model.py

import torch
import torch.nn as nn
import torch.nn.functional as F

class CNNED_Protein(nn.Module):
    def __init__(self, alphabet_size: int, target_size: int,
                 channel: int, depth: int, kernel_size: int, l2norm: bool = True):
        super().__init__()
        C_in = alphabet_size
        C = channel
        K = kernel_size
        pad = K // 2

        blocks = [
            nn.Conv1d(C_in, C, K, stride=1, padding=pad, bias=False),
            nn.BatchNorm1d(C),
            nn.ReLU(inplace=True),
        ]
        for _ in range(depth - 1):
            blocks += [
                nn.Conv1d(C, C, K, stride=1, padding=pad, bias=False),
                nn.BatchNorm1d(C),
                nn.ReLU(inplace=True),
                nn.AvgPool1d(2),
            ]
        self.conv = nn.Sequential(*blocks)
        self.pool = nn.AdaptiveAvgPool1d(1)
        self.proj = nn.Sequential(
            nn.Linear(C, C),
            nn.ReLU(inplace=True),
            nn.Linear(C, target_size),
        )
        self.l2norm = l2norm

    def encode(self, x: torch.Tensor):
        # x: (B, A, L)
        z = self.conv(x)              # (B, C, L')
        z = self.pool(z).squeeze(-1)  # (B, C)
        y = self.proj(z)              # (B, D)
        if self.l2norm:
            y = F.normalize(y, dim=-1)
        return y, z

    def forward(self, a: torch.Tensor, p: torch.Tensor, n: torch.Tensor):
        ay, _ = self.encode(a)
        py, _ = self.encode(p)
        ny, _ = self.encode(n)
        return ay, py, ny