Background Multibreed genomic prediction(MBGP)is crucial for improving prediction accuracy for breeds with small populations,for which limited data are often available.Recent studies have demonstrated that partitionin...Background Multibreed genomic prediction(MBGP)is crucial for improving prediction accuracy for breeds with small populations,for which limited data are often available.Recent studies have demonstrated that partitioning the genome into nonoverlapping blocks to model heterogeneous genetic(co)variance in multitrait models can achieve higher joint prediction accuracy.However,the block partitioning method,a key factor influencing model performance,has not been extensively explored.Results We introduce mbBayesABLD,a novel Bayesian MBGP model that partitions each chromosome into nonoverlapping blocks on the basis of linkage disequilibrium(LD)patterns.In this model,marker effects within each block are assumed to follow normal distributions with block-specific parameters.We employ simulated data as well as empirical datasets from pigs and beans to assess genomic prediction accuracy across different models using cross-validation.The results demonstrate that mbBayesABLD significantly outperforms conventional MBGP models,such as GBLUP and BayesR.For the meat marbling score trait in pigs,compared with GBLUP,which does not account for heterogeneous genetic(co)variance,mbBayesABLD improves the prediction accuracy for the small-population breed Landrace by 15.6%.Furthermore,our findings indicate that a moderate level of similarity in LD patterns between breeds(with an average correlation of 0.6)is sufficient to improve the prediction accuracy of the target breed.Conclusions This study presents a novel LD block-based approach for multibreed genomic prediction.Our work provides a practical tool for livestock breeding programs and offers new insights into leveraging genetic diversity across breeds for improved genomic prediction.展开更多
Impact of satellite elevation cutoff angle and position dilution of precision(PDOP)mask change on epoch-wise variance components of unmodeled effects that accompany relative Global Positioning System(GPS)positioning i...Impact of satellite elevation cutoff angle and position dilution of precision(PDOP)mask change on epoch-wise variance components of unmodeled effects that accompany relative Global Positioning System(GPS)positioning is presented herein.Data used for this study refer to the winter and summer periods of the years with minimal(2008)and maximal(2013)solar activity.These data were collected every 30 s in static mode,at two permanent GPS stations located in Montenegro,establishing a mediumdistance(116-km-long)baseline with a height difference of approximately 760 m between its endpoints.The study showed that changing satellite elevation cutoff angle,with a fixed PDOP mask,affects epochwise two-way nested ANOVA estimates of variances related to the‘far-field’multipath(considered as the nested factor herein)and the combined unmodeled effect of tropospheric and ionospheric refraction(considered as the nesting factor herein).However,changing of PDOP mask,with a fixed satellite elevation cutoff angle,doesn’t affect epoch-wise two-way nested ANOVA estimate of variance of the combined unmodeled effect of tropospheric and ionospheric refraction,but,generally,affects the estimate of variance of the‘far-field’multipath(possibly mixed with a part of a‘shorter-term’ionospheric refraction),which is especially pronounced for the summer period.It should also be noted that there is a significant influence of satellite elevation cutoff angle change on both epoch-wise horizontal and vertical position accuracy,only for the summer period,especially in the presence of maximal solar activity,while there is no significant impact of PDOP mask change on epoch-wise positional accuracy.展开更多
To understand any statistical tool requires not only an understanding of the relevant computational procedures but also an awareness of the assumptions upon which the procedures are based, and the effects of violation...To understand any statistical tool requires not only an understanding of the relevant computational procedures but also an awareness of the assumptions upon which the procedures are based, and the effects of violations of these assumptions. In our earlier articles (Laverty, Miket, & Kelly [1]) and (Laverty & Kelly, [2] [3]) we used Microsoft Excel to simulate both a Hidden Markov model and heteroskedastic models showing different realizations of these models and the performance of the techniques for identifying the underlying hidden states using simulated data. The advantage of using Excel is that the simulations are regenerated when the spreadsheet is recalculated allowing the user to observe the performance of the statistical technique under different realizations of the data. In this article we will show how to use Excel to generate data from a one-way ANOVA (Analysis of Variance) model and how the statistical methods behave both when the fundamental assumptions of the model hold and when these assumptions are violated. The purpose of this article is to provide tools for individuals to gain an intuitive understanding of these violations using this readily available program.展开更多
Sib-pair linkage analysis of complex human diseases has become a method of choice in modern human genetic studies, especially for the diseases with a late age at onset. The traditional parametric methods for sib pair ...Sib-pair linkage analysis of complex human diseases has become a method of choice in modern human genetic studies, especially for the diseases with a late age at onset. The traditional parametric methods for sib pair data need to take the categorical nature of a disease phenotype into account and to explicitly model the non-linear relationship between the discrete phenotype and genetic determinants, or to force their relationship to be linear. The first approach is desirable theoretically, but explicitly modeling the sophisticated genetic architecture of a complex disease can be prohibitively complex and computational demand is high. The second approach, typically a linear regression, relies on a large sample theory and is not appropriate. In this paper, we propose to apply Analysis of Variance (ANOVA) to sib pair linkage analysis of complex human diseases. This approach has avoided building the complicated relationship between the phenotype (the affection group or status of a sib pair) and the underlying genetic determinant (identical-by-decent (IBD) values etc). We have explored its statistical efficiency and properties in sibpair linkage analysis of ordinal complex human diseases via simulation. The simulation suggests that it is a powerful approach for locating genes that presumably control phenotypic expression of complex human diseases.展开更多
The prediction of the fracture plane orientation in fatigue is a scientific topic and remains relevant for every type of material. However, in this work, we compared the orientation of the fracture plane obtained expe...The prediction of the fracture plane orientation in fatigue is a scientific topic and remains relevant for every type of material. However, in this work, we compared the orientation of the fracture plane obtained experimentally through tests on specimens under multiaxial loading with that calculated by the variance method. In the statistical approach criteria, several methods have been developed but we have presented only one method, namely the variance method using the equivalent stress. She assumes that the fracture plane orientation is the one on which the variance of the equivalent stress is maximum. Three types of equivalent stress are defined for this method [1]: normal stress, shear stress and combined normal and shear stress. The results obtained were compared with experimental results for multiaxial cyclic stress states, and it emerges that the variance method for the case of combined loading is conservative as it gives a better prediction of the fracture plane.展开更多
Working toward an efficient duration and timeline for the preconstruction phase should be one of the main objectives for project owners.Failing to plan for and coordinate preconstruction decisions in order to control ...Working toward an efficient duration and timeline for the preconstruction phase should be one of the main objectives for project owners.Failing to plan for and coordinate preconstruction decisions in order to control preconstruction duration and manage time variances can lead to financial insecurities,incomplete contract documents,permitting issues,and unrealistic schedules and resource allocation during this phase.To minimize time variances and ensure a productive decision-making process,project owners should be familiar with critical elements in a project that cause variances in the preconstruction phase timeline.In this study,the impacts of eleven critical preconstruction elements on time variances were analyzed.These eleven preconstruction elements are considered critical in how they impact time variances during the preconstruction phase.They were determined to be critical based either on significantly impacting time variance during the preconstruction phase or believed to be critical from findings from previous studies,however,the findings from this study showed no significant impact on the time variances.In most previous studies focusing on the elements impacting project schedules,data were collected by surveying construction professionals.In this study,objective and quantitative data related to project preconstruction elements were used as opposed to self-reported data.Using the results of this study,project owners and stakeholders will be able to evaluate the critical preconstruction elements impacting the timing of their projects and prioritize decisions related to the critical elements early on during the preconstruction phase.展开更多
The valuation of financial derivatives often assumes risk neutrality with respect to the risk-neutral martingale measure,which prevents arbitrage opportunities.However,casual traders may still incur substantial losses...The valuation of financial derivatives often assumes risk neutrality with respect to the risk-neutral martingale measure,which prevents arbitrage opportunities.However,casual traders may still incur substantial losses when trading at this risk-neutral price,especially when the price has to be paid now and the payoff is only realized in the future.This study proposes a new valuation framework that provides risksensitive investors with an additional safeguard.The proposed framework embraces a worst-case perspective while exploiting the underlier’s stochastic process,representing a combination of robust optimization and stochastic programming.Notably,it aims to mitigate losses in the likelier scenarios of the underlying asset’s prices.When the underlier’s returns are independent and lognormally but not necessarily identically distributed,our approach for pricing variance and volatility swaps could be greatly simplified,benefit from parallel computing,and be solved by a two-dimensional grid search.We further derive a closed-form solution in some special stationary cases and provide experimental results to highlight the effect of risk aversion on fending off sizable trading losses.展开更多
In the variance component estimation(VCE)of geodetic data,the problem of negative VCE is likely to occur.In the ordinary additive error model,there have been related studies to solve the problem of negative variance c...In the variance component estimation(VCE)of geodetic data,the problem of negative VCE is likely to occur.In the ordinary additive error model,there have been related studies to solve the problem of negative variance components.However,there is still no related research in the mixed additive and multiplicative random error model(MAMREM).Based on the MAMREM,this paper applies the nonnegative least squares variance component estimation(NNLS-VCE)algorithm to this model.The correlation formula and iterative algorithm of NNLS-VCE for MAMREM are derived.The problem of negative variance in VCE for MAMREM is solved.This paper uses the digital simulation example and the Digital Terrain Mode(DTM)to prove the proposed algorithm's validity.The experimental results demonstrated that the proposed algorithm can effectively correct the VCE in MAMREM when there is a negative VCE.展开更多
基金supported by the Biological Breeding-Major Projects in National Science and Technology(No.2023ZD0404405)the Earmarked Fund for China Agriculture Research System(No.CARS-pig-35)+2 种基金the National Natural Science Foundation of China(No.3227284,32302708)the 2115 Talent Development Program of China Agricultural University,the Chinese Universities Scientific Fund(No.2023TC196)the Seed Industry Revitalization Action Project of Guangdong Province(No.2024-XPY-06-001)。
文摘Background Multibreed genomic prediction(MBGP)is crucial for improving prediction accuracy for breeds with small populations,for which limited data are often available.Recent studies have demonstrated that partitioning the genome into nonoverlapping blocks to model heterogeneous genetic(co)variance in multitrait models can achieve higher joint prediction accuracy.However,the block partitioning method,a key factor influencing model performance,has not been extensively explored.Results We introduce mbBayesABLD,a novel Bayesian MBGP model that partitions each chromosome into nonoverlapping blocks on the basis of linkage disequilibrium(LD)patterns.In this model,marker effects within each block are assumed to follow normal distributions with block-specific parameters.We employ simulated data as well as empirical datasets from pigs and beans to assess genomic prediction accuracy across different models using cross-validation.The results demonstrate that mbBayesABLD significantly outperforms conventional MBGP models,such as GBLUP and BayesR.For the meat marbling score trait in pigs,compared with GBLUP,which does not account for heterogeneous genetic(co)variance,mbBayesABLD improves the prediction accuracy for the small-population breed Landrace by 15.6%.Furthermore,our findings indicate that a moderate level of similarity in LD patterns between breeds(with an average correlation of 0.6)is sufficient to improve the prediction accuracy of the target breed.Conclusions This study presents a novel LD block-based approach for multibreed genomic prediction.Our work provides a practical tool for livestock breeding programs and offers new insights into leveraging genetic diversity across breeds for improved genomic prediction.
文摘Impact of satellite elevation cutoff angle and position dilution of precision(PDOP)mask change on epoch-wise variance components of unmodeled effects that accompany relative Global Positioning System(GPS)positioning is presented herein.Data used for this study refer to the winter and summer periods of the years with minimal(2008)and maximal(2013)solar activity.These data were collected every 30 s in static mode,at two permanent GPS stations located in Montenegro,establishing a mediumdistance(116-km-long)baseline with a height difference of approximately 760 m between its endpoints.The study showed that changing satellite elevation cutoff angle,with a fixed PDOP mask,affects epochwise two-way nested ANOVA estimates of variances related to the‘far-field’multipath(considered as the nested factor herein)and the combined unmodeled effect of tropospheric and ionospheric refraction(considered as the nesting factor herein).However,changing of PDOP mask,with a fixed satellite elevation cutoff angle,doesn’t affect epoch-wise two-way nested ANOVA estimate of variance of the combined unmodeled effect of tropospheric and ionospheric refraction,but,generally,affects the estimate of variance of the‘far-field’multipath(possibly mixed with a part of a‘shorter-term’ionospheric refraction),which is especially pronounced for the summer period.It should also be noted that there is a significant influence of satellite elevation cutoff angle change on both epoch-wise horizontal and vertical position accuracy,only for the summer period,especially in the presence of maximal solar activity,while there is no significant impact of PDOP mask change on epoch-wise positional accuracy.
文摘To understand any statistical tool requires not only an understanding of the relevant computational procedures but also an awareness of the assumptions upon which the procedures are based, and the effects of violations of these assumptions. In our earlier articles (Laverty, Miket, & Kelly [1]) and (Laverty & Kelly, [2] [3]) we used Microsoft Excel to simulate both a Hidden Markov model and heteroskedastic models showing different realizations of these models and the performance of the techniques for identifying the underlying hidden states using simulated data. The advantage of using Excel is that the simulations are regenerated when the spreadsheet is recalculated allowing the user to observe the performance of the statistical technique under different realizations of the data. In this article we will show how to use Excel to generate data from a one-way ANOVA (Analysis of Variance) model and how the statistical methods behave both when the fundamental assumptions of the model hold and when these assumptions are violated. The purpose of this article is to provide tools for individuals to gain an intuitive understanding of these violations using this readily available program.
文摘Sib-pair linkage analysis of complex human diseases has become a method of choice in modern human genetic studies, especially for the diseases with a late age at onset. The traditional parametric methods for sib pair data need to take the categorical nature of a disease phenotype into account and to explicitly model the non-linear relationship between the discrete phenotype and genetic determinants, or to force their relationship to be linear. The first approach is desirable theoretically, but explicitly modeling the sophisticated genetic architecture of a complex disease can be prohibitively complex and computational demand is high. The second approach, typically a linear regression, relies on a large sample theory and is not appropriate. In this paper, we propose to apply Analysis of Variance (ANOVA) to sib pair linkage analysis of complex human diseases. This approach has avoided building the complicated relationship between the phenotype (the affection group or status of a sib pair) and the underlying genetic determinant (identical-by-decent (IBD) values etc). We have explored its statistical efficiency and properties in sibpair linkage analysis of ordinal complex human diseases via simulation. The simulation suggests that it is a powerful approach for locating genes that presumably control phenotypic expression of complex human diseases.
文摘The prediction of the fracture plane orientation in fatigue is a scientific topic and remains relevant for every type of material. However, in this work, we compared the orientation of the fracture plane obtained experimentally through tests on specimens under multiaxial loading with that calculated by the variance method. In the statistical approach criteria, several methods have been developed but we have presented only one method, namely the variance method using the equivalent stress. She assumes that the fracture plane orientation is the one on which the variance of the equivalent stress is maximum. Three types of equivalent stress are defined for this method [1]: normal stress, shear stress and combined normal and shear stress. The results obtained were compared with experimental results for multiaxial cyclic stress states, and it emerges that the variance method for the case of combined loading is conservative as it gives a better prediction of the fracture plane.
文摘Working toward an efficient duration and timeline for the preconstruction phase should be one of the main objectives for project owners.Failing to plan for and coordinate preconstruction decisions in order to control preconstruction duration and manage time variances can lead to financial insecurities,incomplete contract documents,permitting issues,and unrealistic schedules and resource allocation during this phase.To minimize time variances and ensure a productive decision-making process,project owners should be familiar with critical elements in a project that cause variances in the preconstruction phase timeline.In this study,the impacts of eleven critical preconstruction elements on time variances were analyzed.These eleven preconstruction elements are considered critical in how they impact time variances during the preconstruction phase.They were determined to be critical based either on significantly impacting time variance during the preconstruction phase or believed to be critical from findings from previous studies,however,the findings from this study showed no significant impact on the time variances.In most previous studies focusing on the elements impacting project schedules,data were collected by surveying construction professionals.In this study,objective and quantitative data related to project preconstruction elements were used as opposed to self-reported data.Using the results of this study,project owners and stakeholders will be able to evaluate the critical preconstruction elements impacting the timing of their projects and prioritize decisions related to the critical elements early on during the preconstruction phase.
基金supported by the Ministry of Education,Singapore,under its Academic Research Fund Tier 2 Grant MOE-T2EP20222-0003.
文摘The valuation of financial derivatives often assumes risk neutrality with respect to the risk-neutral martingale measure,which prevents arbitrage opportunities.However,casual traders may still incur substantial losses when trading at this risk-neutral price,especially when the price has to be paid now and the payoff is only realized in the future.This study proposes a new valuation framework that provides risksensitive investors with an additional safeguard.The proposed framework embraces a worst-case perspective while exploiting the underlier’s stochastic process,representing a combination of robust optimization and stochastic programming.Notably,it aims to mitigate losses in the likelier scenarios of the underlying asset’s prices.When the underlier’s returns are independent and lognormally but not necessarily identically distributed,our approach for pricing variance and volatility swaps could be greatly simplified,benefit from parallel computing,and be solved by a two-dimensional grid search.We further derive a closed-form solution in some special stationary cases and provide experimental results to highlight the effect of risk aversion on fending off sizable trading losses.
基金supported by the National Natural Science Foundation of China(No.42174011)。
文摘In the variance component estimation(VCE)of geodetic data,the problem of negative VCE is likely to occur.In the ordinary additive error model,there have been related studies to solve the problem of negative variance components.However,there is still no related research in the mixed additive and multiplicative random error model(MAMREM).Based on the MAMREM,this paper applies the nonnegative least squares variance component estimation(NNLS-VCE)algorithm to this model.The correlation formula and iterative algorithm of NNLS-VCE for MAMREM are derived.The problem of negative variance in VCE for MAMREM is solved.This paper uses the digital simulation example and the Digital Terrain Mode(DTM)to prove the proposed algorithm's validity.The experimental results demonstrated that the proposed algorithm can effectively correct the VCE in MAMREM when there is a negative VCE.
