eugene.models.zoo.ResidualBind

class eugene.models.zoo.ResidualBind(input_len, output_dim, input_chanels=4, conv_channels=[96], conv_kernel_size=[11], conv_stride_size=[1], conv_dilation_rate=[1], conv_padding='valid', conv_activation='relu', conv_batchnorm=True, conv_batchnorm_first=True, conv_dropout_rates=0.1, conv_biases=False, residual_channels=[96, 96, 96], residual_kernel_size=[3, 3, 3], residual_stride_size=[1, 1, 1], residual_dilation_rate=[1, 2, 4], residual_padding='same', residual_activation='relu', residual_batchnorm=True, residual_batchnorm_first=True, residual_dropout_rates=0.1, residual_biases=False, pool_kernel_size=10, pool_dropout_rate=0.2, dense_hidden_dims=[256], dense_activation='relu', dense_batchnorm=True, dense_batchnorm_first=True, dense_dropout_rates=0.5, dense_biases=False)

ResidualBind architecture implemented from Koo et al 2021 in PyTorch

This is a flexible reimplementation of the original ResidualBind architecture that allows users to tweak hyperparameters. If parameters for the CNN and FCN are not passed in, the model will be instantiated with the parameters described in Koo et al 2021.

Parameters:
  • input_len (int) – Length of input sequence

  • output_dim (int) – Number of output neurons

  • input_chanels (int, optional) – Number of input channels, by default 4

  • conv_channels (list, optional) – Number of channels in the first convolutional layer, by default [96]

  • conv_kernel_size (list, optional) – Kernel size of the first convolutional layer, by default [11]

  • conv_stride_size (list, optional) – Stride size of the first convolutional layer, by default [1]

  • conv_dilation_rate (list, optional) – Dilation rate of the first convolutional layer, by default [1]

  • conv_padding (str, optional) – Padding of the first convolutional layer, by default “valid”

  • conv_activation (str, optional) – Activation function of the first convolutional layer, by default “relu”

  • conv_batchnorm (bool, optional) – Whether to use batchnorm in the first convolutional layer, by default True

  • conv_batchnorm_first (bool, optional) – Whether to use batchnorm before or after the activation in the first convolutional layer, by default True

  • conv_dropout_rates (float, optional) – Dropout rate of the first convolutional layer, by default 0.1

  • conv_biases (bool, optional) – Whether to use biases in the first convolutional layer, by default False

  • residual_channels (list, optional) – Number of channels in the residual blocks, by default [96, 96, 96]

  • residual_kernel_size (list, optional) – Kernel size of the residual blocks, by default [3, 3, 3]

  • residual_stride_size (list, optional) – Stride size of the residual blocks, by default [1, 1, 1]

  • residual_dilation_rate (list, optional) – Dilation rate of the residual blocks, by default [1, 2, 4]

  • residual_padding (str, optional) – Padding of the residual blocks, by default “same”

  • residual_activation (str, optional) – Activation function of the residual blocks, by default “relu”

  • residual_batchnorm (bool, optional) – Whether to use batchnorm in the residual blocks, by default True

  • residual_batchnorm_first (bool, optional) – Whether to use batchnorm before or after the activation in the residual blocks, by default True

  • residual_dropout_rates (float, optional) – Dropout rate of the residual blocks, by default 0.1

  • residual_biases (bool, optional) – Whether to use biases in the residual blocks, by default False

  • pool_kernel_size (int, optional) – Kernel size of the average pooling layer, by default 10

  • pool_dropout_rate (float, optional) – Dropout rate of the average pooling layer, by default 0.2

  • dense_hidden_dims (list, optional) – Number of neurons in the fully connected layers, by default [256]

  • dense_activation (str, optional) – Activation function of the fully connected layers, by default “relu”

  • dense_batchnorm (bool, optional) – Whether to use batchnorm in the fully connected layers, by default True

  • dense_batchnorm_first (bool, optional) – Whether to use batchnorm before or after the activation in the fully connected layers, by default True

  • dense_dropout_rates (float, optional) – Dropout rate of the fully connected layers, by default 0.5

  • dense_biases (bool, optional) – Whether to use biases in the fully connected layers, by default False

__init__(input_len, output_dim, input_chanels=4, conv_channels=[96], conv_kernel_size=[11], conv_stride_size=[1], conv_dilation_rate=[1], conv_padding='valid', conv_activation='relu', conv_batchnorm=True, conv_batchnorm_first=True, conv_dropout_rates=0.1, conv_biases=False, residual_channels=[96, 96, 96], residual_kernel_size=[3, 3, 3], residual_stride_size=[1, 1, 1], residual_dilation_rate=[1, 2, 4], residual_padding='same', residual_activation='relu', residual_batchnorm=True, residual_batchnorm_first=True, residual_dropout_rates=0.1, residual_biases=False, pool_kernel_size=10, pool_dropout_rate=0.2, dense_hidden_dims=[256], dense_activation='relu', dense_batchnorm=True, dense_batchnorm_first=True, dense_dropout_rates=0.5, dense_biases=False)

Initializes internal Module state, shared by both nn.Module and ScriptModule.

Methods

__init__(input_len, output_dim[, ...])

Initializes internal Module state, shared by both nn.Module and ScriptModule.

add_module(name, module)

Adds a child module to the current module.

apply(fn)

Applies fn recursively to every submodule (as returned by .children()) as well as self.

bfloat16()

Casts all floating point parameters and buffers to bfloat16 datatype.

buffers([recurse])

Returns an iterator over module buffers.

children()

Returns an iterator over immediate children modules.

cpu()

Moves all model parameters and buffers to the CPU.

cuda([device])

Moves all model parameters and buffers to the GPU.

double()

Casts all floating point parameters and buffers to double datatype.

eval()

Sets the module in evaluation mode.

extra_repr()

Set the extra representation of the module

float()

Casts all floating point parameters and buffers to float datatype.

forward(x)

Defines the computation performed at every call.

get_buffer(target)

Returns the buffer given by target if it exists, otherwise throws an error.

get_extra_state()

Returns any extra state to include in the module's state_dict.

get_parameter(target)

Returns the parameter given by target if it exists, otherwise throws an error.

get_submodule(target)

Returns the submodule given by target if it exists, otherwise throws an error.

half()

Casts all floating point parameters and buffers to half datatype.

ipu([device])

Moves all model parameters and buffers to the IPU.

load_state_dict(state_dict[, strict])

Copies parameters and buffers from state_dict into this module and its descendants.

modules()

Returns an iterator over all modules in the network.

named_buffers([prefix, recurse])

Returns an iterator over module buffers, yielding both the name of the buffer as well as the buffer itself.

named_children()

Returns an iterator over immediate children modules, yielding both the name of the module as well as the module itself.

named_modules([memo, prefix, remove_duplicate])

Returns an iterator over all modules in the network, yielding both the name of the module as well as the module itself.

named_parameters([prefix, recurse])

Returns an iterator over module parameters, yielding both the name of the parameter as well as the parameter itself.

parameters([recurse])

Returns an iterator over module parameters.

register_backward_hook(hook)

Registers a backward hook on the module.

register_buffer(name, tensor[, persistent])

Adds a buffer to the module.

register_forward_hook(hook)

Registers a forward hook on the module.

register_forward_pre_hook(hook)

Registers a forward pre-hook on the module.

register_full_backward_hook(hook)

Registers a backward hook on the module.

register_load_state_dict_post_hook(hook)

Registers a post hook to be run after module's load_state_dict is called.

register_module(name, module)

Alias for add_module().

register_parameter(name, param)

Adds a parameter to the module.

requires_grad_([requires_grad])

Change if autograd should record operations on parameters in this module.

set_extra_state(state)

This function is called from load_state_dict() to handle any extra state found within the state_dict.

share_memory()

See torch.Tensor.share_memory_()

state_dict(*args[, destination, prefix, ...])

Returns a dictionary containing references to the whole state of the module.

to(*args, **kwargs)

Moves and/or casts the parameters and buffers.

to_empty(*, device)

Moves the parameters and buffers to the specified device without copying storage.

train([mode])

Sets the module in training mode.

type(dst_type)

Casts all parameters and buffers to dst_type.

xpu([device])

Moves all model parameters and buffers to the XPU.

zero_grad([set_to_none])

Sets gradients of all model parameters to zero.

Attributes

T_destination

dump_patches

training