torchdms.model.Conditional¶
- class torchdms.model.Conditional(*args, **kwargs)[source]¶
Bases:
torchdms.model.Independent
Allows the latent space for the second output feature (i.e. stability) to feed forward into the network for the first output feature (i.e. binding).
This requires a one-dimensional latent space (see
torchdms.model.Conditional.from_latent_to_output()
to see why).Todo
schematic image: https://user-images.githubusercontent.com/1173298/89943302-d4524d00-dbd2-11ea-827d-6ad6c238ff52.png
- Parameters
args – positional arguments, see
torchdms.model.Independent
kwargs – keyword arguments, see
torchdms.model.Independent
Methods
Adds a child module to the current module.
Applies
fn
recursively to every submodule (as returned by.children()
) as well as self.beta coefficients, skip coefficients only if interaction module.
Casts all floating point parameters and buffers to
bfloat16
datatype.Returns an iterator over module buffers.
Returns an iterator over immediate children modules.
Moves all model parameters and buffers to the CPU.
Moves all model parameters and buffers to the GPU.
Casts all floating point parameters and buffers to
double
datatype.Sets the module in evaluation mode.
Set the extra representation of the module
Perform gauge-fixing procedure on latent space parameters.
Casts all floating point parameters and buffers to
float
datatype.data \(X\) \(\rightarrow\) output \(Y\).
Evaluate the mapping from the latent space to output.
Returns the buffer given by
target
if it exists, otherwise throws an error.Returns any extra state to include in the module's state_dict.
Returns the parameter given by
target
if it exists, otherwise throws an error.Returns the submodule given by
target
if it exists, otherwise throws an error.Casts all floating point parameters and buffers to
half
datatype.Copies parameters and buffers from
state_dict
into this module and its descendants.Returns an iterator over all modules in the network.
Yields parameters to be floored to zero in a monotonic model.
Returns an iterator over module buffers, yielding both the name of the buffer as well as the buffer itself.
Returns an iterator over immediate children modules, yielding both the name of the module as well as the module itself.
Returns an iterator over all modules in the network, yielding both the name of the module as well as the module itself.
Returns an iterator over module parameters, yielding both the name of the parameter as well as the parameter itself.
Single mutant predictions as a numpy array of shape (AAs, sites, outputs).
Returns an iterator over module parameters.
Randomize model parameters.
Registers a backward hook on the module.
Adds a buffer to the module.
Registers a forward hook on the module.
Registers a forward pre-hook on the module.
Registers a backward hook on the module.
Adds a parameter to the module.
Compute regularization penalty, a scalar-valued
torch.Tensor
Change if autograd should record operations on parameters in this module.
Takes a string of amino acids and creates an appropriate one-hot encoding.
This function is called from
load_state_dict()
to handle any extra state found within the state_dict.Set
require_grad
for all parameters.Single mutant predictions as a list (across output dimensions) of Pandas dataframes.
Returns a dictionary containing a whole state of the module.
A one-line summary of the model.
Moves and/or casts the parameters and buffers.
Moves the parameters and buffers to the specified device without copying storage.
Latent space representation \(Z\)
Sets the module in training mode.
Casts all parameters and buffers to
dst_type
.Moves all model parameters and buffers to the XPU.
Sets gradients of all model parameters to zero.
Attributes
T_destination
alias of TypeVar('T_destination', bound=
Mapping
[str
,torch.Tensor
])Salient characteristics of the model that aren't represented in the PyTorch description.
dump_patches
This allows better BC support for
load_state_dict()
.internal_layer_dimensions
Number of dimensions in latent space.
input amino acid sequence length
- from_latent_to_output(z, **kwargs)[source]¶
Evaluate the mapping from the latent space to output.
\[y = g(z)\]
- __call__(*input, **kwargs)¶
Call self as a function.
- add_module(name, module)¶
Adds a child module to the current module.
The module can be accessed as an attribute using the given name.
- Parameters
name (string) – name of the child module. The child module can be accessed from this module using the given name
module (Module) – child module to be added to the module.
- Return type
- apply(fn)¶
Applies
fn
recursively to every submodule (as returned by.children()
) as well as self. Typical use includes initializing the parameters of a model (see also torch.nn.init).- Parameters
fn (
Module
-> None) – function to be applied to each submodule- Returns
self
- Return type
Module
Example:
>>> @torch.no_grad() >>> def init_weights(m): >>> print(m) >>> if type(m) == nn.Linear: >>> m.weight.fill_(1.0) >>> print(m.weight) >>> net = nn.Sequential(nn.Linear(2, 2), nn.Linear(2, 2)) >>> net.apply(init_weights) Linear(in_features=2, out_features=2, bias=True) Parameter containing: tensor([[ 1., 1.], [ 1., 1.]]) Linear(in_features=2, out_features=2, bias=True) Parameter containing: tensor([[ 1., 1.], [ 1., 1.]]) Sequential( (0): Linear(in_features=2, out_features=2, bias=True) (1): Linear(in_features=2, out_features=2, bias=True) ) Sequential( (0): Linear(in_features=2, out_features=2, bias=True) (1): Linear(in_features=2, out_features=2, bias=True) )
- beta_coefficients()¶
beta coefficients, skip coefficients only if interaction module.
- Return type
- bfloat16()¶
Casts all floating point parameters and buffers to
bfloat16
datatype.Note
This method modifies the module in-place.
- Returns
self
- Return type
Module
- buffers(recurse=True)¶
Returns an iterator over module buffers.
- Parameters
recurse (bool) – if True, then yields buffers of this module and all submodules. Otherwise, yields only buffers that are direct members of this module.
- Yields
torch.Tensor – module buffer
Example:
>>> for buf in model.buffers(): >>> print(type(buf), buf.size()) <class 'torch.Tensor'> (20L,) <class 'torch.Tensor'> (20L, 1L, 5L, 5L)
- property characteristics: Dict¶
Salient characteristics of the model that aren’t represented in the PyTorch description.
- Return type
- children()¶
Returns an iterator over immediate children modules.
- Yields
Module – a child module
- Return type
Iterator
[Module
]
- cpu()¶
Moves all model parameters and buffers to the CPU.
Note
This method modifies the module in-place.
- Returns
self
- Return type
Module
- cuda(device=None)¶
Moves all model parameters and buffers to the GPU.
This also makes associated parameters and buffers different objects. So it should be called before constructing optimizer if the module will live on GPU while being optimized.
Note
This method modifies the module in-place.
- Parameters
device (int, optional) – if specified, all parameters will be copied to that device
- Returns
self
- Return type
Module
- double()¶
Casts all floating point parameters and buffers to
double
datatype.Note
This method modifies the module in-place.
- Returns
self
- Return type
Module
- eval()¶
Sets the module in evaluation mode.
This has any effect only on certain modules. See documentations of particular modules for details of their behaviors in training/evaluation mode, if they are affected, e.g.
Dropout
,BatchNorm
, etc.This is equivalent with
self.train(False)
.See Locally disabling gradient computation for a comparison between .eval() and several similar mechanisms that may be confused with it.
- Returns
self
- Return type
Module
- extra_repr()¶
Set the extra representation of the module
To print customized extra information, you should re-implement this method in your own modules. Both single-line and multi-line strings are acceptable.
- Return type
- fix_gauge(gauge_mask)¶
Perform gauge-fixing procedure on latent space parameters.
- Parameters
gauge_mask – 0/1 mask array the same shape as latent space input with 1s for parameters that should be zeroed
- float()¶
Casts all floating point parameters and buffers to
float
datatype.Note
This method modifies the module in-place.
- Returns
self
- Return type
Module
- forward(x, **kwargs)¶
data \(X\) \(\rightarrow\) output \(Y\).
\[y = g(\phi(x))\]
- get_buffer(target)¶
Returns the buffer given by
target
if it exists, otherwise throws an error.See the docstring for
get_submodule
for a more detailed explanation of this method’s functionality as well as how to correctly specifytarget
.- Parameters
target (
str
) – The fully-qualified string name of the buffer to look for. (Seeget_submodule
for how to specify a fully-qualified string.)- Returns
The buffer referenced by
target
- Return type
- Raises
AttributeError – If the target string references an invalid path or resolves to something that is not a buffer
- get_extra_state()¶
Returns any extra state to include in the module’s state_dict. Implement this and a corresponding
set_extra_state()
for your module if you need to store extra state. This function is called when building the module’s state_dict().Note that extra state should be pickleable to ensure working serialization of the state_dict. We only provide provide backwards compatibility guarantees for serializing Tensors; other objects may break backwards compatibility if their serialized pickled form changes.
- Returns
Any extra state to store in the module’s state_dict
- Return type
- get_parameter(target)¶
Returns the parameter given by
target
if it exists, otherwise throws an error.See the docstring for
get_submodule
for a more detailed explanation of this method’s functionality as well as how to correctly specifytarget
.- Parameters
target (
str
) – The fully-qualified string name of the Parameter to look for. (Seeget_submodule
for how to specify a fully-qualified string.)- Returns
The Parameter referenced by
target
- Return type
torch.nn.Parameter
- Raises
AttributeError – If the target string references an invalid path or resolves to something that is not an
nn.Parameter
- get_submodule(target)¶
Returns the submodule given by
target
if it exists, otherwise throws an error.For example, let’s say you have an
nn.Module
A
that looks like this:(The diagram shows an
nn.Module
A
.A
has a nested submodulenet_b
, which itself has two submodulesnet_c
andlinear
.net_c
then has a submoduleconv
.)To check whether or not we have the
linear
submodule, we would callget_submodule("net_b.linear")
. To check whether we have theconv
submodule, we would callget_submodule("net_b.net_c.conv")
.The runtime of
get_submodule
is bounded by the degree of module nesting intarget
. A query againstnamed_modules
achieves the same result, but it is O(N) in the number of transitive modules. So, for a simple check to see if some submodule exists,get_submodule
should always be used.- Parameters
target (
str
) – The fully-qualified string name of the submodule to look for. (See above example for how to specify a fully-qualified string.)- Returns
The submodule referenced by
target
- Return type
- Raises
AttributeError – If the target string references an invalid path or resolves to something that is not an
nn.Module
- half()¶
Casts all floating point parameters and buffers to
half
datatype.Note
This method modifies the module in-place.
- Returns
self
- Return type
Module
- load_state_dict(state_dict, strict=True)¶
Copies parameters and buffers from
state_dict
into this module and its descendants. Ifstrict
isTrue
, then the keys ofstate_dict
must exactly match the keys returned by this module’sstate_dict()
function.- Parameters
state_dict (dict) – a dict containing parameters and persistent buffers.
strict (bool, optional) – whether to strictly enforce that the keys in
state_dict
match the keys returned by this module’sstate_dict()
function. Default:True
- Returns
missing_keys is a list of str containing the missing keys
unexpected_keys is a list of str containing the unexpected keys
- Return type
NamedTuple
withmissing_keys
andunexpected_keys
fields
Note
If a parameter or buffer is registered as
None
and its corresponding key exists instate_dict
,load_state_dict()
will raise aRuntimeError
.
- modules()¶
Returns an iterator over all modules in the network.
- Yields
Module – a module in the network
Note
Duplicate modules are returned only once. In the following example,
l
will be returned only once.Example:
>>> l = nn.Linear(2, 2) >>> net = nn.Sequential(l, l) >>> for idx, m in enumerate(net.modules()): print(idx, '->', m) 0 -> Sequential( (0): Linear(in_features=2, out_features=2, bias=True) (1): Linear(in_features=2, out_features=2, bias=True) ) 1 -> Linear(in_features=2, out_features=2, bias=True)
- Return type
Iterator
[Module
]
- monotonic_params_from_latent_space()¶
Yields parameters to be floored to zero in a monotonic model. This is every parameter after the latent space excluding bias parameters.
We follow the convention that the latent layers of a network are named like
latent_layer*
and the weights and bias are denotedlayer_name*.weight
andlayer_name*.bias
.Layers from nested modules will be prefixed (e.g. with Independent).
- named_buffers(prefix='', recurse=True)¶
Returns an iterator over module buffers, yielding both the name of the buffer as well as the buffer itself.
- Parameters
- Yields
(string, torch.Tensor) – Tuple containing the name and buffer
Example:
>>> for name, buf in self.named_buffers(): >>> if name in ['running_var']: >>> print(buf.size())
- named_children()¶
Returns an iterator over immediate children modules, yielding both the name of the module as well as the module itself.
- Yields
(string, Module) – Tuple containing a name and child module
Example:
>>> for name, module in model.named_children(): >>> if name in ['conv4', 'conv5']: >>> print(module)
- named_modules(memo=None, prefix='', remove_duplicate=True)¶
Returns an iterator over all modules in the network, yielding both the name of the module as well as the module itself.
- Parameters
- Yields
(string, Module) – Tuple of name and module
Note
Duplicate modules are returned only once. In the following example,
l
will be returned only once.Example:
>>> l = nn.Linear(2, 2) >>> net = nn.Sequential(l, l) >>> for idx, m in enumerate(net.named_modules()): print(idx, '->', m) 0 -> ('', Sequential( (0): Linear(in_features=2, out_features=2, bias=True) (1): Linear(in_features=2, out_features=2, bias=True) )) 1 -> ('0', Linear(in_features=2, out_features=2, bias=True))
- named_parameters(prefix='', recurse=True)¶
Returns an iterator over module parameters, yielding both the name of the parameter as well as the parameter itself.
- Parameters
- Yields
(string, Parameter) – Tuple containing the name and parameter
Example:
>>> for name, param in self.named_parameters(): >>> if name in ['bias']: >>> print(param.size())
- numpy_single_mutant_predictions()¶
Single mutant predictions as a numpy array of shape (AAs, sites, outputs).
- Return type
ndarray
- parameters(recurse=True)¶
Returns an iterator over module parameters.
This is typically passed to an optimizer.
- Parameters
recurse (bool) – if True, then yields parameters of this module and all submodules. Otherwise, yields only parameters that are direct members of this module.
- Yields
Parameter – module parameter
Example:
>>> for param in model.parameters(): >>> print(type(param), param.size()) <class 'torch.Tensor'> (20L,) <class 'torch.Tensor'> (20L, 1L, 5L, 5L)
- randomize_parameters()¶
Randomize model parameters.
- register_backward_hook(hook)¶
Registers a backward hook on the module.
This function is deprecated in favor of
register_full_backward_hook()
and the behavior of this function will change in future versions.- Returns
a handle that can be used to remove the added hook by calling
handle.remove()
- Return type
torch.utils.hooks.RemovableHandle
- register_buffer(name, tensor, persistent=True)¶
Adds a buffer to the module.
This is typically used to register a buffer that should not to be considered a model parameter. For example, BatchNorm’s
running_mean
is not a parameter, but is part of the module’s state. Buffers, by default, are persistent and will be saved alongside parameters. This behavior can be changed by settingpersistent
toFalse
. The only difference between a persistent buffer and a non-persistent buffer is that the latter will not be a part of this module’sstate_dict
.Buffers can be accessed as attributes using given names.
- Parameters
name (string) – name of the buffer. The buffer can be accessed from this module using the given name
tensor (Tensor or None) – buffer to be registered. If
None
, then operations that run on buffers, such ascuda
, are ignored. IfNone
, the buffer is not included in the module’sstate_dict
.persistent (bool) – whether the buffer is part of this module’s
state_dict
.
Example:
>>> self.register_buffer('running_mean', torch.zeros(num_features))
- Return type
- register_forward_hook(hook)¶
Registers a forward hook on the module.
The hook will be called every time after
forward()
has computed an output. It should have the following signature:hook(module, input, output) -> None or modified output
The input contains only the positional arguments given to the module. Keyword arguments won’t be passed to the hooks and only to the
forward
. The hook can modify the output. It can modify the input inplace but it will not have effect on forward since this is called afterforward()
is called.- Returns
a handle that can be used to remove the added hook by calling
handle.remove()
- Return type
torch.utils.hooks.RemovableHandle
- register_forward_pre_hook(hook)¶
Registers a forward pre-hook on the module.
The hook will be called every time before
forward()
is invoked. It should have the following signature:hook(module, input) -> None or modified input
The input contains only the positional arguments given to the module. Keyword arguments won’t be passed to the hooks and only to the
forward
. The hook can modify the input. User can either return a tuple or a single modified value in the hook. We will wrap the value into a tuple if a single value is returned(unless that value is already a tuple).- Returns
a handle that can be used to remove the added hook by calling
handle.remove()
- Return type
torch.utils.hooks.RemovableHandle
- register_full_backward_hook(hook)¶
Registers a backward hook on the module.
The hook will be called every time the gradients with respect to module inputs are computed. The hook should have the following signature:
hook(module, grad_input, grad_output) -> tuple(Tensor) or None
The
grad_input
andgrad_output
are tuples that contain the gradients with respect to the inputs and outputs respectively. The hook should not modify its arguments, but it can optionally return a new gradient with respect to the input that will be used in place ofgrad_input
in subsequent computations.grad_input
will only correspond to the inputs given as positional arguments and all kwarg arguments are ignored. Entries ingrad_input
andgrad_output
will beNone
for all non-Tensor arguments.For technical reasons, when this hook is applied to a Module, its forward function will receive a view of each Tensor passed to the Module. Similarly the caller will receive a view of each Tensor returned by the Module’s forward function.
Warning
Modifying inputs or outputs inplace is not allowed when using backward hooks and will raise an error.
- Returns
a handle that can be used to remove the added hook by calling
handle.remove()
- Return type
torch.utils.hooks.RemovableHandle
- register_parameter(name, param)¶
Adds a parameter to the module.
The parameter can be accessed as an attribute using given name.
- Parameters
name (string) – name of the parameter. The parameter can be accessed from this module using the given name
param (Parameter or None) – parameter to be added to the module. If
None
, then operations that run on parameters, such ascuda
, are ignored. IfNone
, the parameter is not included in the module’sstate_dict
.
- Return type
- regularization_loss()¶
Compute regularization penalty, a scalar-valued
torch.Tensor
- Return type
- requires_grad_(requires_grad=True)¶
Change if autograd should record operations on parameters in this module.
This method sets the parameters’
requires_grad
attributes in-place.This method is helpful for freezing part of the module for finetuning or training parts of a model individually (e.g., GAN training).
See Locally disabling gradient computation for a comparison between .requires_grad_() and several similar mechanisms that may be confused with it.
- Parameters
requires_grad (bool) – whether autograd should record operations on parameters in this module. Default:
True
.- Returns
self
- Return type
Module
- seq_to_binary(seq)¶
Takes a string of amino acids and creates an appropriate one-hot encoding.
- property sequence_length¶
input amino acid sequence length
- set_extra_state(state)¶
This function is called from
load_state_dict()
to handle any extra state found within the state_dict. Implement this function and a correspondingget_extra_state()
for your module if you need to store extra state within its state_dict.- Parameters
state (dict) – Extra state from the state_dict
- set_require_grad_for_all_parameters(value)¶
Set
require_grad
for all parameters.- Parameters
value (
bool
) –require_grad=value
for all parameters
See
torch.Tensor.share_memory_()
- Return type
~T
- single_mutant_predictions()¶
Single mutant predictions as a list (across output dimensions) of Pandas dataframes.
- Return type
List
[DataFrame
]
- state_dict(destination=None, prefix='', keep_vars=False)¶
Returns a dictionary containing a whole state of the module.
Both parameters and persistent buffers (e.g. running averages) are included. Keys are corresponding parameter and buffer names. Parameters and buffers set to
None
are not included.- Returns
a dictionary containing a whole state of the module
- Return type
Example:
>>> module.state_dict().keys() ['bias', 'weight']
- to(*args, **kwargs)¶
Moves and/or casts the parameters and buffers.
This can be called as
- to(device=None, dtype=None, non_blocking=False)
- to(dtype, non_blocking=False)
- to(tensor, non_blocking=False)
- to(memory_format=torch.channels_last)
Its signature is similar to
torch.Tensor.to()
, but only accepts floating point or complexdtype
s. In addition, this method will only cast the floating point or complex parameters and buffers todtype
(if given). The integral parameters and buffers will be moveddevice
, if that is given, but with dtypes unchanged. Whennon_blocking
is set, it tries to convert/move asynchronously with respect to the host if possible, e.g., moving CPU Tensors with pinned memory to CUDA devices.See below for examples.
Note
This method modifies the module in-place.
- Parameters
device (
torch.device
) – the desired device of the parameters and buffers in this moduledtype (
torch.dtype
) – the desired floating point or complex dtype of the parameters and buffers in this moduletensor (torch.Tensor) – Tensor whose dtype and device are the desired dtype and device for all parameters and buffers in this module
memory_format (
torch.memory_format
) – the desired memory format for 4D parameters and buffers in this module (keyword only argument)
- Returns
self
- Return type
Module
Examples:
>>> linear = nn.Linear(2, 2) >>> linear.weight Parameter containing: tensor([[ 0.1913, -0.3420], [-0.5113, -0.2325]]) >>> linear.to(torch.double) Linear(in_features=2, out_features=2, bias=True) >>> linear.weight Parameter containing: tensor([[ 0.1913, -0.3420], [-0.5113, -0.2325]], dtype=torch.float64) >>> gpu1 = torch.device("cuda:1") >>> linear.to(gpu1, dtype=torch.half, non_blocking=True) Linear(in_features=2, out_features=2, bias=True) >>> linear.weight Parameter containing: tensor([[ 0.1914, -0.3420], [-0.5112, -0.2324]], dtype=torch.float16, device='cuda:1') >>> cpu = torch.device("cpu") >>> linear.to(cpu) Linear(in_features=2, out_features=2, bias=True) >>> linear.weight Parameter containing: tensor([[ 0.1914, -0.3420], [-0.5112, -0.2324]], dtype=torch.float16) >>> linear = nn.Linear(2, 2, bias=None).to(torch.cdouble) >>> linear.weight Parameter containing: tensor([[ 0.3741+0.j, 0.2382+0.j], [ 0.5593+0.j, -0.4443+0.j]], dtype=torch.complex128) >>> linear(torch.ones(3, 2, dtype=torch.cdouble)) tensor([[0.6122+0.j, 0.1150+0.j], [0.6122+0.j, 0.1150+0.j], [0.6122+0.j, 0.1150+0.j]], dtype=torch.complex128)
- to_empty(*, device)¶
Moves the parameters and buffers to the specified device without copying storage.
- Parameters
device (
torch.device
) – The desired device of the parameters and buffers in this module.- Returns
self
- Return type
Module
- to_latent(x, **kwargs)¶
Latent space representation \(Z\)
\[z \equiv \phi(x) \equiv \beta^\intercal x\]
- train(mode=True)¶
Sets the module in training mode.
This has any effect only on certain modules. See documentations of particular modules for details of their behaviors in training/evaluation mode, if they are affected, e.g.
Dropout
,BatchNorm
, etc.- Parameters
mode (bool) – whether to set training mode (
True
) or evaluation mode (False
). Default:True
.- Returns
self
- Return type
Module
- type(dst_type)¶
Casts all parameters and buffers to
dst_type
.Note
This method modifies the module in-place.
- Parameters
dst_type (type or string) – the desired type
- Returns
self
- Return type
Module
- xpu(device=None)¶
Moves all model parameters and buffers to the XPU.
This also makes associated parameters and buffers different objects. So it should be called before constructing optimizer if the module will live on XPU while being optimized.
Note
This method modifies the module in-place.
- Parameters
device (int, optional) – if specified, all parameters will be copied to that device
- Returns
self
- Return type
Module
- zero_grad(set_to_none=False)¶
Sets gradients of all model parameters to zero. See similar function under
torch.optim.Optimizer
for more context.- Parameters
set_to_none (bool) – instead of setting to zero, set the grads to None. See
torch.optim.Optimizer.zero_grad()
for details.- Return type