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()