Fig. 4: Results of the ablation experiments.
This figure displays the performance of PepNet under different ablation experiments in terms of accuracy (A), recall (B), precision (C), F1-score (D), and MCC (E) on the AMP and AIP test sets. In each figure, the letters A1–A4 represent feature ablation experiments of PepNet by using the amino acid type one-hot encoding, amino acid physicochemical properties, pre-trained features derived from the large protein language model, and the combination of them; B1–B5 represent the residual dilated convolution block ablation experiments of PepNet by removing the residual dilated convolution block, removing the residual connection operation within the block, and substituting the dilated convolution layer with Bi-LSTM, LSTM, and GRU layers, respectively, and B6 represents the residual dilated convolution block applied by PepNet; C1–C6 represent the residual Transformer block ablation experiments of PepNet by removing the residual dilated convolution block, removing the residual connection operation within the block, and with 1–4 Transformer layers in the block; D1 and D2 represent the maximum and average pooling strategies on PepNet.
