Predicting the spatial distribution of ground flora on large domains using a hierarchical Bayesian model

Accomodation of important sources of uncertainty in ecological models is essential to realistically predicting ecological processes. The purpose of this project is to develop a robust methodology for modeling natural processes on a landscape while accounting for the variability in a process by utilizing environmental and spatial random effects. A hierarchical Bayesian framework has allowed the simultaneous integration of these effects. This framework naturally assumes variables to be random and the posterior distribution of the model provides probabilistic information about the process. Two species in the genus Desmodium were used as examples to illustrate the utility of the model in Southeast Missouri, USA. In addition, two validation techniques were applied to evaluate the qualitative and quantitative characteristics of the predictions.This revised version was published online in May 2005 with corrections to the Cover Date.     

基于MCMC模拟的MGPD模型及其在地质灾害风险度量中的应用

基于马尔科夫链蒙特卡洛(简记为MCMC)模拟的参数贝叶斯估计,对改进的广义帕累托分布(简记为MGPD)模型进行了优化,并利用该模型得到了地质灾害损失的在险损失值(简记为VaR)和条件损失值(简记为CVaR).以湖南娄底市地质灾害损失数据进行实证分析及模型适应性检验,结果表明:优化后的模型不仅具有很好的极值数据描述能力,而且具有较强的适用性.     

基于信号博弈的阳澄湖大闸蟹绿色标签市场应用分析

水产品绿色标签对消费者来说是高质量的信号,对卖家来说则是卖出高价的资本.但是欺诈行为的存在损害了消费者和其他卖家的利益,扰乱了市场秩序.以阳澄湖大闸蟹为例,通过信号博彝理论,对螃蟹市场中关卖双方的消费行为进行博彝分析,得到了精炼贝叶斯Nash均衡.     

Bayesian estimation of diagnostic accuracy of a new bead-based antibody detection test to reveal Toxoplasma gondii infections in pig populations

The success of a Toxoplasma gondii surveillance program in European pig production systems depends partly on the quality of the test to detect infection in the population. The test accuracy of a recently developed serological bead-based assay (BBA) was investigated earlier using sera from experimentally infected animals. In this study, the accuracy of the BBA was determined by the use of sera from animals from two field subpopulations. As no T. gondii infection information of these animals was available, test accuracy was determined through a Bayesian approach allowing for conditional dependency between BBA and an ELISA test. The priors for prevalence were based on available information from literature, whereas for specificity vague non-informative priors were used. Priors for sensitivity were based either on available information or specified as non-informative. Posterior estimates for BBA sensitivity and specificity were (mode) 0.855 (Bayesian 95% credibility interval (bCI) 0.702–0.960) and 0.913 (bCI 0.893–0.931), respectively. Comparing the results of BBA and ELISA, sensitivity was higher for the BBA while specificity was higher for ELISA. Alternative priors for the sensitivity affected posterior estimates for sensitivity of both BBA and ELISA, but not for specificity. Because the difference in prevalence between the two subpopulations is small, and the number of infected animals is small as well, the precision of the posterior estimates for sensitivity may be less accurate in comparison to the estimates for specificity. The estimated value for specificity of BBA is at least optimally defined for testing pigs from conventional and organic Dutch farms.     

金融时间序列指标判别框架：以特质波动率为例

基于拐点集合判别的TBUD方法主要思路是分析拐点集合间的关系，并在高维空间进行划分，从而搭建判别模型，并将分析框架应用在特质波动率等若干指标上，利用实证数据得到结论。应用TBUD判别框架可以发现，特质波动率等指标无法对拐点集合进行清晰划分，因而并不具有预测能力。     

A global sensitivity analysis of cultivar trait parameters in a sugarcane growth model for contrasting production environments in Queensland,Australia

New sugarcane cultivars are continuously developed to improve sugar industry productivity. Despite this sugarcane crop models such as the ‘Sugar’ module in the Agricultural Productions System sIMulator (APSIM-Sugar) have not been updated to reflect the most recent cultivars. The implications of misrepresenting cultivar parameters in APSIM-Sugar is difficult to judge as little research has been published on the likely values of these parameters and how uncertainty in parameter values may affect model outputs. A global sensitivity analysis can be used to better understand how cultivar parameters influence simulated yields. A Gaussian emulator was used to perform a global sensitivity analysis on simulated biomass and sucrose yield at harvest for two contrasting sugarcane-growing regions in Queensland, Australia. Biomass and sucrose yields were simulated for 42 years to identify inter-annual variability in output sensitivities to 10 parameters that represent physiological traits and can be used to simulated differences between sugarcane cultivars. Parameter main effect (S_i) and total effect (ST_i) sensitivity indices and emulator accuracy were calculated for all year-region-output combinations. When both regions were considered together parameters representing radiation use efficiency (rue), number of green leaves (green_leaf_no) and a conductance surrogate parameter (k_L) were the most influential parameters for simulated biomass in APSIM-Sugar. Simulated sucrose yield was most sensitive to rue, sucrose_fraction (representing the fraction of biomass partitioned as sucrose in the stem) and green_leaf_no. However, climate and soil differences between regions changed the level of influence cultivar parameters had on simulation outputs. Specifically, model outputs were more sensitive to changes in the transp_eff_cf and k_L parameters in the Burdekin region due to lower rainfall and poor simulated soil conditions. Collecting data on influential traits that are relatively simple to measure (e.g. number of green leaves) during cultivar development would greatly contribute to the simulation of new cultivars in crop models. Influential parameters that are difficult to measure directly such as transp_eff_cf and sucrose_fraction are ideal candidates for statistical calibration. Calibrating crop models either through direct observation or statistical calibration would allow crop modellers to better test how new cultivars will perform in a range of production environments.     

Genomic prediction for meat and carcass traits in Nellore cattle using a Markov blanket algorithm

This study was carried out to evaluate the advantage of preselecting SNP markers using Markov blanket algorithm regarding the accuracy of genomic prediction for carcass and meat quality traits in Nellore cattle. This study considered 3675, 3680, 3660 and 524 records of rib eye area (REA), back fat thickness (BF), rump fat (RF), and Warner–Bratzler shear force (WBSF), respectively, from the Nellore Brazil Breeding Program. The animals have been genotyped using low-density SNP panel (30 k), and subsequently imputed for arrays with 777 k SNPs. Four Bayesian specifications of genomic regression models, namely Bayes A, Bayes B, Bayes Cπ and Bayesian Ridge Regression methods were compared in terms of prediction accuracy using a five folds cross-validation. Prediction accuracy for REA, BF and RF was all similar using the Bayesian Alphabet models, ranging from 0.75 to 0.95. For WBSF, the predictive ability was higher using Bayes B (0.47) than other methods (0.39 to 0.42). Although the prediction accuracies using Markov blanket of SNP markers were lower than those using all SNPs, for WBSF the relative gain was lower than 13%. With a subset of informative SNPs markers, identified using Markov blanket, probably, is possible to capture a large proportion of the genetic variance for WBSF. The development of low-density and customized arrays using Markov blanket might be cost-effective to perform a genomic selection for this trait, increasing the number of evaluated animals, improving the management decisions based on genomic information and applying genomic selection on a large scale.     

基于超参数优化算法下的随机森林模型预测奶牛呼吸频率

奶牛呼吸频率是评估环境造成的奶牛热应激程度的重要指标之一。该研究基于随机森林（random forest,RF）算法提出了适用于生产条件下的奶牛个体呼吸频率准确预测模型,为了平衡模型精度与计算效率问题,利用遗传算法（genetic algorithm,GA）、差分进化（differential evolution,DE）算法、粒子群优化（particle swarm optimization,PSO）算法、贝叶斯优化（Bayesian optimization,BO）算法对模型超参数进行优化,并与网格搜索（grid search,GS）下的人工神经网络（artificial neural network,ANN）和极限梯度提升机（extreme gradient boosting,XGBoost）模型进行了对比分析。研究结果表明,使用融合环境参数的修正温湿指数（adjusted temperature-humidity index,ATHI）、时间区域、奶牛产奶量、泌乳天数、身体姿势以及胎次作为输入特征时,基准RF模型的预测性能最佳。在此基础上,4种智能优化算法下的RF模型性能优于GS-ANN和GS-XGBoost,其中BO-RF的综合性能最优,其决定系数、平均绝对误差、平均绝对百分比误差以及均方根误差分别为0.614、7.723、14.4%、9.737,超参数优化耗时约为DE-RF的1/220。特征重要性分析表明,输入因子对奶牛呼吸频率的影响程度不同,ATHI是影响力最高的因子,相对重要性（relative importance,RI）为0.71,其次是时间区域（RI=0.09）和奶牛产奶量（RI=0.07）。研究为奶牛生产、健康评价及牛舍环境精准调控提供了有效方法和基础。     

基于Bayesian网的蔬菜质量安全追溯模型构建

蔬菜产品的质量安全是当前亟待解决的问题,只有从蔬菜的种植源头抓起,找出蔬菜生产过程中影响蔬菜质量安全的关键因素,结合蔬菜生产流程,建立完善的可追溯模型,才能真正实现蔬菜生产的质量安全监控.为此,建立了基于Bayesian网的蔬菜质量安全追溯初始模型,通过该模型可兼顾"事先"预防和"事后"追踪,从而保障蔬菜的质量安全.     

基于改进残差网络的园林害虫图像识别

针对北方园林害虫识别问题,提出了一种基于改进残差网络的害虫图像识别方法。首先,采用富边缘检测算法,将中值滤波、Sobel算子和Canny算子相结合,对害虫图像进行边缘检测;然后,改进残差网络中的残差块,通过添加卷积层和增加通道数提取更多的害虫图像特征,并将贝叶斯方法运用于改进后的网络中,优化超参数;最后,将预处理的害虫图像输入神经网络中,利用分块共轭算法优化网络权重。对38种北方园林害虫进行了识别,试验结果表明,在相同数据集下,与3种传统害虫识别方法相比,本文方法的平均识别准确率平均提高9. 6个百分点,加权平均分数分别提高16. 3、10. 8、4. 5个百分点。