The marmoset, a highly vocal primate, is a key model for studying social-communicative behavior. Unlike human speech, marmoset vocalizations are less structured, highly variable, and recorded in noisy, low-resource conditions. Learning marmoset communication requires joint call segmentation, classification, and caller identification -- challenging domain tasks. Previous CNNs handle local patterns but struggle with long-range temporal structure. We applied Transformers using self-attention for global dependencies. However, Transformers show overfitting and instability on small, noisy annotated datasets. To address this, we pretrain Transformers with MAE -- a self-supervised method reconstructing masked segments from hundreds of hours of unannotated marmoset recordings. The pretraining improved stability and generalization. Results show MAE-pretrained Transformers outperform CNNs, demonstrating modern self-supervised architectures effectively model low-resource non-human vocal communication.