Predicting dry matter intake in Canadian Holstein dairy cattle using milk mid-infrared reflectance spectroscopy and other commonly available predictors via artificial neural networks

Authors: SHADPOUR, SAEED - University Of Guelph; CHUD, TATIANE - University Of Guelph; HAILEMARIAM, DAGNACHEW - University Of Alberta; DE OLIVEIRA, HINAYAH - Collaborator; PLASTOW, GRAHAM - University Of Alberta; STOTHARD, PAUL - University Of Alberta; LASSEN, JAN - Aarhus University; Baldwin, Ransom - Randy; MIGLIOR, FILIPPO - University Of Guelph; BAES, CHRISTINE - University Of Guelph; TULPAN, DAN - University Of Guelph; SCHENKEL, FLAVIO - University Of Guelph

Submitted to: Journal of Dairy Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/31/2022
Publication Date: 10/1/2022
Citation: Shadpour, S., Chud, T.C., Hailemariam, D., De Oliveira, H.R., Plastow, G., Stothard, P., Lassen, J., Baldwin, R.L., Miglior, F., Baes, C.F., Tulpan, D., Schenkel, F.S. 2022. Predicting dry matter intake in Canadian Holstein dairy cattle using milk mid-infrared reflectance spectroscopy and other commonly available predictors via artificial neural networks. Journal of Dairy Science. 105(10):8257–8271. https://doi.org/10.3168/jds.2021-21297.
DOI: https://doi.org/10.3168/jds.2021-21297

Interpretive Summary: Dry matter intake (DMI) is a fundamental component of the animal's feed efficiency, but measuring DMI of individual cows is expensive. Mid-infrared reflectance spectroscopy (MIRS) on milk samples could be an inexpensive alternative to predict DMI. We asked if milk MIRS data could improve DMI predictions of Canadian Holstein cows using artificial neural networks (ANN) and if various ANN architectures could accurately predict DMI. Finally, we sought to validate the robustness of these models. A total of 7,398 milk samples from 509 dairy cows distributed over Canada, Denmark, and the United States were analyzed. Using statistical approaches to assess different models it was determined that MIRS in association with milk production traits might be limited and needs further investigation. The better predictive ability of nonlinear ANN compared with linear ANN and partial least squares regression indicated possible nonlinear relationships between weekly average DMI and the predictor variables. Some models identified showed more promise than others.

Technical Abstract: Dry matter intake (DMI) is a fundamental component of the animal's feed efficiency, but measuring DMI of individual cows is expensive. Mid-infrared reflectance spectroscopy (MIRS) on milk samples could be an inexpensive alternative to predict DMI. The objectives of this study were (1) to assess if milk MIRS data could improve DMI predictions of Canadian Holstein cows using artificial neural networks (ANN); (2) to investigate the ability of different ANN architectures to predict unobserved DMI; and (3) to validate the robustness of developed prediction models. A total of 7,398 milk samples from 509 dairy cows distributed over Canada, Denmark, and the United States were analyzed. Data from Denmark and the United States were used to increase the training data size and variability to improve the generalization of the prediction models over the lactation. For each milk spectra record, the corresponding weekly average DMI (kg/d), test-day milk yield (MY, kg/d), fat yield (FY, g/d), and protein yield (PY, g/d), metabolic body weight (MBW), age at calving, year of calving, season of calving, days in milk, lactation number, country, and herd were available. The weekly average DMI was predicted with various ANN architectures using 7 predictor sets, which were created by different combinations MY, FY, PY, MBW, and MIRS data. All predictor sets also included age of calving and days in milk. In addition, the classification effects of season of calving, country, and lactation number were included in all models. The explored ANN architectures consisted of 3 training algorithms (Bayesian regularization, Levenberg-Marquardt, and scaled conjugate gradient), 2 types of activation functions (hyperbolic tangent and linear), and from 1 to 10 neurons in hidden layers). In addition, partial least squares regression was also applied to predict the DMI. Models were compared using cross-validation based on leaving out 10% of records (validation A) and leaving out 10% of cows (validation B). Superior fitting statistics of models comprising MIRS information compared with the models fitting milk, fat and protein yields suggest that other unknown milk components may help explain variation in weekly average DMI. For instance, using MY, FY, PY, and MBW as predictor variables produced a predictive accuracy (r) ranging from 0.510 to 0.652 across ANN models and validation sets. Using MIRS together with MY, FY, PY, and MBW as predictors resulted in improved fitting (r = 0.679–0.777). Including MIRS data improved the weekly average DMI prediction of Canadian Holstein cows, but it seems that MIRS predicts DMI mostly through its association with milk production traits and its utility to estimate a measure of feed efficiency that accounts for the level of production, such as residual feed intake, might be limited and needs further investigation. The better predictive ability of nonlinear ANN compared with linear ANN and partial least squares regression indicated possible nonlinear relationships between weekly average DMI and the predictor variables. In general, ANN using Bayesian regularization and scaled conjugate gradient training algorithms yielded slightly better weekly average DMI predictions compared with ANN using the Levenberg-Marquardt training algorithm.