model.py

import torch
import torch.nn as nn
from einops import rearrange, repeat, pack, unpack

class PreNorm(nn.Module):
    def __init__(self, dim, fn):
        super().__init__()
        self.norm = nn.LayerNorm(dim)
        self.fn = fn
    def forward(self, x, **kwargs):
        return self.fn(self.norm(x), **kwargs)

class FeedForward(nn.Module):
    def __init__(self, dim, hidden_dim, dropout = 0.):
        super().__init__()
        self.net = nn.Sequential(
            nn.Linear(dim, hidden_dim),
            nn.GELU(),
            nn.Dropout(dropout),
            nn.Linear(hidden_dim, dim),
            nn.Dropout(dropout)
        )
    def forward(self, x):
        return self.net(x)

class Attention(nn.Module):
    def __init__(self, dim, heads = 8, dim_head = 64, dropout = 0.):
        super().__init__()
        inner_dim = dim_head *  heads
        project_out = not (heads == 1 and dim_head == dim)

        self.heads = heads
        self.scale = dim_head ** -0.5

        self.attend = nn.Softmax(dim = -1)
        self.dropout = nn.Dropout(dropout)

        self.to_qkv = nn.Linear(dim, inner_dim * 3, bias = False)

        self.to_out = nn.Sequential(
            nn.Linear(inner_dim, dim),
            nn.Dropout(dropout)
        ) if project_out else nn.Identity()

    def forward(self, x):
        qkv = self.to_qkv(x).chunk(3, dim = -1)
        q, k, v = map(lambda t: rearrange(t, 'b n (h d) -> b h n d', h = self.heads), qkv)

        dots = torch.matmul(q, k.transpose(-1, -2)) * self.scale

        attn = self.attend(dots)
        attn = self.dropout(attn)

        out = torch.matmul(attn, v)
        out = rearrange(out, 'b h n d -> b n (h d)')
        return self.to_out(out)

class Transformer(nn.Module):
    def __init__(self, dim, depth, heads, dim_head, mlp_dim, dropout = 0.):
        super().__init__()
        self.layers = nn.ModuleList([])
        for _ in range(depth):
            self.layers.append(nn.ModuleList([
                PreNorm(dim, Attention(dim, heads = heads, dim_head = dim_head, dropout = dropout)),
                PreNorm(dim, FeedForward(dim, mlp_dim, dropout = dropout))
            ]))
    def forward(self, x):
        for attn, ff in self.layers:
            x = attn(x) + x
            x = ff(x) + x
        return x

class pathway_guided_transformer(nn.Module):
    def __init__(self, *, num_classes, pathway_number, dim, depth, heads, mlp_dim, dim_head = 64, dropout = 0., emb_dropout = 0.):
        super().__init__()

        self.to_segment_num = pathway_number
        self.mutil_linear_layers =  nn.ModuleList([])
        # for each pathway
        for i in range(len(pathway_number)):
            self.mutil_linear_layers.append(nn.Sequential(
                nn.LayerNorm(pathway_number[i]),
                nn.Linear(pathway_number[i], dim),
                nn.LayerNorm(dim)
            ))
        
        self.cls_token = nn.Parameter(torch.randn(dim))
        self.dropout = nn.Dropout(emb_dropout)
        self.transformer = Transformer(dim, depth, heads, dim_head, mlp_dim, dropout)
        self.mlp_head = nn.Sequential(
            nn.LayerNorm(dim),
            nn.Linear(dim, num_classes)
        )

    def forward(self, series):

        segments = torch.split(series, self.to_segment_num, dim=-1)
        segnum = 0
        transformed_tensors = []
        for layers in self.mutil_linear_layers:
            per_segment = layers(segments[segnum])
            transformed_tensors.append(per_segment)
            segnum = segnum + 1

        concat_segment = torch.cat(transformed_tensors, dim=-2)
        x = concat_segment
        b, n, _ = x.shape
        cls_tokens = repeat(self.cls_token, 'd -> b d', b = b)
        x, ps = pack([cls_tokens, x], 'b * d')
        x = self.dropout(x)
        x = self.transformer(x)
        cls_tokens, _ = unpack(x, ps, 'b * d')

        return self.mlp_head(cls_tokens)

def Pathway_Guided_Transformer(num_classes, pathway_number, dim, depth, heads, mlp_dim, dropout, emb_dropout):
    model = pathway_guided_transformer(
            num_classes = num_classes,
            pathway_number = pathway_number,
            dim = dim,
            depth = depth,
            heads = heads,
            mlp_dim = mlp_dim,
            dropout = dropout,
            emb_dropout = emb_dropout,
        )
    return model