Neural Nets
Fully convolutional neural networks
- class atomai.nets.Unet(nb_classes=1, nb_filters=16, dropout=False, batch_norm=True, upsampling_mode='bilinear', with_dilation=False, **kwargs)[source]
Bases:
torch.nn.Module
Builds a fully convolutional Unet-like neural network model
- Parameters
nb_classes (
int
) – Number of classes in the ground truthnb_filters (
int
) – Number of filters in 1st convolutional block (gets multiplied by 2 in each next block)dropout (
bool
) – Use dropouts to the 3 inner layers (Default: False)batch_norm (
bool
) – Use batch normalization after each convolutional layer (Default: True)upsampling_mode (
str
) – Select between “bilinear” or “nearest” upsampling method. Bilinear is usually more accurate,but adds additional (small) randomness. For full reproducibility, consider using ‘nearest’ (this assumes that all other sources of randomness are fixed)with_dilation (
bool
) – Use dilated convolutions instead of regular ones in the bottleneck layers (Default: False)**layers (list) – List with a number of layers in each block. The first 4 elements in the list are used to determine the number of layers in each block of the encoder (incluidng bottleneck layers), and the number of layers in the decoder is chosen accordingly (to maintain symmetry between encoder and decoder)
- class atomai.nets.dilnet(nb_classes=1, nb_filters=25, dropout=False, batch_norm=True, upsampling_mode='bilinear', **kwargs)[source]
Bases:
torch.nn.Module
Builds a fully convolutional neural network model by utilizing a combination of regular and dilated convolutions
- Parameters
nb_classes (
int
) – Number of classes in the ground truthnb_filters (
int
) – Number of filters in first and last convolutional blocks (gets multiplied by 2 for the bottleneck layer)dropout (
bool
) – Add dropouts to the bottleneck layers (Default: False)batch_norm (
bool
) – Add batch normalization for each convolutional layer (Default: True)upsampling_mode (
str
) – Select between “bilinear” or “nearest” upsampling method. Bilinear is usually more accurate,but adds additional (small) randomness. For full reproducibility, consider using ‘nearest’ (this assumes that all other sources of randomness are fixed)**layers (list) – List with a number of layers for each block (Default: [3, 3, 3, 3])
- class atomai.nets.ResHedNet(nb_classes=1, nb_filters=64, upsampling_mode='bilinear', **kwargs)[source]
Bases:
torch.nn.Module
Holistic edge detector with residual connections in each block
- Parameters
nb_classes (
int
) – Number of classes in the ground truthnb_filters (
int
) – Number of filters in 1st residual block (gets multiplied by 2 in each next block)upsampling_mode (
str
) – Select between “bilinear” or “nearest” upsampling method. Bilinear is usually more accurate,but adds additional (small) randomness. For full reproducibility, consider using ‘nearest’ (this assumes that all other sources of randomness are fixed)**layers (list) – 3-element list with a number of residual blocks in each segment (Default: [3, 4, 5])
- class atomai.nets.SegResNet(nb_classes=1, nb_filters=32, batch_norm=True, upsampling_mode='bilinear', **kwargs)[source]
Bases:
torch.nn.Module
Builds a fully convolutional neural network based on residual blocks for semantic segmentation
- Parameters
nb_classes (
int
) – Number of classes in the ground truthnb_filters (
int
) – Number of filters in 1st residual block (gets multiplied by 2 in each next block)batch_norm (
bool
) – Use batch normalization after each convolutional layer (Default: True)upsampling_mode (
str
) – Select between “bilinear” or “nearest” upsampling method. Bilinear is usually more accurate,but adds additional (small) randomness. For full reproducibility, consider using ‘nearest’ (this assumes that all other sources of randomness are fixed)**layers (list) – 3-element list with a number of residual blocks in each residual segment (Default: [2, 2])
Neural Networks for VAE
- class atomai.nets.fcEncoderNet(in_dim, latent_dim=2, num_layers=2, hidden_dim=32, **kwargs)[source]
Bases:
torch.nn.Module
Encoder/inference network (for variational autoencoder)
- Parameters
in_dim (
Tuple
[int
]) – Input dimensions. For images, it is (height, width) or (height, width, channels). For spectra, it is (length,)latent_dim (
int
) – number of latent dimensions (the first 3 latent dimensions are angle & translations by default)num_layers (
int
) – number of NN layershidden_dim (
int
) – number of neurons in each fully connnected layer (for mlp=True) or number of filters in each convolutional layer (for mlp=False)**softplus_out (bool) – Optionally applies a softplus activation to the output associated with standard deviation of the encoded distribution
- class atomai.nets.convEncoderNet(in_dim, latent_dim=2, num_layers=2, hidden_dim=32, **kwargs)[source]
Bases:
torch.nn.Module
Convolutional encoder/inference network (for variational autoencoder)
- Parameters
in_dim (
Tuple
[int
]) – Input dimensions. For images, it is (height, width) or (height, width, channels). For spectra, it is (length,)latent_dim (
int
) – number of latent dimensions (the first 3 latent dimensions are angle & translations by default)num_layers (
int
) – number of NN layershidden_dim (
int
) – number of neurons in each fully connnected layer (for mlp=True) or number of filters in each convolutional layer (for mlp=False)**softplus_out (bool) – Optionally applies a softplus activation to the output associated with standard deviation of the encoded distribution
- class atomai.nets.fcDecoderNet(out_dim, latent_dim, num_layers=2, hidden_dim=32)[source]
Bases:
torch.nn.Module
Decoder network (for variational autoencoder)
- Parameters
out_dim (
Tuple
[int
]) – Output dimensions. For images, it is (height, width) or (height, width, channels). For spectra, it is (length,)latent_dim (
int
) – number of latent dimensions associated with images contentnum_layers (
int
) – number of fully connected layershidden_dim (
int
) – number of neurons in each fully connected layer
- class atomai.nets.convDecoderNet(out_dim, latent_dim, num_layers=2, hidden_dim=32, **kwargs)[source]
Bases:
torch.nn.Module
Convolutional decoder network (for variational autoencoder)
- Parameters
out_dim (
Tuple
[int
]) – Output dimensions. For images, it is (height, width) or (height, width, channels). For spectra, it is (length,)latent_dim (
int
) – number of latent dimensions associated with images contentnum_layers (
int
) – number of fully connected layershidden_dim (
int
) – number of neurons in each fully connected layer
- class atomai.nets.rDecoderNet(out_dim, latent_dim, num_layers, hidden_dim, skip=False)[source]
Bases:
torch.nn.Module
Spatial decoder network with (optional) skip connections
- Parameters
out_dim (
Tuple
[int
]) – output dimensions: (height, width) or (height, width, channels)latent_dim (
int
) – number of latent dimensions associated with images contentnum_layers (
int
) – number of fully connected layershidden_dim (
int
) – number of neurons in each fully connected layerskip (
bool
) – Use skip connections to propagate latent variables through decoder network (Default: False)
Neural Networks for ImSpec
- class atomai.nets.SignalEncoder(signal_dim, z_dim, nb_layers, nb_filters, **kwargs)[source]
Bases:
torch.nn.Module
Encodes 1D/2D signal into a latent vector
- Parameters
signal_dim (
Tuple
[int
]) – Size of input signal. For images, it is (height, width). For spectra, it is (length,)z_dim (
int
) – Number of fully-connected neurons in a “bottleneck layer” (latent dimensions)nb_layers (
int
) – Number of convolutional layersnb_filters (
int
) – Number of convolutional filters (aka “kernels”) in each layer**batch_norm (bool) – Apply batch normalization after each convolutional layer (Default: True)
**downsampling (int) – Downsamples input data by this factor before passing to convolutional layers (Default: no downsampling)
- class atomai.nets.SignalDecoder(signal_dim, z_dim, nb_layers, nb_filters, **kwargs)[source]
Bases:
torch.nn.Module
Decodes a latent vector into 1D/2D signal
- Parameters
signal_dim (
Tuple
[int
]) – Size of input signal. For images, it is (height, width). For spectra, it is (length,)z_dim (
int
) – Number of fully-connected neurons in a “bottleneck layer” (latent dimensions)nb_layers (
int
) – Number of convolutional layersnb_filters (
int
) – Number of convolutional filters (aka “kernels”) in each layer**batch_norm (bool) – Apply batch normalization after each convolutional layer (Default: True)
**upsampling (bool) – Performs upsampling+convolution operation twice on the reshaped latent vector (starting from image/spectra dims 4x smaller than the target dims) before passing to the decoder
- class atomai.nets.SignalED(feature_dim, target_dim, latent_dim, nblayers_encoder=2, nblayers_decoder=2, nbfilters_encoder=64, nbfilters_decoder=2, batch_norm=True, encoder_downsampling=0, decoder_upsampling=False)[source]
Bases:
torch.nn.Module
Transforms image into spectra (im2spec) and vice versa (spec2im)
- Parameters
feature_dim (
Tuple
[int
]) – Input data dimensions. (height, width) for images or (length,) for spectratarget_dim (
Tuple
[int
]) – Output dimensions. (length,) for spectra or (height, width) for imageslatent_dim (
int
) – Dimensionality of the latent space (number of neurons in a fully connected “bottleneck” layer)nblayers_encoder (
int
) – Number of convolutional layers in the encodernblayers_decoder (
int
) – Number of convolutional layers in the decodernbfilters_encoder (
int
) – number of convolutional filters in each layer of the encodernbfilters_decoder (
int
) – Number of convolutional filters in each layer of the decoderbatch_norm (
bool
) – Apply batch normalization after each convolutional layer (Default: True)encoder_downsampling (
int
) – Downsamples input data by this factor before passing to convolutional layers (Default: no downsampling)decoder_upsampling (
bool
) – Performs upsampling+convolution operation twice on the reshaped latent vector (starting from image/spectra dims 4x smaller than the target dims) before passing to the decoder
Building blocks
- class atomai.nets.ConvBlock(ndim, nb_layers, input_channels, output_channels, kernel_size=3, stride=1, padding=1, batch_norm=False, lrelu_a=0.01, dropout_=0)[source]
Bases:
torch.nn.Module
Creates block of layers each consisting of convolution operation, leaky relu and (optionally) dropout and batch normalization
- Parameters
ndim (
int
) – Data dimensionality (1D or 2D)nb_layers (
int
) – Number of layers in the blockinput_channels (
int
) – Number of input channels for the blockoutput_channels (
int
) – Number of the output channels for the blockkernel_size (
Union
[Tuple
[int
],int
]) – Size of convolutional filter (in pixels)stride (
Union
[Tuple
[int
],int
]) – Stride of convolutional filterpadding (
Union
[Tuple
[int
],int
]) – Value for edge paddingbatch_norm (
bool
) – Add batch normalization to each layer in the blocklrelu_a (
float
) – Value of alpha parameter in leaky ReLU activation for each layer in the blockdropout – Dropout value for each layer in the block
- class atomai.nets.DilatedBlock(ndim, input_channels, output_channels, dilation_values, padding_values, kernel_size=3, stride=1, lrelu_a=0.01, batch_norm=False, dropout_=0)[source]
Bases:
torch.nn.Module
Creates a “cascade” with dilated convolutional layers (aka atrous convolutions)
- Parameters
ndim (
int
) – Data dimensionality (1D or 2D)input_channels (
int
) – Number of input channels for the blockoutput_channels (
int
) – Number of the output channels for the blockdilation_values (
List
[int
]) – List of dilation rates for each convolution layer in the block (for example, dilation_values = [2, 4, 6] means that the dilated block will 3 layers with dilation values of 2, 4, and 6).padding_values (
List
[int
]) – Edge padding for each dilated layer. The number of elements in this list should be equal to that in the dilated_values list and typically they can have the same values.kernel_size (
Union
[Tuple
[int
],int
]) – Size of convolutional filter (in pixels)stride (
Union
[Tuple
[int
],int
]) – Stride of convolutional filterbatch_norm (
bool
) – Add batch normalization to each layer in the blocklrelu_a (
float
) – Value of alpha parameter in leaky ReLU activation for each layer in the blockdropout – Dropout value for each layer in the block
- class atomai.nets.UpsampleBlock(ndim, input_channels, output_channels, scale_factor=2, mode='bilinear')[source]
Bases:
torch.nn.Module
Defines upsampling block performed using bilinear or nearest-neigbor interpolation followed by 1-by-1 convolution (the latter can be used to reduce a number of feature channels)
- Parameters
ndim (
int
) – Data dimensionality (1D or 2D)input_channels (
int
) – Number of input channels for the blockoutput_channels (
int
) – Number of the output channels for the blockscale_factor (
int
) – Scale factor for upsamplingmode (
str
) – Upsampling mode. Select between “bilinear” and “nearest”
- class atomai.nets.ResBlock(ndim, input_channels, output_channels, kernel_size=3, stride=1, padding=1, batch_norm=True, lrelu_a=0.01)[source]
Bases:
torch.nn.Module
Builds a residual block
- Parameters
ndim (
int
) – Data dimensionality (1D or 2D)nb_layers – Number of layers in the block
input_channels (
int
) – Number of input channels for the blockoutput_channels (
int
) – Number of the output channels for the blockkernel_size (
Union
[Tuple
[int
],int
]) – Size of convolutional filter (in pixels)stride (
Union
[Tuple
[int
],int
]) – Stride of convolutional filterpadding (
Union
[Tuple
[int
],int
]) – Value for edge paddingbatch_norm (
bool
) – Add batch normalization to each layer in the blocklrelu_a (
float
) – Value of alpha parameter in leaky ReLU activation for each layer in the block
- class atomai.nets.ResModule(ndim, res_depth, input_channels, output_channels, batch_norm=True, lrelu_a=0.01)[source]
Bases:
torch.nn.Module
Stitches multiple convolutional blocks with residual connections together
- Parameters
ndim (
int
) – Data dimensionality (1D or 2D)res_depth (
int
) – Number of residual blocks in a residual moduleinput_channels (
int
) – Number of filters in the input layeroutput_channels (
int
) – Number of channels in the output layerbatch_norm (
bool
) – Batch normalization for non-unity layers in the blocklrelu_a (
float
) – value of negative slope for LeakyReLU activation