GenerRNA / model.py
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import math
import inspect
from dataclasses import dataclass
import torch
import torch.nn as nn
from torch.nn import functional as F
class LayerNorm(nn.Module):
def __init__(self, ndim, bias):
super().__init__()
self.weight = nn.Parameter(torch.ones(ndim))
self.bias = nn.Parameter(torch.zeros(ndim)) if bias else None
def forward(self, input):
return F.layer_norm(input, self.weight.shape, self.weight, self.bias, 1e-5)
class CausalSelfAttention(nn.Module):
def __init__(self, config):
super().__init__()
assert config.n_embd % config.n_head == 0
# key, query, value projections for all heads, but in a batch
self.c_attn = nn.Linear(config.n_embd, 3 * config.n_embd, bias=config.bias)
# output projection
self.c_proj = nn.Linear(config.n_embd, config.n_embd, bias=config.bias)
# regularization
self.attn_dropout = nn.Dropout(config.dropout)
self.resid_dropout = nn.Dropout(config.dropout)
self.n_head = config.n_head
self.n_embd = config.n_embd
self.dropout = config.dropout
self.flash = hasattr(torch.nn.functional, 'scaled_dot_product_attention')
if not self.flash:
print("WARNING: using slow attention. Flash Attention requires PyTorch >= 2.0")
# causal mask to ensure that attention is only applied to the left in the input sequence
self.register_buffer("bias", torch.tril(torch.ones(config.block_size, config.block_size))
.view(1, 1, config.block_size, config.block_size))
def forward(self, x):
B, T, C = x.size() # batch size, sequence length, embedding dimensionality (n_embd)
# calculate query, key, values for all heads in batch and move head forward to be the batch dim
q, k, v = self.c_attn(x).split(self.n_embd, dim=2)
k = k.view(B, T, self.n_head, C // self.n_head).transpose(1, 2) # (B, nh, T, hs)
q = q.view(B, T, self.n_head, C // self.n_head).transpose(1, 2) # (B, nh, T, hs)
v = v.view(B, T, self.n_head, C // self.n_head).transpose(1, 2) # (B, nh, T, hs)
# causal self-attention; Self-attend: (B, nh, T, hs) x (B, nh, hs, T) -> (B, nh, T, T)
if self.flash:
# efficient attention using Flash Attention CUDA kernels
y = torch.nn.functional.scaled_dot_product_attention(q, k, v, attn_mask=None, dropout_p=self.dropout if self.training else 0, is_causal=True)
else:
# manual implementation of attention
att = (q @ k.transpose(-2, -1)) * (1.0 / math.sqrt(k.size(-1)))
att = att.masked_fill(self.bias[:,:,:T,:T] == 0, float('-inf'))
att = F.softmax(att, dim=-1)
att = self.attn_dropout(att)
y = att @ v # (B, nh, T, T) x (B, nh, T, hs) -> (B, nh, T, hs)
y = y.transpose(1, 2).contiguous().view(B, T, C) # re-assemble all head outputs side by side
# output projection
y = self.resid_dropout(self.c_proj(y))
return y
class MLP(nn.Module):
def __init__(self, config):
super().__init__()
self.c_fc = nn.Linear(config.n_embd, 4 * config.n_embd, bias=config.bias)
self.gelu = nn.GELU()
self.c_proj = nn.Linear(4 * config.n_embd, config.n_embd, bias=config.bias)
self.dropout = nn.Dropout(config.dropout)
def forward(self, x):
x = self.c_fc(x)
x = self.gelu(x)
x = self.c_proj(x)
x = self.dropout(x)
return x
class Block(nn.Module):
def __init__(self, config):
super().__init__()
self.ln_1 = LayerNorm(config.n_embd, bias=config.bias)
self.attn = CausalSelfAttention(config)
self.ln_2 = LayerNorm(config.n_embd, bias=config.bias)
self.mlp = MLP(config)
def forward(self, x):
x = x + self.attn(self.ln_1(x))
x = x + self.mlp(self.ln_2(x))
return x
@dataclass
class GPTConfig:
block_size: int = 1024
vocab_size: int = 50304
n_layer: int = 12
n_head: int = 12
n_embd: int = 768
dropout: float = 0.0
bias: bool = True
class GPT(nn.Module):
def __init__(self, config):
super().__init__()
assert config.vocab_size is not None
assert config.block_size is not None
self.config = config
self.transformer = nn.ModuleDict(dict(
wte = nn.Embedding(config.vocab_size, config.n_embd),
wpe = nn.Embedding(config.block_size, config.n_embd),
drop = nn.Dropout(config.dropout),
h = nn.ModuleList([Block(config) for _ in range(config.n_layer)]),
ln_f = LayerNorm(config.n_embd, bias=config.bias),
))
self.lm_head = nn.Linear(config.n_embd, config.vocab_size, bias=False)
self.transformer.wte.weight = self.lm_head.weight
# init all weights
self.apply(self._init_weights)
# apply special scaled init to the residual projections, per GPT-2 paper
for pn, p in self.named_parameters():
if pn.endswith('c_proj.weight'):
torch.nn.init.normal_(p, mean=0.0, std=0.02/math.sqrt(2 * config.n_layer))
# report number of parameters
print("number of parameters: %.2fM" % (self.get_num_params()/1e6,))
def get_num_params(self, non_embedding=True):
"""
Return the number of parameters in the model.
For non-embedding count (default), the position embeddings get subtracted.
The token embeddings would too, except due to the parameter sharing these
params are actually used as weights in the final layer, so we include them.
"""
n_params = sum(p.numel() for p in self.parameters())
if non_embedding:
n_params -= self.transformer.wpe.weight.numel()
return n_params
def _init_weights(self, module):
if isinstance(module, nn.Linear):
torch.nn.init.kaiming_normal_(module.weight, a=0, mode='fan_in', nonlinearity='relu')
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, idx, targets=None):
device = idx.device
b, t = idx.size()
assert t <= self.config.block_size, f"Cannot forward sequence of length {t}, block size is only {self.config.block_size}"
pos = torch.arange(0, t, dtype=torch.long, device=device) # shape (t)
# forward the GPT model itself
tok_emb = self.transformer.wte(idx) # token embeddings of shape (b, t, n_embd)
pos_emb = self.transformer.wpe(pos) # position embeddings of shape (t, n_embd)
x = self.transformer.drop(tok_emb + pos_emb)
for block in self.transformer.h:
x = block(x)
x = self.transformer.ln_f(x)
if targets is not None:
# if we are given some desired targets also calculate the loss
logits = self.lm_head(x)
loss = F.cross_entropy(logits.view(-1, logits.size(-1)), targets.view(-1), ignore_index=-1)
else:
# inference-time mini-optimization: only forward the lm_head on the very last position
logits = self.lm_head(x[:, [-1], :]) # note: using list [-1] to preserve the time dim
loss = None
return logits, loss
def crop_block_size(self, block_size):
# model surgery to decrease the block size if necessary
# e.g. we may load the GPT2 pretrained model checkpoint (block size 1024)
# but want to use a smaller block size for some smaller, simpler model
assert block_size <= self.config.block_size
self.config.block_size = block_size
self.transformer.wpe.weight = nn.Parameter(self.transformer.wpe.weight[:block_size])
for block in self.transformer.h:
if hasattr(block.attn, 'bias'):
block.attn.bias = block.attn.bias[:,:,:block_size,:block_size]
@classmethod
def from_pretrained(cls, model_type, override_args=None):
assert model_type in {'gpt2', 'gpt2-medium', 'gpt2-large', 'gpt2-xl'}
override_args = override_args or {} # default to empty dict
# only dropout can be overridden see more notes below
assert all(k == 'dropout' for k in override_args)
from transformers import GPT2LMHeadModel
print("loading weights from pretrained gpt: %s" % model_type)
# n_layer, n_head and n_embd are determined from model_type
config_args = {
'gpt2': dict(n_layer=12, n_head=12, n_embd=768), # 124M params
'gpt2-medium': dict(n_layer=24, n_head=16, n_embd=1024), # 350M params
'gpt2-large': dict(n_layer=36, n_head=20, n_embd=1280), # 774M params
'gpt2-xl': dict(n_layer=48, n_head=25, n_embd=1600), # 1558M params
}[model_type]
print("forcing vocab_size=50257, block_size=1024, bias=True")
config_args['vocab_size'] = 50257 # always 50257 for GPT model checkpoints
config_args['block_size'] = 1024 # always 1024 for GPT model checkpoints
config_args['bias'] = True # always True for GPT model checkpoints
# we can override the dropout rate, if desired
if 'dropout' in override_args:
print(f"overriding dropout rate to {override_args['dropout']}")
config_args['dropout'] = override_args['dropout']
# create a from-scratch initialized minGPT model
config = GPTConfig(**config_args)
model = GPT(config)
sd = model.state_dict()
sd_keys = sd.keys()
sd_keys = [k for k in sd_keys if not k.endswith('.attn.bias')] # discard this mask / buffer, not a param
# init a huggingface/transformers model
model_hf = GPT2LMHeadModel.from_pretrained(model_type)
sd_hf = model_hf.state_dict()
# copy while ensuring all of the parameters are aligned and match in names and shapes
sd_keys_hf = sd_hf.keys()
sd_keys_hf = [k for k in sd_keys_hf if not k.endswith('.attn.masked_bias')] # ignore these, just a buffer
sd_keys_hf = [k for k in sd_keys_hf if not k.endswith('.attn.bias')] # same, just the mask (buffer)
transposed = ['attn.c_attn.weight', 'attn.c_proj.weight', 'mlp.c_fc.weight', 'mlp.c_proj.weight']
# basically the openai checkpoints use a "Conv1D" module, but we only want to use a vanilla Linear
# this means that we have to transpose these weights when we import them
assert len(sd_keys_hf) == len(sd_keys), f"mismatched keys: {len(sd_keys_hf)} != {len(sd_keys)}"
for k in sd_keys_hf:
if any(k.endswith(w) for w in transposed):
# special treatment for the Conv1D weights we need to transpose
assert sd_hf[k].shape[::-1] == sd[k].shape
with torch.no_grad():
sd[k].copy_(sd_hf[k].t())
else:
# vanilla copy over the other parameters
assert sd_hf[k].shape == sd[k].shape
with torch.no_grad():
sd[k].copy_(sd_hf[k])
return model
def configure_optimizers(self, weight_decay, learning_rate, betas, device_type):
# start with all of the candidate parameters
param_dict = {pn: p for pn, p in self.named_parameters()}
# filter out those that do not require grad
param_dict = {pn: p for pn, p in param_dict.items() if p.requires_grad}
# create optim groups. Any parameters that is 2D will be weight decayed, otherwise no.
# i.e. all weight tensors in matmuls + embeddings decay, all biases and layernorms don't.
decay_params = [p for n, p in param_dict.items() if p.dim() >= 2]
nodecay_params = [p for n, p in param_dict.items() if p.dim() < 2]
optim_groups = [
{'params': decay_params, 'weight_decay': weight_decay},
{'params': nodecay_params, 'weight_decay': 0.0}
]
num_decay_params = sum(p.numel() for p in decay_params)
num_nodecay_params = sum(p.numel() for p in nodecay_params)
print(f"num decayed parameter tensors: {len(decay_params)}, with {num_decay_params:,} parameters")
print(f"num non-decayed parameter tensors: {len(nodecay_params)}, with {num_nodecay_params:,} parameters")
# Create AdamW optimizer and use the fused version if it is available
fused_available = 'fused' in inspect.signature(torch.optim.AdamW).parameters
use_fused = fused_available and device_type == 'cuda'
extra_args = dict(fused=True) if use_fused else dict()
optimizer = torch.optim.AdamW(optim_groups, lr=learning_rate, betas=betas, **extra_args)
print(f"using fused AdamW: {use_fused}")
return optimizer
def estimate_mfu(self, fwdbwd_per_iter, dt):
""" estimate model flops utilization (MFU) in units of A100 bfloat16 peak FLOPS """
# first estimate the number of flops we do per iteration.
# see PaLM paper Appendix B as ref: https://arxiv.org/abs/2204.02311
N = self.get_num_params()
cfg = self.config
L, H, Q, T = cfg.n_layer, cfg.n_head, cfg.n_embd//cfg.n_head, cfg.block_size
flops_per_token = 6*N + 12*L*H*Q*T
flops_per_fwdbwd = flops_per_token * T
flops_per_iter = flops_per_fwdbwd * fwdbwd_per_iter
# express our flops throughput as ratio of A100 bfloat16 peak flops
flops_achieved = flops_per_iter * (1.0/dt) # per second
flops_promised = 312e12 # A100 GPU bfloat16 peak flops is 312 TFLOPS
mfu = flops_achieved / flops_promised
return mfu
@torch.no_grad()
def generate(self, idx, max_new_tokens, temperature=1.0, top_k=None, strategy='sampling', beam_size=3, eos_token_id=0, repetition_penalty=1.0):
assert strategy in ['greedy_search', 'sampling', 'top_k', 'beam_search']
batch_size = idx.size(0)
if strategy == 'beam_search':
# Initialize beams
beam_seqs = [idx.clone() for _ in range(beam_size)]
beam_scores = torch.zeros((batch_size, beam_size), device=idx.device)
completed_seqs = []
for _ in range(max_new_tokens):
all_candidates = []
for i in range(beam_size):
idx_cond = beam_seqs[i] if beam_seqs[i].size(1) <= self.config.block_size else beam_seqs[i][:, -self.config.block_size:]
logits, _ = self(idx_cond)
logits = logits[:, -1, :] / temperature
if repetition_penalty != 1.0:
for j in range(idx_cond.size(1)):
logits[:, idx_cond[:, j]] /= repetition_penalty
probs = F.log_softmax(logits, dim=-1)
scores, indices = torch.topk(probs, beam_size, dim=-1)
for j in range(beam_size):
candidate_seq = torch.cat([beam_seqs[i], indices[:, j:j+1]], dim=1)
candidate_score = beam_scores[:, i] + scores[:, j]
if indices[0, j] == eos_token_id:
completed_seqs.append((candidate_score, candidate_seq))
else:
all_candidates.append((candidate_score, candidate_seq))
# add random noise when sorting beacause that generated sequences of beam_search remain unchanged if they have the same prefix
all_candidates.sort(key=lambda x: x[0].mean().item() + torch.rand(1).item() * 5e-1, reverse=True)
beam_seqs = [all_candidates[i][1] for i in range(min(beam_size, len(all_candidates)))]
beam_scores = torch.stack([all_candidates[i][0] for i in range(min(beam_size, len(all_candidates)))], dim=1)
if len(completed_seqs) >= beam_size:
break
if not completed_seqs:
completed_seqs = [(beam_scores[:, i], beam_seqs[i]) for i in range(beam_size)]
completed_seqs.sort(key=lambda x: x[0].mean().item(), reverse=True)
return completed_seqs[0][1]
else:
for _ in range(max_new_tokens):
idx_cond = idx if idx.size(1) <= self.config.block_size else idx[:, -self.config.block_size:]
logits, _ = self(idx_cond)
logits = logits[:, -1, :] / temperature
if repetition_penalty != 1.0:
for i in range(idx.size(0)):
for j in range(idx.size(1)):
logits[i, idx[i, j]] /= repetition_penalty
if strategy == 'greedy_search':
idx_next = torch.argmax(logits, dim=-1, keepdim=True)
elif strategy == 'sampling':
probs = F.softmax(logits, dim=-1)
idx_next = torch.multinomial(probs, num_samples=1)
elif strategy == 'top_k':
if top_k is not None:
logits, indices = torch.topk(logits, min(top_k, logits.size(-1)))
probs = F.softmax(logits, dim=-1)
idx_next = torch.multinomial(probs, num_samples=1)
idx_next = torch.gather(indices, dim=-1, index=idx_next)
if idx_next == eos_token_id:
break
idx = torch.cat((idx, idx_next), dim=1)
return idx if idx[0][0] != eos_token_id else idx[:, 1:]