results suggest that topography should be explicitly accounted for in future sampling strategies and that much care must be taken in designing calibration schemes if remote sensing of forest carbon is to achieve its promise.

Use of a structural alphabet to find compatible folds for amino acid sequences

The structural annotation of proteins with no detectable homologs of known 3D structure identified using sequence-search methods is a major challenge today. We propose an original method that computes the conditional probabilities for the amino-acid sequence of a protein to fit to known protein 3D structures using a structural alphabet, known as Protein Blocks (PBs). PBs constitute a library of 16 local structural prototypes that approximate every part of protein backbone structures. It is used to encode 3D protein structures into 1D PB sequences and to capture sequence to structure relationships. Our method relies on amino acid occurrence matrices, one for each PB, to score global and local threading of query amino acid sequences to protein folds encoded into PB sequences. It does not use any information from residue contacts or sequence-search methods or explicit incorporation of hydrophobic effect. The performance of the method was assessed with independent test datasets derived from SCOP 1.75A. With a Z-score cutoff that achieved 95% specificity (i.e., less than 5% false positives), global and local threading showed sensitivity of 64.1% and 34.2%, respectively. We further tested its performance on 57 difficult CASP10 targets that had no known homologs in PDB: 38 compatible templates were identified by our approach and 66% of these hits yielded correctly predicted structures. This method scales-up well and offers promising perspectives for structural annotations at genomic level. It has been implemented in the form of a web-server that is freely available at http://www.bo-protscience.fr/forsa.

Iterated stochastic filters with additive updates for dynamic system identification: Annealing-type iterations and the filter bank

A nonlinear stochastic filtering scheme based on a Gaussian sum representation of the filtering density and an annealing-type iterative update, which is additive and uses an artificial diffusion parameter, is proposed. The additive nature of the update relieves the problem of weight collapse often encountered with filters employing weighted particle based empirical approximation to the filtering density. The proposed Monte Carlo filter bank conforms in structure to the parent nonlinear filtering (Kushner-Stratonovich) equation and possesses excellent mixing properties enabling adequate exploration of the phase space of the state vector. The performance of the filter bank, presently assessed against a few carefully chosen numerical examples, provide ample evidence of its remarkable performance in terms of filter convergence and estimation accuracy vis-a-vis most other competing filters especially in higher dimensional dynamic system identification problems including cases that may demand estimating relatively minor variations in the parameter values from their reference states. (C) 2014 Elsevier Ltd. All rights reserved.

Sparse coding based VLAD for efficient image retrieval

Representing images and videos in the form of compact codes has emerged as an important research interest in the vision community, in the context of web scale image/video search. Recently proposed Vector of Locally Aggregated Descriptors (VLAD), has been shown to outperform the existing retrieval techniques, while giving a desired compact representation. VLAD aggregates the local features of an image in the feature space. In this paper, we propose to represent the local features extracted from an image, as sparse codes over an over-complete dictionary, which is obtained by K-SVD based dictionary training algorithm. The proposed VLAD aggregates the residuals in the space of these sparse codes, to obtain a compact representation for the image. Experiments are performed over the `Holidays' database using SIFT features. The performance of the proposed method is compared with the original VLAD. The 4% increment in the mean average precision (mAP) indicates the better retrieval performance of the proposed sparse coding based VLAD.