flected the sizes of the embeddings rather than their types. This effect was observed due to feature importances being summed across the embedding dimensions, leading to higher PFIs for larger embeddings like those from ESM2 compared to smaller ones from AlphaFold2. Therefore, the type of the model behind the embeddings, as well as different data splits, had minimal impact on model outcomes, indicating that embedding size influenced the observed PFIs rather than any structural or sequential differences (Supp. Table ).