Future direct-imaging flagship missions, such as NASA's Habitable Worlds Observatory (HWO), face critical decisions in prioritizing observations due to extremely stringent time and resource constraints. In this paper, we introduce two advanced machine-learning architectures tailored for predicting biosignature species fluxes from exoplanetary reflected-light spectra: a Bayesian Convolutional Neural Network (BCNN) and our novel model architecture, the Spectral Query Adaptive Transformer (SQuAT). The BCNN robustly quantifies both epistemic and aleatoric uncertainties, offering reliable predictions under diverse observational conditions, whereas SQuAT employs query-driven attention mechanisms to enhance interpretability by explicitly associating spectral features with specific biosignature species. We demonstrate that both models achieve comparably high predictive accuracy on an augmented dataset spanning a wide range of exoplanetary conditions, while highlighting their distinct advantages in uncertainty quantification and spectral interpretability. These capabilities position our methods as promising tools for accelerating target triage, optimizing observation schedules, and maximizing scientific return for upcoming flagship missions such as HWO.