Refactor model and training scripts: remove unused imports and add FactorizedHead class for improved modularity

model.py

@@ -5,12 +5,6 @@ from age_encoder import AgeSinusoidalEncoder, AgeMLPEncoder
 import torch.nn.functional as F
 import torch.nn as nn
 import torch
-import sys
-from pathlib import Path
-
-_PROJECT_ROOT = Path(__file__).resolve().parent
-if str(_PROJECT_ROOT) not in sys.path:
-    sys.path.insert(0, str(_PROJECT_ROOT))
 
 
 class TabularEncoder(nn.Module):
@@ -265,28 +259,77 @@ class AutoDiscretization(nn.Module):
         return emb
 
 
+class FactorizedHead(nn.Module):
+    def __init__(
+            self,
+            n_embd: int,
+            n_disease: int,
+            n_dim: int,
+            rank: int = 16,
+    ):
+        super().__init__()
+        self.n_embd = n_embd
+        self.n_disease = n_disease
+        self.n_dim = n_dim
+        self.rank = rank
+
+        self.disease_base_proj = nn.Sequential(
+            nn.LayerNorm(n_embd),
+            nn.Linear(n_embd, n_dim),
+        )
+        self.context_mod_proj = nn.Sequential(
+            nn.LayerNorm(n_embd),
+            nn.Linear(n_embd, rank, bias=False),
+        )
+        self.disease_mod_proj = nn.Sequential(
+            nn.LayerNorm(n_embd),
+            nn.Linear(n_embd, rank * n_dim, bias=False),
+        )
+        self.delta_scale = nn.Parameter(torch.tensor(1e-3))
+
+        self._init_weights()
+
+    def _init_weights(self):
+        # init disease_base_proj: [LayerNorm, Linear]
+        nn.init.normal_(self.disease_base_proj[1].weight, std=0.02)
+        nn.init.zeros_(self.disease_base_proj[1].bias)
+
+        # init context_mod_proj: [LayerNorm, Linear(bias=False)]
+        nn.init.zeros_(self.context_mod_proj[1].weight)
+
+        # init disease_mod_proj: [LayerNorm, Linear(bias=False)]
+        nn.init.normal_(self.disease_mod_proj[1].weight, std=0.02)
+
+    def forward(
+            self,
+            c: torch.Tensor,  # (M, n_embd)
+            disease_embedding,  # (n_disease, n_embd)
+    ) -> torch.Tensor:
+        M = c.shape[0]
+        K = disease_embedding.shape[0]
+        assert K == self.n_disease
+        base_logits = self.disease_base_proj(disease_embedding)  # (K, n_dim)
+        base_logits = base_logits.unsqueeze(
+            0).expand(M, -1, -1)  # (M, K, n_dim)
+        u = self.context_mod_proj(c)
+        v = self.disease_mod_proj(disease_embedding)
+        v = v.view(K, self.rank, self.n_dim)
+        delta_logits = torch.einsum('mr, krd -> mkd', u, v)
+
+        return base_logits + self.delta_scale * delta_logits
+
+
 def _build_time_padding_mask(
     event_seq: torch.Tensor,
     time_seq: torch.Tensor,
 ) -> torch.Tensor:
-    B, L = event_seq.shape
-    device = event_seq.device
-    key_is_valid = (event_seq != 0)
-
-    cache = getattr(_build_time_padding_mask, "_cache", None)
-    if cache is None:
-        cache = {}
-        setattr(_build_time_padding_mask, "_cache", cache)
-    cache_key = (str(device), L)
-    causal = cache.get(cache_key)
-    if causal is None:
-        causal = torch.ones(L, L, device=device, dtype=torch.bool).triu(1)
-        cache[cache_key] = causal
-
-    causal = causal.unsqueeze(0).unsqueeze(0)  # (1,1,L,L)
-    key_pad = (~key_is_valid).unsqueeze(1).unsqueeze(2)  # (B,1,1,L)
-    attn_mask = causal | key_pad  # (B,1,L,L)
-    return attn_mask
+    t_i = time_seq.unsqueeze(-1)
+    t_j = time_seq.unsqueeze(1)
+    time_mask = (t_j <= t_i)  # allow attending only to past or current
+    key_is_valid = (event_seq != 0)  # disallow padded positions
+    allowed = time_mask & key_is_valid.unsqueeze(1)
+    attn_mask = ~allowed  # True means mask for scaled_dot_product_attention
+    return attn_mask.unsqueeze(1)  # (B, 1, L, L)
 
 
 class DelphiFork(nn.Module):
@@ -322,6 +365,7 @@ class DelphiFork(nn.Module):
             pdrop: float = 0.0,
             token_pdrop: float = 0.0,
             n_dim: int = 1,
+            rank: int = 16,
     ):
         super().__init__()
         self.vocab_size = n_disease + n_tech_tokens
@@ -356,7 +400,12 @@ class DelphiFork(nn.Module):
         self.token_dropout = nn.Dropout(token_pdrop)
 
         # Head layers
-        self.theta_proj = nn.Linear(n_embd, n_disease * n_dim)
+        self.theta_proj = FactorizedHead(
+            n_embd=n_embd,
+            n_disease=n_disease,
+            n_dim=n_dim,
+            rank=rank,
+        )
 
     def forward(
             self,
@@ -404,9 +453,11 @@ class DelphiFork(nn.Module):
         if b_prev is not None and t_prev is not None:
             M = b_prev.numel()
             c = x[b_prev, t_prev]  # (M, D)
+            disease_embeddings = self.token_embedding.weight[
+                self.n_tech_tokens: self.n_tech_tokens + self.n_disease
+            ]
 
-            theta = self.theta_proj(c)  # (M, N_disease * n_dim)
-            theta = theta.view(M, self.n_disease, self.n_dim)
+            theta = self.theta_proj(c, disease_embeddings)
             return theta
         else:
             return x
@@ -428,6 +479,7 @@ class SapDelphi(nn.Module):
             pdrop: float = 0.0,
             token_pdrop: float = 0.0,
             n_dim: int = 1,
+            rank: int = 16,
             pretrained_weights_path: Optional[str] = None,  # 新增参数
             freeze_embeddings: bool = False,               # 新增参数，默认为 False 表示微调
     ):
@@ -438,6 +490,7 @@ class SapDelphi(nn.Module):
         self.n_embd = n_embd
         self.n_head = n_head
         self.n_dim = n_dim
+        self.rank = rank
 
         if pretrained_weights_path is not None:
             print(
@@ -459,7 +512,6 @@ class SapDelphi(nn.Module):
                 self.emb_proj = nn.Sequential(
                     nn.Linear(vocab_dim, n_embd, bias=False),
                     nn.LayerNorm(n_embd),
-                    nn.Dropout(pdrop),
                 )
             else:
                 self.emb_proj = nn.Identity()
@@ -491,7 +543,12 @@ class SapDelphi(nn.Module):
         self.token_dropout = nn.Dropout(token_pdrop)
 
         # Head layers
-        self.theta_proj = nn.Linear(n_embd, n_disease * n_dim)
+        self.theta_proj = FactorizedHead(
+            n_embd=n_embd,
+            n_disease=n_disease,
+            n_dim=n_dim,
+            rank=rank,
+        )
 
     def forward(
             self,
@@ -540,9 +597,12 @@ class SapDelphi(nn.Module):
         if b_prev is not None and t_prev is not None:
             M = b_prev.numel()
             c = x[b_prev, t_prev]  # (M, D)
+            disease_embeddings_raw = self.token_embedding.weight[
+                self.n_tech_tokens: self.n_tech_tokens + self.n_disease
+            ]  # (K, vocab_dim)
 
-            theta = self.theta_proj(c)  # (M, N_disease * n_dim)
-            theta = theta.view(M, self.n_disease, self.n_dim)
+            disease_embeddings = self.emb_proj(disease_embeddings_raw)
+            theta = self.theta_proj(c, disease_embeddings)
             return theta
         else:
             return x

train.py

@@ -16,11 +16,6 @@ import math
 import sys
 from dataclasses import asdict, dataclass, field
 from typing import Literal, Sequence
-from pathlib import Path
-
-_PROJECT_ROOT = Path(__file__).resolve().parent
-if str(_PROJECT_ROOT) not in sys.path:
-    sys.path.insert(0, str(_PROJECT_ROOT))
 
 
 @dataclass