Reply to Pastore, E.P. Comment on “Korkmaz et al. A Deep Learning and Explainable AI-Based Approach for the Classification of Discomycetes Species. Biology 2025, 14, 719”

The comment raises three principal themes: (i) safeguarding statistical independence through grouping at the level of specimen/collector/site prior to splitting, (ii) preventing selection bias via fully nested preprocessing and hyperparameter tuning, and (iii) assessing shortcut learning and reporting probability calibration for decision thresholding in ecological workflows [...].