bioRxiv2025
Recent critiques of the reliability of deep learning (DL) for taphonomic analysis of bone surface modifications (BSM), such as that presented by Courtenay et al. (2024) based on a selection of earlier published studies, have raised concerns about the efficacy of the method. Their critique, however, overlooked fundamental principles regarding the use of small and unbalanced datasets in DL. By reducing the size of the training and validation sets--resulting in a training set only 20% larger than the testing set, and some class validation sets that were under 10 images--these authors may inadvertently have generated underfit models in their attempt to replicate and test the original studies. Moreover, errors in coding during the preprocessing of images have resulted in the development of fundamentally biased models, which fail to effectively evaluate and replicate the reliability of the original studies. In this study, we do not aim to directly refute their critique, but instead use it as an opportunity to reassess the efficiency and resolution of DL in taphonomic research. We revisited the original DL models applied to three targeted datasets, by replicating them as new baseline models for comparison against optimized models designed to address potential biases. Specifically, we accounted for issues stemming from poor-quality image datasets and possible overfitting on validation sets. To ensure the robustness of our findings, we implemented additional methods, including enhanced image data augmentation, k-fold cross-validation of the original training-validation sets, and a few-shot learning approach using model-agnostic meta-learning (MAML). The latter method facilitated the unbiased use of separate training, validation, and testing sets. The results across all approaches were consistent, with comparable--if not almost identical--outcomes to the original baseline models. As a final validation step, we used images of recently generated BSM to act as testing sets with the baseline models. The results also remained virtually invariant. This reinforces the conclusion that the original models were not subject to methodological overfitting and highlights their nuanced efficacy in differentiating BSM. However, it is important to recognize that these models represent pilot studies, constrained by the limitations of the original datasets in terms of image quality and sample size. Future work leveraging larger datasets with higher-quality images has the potential to enhance model generalization, thereby improving the applicability and reliability of deep learning approaches in taphonomic research.