scholarly journals Variety Discrimination Power: An Appraisal Index for Loci Combination Screening Applied to Plant Variety Discrimination

2021 ◽  
Vol 12 ◽  
Author(s):  
Yang Yang ◽  
Hongli Tian ◽  
Rui Wang ◽  
Lu Wang ◽  
Hongmei Yi ◽  
...  
Keyword(s):  
Molecular Marker ◽  
Simulated Data ◽  
Real Data ◽  
Total Probability ◽  
Discrimination Power ◽  
Plant Variety ◽  
Appraisal Index ◽  
Two Phases ◽  
Threshold Setting ◽  
The Cost

Molecular marker technology is used widely in plant variety discrimination, molecular breeding, and other fields. To lower the cost of testing and improve the efficiency of data analysis, molecular marker screening is very important. Screening usually involves two phases: the first to control loci quality and the second to reduce loci quantity. To reduce loci quantity, an appraisal index that is very sensitive to a specific scenario is necessary to select loci combinations. In this study, we focused on loci combination screening for plant variety discrimination. A loci combination appraisal index, variety discrimination power (VDP), is proposed, and three statistical methods, probability-based VDP (P-VDP), comparison-based VDP (C-VDP), and ratio-based VDP (R-VDP), are described and compared. The results using the simulated data showed that VDP was sensitive to statistical populations with convergence toward the same variety, and the total probability of discrimination power (TDP) method was effective only for partial populations. R-VDP was more sensitive to statistical populations with convergence toward various varieties than P-VDP and C-VDP, which both had the same sensitivity; TDP was not sensitive at all. With the real data, R-VDP values for sorghum, wheat, maize and rice data begin to show downward tendency when the number of loci is 20, 7, 100, 100 respectively, while in the case of P-VDP and C-VDP (which have the same results), the number is 6, 4, 9, 19 respectively and in the case of TDP, the number is 6, 4, 4, 11 respectively. For the variety threshold setting, R-VDP values of loci combinations with different numbers of loci responded evenly to different thresholds. C-VDP values responded unevenly to different thresholds, and the extent of the response increased as the number of loci decreased. All the methods gave underestimations when data were missing, with systematic errors for TDP, C-VDP, and R-VDP going from smallest to biggest. We concluded that VDP was a better loci combination appraisal index than TDP for plant variety discrimination and the three VDP methods have different applications. We developed the software called VDPtools, which can calculate the values of TDP, P-VDP, C-VDP, and R-VDP. VDPtools is publicly available athttps://github.com/caurwx1/VDPtools.git.

Accuracy of genomic prediction using mixed low-density marker panels

2020 ◽  
Vol 60 (8) ◽  
pp. 999
Author(s):  
Lianjie Hou ◽  
Wenshuai Liang ◽  
Guli Xu ◽  
Bo Huang ◽  
Xiquan Zhang ◽  
...  
Keyword(s):  
Genomic Selection ◽  
Imputation Accuracy ◽  
Simulated Data ◽  
Real Data ◽  
Substantial Effect ◽  
Low Density ◽  
Snp Panel ◽  
Snp Panels ◽  
The Cost ◽  
Better Than

Low-density single-nucleotide polymorphism (LD-SNP) panel is one effective way to reduce the cost of genomic selection in animal breeding. The present study proposes a new type of LD-SNP panel called mixed low-density (MLD) panel, which considers SNPs with a substantial effect estimated by Bayes method B (BayesB) from many traits and evenly spaced distribution simultaneously. Simulated and real data were used to compare the imputation accuracy and genomic-selection accuracy of two types of LD-SNP panels. The result of genotyping imputation for simulated data showed that the number of quantitative trait loci (QTL) had limited influence on the imputation accuracy only for MLD panels. Evenly spaced (ELD) panel was not affected by QTL. For real data, ELD performed slightly better than did MLD when panel contained 500 and 1000 SNP. However, this advantage vanished quickly as the density increased. The result of genomic selection for simulated data using BayesB showed that MLD performed much better than did ELD when QTL was 100. For real data, MLD also outperformed ELD in growth and carcass traits when using BayesB. In conclusion, the MLD strategy is superior to ELD in genomic selection under most situations.

scholarly journals AdImpute: An Imputation Method for Single-Cell RNA-Seq Data Based on Semi-Supervised Autoencoders

2021 ◽  
Vol 12 ◽  
Author(s):  
Li Xu ◽  
Yin Xu ◽  
Tong Xue ◽  
Xinyu Zhang ◽  
Jin Li
Keyword(s):  
Single Cell ◽  
Missing Values ◽  
Simulated Data ◽  
Real Data ◽  
Imputation Method ◽  
Data Sets ◽  
Silent Genes ◽  
Downstream Analysis ◽  
The Cost ◽  
Simulated Data Sets

Motivation: The emergence of single-cell RNA sequencing (scRNA-seq) technology has paved the way for measuring RNA levels at single-cell resolution to study precise biological functions. However, the presence of a large number of missing values in its data will affect downstream analysis. This paper presents AdImpute: an imputation method based on semi-supervised autoencoders. The method uses another imputation method (DrImpute is used as an example) to fill the results as imputation weights of the autoencoder, and applies the cost function with imputation weights to learn the latent information in the data to achieve more accurate imputation.Results: As shown in clustering experiments with the simulated data sets and the real data sets, AdImpute is more accurate than other four publicly available scRNA-seq imputation methods, and minimally modifies the biologically silent genes. Overall, AdImpute is an accurate and robust imputation method.

Pareto Set as a Model for Dispatching Resources in Emergency Centres (Preprint)

2018 ◽  
Author(s):  
Ricardo Guedes ◽  
Vasco Furtado ◽  
Tarcísio Pequeno ◽  
Joel Rodrigues
Keyword(s):  
Operational Research ◽  
Real Data ◽  
Pareto Set ◽  
Multi Objective Optimization ◽  
Pareto Dominance ◽  
Four Dimensions ◽  
Multi Objective ◽  
The Best Approximation ◽  
One Year ◽  
The Cost

UNSTRUCTURED The article investigates policies for helping emergency-centre authorities for dispatching resources aimed at reducing goals such as response time, the number of unattended calls, the attending of priority calls, and the cost of displacement of vehicles. Pareto Set is shown to be the appropriated way to support the representation of policies of dispatch since it naturally fits the challenges of multi-objective optimization. By means of the concept of Pareto dominance a set with objectives may be ordered in a way that guides the dispatch of resources. Instead of manually trying to identify the best dispatching strategy, a multi-objective evolutionary algorithm coupled with an Emergency Call Simulator uncovers automatically the best approximation of the optimal Pareto Set that would be the responsible for indicating the importance of each objective and consequently the order of attendance of the calls. The scenario of validation is a big metropolis in Brazil using one-year of real data from 911 calls. Comparisons with traditional policies proposed in the literature are done as well as other innovative policies inspired from different domains as computer science and operational research. The results show that strategy of ranking the calls from a Pareto Set discovered by the evolutionary method is a good option because it has the second best (lowest) waiting time, serves almost 100% of priority calls, is the second most economical, and is the second in attendance of calls. That is to say, it is a strategy in which the four dimensions are considered without major impairment to any of them.

scholarly journals Separation of Chromatographic Co-Eluted Compounds by Clustering and by Functional Data Analysis

Metabolites ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 214
Author(s):  
Aneta Sawikowska ◽  
Anna Piasecka ◽  
Piotr Kachlicki ◽  
Paweł Krajewski
Keyword(s):  
Simulated Data ◽  
Principal Component ◽  
Real Data ◽  
Functional Principal Component Analysis ◽  
Additional Advantage ◽  
Time Alignment ◽  
Peak Separation ◽  
Biological Mixtures ◽  
Overlapping Peaks ◽  
Retention Time Alignment

Peak overlapping is a common problem in chromatography, mainly in the case of complex biological mixtures, i.e., metabolites. Due to the existence of the phenomenon of co-elution of different compounds with similar chromatographic properties, peak separation becomes challenging. In this paper, two computational methods of separating peaks, applied, for the first time, to large chromatographic datasets, are described, compared, and experimentally validated. The methods lead from raw observations to data that can form inputs for statistical analysis. First, in both methods, data are normalized by the mass of sample, the baseline is removed, retention time alignment is conducted, and detection of peaks is performed. Then, in the first method, clustering is used to separate overlapping peaks, whereas in the second method, functional principal component analysis (FPCA) is applied for the same purpose. Simulated data and experimental results are used as examples to present both methods and to compare them. Real data were obtained in a study of metabolomic changes in barley (Hordeum vulgare) leaves under drought stress. The results suggest that both methods are suitable for separation of overlapping peaks, but the additional advantage of the FPCA is the possibility to assess the variability of individual compounds present within the same peaks of different chromatograms.

scholarly journals A Closed-Form Solution to Planar Feature-Based Registration of LiDAR Point Clouds

2021 ◽  
Vol 10 (7) ◽  
pp. 435
Author(s):  
Yongbo Wang ◽  
Nanshan Zheng ◽  
Zhengfu Bian
Keyword(s):  
Closed Form ◽  
Closed Form Solution ◽  
Simulated Data ◽  
Real Data ◽  
Point Clouds ◽  
Form Solution ◽  
Spatial Transformation ◽  
Dual Quaternions ◽  
Feature Based ◽  
Planar Feature

Since pairwise registration is a necessary step for the seamless fusion of point clouds from neighboring stations, a closed-form solution to planar feature-based registration of LiDAR (Light Detection and Ranging) point clouds is proposed in this paper. Based on the Plücker coordinate-based representation of linear features in three-dimensional space, a quad tuple-based representation of planar features is introduced, which makes it possible to directly determine the difference between any two planar features. Dual quaternions are employed to represent spatial transformation and operations between dual quaternions and the quad tuple-based representation of planar features are given, with which an error norm is constructed. Based on L2-norm-minimization, detailed derivations of the proposed solution are explained step by step. Two experiments were designed in which simulated data and real data were both used to verify the correctness and the feasibility of the proposed solution. With the simulated data, the calculated registration results were consistent with the pre-established parameters, which verifies the correctness of the presented solution. With the real data, the calculated registration results were consistent with the results calculated by iterative methods. Conclusions can be drawn from the two experiments: (1) The proposed solution does not require any initial estimates of the unknown parameters in advance, which assures the stability and robustness of the solution; (2) Using dual quaternions to represent spatial transformation greatly reduces the additional constraints in the estimation process.

scholarly journals ALPINE: Active Link Prediction Using Network Embedding

2021 ◽  
Vol 11 (11) ◽  
pp. 5043
Author(s):  
Xi Chen ◽  
Bo Kang ◽  
Jefrey Lijffijt ◽  
Tijl De Bie
Keyword(s):  
Active Learning ◽  
Protein Interactions ◽  
Link Prediction ◽  
Prediction Accuracy ◽  
Real Data ◽  
Network Embedding ◽  
Protein Protein Interactions ◽  
Additional Information ◽  
The Cost ◽  
Active Link

Many real-world problems can be formalized as predicting links in a partially observed network. Examples include Facebook friendship suggestions, the prediction of protein–protein interactions, and the identification of hidden relationships in a crime network. Several link prediction algorithms, notably those recently introduced using network embedding, are capable of doing this by just relying on the observed part of the network. Often, whether two nodes are linked can be queried, albeit at a substantial cost (e.g., by questionnaires, wet lab experiments, or undercover work). Such additional information can improve the link prediction accuracy, but owing to the cost, the queries must be made with due consideration. Thus, we argue that an active learning approach is of great potential interest and developed ALPINE (Active Link Prediction usIng Network Embedding), a framework that identifies the most useful link status by estimating the improvement in link prediction accuracy to be gained by querying it. We proposed several query strategies for use in combination with ALPINE, inspired by the optimal experimental design and active learning literature. Experimental results on real data not only showed that ALPINE was scalable and boosted link prediction accuracy with far fewer queries, but also shed light on the relative merits of the strategies, providing actionable guidance for practitioners.

scholarly journals Penalized partial least squares for pleiotropy

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Camilo Broc ◽  
Therese Truong ◽  
Benoit Liquet
Keyword(s):  
Least Squares ◽  
Partial Least Squares ◽  
Association Studies ◽  
A Priori ◽  
Simulated Data ◽  
Real Data ◽  
Genome Wide Association Studies ◽  
Genetic Associations ◽  
Multiple Traits ◽  
Application Fields

Abstract Background The increasing number of genome-wide association studies (GWAS) has revealed several loci that are associated to multiple distinct phenotypes, suggesting the existence of pleiotropic effects. Highlighting these cross-phenotype genetic associations could help to identify and understand common biological mechanisms underlying some diseases. Common approaches test the association between genetic variants and multiple traits at the SNP level. In this paper, we propose a novel gene- and a pathway-level approach in the case where several independent GWAS on independent traits are available. The method is based on a generalization of the sparse group Partial Least Squares (sgPLS) to take into account groups of variables, and a Lasso penalization that links all independent data sets. This method, called joint-sgPLS, is able to convincingly detect signal at the variable level and at the group level. Results Our method has the advantage to propose a global readable model while coping with the architecture of data. It can outperform traditional methods and provides a wider insight in terms of a priori information. We compared the performance of the proposed method to other benchmark methods on simulated data and gave an example of application on real data with the aim to highlight common susceptibility variants to breast and thyroid cancers. Conclusion The joint-sgPLS shows interesting properties for detecting a signal. As an extension of the PLS, the method is suited for data with a large number of variables. The choice of Lasso penalization copes with architectures of groups of variables and observations sets. Furthermore, although the method has been applied to a genetic study, its formulation is adapted to any data with high number of variables and an exposed a priori architecture in other application fields.

scholarly journals Calibration of Camera and Flash LiDAR System with a Triangular Pyramid Target

2021 ◽  
Vol 11 (2) ◽  
pp. 582
Author(s):  
Zean Bu ◽  
Changku Sun ◽  
Peng Wang ◽  
Hang Dong
Keyword(s):  
Simulated Data ◽  
Real Data ◽  
Calibration Method ◽  
Multiple Sensors ◽  
Triangular Pyramid ◽  
World Coordinate System ◽  
Flash Lidar ◽  
Novel Method ◽  
3D Information ◽  
Incremental Validation

Calibration between multiple sensors is a fundamental procedure for data fusion. To address the problems of large errors and tedious operation, we present a novel method to conduct the calibration between light detection and ranging (LiDAR) and camera. We invent a calibration target, which is an arbitrary triangular pyramid with three chessboard patterns on its three planes. The target contains both 3D information and 2D information, which can be utilized to obtain intrinsic parameters of the camera and extrinsic parameters of the system. In the proposed method, the world coordinate system is established through the triangular pyramid. We extract the equations of triangular pyramid planes to find the relative transformation between two sensors. One capture of camera and LiDAR is sufficient for calibration, and errors are reduced by minimizing the distance between points and planes. Furthermore, the accuracy can be increased by more captures. We carried out experiments on simulated data with varying degrees of noise and numbers of frames. Finally, the calibration results were verified by real data through incremental validation and analyzing the root mean square error (RMSE), demonstrating that our calibration method is robust and provides state-of-the-art performance.

scholarly journals Prediction of Fuel Poverty Potential Risk Index Using Six Regression Algorithms: A Case-Study of Chilean Social Dwellings

2021 ◽  
Vol 13 (5) ◽  
pp. 2426
Author(s):  
David Bienvenido-Huertas ◽  
Jesús A. Pulido-Arcas ◽  
Carlos Rubio-Bellido ◽  
Alexis Pérez-Fargallo
Keyword(s):  
Low Income ◽  
Potential Risk ◽  
Energy Use ◽  
Risk Index ◽  
Computing Time ◽  
Simulated Data ◽  
Real Data ◽  
Support Vector ◽  
Energy Poverty ◽  
Regression Algorithms

In recent times, studies about the accuracy of algorithms to predict different aspects of energy use in the building sector have flourished, being energy poverty one of the issues that has received considerable critical attention. Previous studies in this field have characterized it using different indicators, but they have failed to develop instruments to predict the risk of low-income households falling into energy poverty. This research explores the way in which six regression algorithms can accurately forecast the risk of energy poverty by means of the fuel poverty potential risk index. Using data from the national survey of socioeconomic conditions of Chilean households and generating data for different typologies of social dwellings (e.g., form ratio or roof surface area), this study simulated 38,880 cases and compared the accuracy of six algorithms. Multilayer perceptron, M5P and support vector regression delivered the best accuracy, with correlation coefficients over 99.5%. In terms of computing time, M5P outperforms the rest. Although these results suggest that energy poverty can be accurately predicted using simulated data, it remains necessary to test the algorithms against real data. These results can be useful in devising policies to tackle energy poverty in advance.

scholarly journals Constructing Large-Scale Genetic Maps Using an Evolutionary Strategy Algorithm

Genetics ◽  
2003 ◽  
Vol 165 (4) ◽  
pp. 2269-2282
Author(s):  
D Mester ◽  
Y Ronin ◽  
D Minkov ◽  
E Nevo ◽  
A Korol
Keyword(s):  
Discrete Optimization ◽  
High Performance ◽  
Large Scale ◽  
Simulated Data ◽  
Real Data ◽  
Genetic Maps ◽  
Chromosome 1 ◽  
Evolutionary Strategy ◽  
Group A ◽  
The One

Abstract This article is devoted to the problem of ordering in linkage groups with many dozens or even hundreds of markers. The ordering problem belongs to the field of discrete optimization on a set of all possible orders, amounting to n!/2 for n loci; hence it is considered an NP-hard problem. Several authors attempted to employ the methods developed in the well-known traveling salesman problem (TSP) for multilocus ordering, using the assumption that for a set of linked loci the true order will be the one that minimizes the total length of the linkage group. A novel, fast, and reliable algorithm developed for the TSP and based on evolution-strategy discrete optimization was applied in this study for multilocus ordering on the basis of pairwise recombination frequencies. The quality of derived maps under various complications (dominant vs. codominant markers, marker misclassification, negative and positive interference, and missing data) was analyzed using simulated data with ∼50-400 markers. High performance of the employed algorithm allows systematic treatment of the problem of verification of the obtained multilocus orders on the basis of computing-intensive bootstrap and/or jackknife approaches for detecting and removing questionable marker scores, thereby stabilizing the resulting maps. Parallel calculation technology can easily be adopted for further acceleration of the proposed algorithm. Real data analysis (on maize chromosome 1 with 230 markers) is provided to illustrate the proposed methodology.

Sign in / Sign up

Export Citation Format

Share Document