Parallel geostatistics for sparse and dense datasets

Very large spatially-referenced datasets, for example, those derived from satellite-based sensors which sample across the globe or large monitoring networks of individual sensors, are becoming increasingly common and more widely available for use in environmental decision making. In large or dense sensor networks, huge quantities of data can be collected over small time periods. In many applications the generation of maps, or predictions at specific locations, from the data in (near) real-time is crucial. Geostatistical operations such as interpolation are vital in this map-generation process and in emergency situations, the resulting predictions need to be available almost instantly, so that decision makers can make informed decisions and define risk and evacuation zones. It is also helpful when analysing data in less time critical applications, for example when interacting directly with the data for exploratory analysis, that the algorithms are responsive within a reasonable time frame. Performing geostatistical analysis on such large spatial datasets can present a number of problems, particularly in the case where maximum likelihood. Although the storage requirements only scale linearly with the number of observations in the dataset, the computational complexity in terms of memory and speed, scale quadratically and cubically respectively. Most modern commodity hardware has at least 2 processor cores if not more. Other mechanisms for allowing parallel computation such as Grid based systems are also becoming increasingly commonly available. However, currently there seems to be little interest in exploiting this extra processing power within the context of geostatistics. In this paper we review the existing parallel approaches for geostatistics. By recognising that diffeerent natural parallelisms exist and can be exploited depending on whether the dataset is sparsely or densely sampled with respect to the range of variation, we introduce two contrasting novel implementations of parallel algorithms based on approximating the data likelihood extending the methods of Vecchia [1988] and Tresp [2000]. Using parallel maximum likelihood variogram estimation and parallel prediction algorithms we show that computational time can be significantly reduced. We demonstrate this with both sparsely sampled data and densely sampled data on a variety of architectures ranging from the common dual core processor, found in many modern desktop computers, to large multi-node super computers. To highlight the strengths and weaknesses of the diffeerent methods we employ synthetic data sets and go on to show how the methods allow maximum likelihood based inference on the exhaustive Walker Lake data set.

Projected sequential Gaussian processes:a C++ tool for interpolation of large datasets with heterogeneous noise

Heterogeneous datasets arise naturally in most applications due to the use of a variety of sensors and measuring platforms. Such datasets can be heterogeneous in terms of the error characteristics and sensor models. Treating such data is most naturally accomplished using a Bayesian or model-based geostatistical approach; however, such methods generally scale rather badly with the size of dataset, and require computationally expensive Monte Carlo based inference. Recently within the machine learning and spatial statistics communities many papers have explored the potential of reduced rank representations of the covariance matrix, often referred to as projected or fixed rank approaches. In such methods the covariance function of the posterior process is represented by a reduced rank approximation which is chosen such that there is minimal information loss. In this paper a sequential Bayesian framework for inference in such projected processes is presented. The observations are considered one at a time which avoids the need for high dimensional integrals typically required in a Bayesian approach. A C++ library, gptk, which is part of the INTAMAP web service, is introduced which implements projected, sequential estimation and adds several novel features. In particular the library includes the ability to use a generic observation operator, or sensor model, to permit data fusion. It is also possible to cope with a range of observation error characteristics, including non-Gaussian observation errors. Inference for the covariance parameters is explored, including the impact of the projected process approximation on likelihood profiles. We illustrate the projected sequential method in application to synthetic and real datasets. Limitations and extensions are discussed. © 2010 Elsevier Ltd.

PDNAsite:identification of DNA-binding site from protein sequence by incorporating spatial and sequence context

Protein-DNA interactions are involved in many fundamental biological processes essential for cellular function. Most of the existing computational approaches employed only the sequence context of the target residue for its prediction. In the present study, for each target residue, we applied both the spatial context and the sequence context to construct the feature space. Subsequently, Latent Semantic Analysis (LSA) was applied to remove the redundancies in the feature space. Finally, a predictor (PDNAsite) was developed through the integration of the support vector machines (SVM) classifier and ensemble learning. Results on the PDNA-62 and the PDNA-224 datasets demonstrate that features extracted from spatial context provide more information than those from sequence context and the combination of them gives more performance gain. An analysis of the number of binding sites in the spatial context of the target site indicates that the interactions between binding sites next to each other are important for protein-DNA recognition and their binding ability. The comparison between our proposed PDNAsite method and the existing methods indicate that PDNAsite outperforms most of the existing methods and is a useful tool for DNA-binding site identification. A web-server of our predictor (http://hlt.hitsz.edu.cn:8080/PDNAsite/) is made available for free public accessible to the biological research community.