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import math
import numpy as np
import torch
import torch.nn.functional as F
from torch import nn
from torch.cuda.amp import autocast
from einops import rearrange, repeat
from functools import partial
from contextlib import contextmanager
from local_attention import LocalAttention
from performer_pytorch.reversible import ReversibleSequence, SequentialSequence
try:
from apex import amp
APEX_AVAILABLE = True
except:
APEX_AVAILABLE = False
# helpers
def exists(val):
return val is not None
def empty(tensor):
return tensor.numel() == 0
def default(val, d):
return val if exists(val) else d
@contextmanager
def null_context():
yield
def cast_tuple(val):
return (val,) if not isinstance(val, tuple) else val
# def get_module_device(module):
# return next(module.parameters).device
def get_module_device(module):
try:
return next(module.parameters()).device
except StopIteration:
# For nn.DataParallel compatibility in PyTorch 1.5
def find_tensor_attributes(module):
tuples = [(k, v) for k, v in module.__dict__.items() if torch.is_tensor(v)]
return tuples
gen = module._named_members(get_members_fn=find_tensor_attributes)
first_tuple = next(gen)
return first_tuple[1].device
def find_modules(nn_module, type):
return [module for module in nn_module.modules() if isinstance(module, type)]
class Always(nn.Module):
def __init__(self, val):
super().__init__()
self.val = val
def forward(self, *args, **kwargs):
return self.val
# kernel functions
# transcribed from jax to pytorch from
# https://github.com/google-research/google-research/blob/master/performer/fast_attention/jax/fast_attention.py
def softmax_kernel(data, *, projection_matrix, is_query, normalize_data=True, eps=1e-4, device = None):
b, h, *_ = data.shape
data_normalizer = (data.shape[-1] ** -0.25) if normalize_data else 1.
ratio = (projection_matrix.shape[0] ** -0.5)
projection = repeat(projection_matrix, 'j d -> b h j d', b = b, h = h)
projection = projection.type_as(data)
data_dash = torch.einsum('...id,...jd->...ij', (data_normalizer * data), projection)
diag_data = data ** 2
diag_data = torch.sum(diag_data, dim=-1)
diag_data = (diag_data / 2.0) * (data_normalizer ** 2)
diag_data = diag_data.unsqueeze(dim=-1)
if is_query:
data_dash = ratio * (
torch.exp(data_dash - diag_data -
torch.max(data_dash, dim=-1, keepdim=True).values) + eps)
else:
data_dash = ratio * (
torch.exp(data_dash - diag_data - torch.max(data_dash)) + eps)
return data_dash.type_as(data)
def generalized_kernel(data, *, projection_matrix, kernel_fn = nn.ReLU(), kernel_epsilon = 0.001, normalize_data = True, device = None):
b, h, *_ = data.shape
data_normalizer = (data.shape[-1] ** -0.25) if normalize_data else 1.
if projection_matrix is None:
return kernel_fn(data_normalizer * data) + kernel_epsilon
projection = repeat(projection_matrix, 'j d -> b h j d', b = b, h = h)
projection = projection.type_as(data)
data_dash = torch.einsum('...id,...jd->...ij', (data_normalizer * data), projection)
data_prime = kernel_fn(data_dash) + kernel_epsilon
return data_prime.type_as(data)
def orthogonal_matrix_chunk(cols, device = None):
unstructured_block = torch.randn((cols, cols), device = device)
q, r = torch.qr(unstructured_block.cpu(), some = True)
q, r = map(lambda t: t.to(device), (q, r))
return q.t()
def gaussian_orthogonal_random_matrix(nb_rows, nb_columns, scaling = 0, device = None):
nb_full_blocks = int(nb_rows / nb_columns)
block_list = []
for _ in range(nb_full_blocks):
q = orthogonal_matrix_chunk(nb_columns, device = device)
block_list.append(q)
remaining_rows = nb_rows - nb_full_blocks * nb_columns
if remaining_rows > 0:
q = orthogonal_matrix_chunk(nb_columns, device = device)
block_list.append(q[:remaining_rows])
final_matrix = torch.cat(block_list)
if scaling == 0:
multiplier = torch.randn((nb_rows, nb_columns), device = device).norm(dim = 1)
elif scaling == 1:
multiplier = math.sqrt((float(nb_columns))) * torch.ones((nb_rows,), device = device)
else:
raise ValueError(f'Invalid scaling {scaling}')
return torch.diag(multiplier) @ final_matrix
# linear attention classes with softmax kernel
# non-causal linear attention
def linear_attention(q, k, v):
k_cumsum = k.sum(dim = -2)
D_inv = 1. / torch.einsum('...nd,...d->...n', q, k_cumsum.type_as(q))
context = torch.einsum('...nd,...ne->...de', k, v)
out = torch.einsum('...de,...nd,...n->...ne', context, q, D_inv)
return out
# efficient causal linear attention, created by EPFL
# TODO: rewrite EPFL's CUDA kernel to do mixed precision and remove half to float conversion and back
def causal_linear_attention(q, k, v, eps = 1e-6):
from fast_transformers.causal_product import CausalDotProduct
autocast_enabled = torch.is_autocast_enabled()
is_half = isinstance(q, torch.cuda.HalfTensor)
assert not is_half or APEX_AVAILABLE, 'half tensors can only be used if nvidia apex is available'
cuda_context = null_context if not autocast_enabled else partial(autocast, enabled = False)
causal_dot_product_fn = amp.float_function(CausalDotProduct.apply) if is_half else CausalDotProduct.apply
k_cumsum = k.cumsum(dim=-2) + eps
D_inv = 1. / torch.einsum('...nd,...nd->...n', q, k_cumsum.type_as(q))
with cuda_context():
if autocast_enabled:
q, k, v = map(lambda t: t.float(), (q, k, v))
out = causal_dot_product_fn(q, k, v)
out = torch.einsum('...nd,...n->...nd', out, D_inv)
return out
# inefficient causal linear attention, without cuda code, for reader's reference
# not being used
def causal_linear_attention_noncuda(q, k, v, chunk_size = 128):
last_k_cumsum = 0
last_context_cumsum = 0
outs = []
for q, k, v in zip(*map(lambda t: t.chunk(chunk_size, dim = -2), (q, k, v))):
k_cumsum = last_k_cumsum + k.cumsum(dim=-2)
D_inv = 1. / torch.einsum('...nd,...nd->...n', q, k_cumsum.type_as(q))
context = torch.einsum('...nd,...ne->...nde', k, v)
context_cumsum = last_context_cumsum + context.cumsum(dim=-3)
out = torch.einsum('...nde,...nd,...n->...ne', context_cumsum, q, D_inv)
last_k_cumsum = k_cumsum[:, :, -1:]
last_context_cumsum = context_cumsum[:, :, -1:]
outs.append(out)
return torch.cat(outs, dim = -2)
def norm_tensor(tensor, dim=-1):
return tensor / tensor.sum(dim=dim).unsqueeze(dim)
class FastAttention(nn.Module):
def __init__(self, dim_heads, nb_features = None, ortho_scaling = 0, causal = False, generalized_attention = False, kernel_fn = nn.ReLU(), no_projection = False):
super().__init__()
nb_features = default(nb_features, int(dim_heads * math.log(dim_heads)))
self.dim_heads = dim_heads
self.nb_features = nb_features
self.ortho_scaling = ortho_scaling
self.create_projection = partial(gaussian_orthogonal_random_matrix, nb_rows = self.nb_features, nb_columns = dim_heads, scaling = ortho_scaling)
projection_matrix = self.create_projection()
self.register_buffer('projection_matrix', projection_matrix)
self.generalized_attention = generalized_attention
self.kernel_fn = kernel_fn
# if this is turned on, no projection will be used
# queries and keys will be softmax-ed as in the original efficient attention paper
self.no_projection = no_projection
self.causal = causal
if causal:
try:
import fast_transformers.causal_product.causal_product_cuda
self.causal_linear_fn = partial(causal_linear_attention)
except ImportError:
print('unable to import cuda code for auto-regressive Performer. will default to the memory inefficient non-cuda version')
self.causal_linear_fn = causal_linear_attention_noncuda
@torch.no_grad()
def redraw_projection_matrix(self, device):
projections = self.create_projection(device = device)
self.projection_matrix.copy_(projections)
del projections
def forward(self, q, k, v, output_attentions = False):
device = q.device
# inds = [8060, 8064, 6243, 8575, 10342, 10913, 9366, 993, 7796, 5210, 5212, 5504, 6851, 6559, 5508, 13107, 13820]
if self.no_projection:
q = q.softmax(dim = -1)
k = torch.exp(k) if self.causal else k.softmax(dim = -2)
elif self.generalized_attention:
create_kernel = partial(generalized_kernel, kernel_fn = self.kernel_fn, projection_matrix = self.projection_matrix, device = device)
q, k = map(create_kernel, (q, k))
else:
create_kernel = partial(softmax_kernel, projection_matrix = self.projection_matrix, device = device)
q = create_kernel(q, is_query = True)
k = create_kernel(k, is_query = False)
attn_fn = linear_attention if not self.causal else self.causal_linear_fn
out = attn_fn(q, k, v)
if output_attentions:
v_diag = torch.eye(v.shape[-2]).to(device)
v_diag = v_diag.unsqueeze(0).unsqueeze(0).repeat(v.shape[0],v.shape[1],1,1)
# attn_weights = torch.zeros(1, 1, len(inds), len(inds)).to(device).to(torch.float16)
# attn_weights = torch.zeros(1, q.shape[1], len(inds), len(inds)).to(device).to(torch.float16)
attn_weights = torch.zeros(1, 1, q.shape[2], q.shape[2]).to(device).to(torch.float16)
for head_dim in range(q.shape[1]):
# attn_weights[0, head_dim] = torch.abs(attn_fn(q[:,head_dim].to(torch.float16), k[:,head_dim].to(torch.float16), v_diag[:,head_dim].to(torch.float16)))[0, inds][:, inds]
attn_weights += torch.abs(attn_fn(q[:,head_dim].to(torch.float16), k[:,head_dim].to(torch.float16), v_diag[:,head_dim].to(torch.float16)))
# attn_weights += norm_tensor(torch.abs(attn_fn(q[:,head_dim].to(torch.float16), k[:,head_dim].to(torch.float16), v_diag[:,head_dim].to(torch.float16))), dim=-1)
attn_weights /= q.shape[1]
return out, attn_weights
else:
return out
# classes
class ReZero(nn.Module):
def __init__(self, fn):
super().__init__()
self.g = nn.Parameter(torch.tensor(1e-3))
self.fn = fn
def forward(self, x, **kwargs):
return self.fn(x, **kwargs) * self.g
class PreScaleNorm(nn.Module):
def __init__(self, dim, fn, eps=1e-5):
super().__init__()
self.fn = fn
self.g = nn.Parameter(torch.ones(1))
self.eps = eps
def forward(self, x, **kwargs):
n = torch.norm(x, dim=-1, keepdim=True).clamp(min=self.eps)
x = x / n * self.g
return self.fn(x, **kwargs)
class PreLayerNorm(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 Chunk(nn.Module):
def __init__(self, chunks, fn, along_dim = -1):
super().__init__()
self.dim = along_dim
self.chunks = chunks
self.fn = fn
def forward(self, x, **kwargs):
if self.chunks == 1:
return self.fn(x, **kwargs)
chunks = x.chunk(self.chunks, dim = self.dim)
return torch.cat([self.fn(c, **kwargs) for c in chunks], dim = self.dim)
class FeedForward(nn.Module):
def __init__(self, dim, mult = 4, dropout = 0., activation = None, glu = False):
super().__init__()
activation = default(activation, nn.GELU)
self.glu = glu
self.w1 = nn.Linear(dim, dim * mult * (2 if glu else 1))
self.act = activation()
self.dropout = nn.Dropout(dropout)
self.w2 = nn.Linear(dim * mult, dim)
def forward(self, x, **kwargs):
if not self.glu:
x = self.w1(x)
x = self.act(x)
else:
x, v = self.w1(x).chunk(2, dim=-1)
x = self.act(x) * v
x = self.dropout(x)
x = self.w2(x)
return x
class SelfAttention(nn.Module):
def __init__(
self,
dim,
causal = False,
heads = 8,
dim_head = 64,
local_heads = 0,
local_window_size = 256,
nb_features = None,
feature_redraw_interval = 1000,
generalized_attention = False,
kernel_fn = nn.ReLU(),
dropout = 0.,
no_projection = False,
qkv_bias = False
):
super().__init__()
assert dim % heads == 0, 'dimension must be divisible by number of heads'
dim_head = default(dim_head, dim // heads)
inner_dim = dim_head * heads
self.fast_attention = FastAttention(dim_head, nb_features, causal = causal, generalized_attention = generalized_attention, kernel_fn = kernel_fn, no_projection = no_projection)
self.heads = heads
self.global_heads = heads - local_heads
self.local_attn = LocalAttention(window_size = local_window_size, causal = causal, autopad = True, dropout = dropout, look_forward = int(not causal), rel_pos_emb_config = (dim_head, local_heads)) if local_heads > 0 else None
self.to_q = nn.Linear(dim, inner_dim, bias = qkv_bias)
self.to_k = nn.Linear(dim, inner_dim, bias = qkv_bias)
self.to_v = nn.Linear(dim, inner_dim, bias = qkv_bias)
self.to_out = nn.Linear(inner_dim, dim)
self.dropout = nn.Dropout(dropout)
def forward(self, x, pos_emb = None, context = None, mask = None, context_mask = None, output_attentions = False, **kwargs):
b, n, _, h, gh = *x.shape, self.heads, self.global_heads
cross_attend = exists(context)
context = default(context, x)
context_mask = default(context_mask, mask) if not cross_attend else context_mask
q, k, v = self.to_q(x), self.to_k(context), self.to_v(context)
q, k, v = map(lambda t: rearrange(t, 'b n (h d) -> b h n d', h = h), (q, k, v))
(q, lq), (k, lk), (v, lv) = map(lambda t: (t[:, :gh], t[:, gh:]), (q, k, v))
attn_outs = []
if not empty(q):
if exists(context_mask):
global_mask = context_mask[:, None, :, None]
v.masked_fill_(~global_mask, 0.)
if exists(pos_emb) and not cross_attend:
q, k, = apply_rotary_pos_emb(q, k, pos_emb)
if output_attentions:
out, attn_weights = self.fast_attention(q, k, v, output_attentions)
else:
out = self.fast_attention(q, k, v)
attn_outs.append(out)
if not empty(lq):
assert not cross_attend, 'local attention is not compatible with cross attention'
out = self.local_attn(lq, lk, lv, input_mask = mask)
attn_outs.append(out)
out = torch.cat(attn_outs, dim = 1) # combine attn_out and cross_attn_out, here we have only attn_out, that means this line does nothing
out = rearrange(out, 'b h n d -> b n (h d)')
out = self.to_out(out)
if output_attentions:
return self.dropout(out), attn_weights
else:
return self.dropout(out)
# positional embeddings
class AbsolutePositionalEmbedding(nn.Module):
def __init__(self, dim, max_seq_len):
super().__init__()
self.emb = nn.Embedding(max_seq_len, dim)
def forward(self, x):
t = torch.arange(x.shape[1], device=x.device)
return self.emb(t)
# rotary positional embedding helpers
def rotate_every_two(x):
x = rearrange(x, '... (d j) -> ... d j', j = 2)
x1, x2 = x.unbind(dim = -1)
x = torch.stack((-x2, x1), dim = -1)
return rearrange(x, '... d j -> ... (d j)')
def apply_rotary_pos_emb(q, k, sinu_pos):
sinu_pos = rearrange(sinu_pos, '() n (j d) -> n j d', j = 2)
sin, cos = sinu_pos.unbind(dim = -2)
sin, cos = map(lambda t: repeat(t, 'b n -> b (n j)', j = 2), (sin, cos))
q, k = map(lambda t: (t * cos) + (rotate_every_two(t) * sin), (q, k))
return q, k
# sinusoidal positional embeddings
class Gene2VecPositionalEmbedding(nn.Module):
def __init__(self, dim, max_seq_len):
super().__init__()
gene2vec_weight = np.load('./data/gene2vec_16906.npy')
gene2vec_weight = np.concatenate((gene2vec_weight, np.zeros((1, gene2vec_weight.shape[1]))), axis=0)
gene2vec_weight = torch.from_numpy(gene2vec_weight)
self.emb = nn.Embedding.from_pretrained(gene2vec_weight)
def forward(self, x):
t = torch.arange(x.shape[1], device=x.device)
return self.emb(t)
# performer
class Performer(nn.Module):
def __init__(
self,
dim, # dimension
depth, # layers
heads, # heads
dim_head, # dim of head
local_attn_heads = 0, # num of local attention heads, (heads - local_attn_heads) is num of global performers
local_window_size = 256, # window size of local attention
causal = False, # autoregressive or not
ff_mult = 4, # dim of intermediate features after attention / dim of input features
nb_features = None, # number of random features, if not set, will default to (d * log(d)), where d is the dimension of each head ?? what is random feature ??
feature_redraw_interval = 1000, # how frequently to redraw the projection matrix, the more frequent, the slower the training
reversible = False, # reversible layers, from Reformer (save memory)
ff_chunks = 1, # chunk feedforward layer, from Reformer
generalized_attention = False, # defaults to softmax approximation, but can be set to True for generalized attention ?? what is generalized attention ??
kernel_fn = nn.ReLU(), # the kernel function to be used, if generalized attention is turned on, defaults to Relu
use_scalenorm = False, # use scale norm, from 'Transformers without Tears' paper, a substitute for LayerNorm, priority: scalenorm.rezero.layernorm
use_rezero = False, # use Rezero or not, from 'Rezero is all you need' paper, a substitute for LayerNorm, priority: scalenorm.rezero.layernorm
ff_glu = False, # use GLU (Gated Linear Units) variant for feedforward
ff_dropout = 0., # feedforward dropout
attn_dropout = 0., # post-attention dropout
cross_attend = False, # ??
no_projection = False, # ??
auto_check_redraw = True, # ??
qkv_bias = True, # ??
):
super().__init__()
layers = nn.ModuleList([])
local_attn_heads = cast_tuple(local_attn_heads)
local_attn_heads = local_attn_heads * depth if len(local_attn_heads) == 1 else local_attn_heads
assert len(local_attn_heads) == depth, 'tuple specifying number of local attention heads per depth must be equal to the total depth'
assert all(map(lambda n: n >= 0 and n <= heads, local_attn_heads)), 'local attention head value must be less than the total number of heads'
if use_scalenorm:
wrapper_fn = partial(PreScaleNorm, dim)
elif use_rezero:
wrapper_fn = ReZero
else:
wrapper_fn = partial(PreLayerNorm, dim)
for _, local_heads in zip(range(depth), local_attn_heads):
layers.append(nn.ModuleList([
wrapper_fn(SelfAttention(dim, causal = causal, heads = heads, dim_head = dim_head, local_heads = local_heads, local_window_size = local_window_size, nb_features = nb_features, generalized_attention = generalized_attention, kernel_fn = kernel_fn, dropout = attn_dropout, no_projection = no_projection, qkv_bias = qkv_bias)),
wrapper_fn(Chunk(ff_chunks, FeedForward(dim, mult = ff_mult, dropout = ff_dropout, glu = ff_glu), along_dim = 1))
]))
# if no need cross_attend(decoder), begin next cycle
if not cross_attend:
continue
layers.append(nn.ModuleList([
wrapper_fn(SelfAttention(dim, heads = heads, dim_head = dim_head, nb_features = nb_features, generalized_attention = generalized_attention, kernel_fn = kernel_fn, dropout = attn_dropout, no_projection = no_projection)),
wrapper_fn(Chunk(ff_chunks, FeedForward(dim, mult = ff_mult, dropout = ff_dropout, glu = ff_glu), along_dim = 1))
]))
execute_type = ReversibleSequence if reversible else SequentialSequence
route_attn = ((True, False),) * depth * (2 if cross_attend else 1) # ((True, False), (True, False), (True, False), (True, False), (True, False), (True, False))
route_context = ((False, False), (True, False)) * depth
attn_route_map = {'mask': route_attn, 'pos_emb': route_attn}
context_route_map = {'context': route_context, 'context_mask': route_context} if cross_attend else {}
self.net = execute_type(layers, args_route = {**attn_route_map, **context_route_map})
# keeping track of when to redraw projections for all attention layers
self.auto_check_redraw = auto_check_redraw
self.feature_redraw_interval = feature_redraw_interval
self.register_buffer('calls_since_last_redraw', torch.tensor(0))
def fix_projection_matrices_(self):
self.feature_redraw_interval = None
def check_redraw_projections(self):
if not self.training:
return
if exists(self.feature_redraw_interval) and self.calls_since_last_redraw >= self.feature_redraw_interval:
device = get_module_device(self)
fast_attentions = find_modules(self, FastAttention)
for fast_attention in fast_attentions:
fast_attention.redraw_projection_matrix(device)
self.calls_since_last_redraw.zero_()
return
self.calls_since_last_redraw += 1
def forward(self, x, output_attentions = False, **kwargs):
if self.auto_check_redraw:
self.check_redraw_projections()
return self.net(x, output_attentions = output_attentions, **kwargs)
class PerformerLM(nn.Module):
def __init__(
self,
*,
num_tokens, # num of tokens
max_seq_len, # max length of sequence
dim, # dim of tokens
depth, # layers
heads, # num of heads
dim_head = 64, # dim of heads
local_attn_heads = 0,
local_window_size = 256,
causal = False,
ff_mult = 4,
nb_features = None,
feature_redraw_interval = 1000,
reversible = False,
ff_chunks = 1,
ff_glu = False,
emb_dropout = 0.,
ff_dropout = 0.,
attn_dropout = 0.,
generalized_attention = False,
kernel_fn = nn.ReLU(),
use_scalenorm = False,
use_rezero = False,
cross_attend = False,
no_projection = False,
tie_embed = False, # False: output is num of tokens, True: output is dim of tokens //multiply final embeddings with token weights for logits, like gpt decoder//
g2v_position_emb = True, # priority: gene2vec, no embedding
auto_check_redraw = True,
qkv_bias = False
):
super().__init__()
local_attn_heads = cast_tuple(local_attn_heads)
self.max_seq_len = max_seq_len
self.token_emb = nn.Embedding(num_tokens, dim)
if g2v_position_emb:
self.pos_emb = Gene2VecPositionalEmbedding(dim, max_seq_len)
self.layer_pos_emb = Always(None)
else:
self.pos_emb = torch.zeros_like
self.layer_pos_emb = Always(None)
self.dropout = nn.Dropout(emb_dropout)
self.performer = Performer(dim, depth, heads, dim_head, local_attn_heads, local_window_size, causal, ff_mult, nb_features, feature_redraw_interval, reversible, ff_chunks, generalized_attention, kernel_fn, use_scalenorm, use_rezero, ff_glu, ff_dropout, attn_dropout, cross_attend, no_projection, auto_check_redraw, qkv_bias)
self.norm = nn.LayerNorm(dim)
self.to_out = nn.Linear(dim, num_tokens) if not tie_embed else None
def check_redraw_projections(self):
self.performer.check_redraw_projections()
def fix_projection_matrices_(self):
self.performer.fix_projection_matrices_()
def forward(self, x, return_encodings = False, output_attentions = False, **kwargs):
b, n, device = *x.shape, x.device
assert n <= self.max_seq_len, f'sequence length {n} must be less than the max sequence length {self.max_seq_len}'
# token and positional embedding
x = self.token_emb(x)
if output_attentions:
x.requires_grad_() # used for attn_map output
x += self.pos_emb(x)
x = self.dropout(x)
# performer layers
layer_pos_emb = self.layer_pos_emb(x)
if output_attentions:
x, attn_weights = self.performer(x, pos_emb = layer_pos_emb, output_attentions = output_attentions, **kwargs)
# norm and to logits
x = self.norm(x)
if return_encodings:
return x, attn_weights
if exists(self.to_out):
return self.to_out(x), attn_weights
return (x @ self.token_emb.weight.t()), attn_weights
else:
x = self.performer(x, pos_emb = layer_pos_emb, output_attentions = output_attentions, **kwargs)
# norm and to logits
x = self.norm(x)
if return_encodings:
return x
if exists(self.to_out):
x = self.to_out(x)
return x
return x @ self.token_emb.weight.t()
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