Energy expenditure estimation aims to infer human metabolic rate from physiological signals such as heart rate, respiration, or accelerometer data, and has been studied primarily with classical regression methods. The few existing deep learning approaches rarely disentangle the role of neural architecture from that of signal choice. In this work, we systematically evaluate both aspects. We compare classical baselines with newer neural architectures across single signals, signal pairs, and grouped sensor inputs for diverse physical activities. Our results show that minute ventilation is the most predictive individual signal, with a transformer model achieving the lowest root mean square error (RMSE) of 0.87 W/kg across all activities. Paired and grouped signals, such as those from the Hexoskin smart shirt (five signals), offer good alternatives for faster models like CNN and ResNet with attention. Per-activity evaluation revealed mixed outcomes: notably better results in low-intensity activities (RMSE down to 0.29 W/kg; NRMSE = 0.04), while higher-intensity tasks showed larger RMSE but more comparable normalized errors. Finally, subject-level analysis highlights strong inter-individual variability, motivating the need for adaptive modeling strategies. Our code and models will be publicly available at https://github.com/Sarvibabakhani/deeplearning-biosignals-ee .