Image Segmentation
Transformers
PyTorch
repcontur
feature-extraction
medical
radiology
ct
3d
tumor-segmentation
referring-segmentation
report-generation
visual-question-answering
custom_code
Instructions to use Oncosoft-Research/RepConTUR with libraries, inference providers, notebooks, and local apps. Follow these links to get started.
- Libraries
- Transformers
How to use Oncosoft-Research/RepConTUR with Transformers:
# Use a pipeline as a high-level helper from transformers import pipeline pipe = pipeline("image-segmentation", model="Oncosoft-Research/RepConTUR", trust_remote_code=True)# pip install -U transformers accelerate # Load model directly from transformers import AutoModel model = AutoModel.from_pretrained("Oncosoft-Research/RepConTUR", trust_remote_code=True, device_map="auto") - Notebooks
- Google Colab
- Kaggle
File size: 10,637 Bytes
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import torch
import torch.nn.functional as F
from torch import nn, einsum
from beartype import beartype
from typing import Tuple
from einops import rearrange, repeat
# helpers
def exists(val):
return val is not None
def default(val, d):
return val if exists(val) else d
def leaky_relu(p = 0.1):
return nn.LeakyReLU(p)
def l2norm(t):
return F.normalize(t, dim = -1)
# bias-less layernorm, being used in more recent T5s, PaLM, also in @borisdayma 's experiments shared with me
# greater stability
class LayerNorm(nn.Module):
def __init__(self, dim):
super().__init__()
self.gamma = nn.Parameter(torch.ones(dim))
self.register_buffer("beta", torch.zeros(dim))
def forward(self, x):
return F.layer_norm(x, x.shape[-1:],
self.gamma.to(x.dtype), self.beta.to(x.dtype))
# feedforward
class GEGLU(nn.Module):
def forward(self, x):
x, gate = x.chunk(2, dim = -1)
return F.gelu(gate) * x
def FeedForward(dim, mult = 4, dropout = 0.):
inner_dim = int(mult * (2 / 3) * dim)
return nn.Sequential(
nn.LayerNorm(dim),
nn.Linear(dim, inner_dim * 2, bias = False),
GEGLU(),
nn.Dropout(dropout),
nn.Linear(inner_dim, dim, bias = False)
)
# PEG - position generating module
class PEG(nn.Module):
def __init__(self, dim, causal = False):
super().__init__()
self.causal = causal
self.dsconv = nn.Conv3d(dim, dim, 3, groups = dim)
@beartype
def forward(self, x, shape: Tuple[int, int, int, int] = None):
needs_shape = x.ndim == 3
assert not (needs_shape and not exists(shape))
orig_shape = x.shape
if needs_shape:
x = x.reshape(*shape, -1)
x = rearrange(x, 'b ... d -> b d ...')
frame_padding = (2, 0) if self.causal else (1, 1)
x = F.pad(x, (1, 1, 1, 1, *frame_padding), value = 0.)
x = self.dsconv(x)
x = rearrange(x, 'b d ... -> b ... d')
if needs_shape:
x = rearrange(x, 'b ... d -> b (...) d')
return x.reshape(orig_shape)
# attention
class Attention(nn.Module):
def __init__(
self,
dim,
dim_context = None,
dim_head = 64,
heads = 8,
causal = False,
num_null_kv = 0,
norm_context = True,
dropout = 0.,
scale = 8
):
super().__init__()
self.heads = heads
self.causal = causal
self.scale = scale
inner_dim = dim_head * heads
dim_context = default(dim_context, dim)
if causal:
self.rel_pos_bias = AlibiPositionalBias(heads = heads)
self.attn_dropout = nn.Dropout(dropout)
self.norm = LayerNorm(dim)
self.context_norm = LayerNorm(dim_context) if norm_context else nn.Identity()
self.num_null_kv = num_null_kv
# Only create null_kv parameter if num_null_kv > 0
# Zero-element parameters cause DeepSpeed ZeRO partitioning issues
if num_null_kv > 0:
self.null_kv = nn.Parameter(torch.randn(heads, 2 * num_null_kv, dim_head))
else:
self.register_buffer('null_kv', None)
self.to_q = nn.Linear(dim, inner_dim, bias = False)
self.to_kv = nn.Linear(dim_context, inner_dim * 2, bias = False)
self.q_scale = nn.Parameter(torch.ones(dim_head))
self.k_scale = nn.Parameter(torch.ones(dim_head))
self.to_out = nn.Linear(inner_dim, dim, bias = False)
def forward(
self,
x,
mask = None,
context = None,
attn_bias = None
):
batch, device, dtype = x.shape[0], x.device, x.dtype
device=torch.device('cuda')
if exists(context):
context = self.context_norm(context)
kv_input = default(context, x)
x = self.norm(x)
q, k, v = self.to_q(x), *self.to_kv(kv_input).chunk(2, dim = -1)
q, k, v = map(lambda t: rearrange(t, 'b n (h d) -> b h n d', h = self.heads), (q, k, v))
# Only add null key-values if they exist
if self.null_kv is not None:
nk, nv = repeat(self.null_kv, 'h (n r) d -> b h n r d', b = batch, r = 2).unbind(dim = -2)
k = torch.cat((nk, k), dim = -2)
v = torch.cat((nv, v), dim = -2)
q, k = map(l2norm, (q, k))
q = q * self.q_scale
k = k * self.k_scale
sim = einsum('b h i d, b h j d -> b h i j', q, k) * self.scale
i, j = sim.shape[-2:]
if exists(attn_bias):
attn_bias = F.pad(attn_bias, (self.num_null_kv, 0), value = 0.)
sim = sim + attn_bias
if exists(mask):
mask = F.pad(mask, (self.num_null_kv, 0), value = True)
mask = rearrange(mask, 'b j -> b 1 1 j')
sim = sim.masked_fill(~mask, -torch.finfo(sim.dtype).max)
if self.causal:
sim = sim + self.rel_pos_bias(sim)
device=torch.device('cuda')
causal_mask = torch.ones((i, j), device = device, dtype = torch.bool).triu(j - i + 1)
sim = sim.masked_fill(causal_mask, -torch.finfo(sim.dtype).max)
attn = sim.softmax(dim = -1)
attn = self.attn_dropout(attn)
out = einsum('b h i j, b h j d -> b h i d', attn, v)
out = rearrange(out, 'b h n d -> b n (h d)')
return self.to_out(out)
# alibi positional bias for extrapolation
class AlibiPositionalBias(nn.Module):
def __init__(self, heads):
super().__init__()
self.heads = heads
slopes = torch.Tensor(self._get_slopes(heads))
slopes = rearrange(slopes, 'h -> h 1 1')
self.register_buffer('slopes', slopes, persistent = False)
self.register_buffer('bias', None, persistent = False)
def get_bias(self, i, j, device):
device=torch.device('cuda')
i_arange = torch.arange(j - i, j, device = device)
j_arange = torch.arange(j, device = device)
bias = -torch.abs(rearrange(j_arange, 'j -> 1 1 j') - rearrange(i_arange, 'i -> 1 i 1'))
return bias
@staticmethod
def _get_slopes(heads):
def get_slopes_power_of_2(n):
start = (2**(-2**-(math.log2(n)-3)))
ratio = start
return [start*ratio**i for i in range(n)]
if math.log2(heads).is_integer():
return get_slopes_power_of_2(heads)
closest_power_of_2 = 2 ** math.floor(math.log2(heads))
return get_slopes_power_of_2(closest_power_of_2) + get_slopes_power_of_2(2 * closest_power_of_2)[0::2][:heads-closest_power_of_2]
def forward(self, sim):
h, i, j, device = *sim.shape[-3:], sim.device
if exists(self.bias) and self.bias.shape[-1] >= j:
return self.bias[..., :i, :j]
device=torch.device('cuda')
bias = self.get_bias(i, j, device)
bias = bias * self.slopes
num_heads_unalibied = h - bias.shape[0]
bias = F.pad(bias, (0, 0, 0, 0, 0, num_heads_unalibied))
self.register_buffer('bias', bias, persistent = False)
return self.bias
class ContinuousPositionBias(nn.Module):
""" from https://arxiv.org/abs/2111.09883 """
def __init__(
self,
*,
dim,
heads,
num_dims = 2, # 2 for images, 3 for video
layers = 2,
log_dist = True,
cache_rel_pos = False
):
super().__init__()
self.num_dims = num_dims
self.log_dist = log_dist
self.net = nn.ModuleList([])
self.net.append(nn.Sequential(nn.Linear(self.num_dims, dim), leaky_relu()))
for _ in range(layers - 1):
self.net.append(nn.Sequential(nn.Linear(dim, dim), leaky_relu()))
self.net.append(nn.Linear(dim, heads))
self.cache_rel_pos = cache_rel_pos
self.register_buffer('rel_pos', None, persistent = False)
def forward(self, *dimensions, device = torch.device('cpu')):
if not exists(self.rel_pos) or not self.cache_rel_pos:
device=torch.device('cuda')
positions = [torch.arange(d, device = device) for d in dimensions]
grid = torch.stack(torch.meshgrid(*positions, indexing = 'ij'))
grid = rearrange(grid, 'c ... -> (...) c')
rel_pos = rearrange(grid, 'i c -> i 1 c') - rearrange(grid, 'j c -> 1 j c')
if self.log_dist:
rel_pos = torch.sign(rel_pos) * torch.log(rel_pos.abs() + 1)
self.register_buffer('rel_pos', rel_pos, persistent = False)
# Get the dtype of the model weights for consistent computation
target_dtype = self.net[0][0].weight.dtype if len(self.net) > 0 else torch.float32
rel_pos = self.rel_pos.to(target_dtype)
for layer in self.net:
rel_pos = layer(rel_pos)
return rearrange(rel_pos, 'i j h -> h i j')
# transformer
class Transformer(nn.Module):
def __init__(
self,
dim,
*,
depth,
dim_context = None,
causal = False,
dim_head = 64,
heads = 8,
ff_mult = 4,
peg = False,
peg_causal = False,
attn_num_null_kv = 2,
has_cross_attn = False,
attn_dropout = 0.,
ff_dropout = 0.
):
super().__init__()
self.layers = nn.ModuleList([])
for _ in range(depth):
self.layers.append(nn.ModuleList([
PEG(dim = dim, causal = peg_causal) if peg else None,
Attention(dim = dim, dim_head = dim_head, heads = heads, causal = causal, dropout = attn_dropout),
Attention(dim = dim, dim_head = dim_head, dim_context = dim_context, heads = heads, causal = False, num_null_kv = attn_num_null_kv, dropout = attn_dropout) if has_cross_attn else None,
FeedForward(dim = dim, mult = ff_mult, dropout = ff_dropout)
]))
self.norm_out = LayerNorm(dim)
@beartype
def forward(
self,
x,
video_shape: Tuple[int, int, int, int] = None,
attn_bias = None,
context = None,
self_attn_mask = None,
cross_attn_context_mask = None
):
for peg, self_attn, cross_attn, ff in self.layers:
if exists(peg):
x = peg(x, shape = video_shape) + x
x = self_attn(x, attn_bias = attn_bias, mask = self_attn_mask) + x
if exists(cross_attn) and exists(context):
x = cross_attn(x, context = context, mask = cross_attn_context_mask) + x
x = ff(x) + x
return self.norm_out(x)
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