关于深度学习:恒源云GpuShare医学图像分割MTUNet

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文章起源 | 恒源云社区

原文地址 | 新的混合 Transformer 模块(MTM)

原文作者 | 咚咚


摘要

存在问题 尽管 U -Net 在医学图像宰割方面获得了微小的胜利,但它不足对长期依赖关系进行显式建模的能力。视觉 Transformer 因为其固有的通过自留神(SA)捕获长程相关性的能力,近年来成为一种可代替的宰割构造。
存在问题 然而,Transformer 通常依赖于大规模的预训练,具备较高的计算复杂度。此外,SA 只能在单个样本中建模 self-affinities,疏忽了整个数据集的潜在相关性
论文办法 提出了一种新的混合 Transformer 模块 (MTM),用于同时进行 inter-affinities 学习和 intra-affinities 学习。MTM 首先通过部分 - 全局高斯加权自留神(LGG-SA) 无效地计算窗口外部 affinities。而后,通过内部留神开掘数据样本之间的分割。利用 MTM 算法,结构了一种用于医学图像宰割的 MT-UNet 模型

Method


如图 1 所示。该网络基于 编码器 - 解码器构造

  1. 为了升高计算成本,MTMs只对空间大小较小的深层应用,
  2. 浅层依然应用经典的卷积运算。这是因为浅层次要关注部分信息,蕴含更多高分辨率的细节。

MTM

如图 2 所示。MTM 次要由 LGG-SA 和 EA 组成。

LGG-SA 用于对不同粒度的短期和长期依赖进行建模,而 EA 用于开掘样本间的相关性。

该模块是为了代替原来的 Transformer 编码器,以进步其在视觉工作上的性能和升高工夫复杂度

LGG-SA(Local-Global Gaussian-Weighted Self-Attention)

传统的 SA 模块对所有 tokens 赋予雷同的关注度,而 LGG -SA 则不同,利用 local-global 自注意力和高斯 mask 使其能够更专一于邻近区域。试验证实,该办法能够进步模型的性能,节俭计算资源。该模块的具体设计如图 3 所示

local-global 自注意力

在计算机视觉中,邻近区域之间的相关性往往比边远区域之间的相关性更重要,在计算留神图时,不须要为更远的区域破费雷同的代价。

因而,提出local-global 自注意力

  1. 上图 stage1 中的每个部分窗口中含有四个 token,local SA 计算每个窗口内的外在 affinities。
  2. 每个窗口中的 token 被 aggregate 聚合为一个全局 token,示意窗口的次要信息。对于 聚合函数 ,轻量级动静卷积(Lightweight Dynamic convolution, LDConv) 的性能最好。
  3. 在失去下采样的整个特色图后,能够以更少的开销执行 global SA(上图 stage2)。


其中 \(X \in R^{H \times W \times C} \)

其中,stage1 中的部分窗口自注意力代码如下:

class WinAttention(nn.Module):
    def __init__(self, configs, dim):
        super(WinAttention, self).__init__()
        self.window_size = configs["win_size"]
        self.attention = Attention(dim, configs)

    def forward(self, x):
        b, n, c = x.shape
        h, w = int(np.sqrt(n)), int(np.sqrt(n))
        x = x.permute(0, 2, 1).contiguous().view(b, c, h, w)
        if h % self.window_size != 0:
            right_size = h + self.window_size - h % self.window_size
            new_x = torch.zeros((b, c, right_size, right_size))
            new_x[:, :, 0:x.shape[2], 0:x.shape[3]] = x[:]
            new_x[:, :, x.shape[2]:,
                  x.shape[3]:] = x[:, :, (x.shape[2] - right_size):,
                                   (x.shape[3] - right_size):]
            x = new_x
            b, c, h, w = x.shape
        x = x.view(b, c, h // self.window_size, self.window_size,
                   w // self.window_size, self.window_size)  
        x = x.permute(0, 2, 4, 3, 5,
                      1).contiguous().view(b, h // self.window_size,
                                           w // self.window_size,
                                           self.window_size * self.window_size,
                                           c).cuda()
        x = self.attention(x)  #  (b, p, p, win, c) 对部分窗口内的 tokens 进行自注意力计算
        return x

聚合函数 代码如下

class DlightConv(nn.Module):
    def __init__(self, dim, configs):
        super(DlightConv, self).__init__()
        self.linear = nn.Linear(dim, configs["win_size"] * configs["win_size"])
        self.softmax = nn.Softmax(dim=-1)

    def forward(self, x):  # (b, p, p, win, c)
        h = x
        avg_x = torch.mean(x, dim=-2)  # (b, p, p, c)
        x_prob = self.softmax(self.linear(avg_x))  # (b, p, p, win)

        x = torch.mul(h,
                      x_prob.unsqueeze(-1))  # (b, p, p, win, c) 
        x = torch.sum(x, dim=-2)  # (b, p, p, c)
        return x

Gaussian-Weighted Axial Attention

与应用原始 SA 的 LSA 不同,提出了高斯加权轴向留神 (GWAA) 的办法。GWAA 通过一个可学习的高斯矩阵加强了相邻区域的感知全权重,同时因为具备轴向注意力而升高了工夫复杂度。

  1. 上图中 stage2 中特色图的第三行第三列特色进行 linear projection 失去 \(q_{i, j} \)
  2. 将该特色点所在行和列的所有特色别离进行 linear projection 失去 \(K_{i, j} \)
    和 \(V_{i, j} \)
  3. 将该特色点与所有的 K 和 V 的欧式间隔定义为 \(D_{i, j} \)

最终的高斯加权轴向注意力输入后果为

并简化为

轴向注意力 代码如下:

class Attention(nn.Module):
    def __init__(self, dim, configs, axial=False):
        super(Attention, self).__init__()
        self.axial = axial
        self.dim = dim
        self.num_head = configs["head"]
        self.attention_head_size = int(self.dim / configs["head"])
        self.all_head_size = self.num_head * self.attention_head_size

        self.query_layer = nn.Linear(self.dim, self.all_head_size)
        self.key_layer = nn.Linear(self.dim, self.all_head_size)
        self.value_layer = nn.Linear(self.dim, self.all_head_size)

        self.out = nn.Linear(self.dim, self.dim)
        self.softmax = nn.Softmax(dim=-1)

    def transpose_for_scores(self, x):
        new_x_shape = x.size()[:-1] + (self.num_head, self.attention_head_size)
        x = x.view(*new_x_shape)
        return x

    def forward(self, x):
        # first row and col attention
        if self.axial:
             # x: (b, p, p, c)
            # row attention (single head attention)
            b, h, w, c = x.shape
            mixed_query_layer = self.query_layer(x)
            mixed_key_layer = self.key_layer(x)
            mixed_value_layer = self.value_layer(x)

            query_layer_x = mixed_query_layer.view(b * h, w, -1)
            key_layer_x = mixed_key_layer.view(b * h, w, -1).transpose(-1, -2)  # (b*h, -1, w)
            attention_scores_x = torch.matmul(query_layer_x,
                                              key_layer_x)  # (b*h, w, w)
            attention_scores_x = attention_scores_x.view(b, -1, w,
                                                         w)  # (b, h, w, w)

            # col attention  (single head attention)
            query_layer_y = mixed_query_layer.permute(0, 2, 1,
                                                      3).contiguous().view(b * w, h, -1)
            key_layer_y = mixed_key_layer.permute(0, 2, 1, 3).contiguous().view(b * w, h, -1).transpose(-1, -2)  # (b*w, -1, h)
            attention_scores_y = torch.matmul(query_layer_y,
                                              key_layer_y)  # (b*w, h, h)
            attention_scores_y = attention_scores_y.view(b, -1, h,
                                                         h)  # (b, w, h, h)

            return attention_scores_x, attention_scores_y, mixed_value_layer

        else:
          
            mixed_query_layer = self.query_layer(x)
            mixed_key_layer = self.key_layer(x)
            mixed_value_layer = self.value_layer(x)

            query_layer = self.transpose_for_scores(mixed_query_layer).permute(0, 1, 2, 4, 3, 5).contiguous()  # (b, p, p, head, n, c)
            key_layer = self.transpose_for_scores(mixed_key_layer).permute(0, 1, 2, 4, 3, 5).contiguous()
            value_layer = self.transpose_for_scores(mixed_value_layer).permute(0, 1, 2, 4, 3, 5).contiguous()

            attention_scores = torch.matmul(query_layer,
                                            key_layer.transpose(-1, -2))
            attention_scores = attention_scores / math.sqrt(self.attention_head_size)
            atten_probs = self.softmax(attention_scores)

            context_layer = torch.matmul(atten_probs, value_layer)  # (b, p, p, head, win, h)
            context_layer = context_layer.permute(0, 1, 2, 4, 3,
                                                  5).contiguous()
            new_context_layer_shape = context_layer.size()[:-2] + (self.all_head_size,)
            context_layer = context_layer.view(*new_context_layer_shape)
            attention_output = self.out(context_layer)

        return attention_output

高斯加权 代码如下:

class GaussianTrans(nn.Module):
    def __init__(self):
        super(GaussianTrans, self).__init__()
        self.bias = nn.Parameter(-torch.abs(torch.randn(1)))
        self.shift = nn.Parameter(torch.abs(torch.randn(1)))
        self.softmax = nn.Softmax(dim=-1)

    def forward(self, x): 
        x, atten_x_full, atten_y_full, value_full = x  #x(b, h, w, c) atten_x_full(b, h, w, w)   atten_y_full(b, w, h, h) value_full(b, h, w, c)
        new_value_full = torch.zeros_like(value_full)

        for r in range(x.shape[1]):  # row
            for c in range(x.shape[2]):  # col
                atten_x = atten_x_full[:, r, c, :]  # (b, w)
                atten_y = atten_y_full[:, c, r, :]  # (b, h)

                dis_x = torch.tensor([(h - c)**2 for h in range(x.shape[2])
                                      ]).cuda()  # (b, w)
                dis_y = torch.tensor([(w - r)**2 for w in range(x.shape[1])
                                      ]).cuda()  # (b, h)

                dis_x = -(self.shift * dis_x + self.bias).cuda()
                dis_y = -(self.shift * dis_y + self.bias).cuda()

                atten_x = self.softmax(dis_x + atten_x)
                atten_y = self.softmax(dis_y + atten_y)

                new_value_full[:, r, c, :] = torch.sum(atten_x.unsqueeze(dim=-1) * value_full[:, r, :, :] +
                    atten_y.unsqueeze(dim=-1) * value_full[:, :, c, :],
                    dim=-2)
        return new_value_full

local-global 自注意力 残缺代码如下:

class CSAttention(nn.Module):
    def __init__(self, dim, configs):
        super(CSAttention, self).__init__()
        self.win_atten = WinAttention(configs, dim)
        self.dlightconv = DlightConv(dim, configs)
        self.global_atten = Attention(dim, configs, axial=True)
        self.gaussiantrans = GaussianTrans()
        #self.conv = nn.Conv2d(dim, dim, 3, padding=1)
        #self.maxpool = nn.MaxPool2d(2)
        self.up = nn.UpsamplingBilinear2d(scale_factor=4)
        self.queeze = nn.Conv2d(2 * dim, dim, 1)

    def forward(self, x):
        '''
        :param x: size(b, n, c)
        :return:
        '''
        origin_size = x.shape
        _, origin_h, origin_w, _ = origin_size[0], int(np.sqrt(origin_size[1])), int(np.sqrt(origin_size[1])), origin_size[2]
        x = self.win_atten(x)  # (b, p, p, win, c)
        b, p, p, win, c = x.shape
        h = x.view(b, p, p, int(np.sqrt(win)), int(np.sqrt(win)),
                   c).permute(0, 1, 3, 2, 4, 5).contiguous()
        h = h.view(b, p * int(np.sqrt(win)), p * int(np.sqrt(win)),
                   c).permute(0, 3, 1, 2).contiguous()  # (b, c, h, w)

        x = self.dlightconv(x)  # (b, p, p, c)
        atten_x, atten_y, mixed_value = self.global_atten(x)  # (b, h, w, w) (b, w, h, h) (b, h, w, c)这里的 h w 就是 p
        gaussian_input = (x, atten_x, atten_y, mixed_value)
        x = self.gaussiantrans(gaussian_input)  # (b, h, w, c)
        x = x.permute(0, 3, 1, 2).contiguous()  # (b, c, h, w)

        x = self.up(x)
        x = self.queeze(torch.cat((x, h), dim=1)).permute(0, 2, 3,
                                                          1).contiguous()
        x = x[:, :origin_h, :origin_w, :].contiguous()
        x = x.view(b, -1, c)

        return x
EA

内部留神 (External Attention, EA),是用于解决 SA 无奈利用 不同输出数据样本之间关系 的问题。

与应用每个样本本人的线性变换来计算留神分数的自我留神不同,在 EA 中,所有的数据样本共享两个记忆单元 MKMV(如图 2 所示),形容了整个数据集的最重要信息。

EA 代码如下:

class MEAttention(nn.Module):
    def __init__(self, dim, configs):
        super(MEAttention, self).__init__()
        self.num_heads = configs["head"]
        self.coef = 4
        self.query_liner = nn.Linear(dim, dim * self.coef)
        self.num_heads = self.coef * self.num_heads
        self.k = 256 // self.coef
        self.linear_0 = nn.Linear(dim * self.coef // self.num_heads, self.k)
        self.linear_1 = nn.Linear(self.k, dim * self.coef // self.num_heads)

        self.proj = nn.Linear(dim * self.coef, dim)

    def forward(self, x):
        B, N, C = x.shape
        x = self.query_liner(x)  # (b, n, 4c)
        x = x.view(B, N, self.num_heads, -1).permute(0, 2, 1,
                                                     3)  #  (b, h, n, 4c/h)

        attn = self.linear_0(x)  # (b, h, n, 256/4)

        attn = attn.softmax(dim=-2)  # (b, h, 256/4)
        attn = attn / (1e-9 + attn.sum(dim=-1, keepdim=True))  # (b, h, 256/4)

        x = self.linear_1(attn).permute(0, 2, 1, 3).reshape(B, N, -1)

        x = self.proj(x)

        return x

EXPERIMENTS



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