Numerous statistical machine learning methods suitable for application to highly correlated features, as those that exist for spectral data, could potentially improve prediction performance over the commonly used partial least squares approach. Milk samples from 622 individual cows with known detailed protein composition and technological trait data accompanied by mid-infrared spectra were available to assess the predictive ability of different regression and classification algorithms. The regression-based approaches were partial least squares regression (PLSR), ridge regression (RR), least absolute shrinkage and selection operator (LASSO), elastic net, principal component regression, projection pursuit regression, spike and slab regression, random forests, boosting decision trees, neural networks (NN), and a post-hoc approach of model averaging (MA). Several classification methods (i.e., partial least squares discriminant analysis (PLSDA), random forests, boosting decision trees, and support vector machines (SVM)) were also used after stratifying the traits of interest into categories. In the regression analyses, MA was the best prediction method for 6 of the 14 traits investigated [curd firmness at 60 min, α_S1-casein (CN), α_S2-CN, κ-CN, α-lactalbumin, and β-lactoglobulin B], whereas NN and RR were the best algorithms for 3 traits each (rennet coagulation time, curd-firming time, and heat stability, and curd firmness at 30 min, β-CN, and β-lactoglobulin A, respectively), PLSR was best for pH, and LASSO was best for CN micelle size. When traits were divided into 2 classes, SVM had the greatest accuracy for the majority of the traits investigated. Although the well-established PLSR-based method performed competitively, the application of statistical machine learning methods for regression analyses reduced the root mean square error compared with PLSR from between 0.18% (κ-CN) to 3.67% (heat stability). The use of modern statistical machine learning methods for trait prediction from mid-infrared spectroscopy may improve the prediction accuracy for some traits.

The prevalence of "grass-fed" labeled food products on the market has increased in recent years, often commanding a premium price. To date, the majority of methods used for the authentication of grass-fed source products are driven by auditing and inspection of farm records. As such, the ability to verify grass-fed source claims to ensure consumer confidence will be important in the future. Mid-infrared (MIR) spectroscopy is widely used in the dairy industry as a rapid method for the routine monitoring of individual herd milk composition and quality. Further harnessing the data from individual spectra offers a promising and readily implementable strategy to authenticate the milk source at both farm and processor levels. Herein, a comprehensive comparison of the robustness, specificity, and accuracy of 11 machine-learning statistical analysis methods were tested for the discrimination of grass-fed versus non-grass-fed milks based on the MIR spectra of 4,320 milk samples collected from cows on pasture or indoor total mixed ration-based feeding systems over a 3-yr period. Linear discriminant analysis and partial least squares discriminant analysis (PLS-DA) were demonstrated to offer the greatest level of accuracy for the prediction of cow diet from MIR spectra. Parsimonious strategies for the selection of the most discriminating wavelengths within the spectra are also highlighted.

Bovine milk fat contains ∼400 different fatty acids, with their relative concentration being highly variable and influenced by (or associated with) intrinsic and extrinsic factors such as diet, breed, and lactation stage. Using predicted fatty acids from milk mid-infrared spectra, the objectives of the present study were to (1) quantify the association between cow parity, lactation stage, breed, heterosis, and recombination loss with milk fatty acid composition, and (2) quantify the association between parental average genetic merit for both milk fat concentration and yield with a series of different fatty acids. The dataset used included 644,752 milk test-day records from 303,089 cows across 2,406 commercial dairy farms. The concentration of 17 individual fatty acids as well as 16 fatty acid indices were predicted from spectral analyses of milk samples. Factors associated with all the investigated traits were individually explored using linear mixed models. The fixed effects considered in all models were the interaction between parity and stage of lactation, the calendar month of test, breed composition, heterosis, and recombination; the random effects were contemporary group and a within-lactation repeated effect. In a separate series of analyses, cow genetic merit for fat yield and fat percentage were separately included in the model as linear covariates. The concentration of the different fatty acids changed throughout lactation and across calendar months, coinciding with the seasonal profile in pasture quality, especially during the summer months. Multiparous cows were characterized by milk with a higher concentration of saturated and short-chain fatty acids, along with a lower concentration of unsaturated, medium-chain, and long-chain fatty acids. Jersey bloodline was associated with a higher concentration of milk saturated and short-chain fatty acids, along with a lower concentration of unsaturated, medium-chain, and long-chain fatty acids compared with Holstein-Friesians. Genetic merit for fat yield or fat percentage was associated with a higher concentration of saturated fatty acids and a lower concentration of unsaturated fatty acids.

Directly measuring individual cow energy balance is not trivial. Other traits, like body condition score (BCS) and BCS change (ΔBCS) can, however, be used as an indicator of cow energy status. Body condition score is a metric used world-wide to estimate cow body reserves and the estimation of ΔBCS was, until now, conditional on the availability of multiple BCS assessments. The aim of the present study was to estimate ΔBCS from milk mid-infrared (MIR) spectra and days in milk (DIM) in intensively-fed dairy cows using statistical prediction methods. Daily BCS was interpolated from cubic splines fitted through the BCS records and daily ΔBCS was calculated from these splines. Body condition score change records were merged with milk MIR spectra recorded on the same week. The data set comprised 37,077 ΔBCS phenotypes across 9,403 lactations from 6,988 cows in 151 herds based in Quebec (Canada). Partial least squares regression (PLSR) and a neural network (NN) were then used to estimate ΔBCS from 1) MIR spectra only, 2) DIM only, or 3) MIR spectra and DIM together. ΔBCS data in both the first 120 DIM and 305 DIM of lactation were used to develop the estimates. Daily ΔBCS had a standard deviation of 4.40*10^-3 BCS units in the 120-d data set and of 3.63*10^-3 BCS units in the 305-d data set. 4-fold cross-validation was used to calibrate and test the prediction equations. External validation was also conducted using more recent years of data. Irrespective of whether based on the first 120 or 305 DIM, or when MIR spectra only, DIM only or MIR spectra and DIM were jointly used as prediction variables, NN produced the lowest root mean square error (RMSE) of cross-validation (1.81*10^-3 BCS units and 1.51*10^-3 BCS units, respectively, using the 120-d and 305-d data set). Relative to predictions for the entire 305 DIM, the RMSE of cross-validation was 15.4% and 1.5% lower in the first 120 DIM when using PLSR and NN, respectively. Predictions from DIM only were more accurate than those using just MIR spectra data but, irrespective of the data set and of the prediction model used, the combining DIM information with MIR spectral data as prediction variables reduced the RMSE compared with inclusion of DIM alone, albeit the benefit was small (the RMSE from cross-validation was reduced up to 5.5% when DIM and spectral data were jointly used as model features instead of DIM only). However, when predicting extreme ΔBCS records, the MIR spectral data was more informative than DIM. Model performance when predicting ΔBCS records in future years was similar to that from cross-validation demonstrating the ability of MIR spectra of milk and DIM combined to estimate ΔBCS, particularly in early lactation. This can be used to routinely generate estimates of ΔBCS to aid in day-to-day individual cow management.