Mastitis detection with recurrent neural networks in farms using automated milking systems

Mastitis is the most important disease in the dairy industry. With widespread adoption of automated milking systems (AMS) in Canada, there is an increasing need for automated detection of mastitis in AMS farms. The main objective of this study was to develop a recurrent neural network (RNN) model for the detection of clinical mastitis (CM) in dairy cows on farms using AMS. Producer-recorded treatment records and AMS data were collected over 3 time periods from a total of 89 dairy farms in 7 provinces across Canada. In addition to developing effective models for the detection of CM, our study also evaluated different windows around the day of diagnosis when the cow would be considered CM-positive to guide practical implementation of models. We also compared numerous subsets of variables including milk and behavioural characteristics, cow traits and farmlevel/environmental variables to determine their importance and impact on model performance. Data were randomly divided into a training and a hold-out test set, consisting of all records from 66 and 23 farms, respectively. A 10-fold internal cross-validation was also employed on the training set for model development. When comparing different windows of time around diagnosis, considering animals as CM-positive for 3 d prior to recorded diagnosis resulted in the most timely and effective detection of CM with a per-case sensitivity of 89.8% (range: 83.3-96.0%), and per-day specificity of 84.3% (range: 83.4-85.8%) over the validation folds. These levels of sensitivity and specificity were achieved when using all recorded variables and their daily variances, although the inclusion of behavioural variables and farm-level/environmental variables provided marginal performance improvement over using milk traits alone. Performance of the model was worse on the hold-out test set with a per-case sensitivity of 83.5% (range: 77.9-86.3%) and a per-day specificity of 80.4 % (range: 78.1-82.4%), likely due to farm-specific heterogeneity not encountered in the training data. Over 90% of cases of severe CM (defined by an increase in milk temperature over the pre-CM baseline) were identified by the model, indicating effective performance for the detection of CM requiring the most immediate treatment. Somatic cell count, daily variance in milking interval and milk temperature were identified as the 3 most important variables defined by their impact on model predictions. In addition to milking traits, 8 of the top 20 variables were behavioural measurements, suggesting they can play a role in the detection of CM. Daily variances also represented 8 of the 20 most important variables indicating that CM onset may be associated with sudden, within-day changes in the animal. In conclusion, this study demonstrates that RNNs are able to effectively detect CM by integrating a number of variables that are regularly measured on AMS farms but have typically been excluded from CM detection models.