Fourier series approximation of separable models

n/

A Network-Constrain Weibull AFT Model for Biomarkers Discovery

We propose AFTNet, a novel network-constraint survival analysis method based on the Weibull accelerated failure time (AFT) model solved by a penalized likelihood approach for variable selection and estimation. When using the log-linear representation, the inference problem becomes a structured sparse regression problem for which we explicitly incorporate the correlation patterns among predictors using a double penalty that promotes both sparsity and grouping effect. Moreover, we establish the theoretical consistency for the AFTNet estimator and present an efficient iterative computational algorithm based on the proximal gradient descent method. Finally, we evaluate AFTNet performance both on synthetic and real data examples

Kalman filter physical retrieval of surface emissivity and temperature from geostationary infrared radiances

The high temporal resolution of data acquisition by geostationary satellites and their capability to resolve the diurnal cycle allows for the retrieval of a valuable source of information about geophysical parameters. In this paper, we implement a Kalman filter approach to applying tempo-ral constraints on the retrieval of surface emissivity and temperature from radiance measurements made from geostationary platforms. Although we consider a case study in which we apply a strictly temporal constraint alone, the methodology will be presented in its general four-dimensional, i.e., space-time, setting. The case study we consider is the retrieval of emissivity and surface temperature from SEVIRI (Spinning Enhanced Visible and Infrared Imager) observations over a target area encompassing the Iberian Peninsula and northwestern Africa. The retrievals are then compared with in situ data and other similar satellite products. Our findings show that the Kalman filter strategy can simultaneously retrieve surface emissivity and temperature with an accuracy of ± 0.005 and ±0.2 K, respectively

Technical note: Functional sliced inverse regression to infer temperature, water vapour and ozone from IASI data.

A retrieval algorithm that uses a statistical strategy based on dimension reduction is proposed. The methodology and details of the implementation of the new algorithm are presented and discussed. The algorithm has been applied to high resolution spectra measured by the Infrared Atmospheric Sounding Interferometer instrument to retrieve atmospheric profiles of temperature, water vapour and ozone. The performance of the inversion strategy has been assessed by comparing the retrieved profiles to the ones obtained by co-locating in space and time profiles from the European Centre for Medium-Range Weather Forecasts analysi

Spatio-temporal constraints for emissivity and surface temperature retrieval: Preliminary results and comparisons for SEVIRI and IASI observation

Infrared instrumentation on geostationary satellites is now rapidly approaching the spectral quality and accuracy of modern sensors flying on polar platforms. Currently, the core of EUMETSAT geostationary meteorological programme is the Meteosat Second Generation (MSG). However, EUMETSAT is preparing for the Meteosat Third Generation (MTG). The capability of geostationary satellites to resolve the diurnal cycle and hence to provide time-resolved sequences or times series of observations is a source of information which could suitably constrain the derivation of geophysical parameters. Nowadays, also because of lack of time continuity, when dealing with observations from polar platforms, the problem of deriving geophysical parameters is normally solved by considering each single observation as independent of past and future events. For historical reason, the same approach is currently pursued with geostationary observations, which are still being dealt with as they were with polar observations. In this study we show some preliminary results on emissivity and surface temperature retrieval for SEVIRI observations, using the Kalman filter methodology (KF) and compare the retrievals with those obtained using IASI observations co-localized with SEVIRI ones using the times accumulation approach (Optimal Estimation OE). The Sahara desert was chosen as target area, and both SEVIRI and IASI data (infrared radiances and cloud mask) were acquired. The time period considered is that of July 2010 (the whole month). ECMWF analyses for the same date and target area have also been acquired, which comprise Ts, T(p), O(p), Q(p) for the canonical hours 0:00, 6:00, 12:00 and 18:00. Moreover, for the purpose of developing a suitable background for emissivity, the Global Infrared Land Surface Emissivity database developed at CIMSS, University of Wisconsin, derived by MODIS observations was used and was available from the year 2003 till 2011. Concerning the performance of the two methodologies, the retrieval of skin temperature is almost equivalent. The agreement between OE and KF is fairly good if compared with ECMWF analysis for sea surface, while for land surface, OE and KF agree fairly well with ECMWF during the night, but at midday ECMWF shows a cold bias of 10 K and more. For emissivity the comparison with the UW/BFEMIS database for the same date and location is fairly good for both methods

Cosmonet: An r package for survival analysis using screening-network methods

Identifying relevant genomic features that can act as prognostic markers for building predictive survival models is one of the central themes in medical research, affecting the future of personalized medicine and omics technologies. However, the high dimension of genome-wide omic data, the strong correlation among the features, and the low sample size significantly increase the complexity of cancer survival analysis, demanding the development of specific statistical methods and software. Here, we present a novel R package, COSMONET (COx Survival Methods based On NETworks), that provides a complete workflow from the pre-processing of omics data to the selection of gene signatures and prediction of survival outcomes. In particular, COSMONET implements (i) three different screening approaches to reduce the initial dimension of the data from a high-dimensional space p to a moderate scale d, (ii) a network-penalized Cox regression algorithm to identify the gene signature, (iii) several approaches to determine an optimal cut-off on the prognostic index (PI) to separate high- and low-risk patients, and (iv) a prediction step for patients’ risk class based on the evaluation of PIs. Moreover, COSMONET provides functions for data pre-processing, visualization, survival prediction, and gene enrichment analysis. We illustrate COSMONET through a step-by-step R vignette using two cancer datasets.</jats:p

The IASI Water Deficit Index to Monitor Vegetation Stress and Early Drying in Summer Heatwaves: An Application to Southern Italy

The boreal hemisphere has been experiencing increasing extreme hot and dry conditions over the past few decades, consistent with anthropogenic climate change. The continental extension of this phenomenon calls for tools and techniques capable of monitoring the global to regional scales. In this context, satellite data can satisfy the need for global coverage. The main objective we have addressed in the present paper is the capability of infrared satellite observations to monitor the vegetation stress due to increasing drought and heatwaves in summer. We have designed and implemented a new water deficit index (wdi) that exploits satellite observations in the infrared to retrieve humidity, air temperature, and surface temperature simultaneously. These three parameters are combined to provide the water deficit index. The index has been developed based on the Infrared Atmospheric Sounder Interferometer or IASI, which covers the infrared spectral range 645 to 2760 cm−1 with a sampling of 0.25 cm−1. The index has been used to study the 2017 heatwave, which hit continental Europe from May to October. In particular, we have examined southern Italy, where Mediterranean forests suffer from climate change. We have computed the index’s time series and show that it can be used to indicate the atmospheric background conditions associated with meteorological drought. We have also found a good agreement with soil moisture, which suggests that the persistence of an anomalously high water deficit index was an essential driver of the rapid development and evolution of the exceptionally severe 2017 droughts

ROBustness In Network (robin): an R Package for Comparison and Validation of Communities

In network analysis, many community detection algorithms have been developed. However, their implementation leaves unaddressed the question of the statistical validation of the results. Here, we present robin (ROBustness In Network), an R package to assess the robustness of the community structure of a network found by one or more methods to give indications about their reliability. The procedure initially detects if the community structure found by a set of algorithms is statistically significant and then compares two selected detection algorithms on the same graph to choose the one that better fits the network of interest. We demonstrate the use of our package on the American College Football benchmark dataset

How Do They Do It? – Understanding the Success of Marine Invasive Species

From the depths of the oceans to the shallow estuaries and wetlands of our coasts, organisms of the marine environment are teeming with unique adaptations to cope with a multitude of varying environmental conditions. With millions of years and a vast volume of water to call their home, they have become quite adept at developing specialized and unique techniques for survival and – given increasing human mediated transport – biological invasions. A growing world human population and a global economy drives the transportation of goods across the oceans and with them invasive species via ballast water and attached to ship hulls. In any given 24-hour period, there are about 10,000 species being transported across different biogeographic regions. If any of them manage to take hold and establish a range in an exotic habitat, the implications for local ecosystems can be costly. This review on marine invasions highlights trends among successful non-indigenous species (NIS), from vectors of transport to ecological and physiological plasticity. Apart from summarizing patterns of successful invasions, it discusses the implications of how successfully established NIS impact the local environment, economy and human health. Finally, it looks to the future and discusses what questions need to be addressed and what models can tell us about what the outlook on future marine invasions is