Linear Prediction Method Research Articles

Genomic evaluation of Brown Swiss dairy cattle with limited national genotype data and integrated external information

This study demonstrated the feasibility of a genomic evaluation for the dairy cattle population for which the small national training population can be complemented with foreign information from international evaluations. National test-day milk yield data records for the Slovenian Brown Swiss cattle population were analyzed. Genomic evaluation was carried out using the single-step genomic best linear unbiased prediction method (ssGBLUP), resulting in genomic estimated breeding values (GEBV). The predominantly female group of genotyped animals, representing the national training population in the single-step genomic evaluation, was further augmented with 7,024 genotypes of foreign progeny-tested sires from an international Brown Swiss InterGenomics genomic evaluation (https://interbull.org/ib/whole_cop). Additionally, the estimated breeding values for the altogether 7,246 genotyped domestic and foreign sires from the 2019 sire multiple across-country evaluation(MACE), were added to the ssGBLUP as external pseudophenotypic information. The ssGBLUP method, with integration of MACE information by avoiding double counting, was then performed, resulting in MACE-enhanced GEBV (GEBVM). The methods were empirically validated with forward prediction. The validation group consisted of 315 domestic males and 1,041 domestic females born after 2012. Increase, inflation, and bias of the GEBV(M) reliability (REL) were assessed for the validation group with a focus on females. All individuals in the validation benefited from genomic evaluations using both methods, but the GEBV(M) REL increased most for the youngest selection candidates. Up to 35 points of GEBV REL could be assigned to national genomic information, and up to 17 points of GEBVM REL could additionally be attributed to the integration of foreign sire genomic and MACE information. Results indicated that the combined foreign progeny-tested sire genomic and external MACE information can be used in the single-step genomic evaluation as an equivalent replacement for domestic phenotypic information. Thus, an equal or slightly higher genomic breeding value REL was obtained sooner than the pedigree-based breeding value REL for the female selection candidates. When the abundant foreign progeny-tested sire genomic and MACE information was used to complement available national genomic and phenotypic information in single-step genomic evaluation, the genomic breeding value REL for young-female selection candidates increased approximately 10 points. Use of international information provides the possibility to upgrade small national training populations and obtain satisfying reliability of genomic breeding values even for the youngest female selection candidates, which will help to increase selection efficiency in the future.

Genome-Wide Marker Analysis for Traits of Economic Importance in Asian Seabass Lates calcarifer

To date, it is not known whether animal breeding values in Asian seabass (Lates calcarifer) can be estimated using single nucleotide polymorphisms (SNPs) generated from new high-throughput genotyping by sequencing platforms. The principal aim of the present study was to assess the genomic prediction accuracy for growth traits, survival, cannibalism, and disease resistance against Streptococcus iniae in this species L. calcarifer. Additionally, this study attempted to identify markers associated with the five traits studied as well as to understand if the genotype data can be used to estimate genetic parameters for these complex traits. The genomic best linear unbiased prediction (gBLUP) method was used to analyze 11,084 SNPs and showed that the prediction accuracies for growth traits (weight and length) were high (0.67–0.75). By contrast, these estimates for survival were low (0.25). Multi-locus mixed model analyses identified four SNPs significantly associated with body weight (p < 5 × 10−8 or −log10 p ≥ 5). There were, however, no significant associations detected for other traits. Similarly, the SNP heritability was moderate, while the estimates for other traits were approximated to zero and not significant. Genetic correlations between body weight and standard length were close to unity. Collectively, the results obtained from this study suggest that genotyping by sequencing platforms can provide informative DNA markers to conduct genome-wide association analysis, estimation of genetic parameters, and evaluation of genomic prediction accuracy for complex traits in Asian seabass.

Genomic Analysis, Progress and Future Perspectives in Dairy Cattle Selection: A Review.

Simple SummaryThe discovery of the genome has been one of the greatest advances in the development of tools for the genetic improvement of cattle in the last decades. The use of information derived from genomics has been demonstrated to be an efficient alternative for the validation of kinship, adjusted mating, and conservation strategies to generate dairy cattle with desirable traits. However, the impact of the genetic improvement strategies in breeding programs has closed bloodlines in several milk breeds, consequently generating inbreeding depression. Thus, to mitigate the negative effects of inbreeding, several tools associated with genomic analysis are currently available that may be useful to reverse undesirable genetic trends. The present review will provide an understanding of the importance of genomic analysis and how it can be used to mitigate the negative effects of inbreeding depression on different traits related to production, reproduction, health, animal welfare, linear type traits, and adaptability in dairy cattle. A historical overview of genomics and future perspectives will also be covered.Genomics comprises a set of current and valuable technologies implemented as selection tools in dairy cattle commercial breeding programs. The intensive progeny testing for production and reproductive traits based on genomic breeding values (GEBVs) has been crucial to increasing dairy cattle productivity. The knowledge of key genes and haplotypes, including their regulation mechanisms, as markers for productivity traits, may improve the strategies on the present and future for dairy cattle selection. Genome-wide association studies (GWAS) such as quantitative trait loci (QTL), single nucleotide polymorphisms (SNPs), or single-step genomic best linear unbiased prediction (ssGBLUP) methods have already been included in global dairy programs for the estimation of marker-assisted selection-derived effects. The increase in genetic progress based on genomic predicting accuracy has also contributed to the understanding of genetic effects in dairy cattle offspring. However, the crossing within inbred-lines critically increased homozygosis with accumulated negative effects of inbreeding like a decline in reproductive performance. Thus, inaccurate-biased estimations based on empirical-conventional models of dairy production systems face an increased risk of providing suboptimal results derived from errors in the selection of candidates of high genetic merit-based just on low-heritability phenotypic traits. This extends the generation intervals and increases costs due to the significant reduction of genetic gains. The remarkable progress of genomic prediction increases the accurate selection of superior candidates. The scope of the present review is to summarize and discuss the advances and challenges of genomic tools for dairy cattle selection for optimizing breeding programs and controlling negative inbreeding depression effects on productivity and consequently, achieving economic-effective advances in food production efficiency. Particular attention is given to the potential genomic selection-derived results to facilitate precision management on modern dairy farms, including an overview of novel genome editing methodologies as perspectives toward the future.

Towards link inference attack against network structure perturbation

The increasing popularity and diversity of social media sites have resulted in an emergent number of available social networks. These social networks are now the source of information for third-party consumers, such as researchers and advertisers, to understand user social activities. In a privacy-preserving viewpoint, a full assessment of social relationships between individuals may violate privacy. Different network structure perturbation methods have been proposed to limit the disclosure of sensitive user data. However, despite the proliferation of these methods, currently, there are no robustness studies on the methods for link prediction-based hidden inference structure. In this study, we survey the state-of-the-art network structure perturbation methods for privacy-preservation and the classic link prediction methods for structure inference. To restore the perturbed network structure effectively, we propose a novel Multi-Layer Linear Coding-based link prediction method (MLLC) with a closed-form solution. Furthermore, we provide vulnerability analysis on network structure perturbation methods in the context of link prediction-based structure inference. We also compare the methods on the preservation of utility metrics for social network analysis, where a structure perturbation method is preferred if the metrics of the perturbed network are similar to those of the original network. Our experimental study indicates that the MLLC algorithm outperforms conventional methods for hidden structure inference, and that it is important to provide robustness to network structure perturbation methods against these attacks.

Genomic Prediction Using Alternative Strategies of Weighted Single-Step Genomic BLUP for Yearling Weight and Carcass Traits in Hanwoo Beef Cattle.

The weighted single-step genomic best linear unbiased prediction (GBLUP) method has been proposed to exploit information from genotyped and non-genotyped relatives, allowing the use of weights for single-nucleotide polymorphism in the construction of the genomic relationship matrix. The purpose of this study was to investigate the accuracy of genetic prediction using the following single-trait best linear unbiased prediction methods in Hanwoo beef cattle: pedigree-based (PBLUP), un-weighted (ssGBLUP), and weighted (WssGBLUP) single-step genomic methods. We also assessed the impact of alternative single and window weighting methods according to their effects on the traits of interest. The data was comprised of 15,796 phenotypic records for yearling weight (YW) and 5622 records for carcass traits (backfat thickness: BFT, carcass weight: CW, eye muscle area: EMA, and marbling score: MS). Also, the genotypic data included 6616 animals for YW and 5134 for carcass traits on the 43,950 single-nucleotide polymorphisms. The ssGBLUP showed significant improvement in genomic prediction accuracy for carcass traits (71%) and yearling weight (99%) compared to the pedigree-based method. The window weighting procedures performed better than single SNP weighting for CW (11%), EMA (11%), MS (3%), and YW (6%), whereas no gain in accuracy was observed for BFT. Besides, the improvement in accuracy between window WssGBLUP and the un-weighted method was low for BFT and MS, while for CW, EMA, and YW resulted in a gain of 22%, 15%, and 20%, respectively, which indicates the presence of relevant quantitative trait loci for these traits. These findings indicate that WssGBLUP is an appropriate method for traits with a large quantitative trait loci effect.

Performance of genome prediction for morphological and growth-related traits in Yellow River carp

Common Carp (Cyprinus carpio) is the earliest truly domesticated fish, and genetic improvement of its economic traits is important for satisfying human protein demand.However, very little is known about the performance of Genomic selection (GS) in common carp by used SNP array data. Here we estimated the genetic parameters and evaluated the performance of GS for 24 morphological and growth-related traits in Yellow River carp. The result showed that the heritability of these traits ranged from medium to high. The predictive ability of most traits based on family cross-validation was higher than that of random cross-validation. Compared with best linear unbiased prediction (BLUP) method, genomic BLUP (GBLUP) method has more advantage on predictive ability of low heritability traits, with a maximum increase ratio of 37.5%. Gene annotation information is not helpful to improving predictive ability, but GBLUP based on haplotype information obtained highest accuracy on 6 of 24 traits, and compared with GBLUP, the average ratio of prediction abilities increased by 2%. This study shows that it is necessary to assess the effect of family structure on reference group construction before calculated the breeding value. In additon, biological information has a certain potential for improving prediction ability. Low density array genotyping, as a kind of method can decrease the cost of genotyping and facilitate the implementation of genomic selection in aquatic breeding.

Bias Not Linear Prediction Method The Best for Small Area on Empirical Suspect Spending Per Capita (Case: South Sulawesi Province District Gowa)

Indirect estimation is the estimation of parameters that use additional information about the same parameters in a small area. The combination of the basic assumption of random effects and fixed effects forms a mixed influence model. In this study, the data used are secondary data from the SUSENAS and Regression methods. The value of Average Root Mean Square Error (ARSME) estimator in the EBLUP estimator is smaller when compared to the direct estimator and simple linear regression. So it can be said that the EBLUP estimator is better than the direct estimator of per household at the District level in Gowa Regency based on SUSENAS data for 2017.

Prediction Accuracies of Genomic Selection for Nine Commercially Important Traits in the Portuguese Oyster (Crassostrea angulata) Using DArT-Seq Technology.

Genomic selection has been widely used in terrestrial animals but has had limited application in aquaculture due to relatively high genotyping costs. Genomic information has an important role in improving the prediction accuracy of breeding values, especially for traits that are difficult or expensive to measure. The purposes of this study were to (i) further evaluate the use of genomic information to improve prediction accuracies of breeding values from, (ii) compare different prediction methods (BayesA, BayesCπ and GBLUP) on prediction accuracies in our field data, and (iii) investigate the effects of different SNP marker densities on prediction accuracies of traits in the Portuguese oyster (Crassostrea angulata). The traits studied are all of economic importance and included morphometric traits (shell length, shell width, shell depth, shell weight), edibility traits (tenderness, taste, moisture content), and disease traits (Polydora sp. and Marteilioides chungmuensis). A total of 18,849 single nucleotide polymorphisms were obtained from genotyping by sequencing and used to estimate genetic parameters (heritability and genetic correlation) and the prediction accuracy of genomic selection for these traits. Multi-locus mixed model analysis indicated high estimates of heritability for edibility traits; 0.44 for moisture content, 0.59 for taste, and 0.72 for tenderness. The morphometric traits, shell length, shell width, shell depth and shell weight had estimated genomic heritabilities ranging from 0.28 to 0.55. The genomic heritabilities were relatively low for the disease related traits: Polydora sp. prevalence (0.11) and M. chungmuensis (0.10). Genomic correlations between whole weight and other morphometric traits were from moderate to high and positive (0.58–0.90). However, unfavourably positive genomic correlations were observed between whole weight and the disease traits (0.35–0.37). The genomic best linear unbiased prediction method (GBLUP) showed slightly higher accuracy for the traits studied (0.240–0.794) compared with both BayesA and BayesCπ methods but these differences were not significant. In addition, there is a large potential for using low-density SNP markers for genomic selection in this population at a number of 3000 SNPs. Therefore, there is the prospect to improve morphometric, edibility and disease related traits using genomic information in this species.

Protecting surface and buried structures from tunnelling using pile walls: a prediction model

When tunnelling poses excessive risks for buildings and buried foundations, a pile row barrier may shield the existing structure from ground movements. This paper presents a three-dimensional linear elastic prediction method to evaluate the protective action of pile walls against surface and subsurface ground movements due to new tunnels, both directly behind the wall as well as within the entire ground. Analyses are carried out to evaluate the vertical and horizontal movements of the ground and the pile wall as the result of soil–pile row interaction. New factors that quantify the wall efficiency in reducing settlements and deflections behind the wall are proposed; the results indicate that the effectiveness of the pile wall at reducing horizontal displacements is limited. Subsequently, predictions are compared against field and numerical data to demonstrate that the elastic solution is applicable, particularly for small ground losses. Finally, the barrier efficiency in reducing settlements is discussed comparing pile walls and diaphragm walls.

An Improved Rainflow Algorithm Combined with Linear Criterion for the Accurate Li-ion Battery Residual Life Prediction

Li-ion battery health assessment has been widely used in electric vehicles, unmanned aerial vehicle and other fields. In this paper, a new linear prediction method is proposed. By weakening the sensitivity of the Rainflow algorithm to the peak data, it can be applied to the field of battery, and can accurately count the number of Li-ion battery cycles, and skip the cumbersome link of parameter identification. Then, a linear criterion is proposed based on the idea of proportion, which makes the life prediction of Li-ion battery linear. Under the verification of multiple sets of data, the prediction error of this method is kept within 2.53%. This method has the advantages of high operation efficiency and simple operation, which provides a new idea for battery life prediction in the field of electric vehicles and aerospace.

Cobalt crust recognition based on kernel Fisher discriminant analysis and genetic algorithm in reverberation environment

Recognition of substrates in cobalt crust mining areas can improve mining efficiency. Aiming at the problem of unsatisfactory performance of using single feature to recognize the seabed material of the cobalt crust mining area, a method based on multiple-feature sets is proposed. Features of the target echoes are extracted by linear prediction method and wavelet analysis methods, and the linear prediction coefficient and linear prediction cepstrum coefficient are also extracted. Meanwhile, the characteristic matrices of modulus maxima, sub-band energy and multi-resolution singular spectrum entropy are obtained, respectively. The resulting features are subsequently compressed by kernel Fisher discriminant analysis (KFDA), the output features are selected using genetic algorithm (GA) to obtain optimal feature subsets, and recognition results of classifier are chosen as genetic fitness function. The advantages of this method are that it can describe the signal features more comprehensively and select the favorable features and remove the redundant features to the greatest extent. The experimental results show the better performance of the proposed method in comparison with only using KFDA or GA.

A genome-wide association study (GWAS) for pH value in the meat of Berkshire pigs.

The purpose of this study is to estimate the single nucleotide polymorphism (SNP) effect for pH values affecting Berkshire meat quality. A total of 39,603 SNPs from 1,978 heads after quality control and 882 pH values were used estimate SNP effect by single step genomic best linear unbiased prediction (ssGBLUP) method. The average physical distance between adjacent SNP pairs was 61.7kbp and the number and proportion of SNPs whose minor allele frequency was below 10% were 9,573 and 24.2%, respectively. The average of observed heterozygosity and polymorphic information content was 0.32 ± 0.16 and 0.26 ± 0.11, respectively and the estimate for average linkage disequilibrium was 0.40. The heritability of pH45m and pH24h were 0.10 and 0.15 respectively. SNPs with an absolute value more than 4 standard deviations from the mean were selected as threshold markers, among the selected SNPs, protein-coding genes of pH45m and pH24h were detected in 6 and 4 SNPs, respectively. The distribution of coding genes <RFX8, CREG2, TBC1D8, EXOC6B> were detected at pH45m and <C12orf49, LOC106506010, BICC1, ANK3> were detected at pH24h.

Using Formants to Extract Short Vowels from Arabic Words with (Consonant Vowel)&amp;lt;sup&amp;gt;3&amp;lt;/sup&amp;gt; Structure

Arabic texts suffer from missing short vowels. Arabic Speech Recognition is not as good as English speech recognition due to the short vowels not being recognized. And the Arabic language is unlike the English language in characteristics such as the number of vowels. English has more than 24 vowels that are close to each other in pronunciation. The Arabic language only has three short vowels that are far from each other in utter and measurement, by elongating those short vowels, long vowels arose. Researchers said that the vowels could be recognized using formants. The formants’ measurements of Arabic vowels are far from each other too, so it is possible to recognize them so that Arabic Speech recognition can give more accurate results. The paper applies this idea to the corpus Phonemes of Arabic. It uses the Euclidian distance method to measure the distances between formant values to recognize Arabic from words with a CV3 structure, the Linear Predictive Coding method and MATLAB to develop the programs that will extract the formants and calculate the means of the short vowels by using the corpus to identify the short vowels within words in the corpus. The results showed that if highly qualified readers were chosen to read the Arabic text, then higher rates of recognition of the short vowels involved in words will be achieved. This paper revealed that some of the characteristics of a language can be utilized for vowel recognition or to enhance the existing methods for speech recognition.

Predicting dissolved organic carbon concentration in a dynamic salt marsh creek via machine learning

AbstractDissolved organic carbon (DOC) is a master variable in aquatic systems. Resolving DOC dynamics requires high‐temporal resolution data. However, DOC concentration cannot be directly measured in situ, and discrete sample collection and analysis becomes expensive as temporal resolution increases. To surmount this problem, an option is to predict site‐specific DOC concentration with linear modeling and optical data predictors collected from high‐cost, high‐maintenance in situ spectrophotometers. This study sought to improve upon the accuracy and field costs of linear predictive DOC methods by using machine learning modeling coupled to low‐to‐zero cost predictors. To do this, we collected 16 months of in situ data (e.g., spectrophotometer attenuation, salinity, temperature), assembled freely available predictors (e.g., point in year, rainfall), and collected samples for DOC analysis, all in a salt marsh creek. At seasonal timescales, machine learning (coefficient of determination [R2] = 0.90) modestly improved upon the accuracy of linear methods (R2 = 0.80) but offered substantial instrumentation cost reductions (~ 90%) by requiring only cost‐free predictors (online data) or cost‐free predictors paired with low‐cost in situ predictors (temperature, salinity, depth). At intertidal timescales, linear methods proved ill‐equipped to predict DOC concentration compared to machine learning, and again, machine learning offered a substantial instrumentation cost reduction (~ 90%). Although our models were developed for and applicable to a single site, the use of machine learning with low‐to‐zero cost predictors provides a blueprint for others trying to model DOC dynamics and other analytes in any complex aquatic system.

Genome-enabled prediction of meat and carcass traits using Bayesian regression, single-step genomic best linear unbiased prediction and blending methods in Nelore cattle

Several methods have been used for genome-enabled prediction (or genomic selection) of complex traits, for example, multiple regression models describing a target trait with a linear function of a set of genetic markers. Genomic selection studies have been focused mostly on single-trait analyses. However, most profitability traits are genetically correlated, and an increase in prediction accuracy of genomic breeding values for genetically correlated traits is expected when using multiple-trait models. Thus, this study was carried out to assess the accuracy of genomic prediction for carcass and meat quality traits in Nelore cattle, using single- and multiple-trait approaches. The study considered 15 780, 15 784, 15 742 and 526 records of rib eye area (REA, cm2), back fat thickness (BF, mm), rump fat (RF, mm) and Warner–Bratzler shear force (WBSF, kg), respectively, in Nelore cattle, from the Nelore Brazil Breeding Program. Animals were genotyped with a low-density single nucleotide polymorphism (SNP) panel and subsequently imputed to arrays with 54 and 777 k SNPs. Four Bayesian specifications of genomic regression models, namely, Bayes A, Bayes B, Bayes Cπ and Bayesian Ridge Regression; blending methods, BLUP; and single-step genomic best linear unbiased prediction (ssGBLUP) methods were compared in terms of prediction accuracy using a fivefold cross-validation. Estimates of heritability ranged from 0.20 to 0.35 and from 0.21 to 0.46 for RF and WBSF on single- and multiple-trait analyses, respectively. Prediction accuracies for REA, BF, RF and WBSF were all similar using the different specifications of regression models. In addition, this study has shown the impact of genomic information upon genetic evaluations in beef cattle using the multiple-trait model, which was also advantageous compared to the single-trait model because it accounted for the selection process using multiple traits at the same time. The advantage of multi-trait analyses is attributed to the consideration of correlations and genetic influences between the traits, in addition to the non-random association of alleles.

Improving the accuracy of genomic evaluation for linear body measurement traits using single-step genomic best linear unbiased prediction in Hanwoo beef cattle

BackgroundRecently, there has been a growing interest in the genetic improvement of body measurement traits in farm animals. They are widely used as predictors of performance, longevity, and production traits, and it is worthwhile to investigate the prediction accuracies of genomic selection for these traits. In genomic prediction, the single-step genomic best linear unbiased prediction (ssGBLUP) method allows the inclusion of information from genotyped and non-genotyped relatives in the analysis. Hence, we aimed to compare the prediction accuracy obtained from a pedigree-based BLUP only on genotyped animals (PBLUP-G), a traditional pedigree-based BLUP (PBLUP), a genomic BLUP (GBLUP), and a single-step genomic BLUP (ssGBLUP) method for the following 10 body measurement traits at yearling age of Hanwoo cattle: body height (BH), body length (BL), chest depth (CD), chest girth (CG), chest width (CW), hip height (HH), hip width (HW), rump length (RL), rump width (RW), and thurl width (TW). The data set comprised 13,067 phenotypic records for body measurement traits and 1523 genotyped animals with 34,460 single-nucleotide polymorphisms. The accuracy for each trait and model was estimated only for genotyped animals using five-fold cross-validations.ResultsThe accuracies ranged from 0.02 to 0.19, 0.22 to 0.42, 0.21 to 0.44, and from 0.36 to 0.55 as assessed using the PBLUP-G, PBLUP, GBLUP, and ssGBLUP methods, respectively. The average predictive accuracies across traits were 0.13 for PBLUP-G, 0.34 for PBLUP, 0.33 for GBLUP, and 0.45 for ssGBLUP methods. Our results demonstrated that averaged across all traits, ssGBLUP outperformed PBLUP and GBLUP by 33 and 43%, respectively, in terms of prediction accuracy. Moreover, the least root of mean square error was obtained by ssGBLUP method.ConclusionsOur findings suggest that considering the ssGBLUP model may be a promising way to ensure acceptable accuracy of predictions for body measurement traits, especially for improving the prediction accuracy of selection candidates in ongoing Hanwoo breeding programs.

9 A comparison of different genomic prediction methods in the Canadian Landrace swine population

Abstract Increasing the accuracy of breeding value prediction can lead to more profitability through accelerating genetic progress for economic traits. The objective of this study was to assess the predictive abilities and unbiasedness of best linear unbiased prediction (BLUP) and popular genomic prediction methods of BayesC, BayesC(π = 0.99), genomic BLUP (GBLUP), and single-step GBLUP (ssGBLUP). Genotypic information (50K and 60K) of 4,890 performance tested Landrace pigs before February 2019 and 471 validation Landrace pigs that both had phenotypic information on backfat thickness (BFT), average daily gain (ADG), and loin muscle depth (LMD) from two Canadian pig breeding companies (AlphaGene and Alliance Genetics Canada) were used. The de-regressed breeding values (DEBV) were employed in GBLUP and Bayesian methods. A total number of 48,580 single nucleotide polymorphisms remained after quality control and imputation steps. The prediction accuracies were calculated using the correlation between predicted breeding values before performance test and DEBVs after performance test. All employed genomic prediction methods showed higher prediction accuracies for BFT (50.80–52.68%), ADG (26.61–34.47%), and LMD (18.25–25.08%) compared to BLUP method (BFT = 28.54%, ADG = 16.41%, LMD = 17.15%). The highest prediction accuracies for BFT and ADG were obtained using ssGBLUP method, and for LMD it was obtained using BayesC(π = 0.99). The BayesC(π = 0.99) showed also the lowest prediction biases across the studied traits (+0.05 for BFT, 0.00 for AGD, and -0.10 for LMD). In conclusion, our results revealed the superiority of ssGBLUP (for BFT and ADG) and BayesC(π = 0.99) (for LMD) over other tested methods in this study. However, the prediction accuracies from the tested genomic prediction methods were not significantly different from each other. Thus, employing these methods can be helpful for accelerating the genetic improvement of BFT, ADG, and LMD in the moderate population size of Canadian Landrace.

A simple, cost-effective high-throughput image analysis pipeline improves genomic prediction accuracy for days to maturity in wheat

BackgroundHigh-throughput phenotyping and genomic selection accelerate genetic gain in breeding programs by advances in phenotyping and genotyping methods. This study developed a simple, cost-effective high-throughput image analysis pipeline to quantify digital images taken in a panel of 286 Iran bread wheat accessions under terminal drought stress and well-watered conditions. The color proportion of green to yellow (tolerance ratio) and the color proportion of yellow to green (stress ratio) was assessed for each canopy using the pipeline. The estimated tolerance and stress ratios were used as covariates in the genomic prediction models to evaluate the effect of change in canopy color on the improvement of the genomic prediction accuracy of different agronomic traits in wheat.ResultsThe reliability of the high-throughput image analysis pipeline was proved by three to four times of improvement in the accuracy of genomic predictions for days to maturity with the use of tolerance and stress ratios as covariates in the univariate genomic selection models. The higher prediction accuracies were attained for days to maturity when both tolerance and stress ratios were used as fixed effects in the univariate models. The results of this study indicated that the Bayesian ridge regression and ridge regression-best linear unbiased prediction methods were superior to other genomic prediction methods which were used in this study under terminal drought stress and well-watered conditions, respectively.ConclusionsThis study provided a robust, quick, and cost-effective machine learning-enabled image-phenotyping pipeline to improve the genomic prediction accuracy for days to maturity in wheat. The results encouraged the integration of phenomics and genomics in breeding programs.

Toward a Reinforcement Learning Environment Toolbox for Intelligent Electric Motor Control.

Electric motors are used in many applications, and their efficiency is strongly dependent on their control. Among others, linear feedback approaches or model predictive control methods are well known in the scientific literature and industrial practice. A novel approach is to use reinforcement learning (RL) to have an agent learn electric drive control from scratch merely by interacting with a suitable control environment. RL achieved remarkable results with superhuman performance in many games (e.g., Atari classics or Go) and also becomes more popular in control tasks, such as cart-pole or swinging pendulum benchmarks. In this work, the open-source Python package gym-electric-motor (GEM) is developed for ease of training of RL-agents for electric motor control. Furthermore, this package can be used to compare the trained agents with other state-of-the-art control approaches. It is based on the OpenAI Gym framework that provides a widely used interface for the evaluation of RL-agents. The package covers different dc and three-phase motor variants, as well as different power electronic converters and mechanical load models. Due to the modular setup of the proposed toolbox, additional motor, load, and power electronic devices can be easily extended in the future. Furthermore, different secondary effects, such as converter interlocking time or noise, are considered. An intelligent controller example based on the deep deterministic policy gradient algorithm that controls a series dc motor is presented and compared to a cascaded proportional-integral controller as a baseline for future research. Here, safety requirements are particularly highlighted as an important constraint for data-driven control algorithms applied to electric energy systems. Fellow researchers are encouraged to use the GEM framework in their RL investigations or contribute to the functional scope (e.g., further motor types) of the package.

Speech Recognition Using Elman Artificial Neural Network and Linear Predictive Coding

Background: Today, the automatic intelligent system requirement has caused an increasing consideration on the interactive modern techniques between human being and machine. These techniques generally consist of two types: audio and visual methods. Meanwhile, the need for developing the algorithms that enable the human speech recognition by machine is of high importance and frequently studied by the researchers. Objective: Using artificial intelligence methods has led to better results in human speech recognition, but the basic problem is the lack of an appropriate strategy to select the recognition data among the huge amount of speech information that practically makes it impossible for the available algorithms to work. Method: In this article, to solve the problem, the linear predictive coding coefficients extraction method is used to sum up the data related to the English digits pronunciation. After extracting the database, it is utilized to an Elman neural network to recognize the relation between the linear coding coefficients of an audio file with the pronounced digit. Results: The results show that this method has a good performance compared to other methods. According to the experiments, the obtained results of network training (99% recognition accuracy) indicate that the network still has better performance than RBF despite many errors. Conclusion: The results of the experiments showed that the Elman memory neural network has had an acceptable performance in recognizing the speech signal compared to the other algorithms. The use of the linear predictive coding coefficients along with the Elman neural network has led to higher recognition accuracy and improved the speech recognition system.