Infrared spectroscopy coupled with machine learning algorithms for predicting the detailed milk mineral profile in dairy cattle

Milk minerals are not only essential components for human health, but they can be informative for milk quality and cow's health. Herein, we investigated the feasibility of Fourier Transformed mid Infrared (FTIR) spectroscopy for the prediction of a detailed panel of 17 macro, trace, and environmental elements in bovine milk, using partial least squares regression (PLS) and machine learning approaches. The automatic machine learning significantly outperformed the PLS regression in terms of prediction performances of the mineral elements. For macrominerals, the R2 ranged from 0.59 to 0.78. Promising predictability was achieved for Cu and B (R2 = 0.66 and 0.74, respectively) and more moderate ones for Fe, Mn, Zn, and Al (R2 from 0.48 to 0.58). These results provide a reliable basis for a rapid and cost-effective quantification of these traits, serving as a resource for dairy farmers seeking to enhance the quality of milk production and optimize cheese properties.

Implementation of plant extracts for cheddar-type cheese production in conjunction with FTIR and Raman spectroscopy comparison

Plant extracts have demonstrated the ability to act as coagulants for milk coagulation at an adequate concentration, wide temperatures and pH ranges. This research is focused on the use of different vegetative extracts such as Citrus aurnatium flower extract (CAFE), bromelain, fig latex, and melon extract as economical and beneficial coagulants in the development of plant-based cheddar-type cheese. The cheddar-type cheese samples were subjected to physicochemical analysis in comparison to controlled cheese samples made from acetic acid and rennet. The fat, moisture, protein, and salt contents remained the same over the storage period, but a slight decline was observed in pH. The Ferric reducing antioxidant power (FRAP) increased with the passage of the ripening period. The FTIR and Raman spectra showed exponential changes and qualitative estimates in the binding and vibrational structure of lipids and protein in plant-based cheeses. The higher FTIR and Raman spectra bands were observed in acid, rennet, bromelain, and CAFE due to their firm and strong texture of cheese while lower spectra were observed in cheese made from melon extract due to weak curdling and textural properties. These plant extracts are economical and easily available alternative sources for cheese production with higher protein and nutritional contents.

Combining genetic markers, on-farm information and infrared data for the in-line prediction of blood biomarkers of metabolic disorders in Holstein cattle

BACKGROUND

Various blood metabolites are known to be useful indicators of health status in dairy cattle, but their routine assessment is time-consuming, expensive, and stressful for the cows at the herd level. Thus, we evaluated the effectiveness of combining in-line near infrared (NIR) milk spectra with on-farm (days in milk [DIM] and parity) and genetic markers for predicting blood metabolites in Holstein cattle. Data were obtained from 388 Holstein cows from a farm with an AfiLab system. NIR spectra, on-farm information, and single nucleotide polymorphisms (SNP) markers were blended to develop calibration equations for blood metabolites using the elastic net (ENet) approach, considering 3 models: (1) Model 1 (M1) including only NIR information, (2) Model 2 (M2) with both NIR and on-farm information, and (3) Model 3 (M3) combining NIR, on-farm and genomic information. Dimension reduction was considered for M3 by preselecting SNP markers from genome-wide association study (GWAS) results.

RESULTS

Results indicate that M2 improved the predictive ability by an average of 19% for energy-related metabolites (glucose, cholesterol, NEFA, BHB, urea, and creatinine), 20% for liver function/hepatic damage, 7% for inflammation/innate immunity, 24% for oxidative stress metabolites, and 23% for minerals compared to M1. Meanwhile, M3 further enhanced the predictive ability by 34% for energy-related metabolites, 32% for liver function/hepatic damage, 22% for inflammation/innate immunity, 42.1% for oxidative stress metabolites, and 41% for minerals, compared to M1. We found improved predictive ability of M3 using selected SNP markers from GWAS results using a threshold of > 2.0 by 5% for energy-related metabolites, 9% for liver function/hepatic damage, 8% for inflammation/innate immunity, 22% for oxidative stress metabolites, and 9% for minerals. Slight reductions were observed for phosphorus (2%), ferric-reducing antioxidant power (1%), and glucose (3%). Furthermore, it was found that prediction accuracies are influenced by using more restrictive thresholds (-log10(P-value) > 2.5 and 3.0), with a lower increase in the predictive ability.

CONCLUSION

Our results highlighted the potential of combining several sources of information, such as genetic markers, on-farm information, and in-line NIR infrared data improves the predictive ability of blood metabolites in dairy cattle, representing an effective strategy for large-scale in-line health monitoring in commercial herds.

Staging of Liver Fibrosis Based on Energy Valley Optimization Multiple Stacking (EVO-MS) Model

Currently, staging the degree of liver fibrosis predominantly relies on liver biopsy, a method fraught with potential risks, such as bleeding and infection. With the rapid development of medical imaging devices, quantification of liver fibrosis through image processing technology has become feasible. Stacking technology is one of the effective ensemble techniques for potential usage, but precise tuning to find the optimal configuration manually is challenging. Therefore, this paper proposes a novel EVO-MS model-a multiple stacking ensemble learning model optimized by the energy valley optimization (EVO) algorithm to select most informatic features for fibrosis quantification. Liver contours are profiled from 415 biopsied proven CT cases, from which 10 shape features are calculated and inputted into a Support Vector Machine (SVM) classifier to generate the accurate predictions, then the EVO algorithm is applied to find the optimal parameter combination to fuse six base models: K-Nearest Neighbors (KNNs), Decision Tree (DT), Naive Bayes (NB), Extreme Gradient Boosting (XGB), Gradient Boosting Decision Tree (GBDT), and Random Forest (RF), to create a well-performing ensemble model. Experimental results indicate that selecting 3-5 feature parameters yields satisfactory results in classification, with features such as the contour roundness non-uniformity (Rmax), maximum peak height of contour (Rp), and maximum valley depth of contour (Rm) significantly influencing classification accuracy. The improved EVO algorithm, combined with a multiple stacking model, achieves an accuracy of 0.864, a precision of 0.813, a sensitivity of 0.912, a specificity of 0.824, and an F1-score of 0.860, which demonstrates the effectiveness of our EVO-MS model in staging the degree of liver fibrosis.

Genomic prediction of blood biomarkers of metabolic disorders in Holstein cattle using parametric and nonparametric models

BACKGROUND

Metabolic disturbances adversely impact productive and reproductive performance of dairy cattle due to changes in endocrine status and immune function, which increase the risk of disease. This may occur in the post-partum phase, but also throughout lactation, with sub-clinical symptoms. Recently, increased attention has been directed towards improved health and resilience in dairy cattle, and genomic selection (GS) could be a helpful tool for selecting animals that are more resilient to metabolic disturbances throughout lactation. Hence, we evaluated the genomic prediction of serum biomarkers levels for metabolic distress in 1353 Holsteins genotyped with the 100K single nucleotide polymorphism (SNP) chip assay. The GS was evaluated using parametric models best linear unbiased prediction (GBLUP), Bayesian B (BayesB), elastic net (ENET), and nonparametric models, gradient boosting machine (GBM) and stacking ensemble (Stack), which combines ENET and GBM approaches.

RESULTS

The results show that the Stack approach outperformed other methods with a relative difference (RD), calculated as an increment in prediction accuracy, of approximately 18.0% compared to GBLUP, 12.6% compared to BayesB, 8.7% compared to ENET, and 4.4% compared to GBM. The highest RD in prediction accuracy between other models with respect to GBLUP was observed for haptoglobin (hapto) from 17.7% for BayesB to 41.2% for Stack; for Zn from 9.8% (BayesB) to 29.3% (Stack); for ceruloplasmin (CuCp) from 9.3% (BayesB) to 27.9% (Stack); for ferric reducing antioxidant power (FRAP) from 8.0% (BayesB) to 40.0% (Stack); and for total protein (PROTt) from 5.7% (BayesB) to 22.9% (Stack). Using a subset of top SNPs (1.5k) selected from the GBM approach improved the accuracy for GBLUP from 1.8 to 76.5%. However, for the other models reductions in prediction accuracy of 4.8% for ENET (average of 10 traits), 5.9% for GBM (average of 21 traits), and 6.6% for Stack (average of 16 traits) were observed.

CONCLUSIONS

Our results indicate that the Stack approach was more accurate in predicting metabolic disturbances than GBLUP, BayesB, ENET, and GBM and seemed to be competitive for predicting complex phenotypes with various degrees of mode of inheritance, i.e. additive and non-additive effects. Selecting markers based on GBM improved accuracy of GBLUP.

Prediction of detailed blood metabolic profile using milk infrared spectra and machine learning methods in dairy cattle

The adoption of preventive management decisions is crucial to dealing with metabolic impairments in dairy cattle. Various serum metabolites are known to be useful indicators of the health status of cows. In this study, we used milk Fourier-transform mid-infrared (FTIR) spectra and various machine learning (ML) algorithms to develop prediction equations for a panel of 29 blood metabolites, including those related to energy metabolism, liver function/hepatic damage, oxidative stress, inflammation/innate immunity, and minerals. For most traits, the data set comprised observations from 1,204 Holstein-Friesian dairy cows belonging to 5 herds. An exception was represented by β-hydroxybutyrate prediction, which contained observations from 2,701 multibreed cows pertaining to 33 herds. The best predictive model was developed using an automatic ML algorithm that tested various methods, including elastic net, distributed random forest, gradient boosting machine, artificial neural network, and stacking ensemble. These ML predictions were compared with partial least squares regression, the most commonly used method for FTIR prediction of blood traits. Performance of each model was evaluated using 2 cross-validation (CV) scenarios: 5-fold random (CV_r) and herd-out (CV_h). We also tested the best model's ability to classify values precisely in the 2 extreme tails, namely, the 25th (Q25) and 75th (Q75) percentiles (true-positive prediction scenario). Compared with partial least squares regression, ML algorithms achieved more accurate performance. Specifically, elastic net increased the R² value from 5% to 75% for CV_r and 2% to 139% for CV_h, whereas the stacking ensemble increased the R² value from 4% to 70% for CV_r and 4% to 150% for CV_h. Considering the best model, with the CV_r scenario, good prediction accuracies were obtained for glucose (R² = 0.81), urea (R² = 0.73), albumin (R² = 0.75), total reactive oxygen metabolites (R² = 0.79), total thiol groups (R² = 0.76), ceruloplasmin (R² = 0.74), total proteins (R² = 0.81), globulins (R² = 0.87), and Na (R² = 0.72). Good prediction accuracy in classifying extreme values was achieved for glucose (Q25 = 70.8%, Q75 = 69.9%), albumin (Q25 = 72.3%), total reactive oxygen metabolites (Q25 = 75.1%, Q75 = 74%), thiol groups (Q75 = 70.4%), total proteins (Q25 = 72.4%, Q75 = 77.2.%), globulins (Q25 = 74.8%, Q75 = 81.5%), and haptoglobin (Q75 = 74.4%). In conclusion, our study shows that FTIR spectra can be used to predict blood metabolites with relatively good accuracy, depending on trait, and are a promising tool for large-scale monitoring.

Integrating on-farm and genomic information improves the predictive ability of milk infrared prediction of blood indicators of metabolic disorders in dairy cows

BACKGROUND

Blood metabolic profiles can be used to assess metabolic disorders and to evaluate the health status of dairy cows. Given that these analyses are time-consuming, expensive, and stressful for the cows, there has been increased interest in Fourier transform infrared (FTIR) spectroscopy of milk samples as a rapid, cost-effective alternative for predicting metabolic disturbances. The integration of FTIR data with other layers of information such as genomic and on-farm data (days in milk (DIM) and parity) has been proposed to further enhance the predictive ability of statistical methods. Here, we developed a phenotype prediction approach for a panel of blood metabolites based on a combination of milk FTIR data, on-farm data, and genomic information recorded on 1150 Holstein cows, using BayesB and gradient boosting machine (GBM) models, with tenfold, batch-out and herd-out cross-validation (CV) scenarios.

RESULTS

The predictive ability of these approaches was measured by the coefficient of determination (R²). The results show that, compared to the model that includes only FTIR data, integration of both on-farm (DIM and parity) and genomic information with FTIR data improves the R² for blood metabolites across the three CV scenarios, especially with the herd-out CV: R² values ranged from 5.9 to 17.8% for BayesB, from 8.2 to 16.9% for GBM with the tenfold random CV, from 3.8 to 13.5% for BayesB and from 8.6 to 17.5% for GBM with the batch-out CV, and from 8.4 to 23.0% for BayesB and from 8.1 to 23.8% for GBM with the herd-out CV. Overall, with the model that includes the three sources of data, GBM was more accurate than BayesB with accuracies across the CV scenarios increasing by 7.1% for energy-related metabolites, 10.7% for liver function/hepatic damage, 9.6% for oxidative stress, 6.1% for inflammation/innate immunity, and 11.4% for mineral indicators.

CONCLUSIONS

Our results show that, compared to using only milk FTIR data, a model integrating milk FTIR spectra with on-farm and genomic information improves the prediction of blood metabolic traits in Holstein cattle and that GBM is more accurate in predicting blood metabolites than BayesB, especially for the batch-out CV and herd-out CV scenarios.

Hyperspectral technique combined with stacking and blending ensemble learning method for detection of cadmium content in oilseed rape leaves

BACKGROUND

Oilseed rape, as one of the most important oil crops, is an important source of vegetable oil and protein for mankind. As a non-essential element for plant growth, heavy metal cadmium (Cd) is easily absorbed by plants. Cd will inhibit the photosynthesis of plants, destroy the cell structure, slow the growth of plants, and affect their development and yield. It is necessary to develop a method based on visible near-infrared (NIR) hyperspectral imaging (HSI) technology to quickly and nondestructively determine the Cd content in rape leaves.

RESULTS

Two-layer estimation models were established by combining visible-NIR HSI with ensemble learning methods (stacking and blending). One layer used support vector regression, extreme learning machine, decision tree, and random forest (RF) as basic learners, and the other layer used support vector regression or RF as a meta learner. Different models were used to analyze the spectra of rape treated with five Cd concentrations to obtain the best prediction method. The results showed that the best model to predict Cd content was the stacking ensemble model with RF as the meta learner, with coefficient of determination for prediction of 0.9815 and root-mean-square error for prediction of 5.8969 mg kg^-1 . A pseudo-color image was developed using this stacking model to visualize the content and distribution of Cd.

CONCLUSION

The combination of visible-NIR HSI technology and the stacking ensemble learning method is a feasible method to detect the Cd content in rape leaves, which has the potential of being rapid and nondestructive. © 2022 Society of Chemical Industry.

Establishment and Validation of Fourier Transform Infrared Spectroscopy (FT–MIR) Methodology for the Detection of Linoleic Acid in Buffalo Milk

Buffalo milk is a dairy product that is considered to have a higher nutritional value compared to cow’s milk. Linoleic acid (LA) is an essential fatty acid that is important for human health. This study aimed to investigate and validate the use of Fourier transform mid-infrared spectroscopy (FT-MIR) for the quantification of the linoleic acid in buffalo milk. Three machine learning models were used to predict linoleic acid content, and random forest was employed to select the most important subset of spectra for improved model performance. The validity of the FT-MIR methods was evaluated in accordance with ICH Q2 (R1) guidelines using the accuracy profile method, and the precision, the accuracy, and the limit of quantification were determined. The results showed that Fourier transform infrared spectroscopy is a suitable technique for the analysis of linoleic acid, with a lower limit of quantification of 0.15 mg/mL milk. Our results showed that FT-MIR spectroscopy is a viable method for LA concentration analysis.

Predicting milk protein fractions using infrared spectroscopy and a gradient boosting machine for breeding purposes in Holstein cattle

In recent years, increasing attention has been focused on the genetic evaluation of protein fractions in cow milk with the aim of improving milk quality and technological characteristics. In this context, advances in high-throughput phenotyping by Fourier transform infrared (FTIR) spectroscopy offer the opportunity for large-scale, efficient measurement of novel traits that can be exploited in breeding programs as indicator traits. We took milk samples from 2,558 Holstein cows belonging to 38 herds in northern Italy, operating under different production systems. Fourier transform infrared spectra were collected on the same day as milk sampling and stored for subsequent analysis. Two sets of data (i.e., phenotypes and FTIR spectra) collected in 2 different years (2013 and 2019-2020) were compiled. The following traits were assessed using HPLC: true protein, major casein fractions [α_S1-casein (CN), α_S2-CN, β-CN, κ-CN, and glycosylated-κ-CN], and major whey proteins (β-lactoglobulin and α-lactalbumin), all of which were measured both in grams per liter (g/L) and proportion of total nitrogen (% N). The FTIR predictions were calculated using the gradient boosting machine technique and tested by 3 different cross-validation (CRV) methods. We used the following CRV scenarios: (1) random 10-fold, which randomly split the whole into 10-folds of equal size (9-folds for training and 1-fold for validation); (2) herd/date-out CRV, which assigned 80% of herd/date as the training set with independence of 20% of herd/date assigned as the validation set; (3) forward/backward CRV, which split the data set in training and validation set according with the year of milk sampling (FTIR and gold standard data assessed in 2013 or 2019-2020) using the "old" and "new" databases for training and validation, and vice-versa with independence among them; (4) the CRV for genetic parameters (CRV-gen), where animals without pedigree as assigned as a fixed training population and animals with pedigree information was split in 5-folds, in which 1-fold was assigned to the fixed training population, and 4-folds were assigned to the validation set (independent from the training set). The results (i.e., measures and predictions) of CRV-gen were used to infer the genetic parameters for gold standard laboratory measurements (i.e., proteins assessed with HPLC) and FTIR-based predictions considering the CRV-gen scenario from a bi-trait animal model using single-step genomic BLUP. We found that the prediction accuracies of the gradient boosting machine equations differed according to the way in which the proteins were expressed, achieving higher accuracy when expressed in g/L than when expressed as % N in all CRV scenarios. Concerning the reproducibility of the equations over the different years, the results showed no relevant differences in predictive ability between using "old" data as the training set and "new" data as the validation set and vice-versa. Comparing the additive genetic variance estimates for milk protein fractions between the FTIR predicted and HPLC measures, we found reductions of -19.7% for milk protein fractions expressed in g/L, and -21.19% expressed as % N. Although we found reductions in the heritability estimates, they were small, with values ranging from -1.9 to -7.25% for g/L, and -1.6 to -7.9% for % N. The posterior distributions of the additive genetic correlations (r_a) between the FTIR predictions and the laboratory measurements were generally high (>0.8), even when the milk protein fractions were expressed as % N. Our results show the potential of using FTIR predictions in breeding programs as indicator traits for the selection of animals to enhance milk protein fraction contents. We expect acceptable responses to selection due to the high genetic correlations between HPLC measurements and FTIR predictions.

Comparison of machine learning models for bluetongue risk prediction: a seroprevalence study on small ruminants

Background

Bluetongue (BT) is a disease of concern to animal breeders, so the question on their minds is whether they can predict the risk of the disease before it occurs. The main objective of this study is to enhance the accuracy of BT risk prediction by relying on machine learning (ML) approaches to help in fulfilling this inquiry. Several risk factors of BT that affect the occurrence and magnitude of animal infection with the virus have been reported globally. Additionally, risk factors, such as sex, age, species, and season, unevenly affect animal health and welfare. Therefore, the seroprevalence study data of 233 apparently healthy animals (125 sheep and 108 goats) from five different provinces in Egypt were used to analyze and compare the performance of the algorithms in predicting BT risk.

Results

Logistic regression (LR), decision tree (DT), random forest (RF), and a feedforward artificial neural network (ANN) were used to develop predictive BT risk models and compare their performance to the base model (LR). Model performance was assessed by the area under the receiver operating characteristics curve (AUC), accuracy, true positive rate (TPR), false positive rate (FPR), false negative rate (FNR), precision, and F1 score. The results indicated that RF performed better than other models, with an AUC score of 81%, ANN of 79.6%, and DT of 72.85%. In terms of performance and prediction, LR showed a much lower value (AUC = 69%). Upon further observation of the results, it was discovered that age and season were the most important predictor variables reported in classification and prediction.

Conclusion

The findings of this study can be utilized to predict and control BT risk factors in sheep and goats, with better diagnostic discrimination in terms of accuracy, TPR, FNR, FPR, and precision of ML models over traditional and commonly used LR models. Our findings advocate that the implementation of ML algorithms, mainly RF, in farm decision making and prediction is a promising technique for analyzing cross-section studies, providing adequate predictive power and significant competence in identifying and ranking predictors representing potential risk factors for BT.

In-line near-infrared analysis of milk coupled with machine learning methods for the daily prediction of blood metabolic profile in dairy cattle

Precision livestock farming technologies are used to monitor animal health and welfare parameters continuously and in real time in order to optimize nutrition and productivity and to detect health issues at an early stage. The possibility of predicting blood metabolites from milk samples obtained during routine milking by means of infrared spectroscopy has become increasingly attractive. We developed, for the first time, prediction equations for a set of blood metabolites using diverse machine learning methods and milk near-infrared spectra collected by the AfiLab instrument. Our dataset was obtained from 385 Holstein Friesian dairy cows. Stacking ensemble and multi-layer feedforward artificial neural network outperformed the other machine learning methods tested, with a reduction in the root mean square error of between 3 and 6% in most blood parameters. We obtained moderate correlations (r) between the observed and predicted phenotypes for γ-glutamyl transferase (r = 0.58), alkaline phosphatase (0.54), haptoglobin (0.66), globulins (0.61), total reactive oxygen metabolites (0.60) and thiol groups (0.57). The AfiLab instrument has strong potential but may not yet be ready to predict the metabolic stress of dairy cows in practice. Further research is needed to find out methods that allow an improvement in accuracy of prediction equations.