pubmedbert-bio-ext-summ / transformerutils.py
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import torch
import torch.nn as nn
import math
# Source: https://pytorch.org/tutorials/beginner/transformer_tutorial.html
class PositionalEncoding(nn.Module):
def __init__(self, d_model, dropout=0.1, max_len=5000):
super().__init__()
self.dropout = nn.Dropout(p=dropout)
position = torch.arange(max_len).unsqueeze(1)
div_term = torch.exp(torch.arange(0, d_model, 2) * (-math.log(10000.0) / d_model))
pe = torch.zeros(max_len, d_model)
pe[:, 0::2] = torch.sin(position * div_term)
pe[:, 1::2] = torch.cos(position * div_term)
self.register_buffer("pe", pe)
def forward(self, x):
x = x + self.pe[:x.size(0)]
return self.dropout(x)
"""
Same scheduler as in "Attention Is All You Need"
"""
class NoamScheduler():
def __init__(self, optimizer, warmup, model_size):
self.epoch = 0
self.optimizer = optimizer
self.warmup = warmup
self.model_size = model_size
def step(self):
self.epoch += 1
new_lr = self.model_size**(-0.5) * min(self.epoch**(-0.5), self.epoch * self.warmup**(-1.5))
for param in self.optimizer.param_groups:
param["lr"] = new_lr
"""
Encoders to attend sentence level features.
"""
class TransformerInterEncoder(nn.Module):
def __init__(self, d_model, d_ff=2048, nheads=8, num_encoders=2, dropout=0.1, max_len=512):
super().__init__()
self.positional_enc = PositionalEncoding(d_model, dropout, max_len)
self.encoders = nn.TransformerEncoder(
nn.TransformerEncoderLayer(d_model=d_model, nhead=nheads, dim_feedforward=d_ff),
num_layers=num_encoders
)
self.layer_norm = nn.LayerNorm(d_model)
self.linear = nn.Linear(d_model, 1)
self.sigmoid = nn.Sigmoid()
def forward(self, x):
x = self.positional_enc(x)
x = self.encoders(x)
x = self.layer_norm(x)
logit = self.linear(x)
sentences_scores = self.sigmoid(logit)
return sentences_scores.squeeze(-1), logit.squeeze(-1)