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b/BioSeqNet/resnest/torch/resnet.py |
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##+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ |
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## Created by: Hang Zhang |
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## Email: zhanghang0704@gmail.com |
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## Copyright (c) 2020 |
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## |
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## LICENSE file in the root directory of this source tree |
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##+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ |
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"""ResNet variants""" |
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import math |
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import torch |
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import torch.nn as nn |
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from .splat import SplAtConv1d |
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__all__ = ['ResNet', 'Bottleneck'] |
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class DropBlock2D(object): |
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def __init__(self, *args, **kwargs): |
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raise NotImplementedError |
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class GlobalAvgPool1d(nn.Module): |
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def __init__(self): |
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"""Global average pooling over the input's spatial dimensions""" |
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super(GlobalAvgPool1d, self).__init__() |
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def forward(self, inputs): |
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return nn.functional.adaptive_avg_pool1d(inputs, 1).view(inputs.size(0), -1) |
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class Bottleneck(nn.Module): |
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"""ResNet Bottleneck |
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""" |
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# pylint: disable=unused-argument |
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expansion = 4 |
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def __init__(self, inplanes, planes, stride=1, downsample=None, |
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radix=1, cardinality=1, bottleneck_width=64, |
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avd=False, avd_first=False, dilation=1, is_first=False, |
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rectified_conv=False, rectify_avg=False, |
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norm_layer=None, dropblock_prob=0.0, last_gamma=False): |
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super(Bottleneck, self).__init__() |
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group_width = int(planes * (bottleneck_width / 64.)) * cardinality |
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self.conv1 = nn.Conv1d(inplanes, group_width, kernel_size=1, bias=False) |
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self.bn1 = norm_layer(group_width) |
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self.dropblock_prob = dropblock_prob |
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self.radix = radix |
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self.avd = avd and (stride > 1 or is_first) |
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self.avd_first = avd_first |
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if self.avd: |
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self.avd_layer = nn.AvgPool1d(3, stride, padding=1) |
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stride = 1 |
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if dropblock_prob > 0.0: |
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self.dropblock1 = DropBlock2D(dropblock_prob, 3) |
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if radix == 1: |
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self.dropblock2 = DropBlock2D(dropblock_prob, 3) |
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self.dropblock3 = DropBlock2D(dropblock_prob, 3) |
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if radix >= 1: |
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self.conv2 = SplAtConv1d( |
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group_width, group_width, kernel_size=3, |
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stride=stride, padding=dilation, |
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dilation=dilation, groups=cardinality, bias=False, |
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radix=radix, rectify=rectified_conv, |
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rectify_avg=rectify_avg, |
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norm_layer=norm_layer, |
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dropblock_prob=dropblock_prob) |
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elif rectified_conv: |
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from rfconv import RFConv1d |
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self.conv2 = RFConv1d( |
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group_width, group_width, kernel_size=3, stride=stride, |
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padding=dilation, dilation=dilation, |
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groups=cardinality, bias=False, |
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average_mode=rectify_avg) |
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self.bn2 = norm_layer(group_width) |
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else: |
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self.conv2 = nn.Conv1d( |
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group_width, group_width, kernel_size=3, stride=stride, |
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padding=dilation, dilation=dilation, |
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groups=cardinality, bias=False) |
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self.bn2 = norm_layer(group_width) |
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self.conv3 = nn.Conv1d( |
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group_width, planes * 4, kernel_size=1, bias=False) |
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self.bn3 = norm_layer(planes*4) |
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if last_gamma: |
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from torch.nn.init import zeros_ |
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zeros_(self.bn3.weight) |
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self.relu = nn.ReLU(inplace=True) |
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self.downsample = downsample |
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self.dilation = dilation |
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self.stride = stride |
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def forward(self, x): |
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residual = x |
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out = self.conv1(x) |
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out = self.bn1(out) |
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if self.dropblock_prob > 0.0: |
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out = self.dropblock1(out) |
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out = self.relu(out) |
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if self.avd and self.avd_first: |
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out = self.avd_layer(out) |
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out = self.conv2(out) |
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if self.radix == 0: |
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out = self.bn2(out) |
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if self.dropblock_prob > 0.0: |
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out = self.dropblock2(out) |
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out = self.relu(out) |
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if self.avd and not self.avd_first: |
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out = self.avd_layer(out) |
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out = self.conv3(out) |
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out = self.bn3(out) |
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if self.dropblock_prob > 0.0: |
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out = self.dropblock3(out) |
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if self.downsample is not None: |
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residual = self.downsample(x) |
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out += residual |
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out = self.relu(out) |
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return out |
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class ResNet(nn.Module): |
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"""ResNet Variants |
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Parameters |
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---------- |
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block : Block |
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Class for the residual block. Options are BasicBlockV1, BottleneckV1. |
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layers : list of int |
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Numbers of layers in each block |
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classes : int, default 1000 |
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Number of classification classes. |
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dilated : bool, default False |
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Applying dilation strategy to pretrained ResNet yielding a stride-8 model, |
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typically used in Semantic Segmentation. |
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norm_layer : object |
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Normalization layer used in backbone network (default: :class:`mxnet.gluon.nn.BatchNorm`; |
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for Synchronized Cross-GPU BachNormalization). |
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Reference: |
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- He, Kaiming, et al. "Deep residual learning for image recognition." Proceedings of the IEEE conference on computer vision and pattern recognition. 2016. |
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- Yu, Fisher, and Vladlen Koltun. "Multi-scale context aggregation by dilated convolutions." |
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""" |
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# pylint: disable=unused-variable |
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def __init__(self, block, layers, radix=1, groups=1, bottleneck_width=64, |
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num_classes=1000, dilated=False, dilation=1, |
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deep_stem=False, stem_width=64, avg_down=False, |
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rectified_conv=False, rectify_avg=False, |
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avd=False, avd_first=False, |
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final_drop=0.0, dropblock_prob=0, |
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last_gamma=False, norm_layer=nn.BatchNorm1d, num_channels=4): |
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self.cardinality = groups |
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self.bottleneck_width = bottleneck_width |
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# ResNet-D params |
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self.inplanes = stem_width*2 if deep_stem else 64 |
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self.avg_down = avg_down |
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self.last_gamma = last_gamma |
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# ResNeSt params |
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self.radix = radix |
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self.avd = avd |
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self.avd_first = avd_first |
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super(ResNet, self).__init__() |
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self.rectified_conv = rectified_conv |
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self.rectify_avg = rectify_avg |
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if rectified_conv: |
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from rfconv import RFConv1d |
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conv_layer = RFConv1d |
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else: |
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conv_layer = nn.Conv1d |
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conv_kwargs = {'average_mode': rectify_avg} if rectified_conv else {} |
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if deep_stem: |
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self.conv1 = nn.Sequential( |
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conv_layer(num_channels, stem_width, kernel_size=3, stride=2, padding=1, bias=False, **conv_kwargs), |
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norm_layer(stem_width), |
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nn.ReLU(inplace=True), |
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conv_layer(stem_width, stem_width, kernel_size=3, stride=1, padding=1, bias=False, **conv_kwargs), |
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norm_layer(stem_width), |
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nn.ReLU(inplace=True), |
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conv_layer(stem_width, stem_width*2, kernel_size=3, stride=1, padding=1, bias=False, **conv_kwargs), |
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) |
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else: |
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self.conv1 = conv_layer(num_channels, 64, kernel_size=7, stride=2, padding=3, |
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bias=False, **conv_kwargs) |
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self.bn1 = norm_layer(self.inplanes) |
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self.relu = nn.ReLU(inplace=True) |
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self.maxpool = nn.MaxPool1d(kernel_size=3, stride=2, padding=1) |
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self.layer1 = self._make_layer(block, 64, layers[0], norm_layer=norm_layer, is_first=False) |
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self.layer2 = self._make_layer(block, 128, layers[1], stride=2, norm_layer=norm_layer) |
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if dilated or dilation == 4: |
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self.layer3 = self._make_layer(block, 256, layers[2], stride=1, |
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dilation=2, norm_layer=norm_layer, |
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dropblock_prob=dropblock_prob) |
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self.layer4 = self._make_layer(block, 512, layers[3], stride=1, |
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dilation=4, norm_layer=norm_layer, |
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dropblock_prob=dropblock_prob) |
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elif dilation==2: |
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self.layer3 = self._make_layer(block, 256, layers[2], stride=2, |
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dilation=1, norm_layer=norm_layer, |
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dropblock_prob=dropblock_prob) |
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self.layer4 = self._make_layer(block, 512, layers[3], stride=1, |
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dilation=2, norm_layer=norm_layer, |
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dropblock_prob=dropblock_prob) |
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else: |
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self.layer3 = self._make_layer(block, 256, layers[2], stride=2, |
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norm_layer=norm_layer, |
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dropblock_prob=dropblock_prob) |
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self.layer4 = self._make_layer(block, 512, layers[3], stride=2, |
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norm_layer=norm_layer, |
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dropblock_prob=dropblock_prob) |
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self.avgpool = GlobalAvgPool1d() |
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self.drop = nn.Dropout(final_drop) if final_drop > 0.0 else None |
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self.fc = nn.Linear(512 * block.expansion, num_classes) |
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#for m in self.modules(): |
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# if isinstance(m, nn.Conv1d): |
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# n = m.kernel_size[0] * m.kernel_size[1] * m.out_channels |
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# m.weight.data.normal_(0, math.sqrt(2. / n)) |
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# elif isinstance(m, norm_layer): |
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# m.weight.data.fill_(1) |
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# m.bias.data.zero_() |
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def _make_layer(self, block, planes, blocks, stride=1, dilation=1, norm_layer=None, |
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dropblock_prob=0.0, is_first=True): |
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downsample = None |
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if stride != 1 or self.inplanes != planes * block.expansion: |
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down_layers = [] |
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if self.avg_down: |
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if dilation == 1: |
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down_layers.append(nn.AvgPool1d(kernel_size=stride, stride=stride, |
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ceil_mode=True, count_include_pad=False)) |
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else: |
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down_layers.append(nn.AvgPool1d(kernel_size=1, stride=1, |
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ceil_mode=True, count_include_pad=False)) |
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down_layers.append(nn.Conv1d(self.inplanes, planes * block.expansion, |
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kernel_size=1, stride=1, bias=False)) |
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else: |
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down_layers.append(nn.Conv1d(self.inplanes, planes * block.expansion, |
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kernel_size=1, stride=stride, bias=False)) |
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down_layers.append(norm_layer(planes * block.expansion)) |
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downsample = nn.Sequential(*down_layers) |
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layers = [] |
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if dilation == 1 or dilation == 2: |
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layers.append(block(self.inplanes, planes, stride, downsample=downsample, |
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radix=self.radix, cardinality=self.cardinality, |
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bottleneck_width=self.bottleneck_width, |
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avd=self.avd, avd_first=self.avd_first, |
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dilation=1, is_first=is_first, rectified_conv=self.rectified_conv, |
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rectify_avg=self.rectify_avg, |
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norm_layer=norm_layer, dropblock_prob=dropblock_prob, |
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last_gamma=self.last_gamma)) |
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elif dilation == 4: |
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layers.append(block(self.inplanes, planes, stride, downsample=downsample, |
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radix=self.radix, cardinality=self.cardinality, |
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bottleneck_width=self.bottleneck_width, |
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avd=self.avd, avd_first=self.avd_first, |
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dilation=2, is_first=is_first, rectified_conv=self.rectified_conv, |
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rectify_avg=self.rectify_avg, |
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norm_layer=norm_layer, dropblock_prob=dropblock_prob, |
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last_gamma=self.last_gamma)) |
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else: |
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raise RuntimeError("=> unknown dilation size: {}".format(dilation)) |
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self.inplanes = planes * block.expansion |
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for i in range(1, blocks): |
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layers.append(block(self.inplanes, planes, |
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radix=self.radix, cardinality=self.cardinality, |
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bottleneck_width=self.bottleneck_width, |
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avd=self.avd, avd_first=self.avd_first, |
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dilation=dilation, rectified_conv=self.rectified_conv, |
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rectify_avg=self.rectify_avg, |
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norm_layer=norm_layer, dropblock_prob=dropblock_prob, |
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last_gamma=self.last_gamma)) |
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return nn.Sequential(*layers) |
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def forward(self, x): |
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x = self.conv1(x) |
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x = self.bn1(x) |
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x = self.relu(x) |
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x = self.maxpool(x) |
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x = self.layer1(x) |
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x = self.layer2(x) |
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x = self.layer3(x) |
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x = self.layer4(x) |
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x = self.avgpool(x) |
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#x = x.view(x.size(0), -1) |
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x = torch.flatten(x, 1) |
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if self.drop: |
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x = self.drop(x) |
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x = self.fc(x) |
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return x |