from transformers import PreTrainedModel import torch import torch.nn as nn from torch.nn import functional as F from .configuration_medts import MedTSConfig class FeedFoward(nn.Module): """ a simple linear layer followed by a non-linearity """ def __init__(self, n_embd, dropout): super().__init__() self.net = nn.Sequential( nn.Linear(n_embd, 4 * n_embd), nn.ReLU(), nn.Linear(4 * n_embd, n_embd), nn.Dropout(dropout), ) def forward(self, x): return self.net(x) class Head(nn.Module): """ one head of self-attention """ def __init__(self, head_size, n_embd, block_size): super().__init__() self.key = nn.Linear(n_embd, head_size, bias=False) self.query = nn.Linear(n_embd, head_size, bias=False) self.value = nn.Linear(n_embd, head_size, bias=False) self.register_buffer('tril', torch.tril(torch.ones(block_size, block_size))) def forward(self, x): # input of size (batch, time-step, channels) # output of size (batch, time-step, head size) B,T,C = x.shape k = self.key(x) # (B,T,hs) q = self.query(x) # (B,T,hs) # compute attention scores ("affinities") wei = q @ k.transpose(-2,-1) * k.shape[-1]**-0.5 # (B, T, hs) @ (B, hs, T) -> (B, T, T) wei = wei.masked_fill(self.tril[:T, :T] == 0, float('-inf')) # (B, T, T) wei = F.softmax(wei, dim=-1) # (B, T, T) # perform the weighted aggregation of the values v = self.value(x) # (B,T,hs) out = wei @ v # (B, T, T) @ (B, T, hs) -> (B, T, hs) return out class MultiHeadAttention(nn.Module): """ multiple heads of self-attention in parallel """ def __init__(self, num_heads, head_size, n_embd, dropout, block_size): super().__init__() self.heads = nn.ModuleList([Head(head_size, n_embd, block_size) for _ in range(num_heads)]) self.proj = nn.Linear(head_size * num_heads, n_embd) self.dropout = nn.Dropout(dropout) def forward(self, x): out = torch.cat([h(x) for h in self.heads], dim=-1) out = self.dropout(self.proj(out)) return out class Block(nn.Module): """ Transformer block: communication followed by computation """ def __init__(self, n_embd, n_head, dropout, block_size): # n_embd: embedding dimension, n_head: the number of heads we'd like super().__init__() head_size = n_embd // n_head self.sa = MultiHeadAttention(n_head, head_size, n_embd, dropout, block_size) self.ffwd = FeedFoward(n_embd, dropout) self.ln1 = nn.LayerNorm(n_embd) self.ln2 = nn.LayerNorm(n_embd) def forward(self, x): x = x + self.sa(self.ln1(x)) x = x + self.ffwd(self.ln2(x)) return x class PatientsTimeSeriesModel(nn.Module): def __init__(self, vocab_size, n_embd, block_size, device, n_layer, n_head, dropout): ''' args: - vocab_size: int, the number of unique tokens in the vocabulary, i.e. the number of unique tests results - n_embd: int, the dimension of the embedding, i.e. the number of tests results (same as vocab_size) - block_size: int, the length of the context ''' super().__init__() # each token directly reads off the logits for the next token from a lookup table self.position_embedding_table = nn.Embedding(block_size, vocab_size) # self.sa =Head(n_embd, n_embd, block_size) self.blocks = nn.Sequential(*[Block(n_embd, n_head, dropout, block_size) for _ in range(n_layer)]) self.ln_f = nn.LayerNorm(n_embd) # final layer norm self.lm_prefix = nn.Linear(vocab_size, n_embd) # linear layer to project the tokens to the embedding dimension self.lm_head = nn.Linear(n_embd, vocab_size) # linear layer to project the embeddings to the vocabulary size self.device = device self.apply(self._init_weights) def _init_weights(self, module): if isinstance(module, nn.Linear): torch.nn.init.normal_(module.weight, mean=0.0, std=0.02) if module.bias is not None: torch.nn.init.zeros_(module.bias) elif isinstance(module, nn.Embedding): torch.nn.init.normal_(module.weight, mean=0.0, std=0.02) def forward(self, tok_emb, targets=None): # tok_emb and targets are both (B,T,C) tensors # where B is the batch size, T is the number of time steps and C is the number of tests results B, T, C = tok_emb.shape pos_emb = self.position_embedding_table(torch.arange(T, device=self.device)) # (T,Vocab_size) x = tok_emb + pos_emb # (B,T,Vocab_size) x = self.lm_prefix(x) # (B,T,C) x = self.blocks(x) # (B,T,C) x = self.ln_f(x) # (B,T,C) logits = self.lm_head(x) # (B,T,vocab_size) if targets is None: return {"logits": logits} else: B, T, C = logits.shape logits = logits.view(B*T, C) targets = targets.view(B*T, C) # TODO: Add padding mask to the loss computation # loss = F.mse_loss(logits, targets) loss = self.mse_loss(logits, targets, reduction="mean") return {"logits": logits, "loss": loss} def mse_loss(self, out, target, reduction): mask = (target == 0) loss = (out[~mask]-target[~mask])**2 if reduction == "mean": return loss.mean() elif reduction == "None": return loss class MedTSModel(PreTrainedModel): config_class = MedTSConfig def __init__(self, config): super().__init__(config) self.model = PatientsTimeSeriesModel( vocab_size=config.vocab_size, n_embd=config.n_embd, block_size=config.block_size, device= 'mps' if torch.backends.mps.is_available() else 'cuda' if torch.cuda.is_available() else 'cpu', n_layer=config.n_layer, n_head=config.n_head, dropout=config.dropout ) def forward(self, tensor, targets=None): return self.model(tensor, targets)