Hierarchical Acoustic Encoding Distress in Pigs: Disentangling Individual, Developmental, and Emotional Effects with Subject-Wise Validation

Automated pig-welfare monitoring needs scalable, non-invasive signals that work across ages and individuals. A key methodological contribution of this study is the use of subject-wise validation, which ensures generalization to unseen animals and prevents inflated accuracy caused by growth-related and individual ‘voice’ differences. Vocalizations can help, but growth and individual “voice” differences can confound distress patterns and overstate accuracy without subject-wise validation. In our study, we explicitly accounted for individual variability by including animal identity as a random effect in mixed models and by using grouped cross-validation, where models were tested only on pigs not seen during training. This approach ensures that the reported accuracy reflects generalization across different individuals rather than memorization of specific vocal signatures. We analyzed 2221 vocal samples from 40 pigs (20 males, 20 females) recorded across four growth phases (farrowing, nursery, growing, finishing) under six conditions (pain, hunger, thirst, cold stress, heat stress, normal). Acoustic features extracted in Praat included energy, duration, intensity, pitch, and formants (F1–F4). Using blockwise variance decomposition, we quantified contributions of distress exposure, growth phase, and sex, and estimated the additional variance explained by animal identity. Distress exposure dominated intensity and spectral traits, particularly Formant 2, whereas the growth phase produced systematic shifts in duration and pitch. Animal identity added a modest but consistent increment in explained variance (~+0.02–0.03 R2 beyond sex, phase, and distress). For prediction, we used 5-fold cross-validation grouped by animal. A Random Forest achieved a modest balanced accuracy of 0.609 and macro-F1 of 0.597; pain was most separable (recall 0.825), while other states showed moderate recall, indicating overlap. These results support hierarchical acoustic encoding of distress and establish a benchmark for precision welfare monitoring. Furthermore, they highlight that resolving complex physiological overlaps, such as heat stress and resource competition, requires a shift from unimodal acoustic models to multimodal Precision Livestock Farming (PLF) systems that integrate bioacoustics with continuous environmental and behavioral data streams.