Neural Network¶
Modules¶
- class metatensor.learn.nn.ModuleMap(in_keys: Labels, modules: List[Module], out_properties: List[Labels] | None = None)[source]¶
A class that imitates
torch.nn.ModuleDict
. In its forward function the module at position i given on construction by :param modules: is applied to the tensor block that corresponding to the`i`th key in :param in_keys:.- Parameters:
in_keys (Labels) – A
metatensor.Labels
object with the keys of the module map that are assumed to be in the input tensor map in theforward()
function.modules (List[Module]) – A sequence of modules applied in the
forward()
function on the inputTensorMap
. Each module corresponds to oneLabelsEntry
in :param in_keys: that determines on whichTensorBlock
the module is applied on. :param modules: and :param in_keys: must match in length.out_properties (List[Labels] | None) –
A list of labels that is used to determine the properties labels of the output. Because a module could change the number of properties, the labels of the properties cannot be persevered. By default the output properties are relabeled using Labels.range with “_” as key.
>>> import torch >>> import numpy as np >>> from copy import deepcopy >>> from metatensor import Labels, TensorBlock, TensorMap >>> from metatensor.learn.nn import ModuleMap
Create simple block
>>> block_1 = TensorBlock( ... values=torch.tensor( ... [ ... [1.0, 2.0, 4.0], ... [3.0, 5.0, 6.0], ... ] ... ), ... samples=Labels( ... ["system", "atom"], ... np.array( ... [ ... [0, 0], ... [0, 1], ... ] ... ), ... ), ... components=[], ... properties=Labels(["properties"], np.array([[0], [1], [2]])), ... ) >>> block_2 = TensorBlock( ... values=torch.tensor( ... [ ... [5.0, 8.0, 2.0], ... [1.0, 2.0, 8.0], ... ] ... ), ... samples=Labels( ... ["system", "atom"], ... np.array( ... [ ... [0, 0], ... [0, 1], ... ] ... ), ... ), ... components=[], ... properties=Labels(["properties"], np.array([[3], [4], [5]])), ... ) >>> keys = Labels(names=["key"], values=np.array([[0], [1]])) >>> tensor = TensorMap(keys, [block_1, block_2])
Create modules
>>> linear = torch.nn.Linear(3, 1, bias=False) >>> with torch.no_grad(): ... _ = linear.weight.copy_(torch.tensor([1.0, 1.0, 1.0])) ... >>> modules = [linear, deepcopy(linear)] >>> # you could also extend the module by some nonlinear activation function
Create ModuleMap from this ModucDict and apply it
>>> module_map = ModuleMap(tensor.keys, modules) >>> out = module_map(tensor) >>> out TensorMap with 2 blocks keys: key 0 1 >>> out[0].values tensor([[ 7.], [14.]], grad_fn=<MmBackward0>) >>> out[1].values tensor([[15.], [11.]], grad_fn=<MmBackward0>)
Let’s look at the metadata
>>> tensor[0] TensorBlock samples (2): ['system', 'atom'] components (): [] properties (3): ['properties'] gradients: None >>> out[0] TensorBlock samples (2): ['system', 'atom'] components (): [] properties (1): ['_'] gradients: None
It got completely lost because we cannot know in general what the output is. You can add in the initialization of the ModuleMap a TensorMap that contains the intended output Labels.
Initialize internal Module state, shared by both nn.Module and ScriptModule.
- classmethod from_module(in_keys: Labels, module: Module, out_properties: List[Labels] | None = None)[source]¶
A wrapper around one
torch.nn.Module
applying the same type of module on each tensor block.- Parameters:
in_keys (Labels) – A
metatensor.Labels
object that determines the keys of the module map that are ass the TensorMaps that are assumed to be in the input tensor map in theforward()
function.module (Module) – The module that is applied on each block.
out_properties (List[Labels] | None) – A list of labels that is used to determine the properties labels of the output. Because a module could change the number of properties, the labels of the properties cannot be persevered. By default the output properties are relabeled using Labels.range with “_” as key.
>>> import torch >>> import numpy as np >>> from metatensor import Labels, TensorBlock, TensorMap >>> block_1 = TensorBlock( ... values=torch.tensor( ... [ ... [1.0, 2.0, 4.0], ... [3.0, 5.0, 6.0], ... ] ... ), ... samples=Labels( ... ["system", "atom"], ... np.array( ... [ ... [0, 0], ... [0, 1], ... ] ... ), ... ), ... components=[], ... properties=Labels(["properties"], np.array([[0], [1], [2]])), ... ) >>> block_2 = TensorBlock( ... values=torch.tensor( ... [ ... [5.0, 8.0, 2.0], ... [1.0, 2.0, 8.0], ... ] ... ), ... samples=Labels( ... ["system", "atom"], ... np.array( ... [ ... [0, 0], ... [0, 1], ... ] ... ), ... ), ... components=[], ... properties=Labels(["properties"], np.array([[0], [1], [2]])), ... ) >>> keys = Labels(names=["key"], values=np.array([[0], [1]])) >>> tensor = TensorMap(keys, [block_1, block_2]) >>> linear = torch.nn.Linear(3, 1, bias=False) >>> with torch.no_grad(): ... _ = linear.weight.copy_(torch.tensor([1.0, 1.0, 1.0])) ... >>> # you could also extend the module by some nonlinear activation function >>> from metatensor.learn.nn import ModuleMap >>> module_map = ModuleMap.from_module(tensor.keys, linear) >>> out = module_map(tensor) >>> out[0].values tensor([[ 7.], [14.]], grad_fn=<MmBackward0>) >>> out[1].values tensor([[15.], [11.]], grad_fn=<MmBackward0>)
- forward(tensor: TensorMap) TensorMap [source]¶
Apply the modules on each block in
tensor
.tensor
must have the same set of keys as the modules used to initialize thisModuleMap
.
- get_module(key: LabelsEntry)[source]¶
- Parameters:
key (LabelsEntry) – key of module which should be returned
- Return module:
returns he torch.nn.Module corresponding to the :param key:
- property in_keys: Labels¶
A list of labels that defines the initialized keys with corresponding modules of this module map.
- class metatensor.learn.nn.Sequential(in_keys: Labels, *args: List[ModuleMap])[source]¶
A sequential model that applies a list of ModuleMaps to the input in order.
- Parameters:
Initialize internal Module state, shared by both nn.Module and ScriptModule.
- class metatensor.learn.nn.Linear(in_keys: Labels, in_features: int | List[int], out_features: List[int] | int | None = None, out_properties: List[Labels] | None = None, *, bias: bool = True, device: device | None = None, dtype: dtype | None = None)[source]¶
Module similar to
torch.nn.Linear
that works withmetatensor.torch.TensorMap
.Applies a linear transformation to each block of a
TensorMap
passed to its forward method, indexed by :param in_keys:.Refer to the :py:class`torch.nn.Linear` documentation for a more detailed description of the other parameters.
Each parameter is passed as a single value of its expected type, which is used as the parameter for all blocks.
- Parameters:
in_keys (Labels) –
Labels
, the keys that are assumed to be in the input tensor map in theforward()
method.in_features (int | List[int]) –
int
orlist
ofint
, the number of input features for each block. If passed as a single value, the same feature size is taken for all blocks.out_features (List[int] | int | None) –
int
orlint
ofint
, the number of output features for each block. If passed as a single value, the same feature size is taken for all blocks.out_properties (List[Labels] | None) – list of :py:class`Labels` (optional), the properties labels of the output. By default the output properties are relabeled using Labels.range. If provided, :param out_features: can be inferred and need not be provided.
bias (bool)
device (device | None)
dtype (dtype | None)
Initialize internal Module state, shared by both nn.Module and ScriptModule.
- class metatensor.learn.nn.EquivariantLinear(in_keys: Labels, in_features: int | List[int], out_features: List[int] | int | None = None, out_properties: List[Labels] | None = None, invariant_keys: Labels | None = None, *, bias: bool = True, device: device | None = None, dtype: dtype | None = None)[source]¶
Module similar to
torch.nn.Linear
that works with equivariantmetatensor.torch.TensorMap
objects.Applies a linear transformation to each block of a
TensorMap
passed to its forward method, indexed by :param in_keys:.Refer to the :py:class`torch.nn.Linear` documentation for a more detailed description of the other parameters.
For
EquivariantLinear
, by contrast toLinear
, the parameter :param bias: is only applied to modules corresponding to invariant blocks, i.e. keys in :param in_keys: that correspond to the selection in :param invariant_keys:.- Parameters:
in_keys (Labels) –
Labels
, the keys that are assumed to be in the input tensor map in theforward()
method.in_features (int | List[int]) –
int
orlist
ofint
, the number of input features for each block. If passed as a single value, the same feature size is taken for all blocks.out_features (List[int] | int | None) –
int
orlint
ofint
, the number of output features for each block. If passed as a single value, the same feature size is taken for all blocks.out_properties (List[Labels] | None) – list of :py:class`Labels` (optional), the properties labels of the output. By default the output properties are relabeled using Labels.range. If provided, :param out_features: can be inferred and need not be provided.
invariant_keys (Labels | None) – a
Labels
object that is used to select the invariant keys fromin_keys
. If not provided, the invariant keys are assumed to be those where key dimensions["o3_lambda", "o3_sigma"]
are equal to[0, 1]
.bias (bool)
device (device | None)
dtype (dtype | None)
Initialize internal Module state, shared by both nn.Module and ScriptModule.
- class metatensor.learn.nn.Tanh(in_keys: Labels, out_properties: Labels | None = None)[source]¶
Module similar to
torch.nn.Tanh
that works withmetatensor.torch.TensorMap
objects.Applies a hyperbolic tangent transformation to each block of a
TensorMap
passed to its forward method, indexed by :param in_keys:.Refer to the :py:class`torch.nn.Tanh` documentation for a more detailed description of the parameters.
- Parameters:
Initialize internal Module state, shared by both nn.Module and ScriptModule.
- class metatensor.learn.nn.InvariantTanh(in_keys: Labels, out_properties: Labels | None = None, invariant_keys: Labels | None = None)[source]¶
Module similar to
torch.nn.Tanh
that works withmetatensor.torch.TensorMap
objects, applying the transformation only to the invariant blocks.Applies a hyperbolic tangent transformation to each invariant block of a
TensorMap
passed to itsforward()
method. These are indexed by the keys in :param in_keys: that correspond to the selection passed in :param invariant_keys:.Refer to the :py:class`torch.nn.Tanh` documentation for a more detailed description of the parameters.
- Parameters:
in_keys (Labels) –
Labels
, the keys that are assumed to be in the input tensor map in theforward()
method.out_properties (Labels | None) – list of :py:class`Labels` (optional), the properties labels of the output. By default the output properties are relabeled using Labels.range.
invariant_keys (Labels | None) – a
Labels
object that is used to select the invariant keys fromin_keys
. If not provided, the invariant keys are assumed to be those where key dimensions["o3_lambda", "o3_sigma"]
are equal to[0, 1]
.
Initialize internal Module state, shared by both nn.Module and ScriptModule.
- class metatensor.learn.nn.ReLU(in_keys: Labels, out_properties: Labels | None = None, *, in_place: bool = False)[source]¶
Module similar to
torch.nn.ReLU
that works withmetatensor.torch.TensorMap
objects.Applies a rectified linear unit transformation transformation to each block of a
TensorMap
passed to its forward method, indexed by :param in_keys:.Refer to the :py:class`torch.nn.ReLU` documentation for a more detailed description of the parameters.
- Parameters:
Initialize internal Module state, shared by both nn.Module and ScriptModule.
- class metatensor.learn.nn.InvariantReLU(in_keys: Labels, out_properties: Labels | None = None, invariant_keys: Labels | None = None, *, in_place: bool = False)[source]¶
Module similar to
torch.nn.ReLU
that works withmetatensor.torch.TensorMap
objects, applying the transformation only to the invariant blocks.Applies a rectified linear unit transformation to each invariant block of a
TensorMap
passed to itsforward()
method. These are indexed by the keys in :param in_keys: that correspond to the selection passed in :param invariant_keys:.Refer to the :py:class`torch.nn.ReLU` documentation for a more detailed description of the parameters.
- Parameters:
in_keys (Labels) –
Labels
, the keys that are assumed to be in the input tensor map in theforward()
method.out_properties (Labels | None) – list of :py:class`Labels` (optional), the properties labels of the output. By default the output properties are relabeled using Labels.range.
invariant_keys (Labels | None) – a
Labels
object that is used to select the invariant keys fromin_keys
. If not provided, the invariant keys are assumed to be those where key dimensions["o3_lambda", "o3_sigma"]
are equal to[0, 1]
.in_place (bool)
Initialize internal Module state, shared by both nn.Module and ScriptModule.
- class metatensor.learn.nn.SiLU(in_keys: Labels, out_properties: Labels | None = None, *, in_place: bool = False)[source]¶
Module similar to
torch.nn.SiLU
that works withmetatensor.torch.TensorMap
objects.Applies a sigmoid linear unit transformation transformation to each block of a
TensorMap
passed to its forward method, indexed by :param in_keys:.Refer to the :py:class`torch.nn.SiLU` documentation for a more detailed description of the parameters.
- Parameters:
Initialize internal Module state, shared by both nn.Module and ScriptModule.
- class metatensor.learn.nn.InvariantSiLU(in_keys: Labels, out_properties: Labels | None = None, invariant_keys: Labels | None = None, *, in_place: bool = False)[source]¶
Module similar to
torch.nn.SiLU
that works withmetatensor.torch.TensorMap
objects, applying the transformation only to the invariant blocks.Applies a sigmoid linear unit transformation to each invariant block of a
TensorMap
passed to itsforward()
method. These are indexed by the keys in :param in_keys: that correspond to the selection passed in :param invariant_keys:.Refer to the :py:class`torch.nn.SiLU` documentation for a more detailed description of the parameters.
- Parameters:
in_keys (Labels) –
Labels
, the keys that are assumed to be in the input tensor map in theforward()
method.out_properties (Labels | None) – list of :py:class`Labels` (optional), the properties labels of the output. By default the output properties are relabeled using Labels.range.
invariant_keys (Labels | None) – a
Labels
object that is used to select the invariant keys fromin_keys
. If not provided, the invariant keys are assumed to be those where key dimensions["o3_lambda", "o3_sigma"]
are equal to[0, 1]
.in_place (bool)
Initialize internal Module state, shared by both nn.Module and ScriptModule.
- class metatensor.learn.nn.LayerNorm(in_keys: Labels, in_features: List[int], out_properties: List[Labels] | None = None, *, eps: float = 1e-05, elementwise_affine: bool = True, bias: bool = True, mean: bool = True, device: device | None = None, dtype: dtype | None = None)[source]¶
Module similar to
torch.nn.LayerNorm
that works withmetatensor.torch.TensorMap
objects.Applies a layer normalization to each block of a
TensorMap
passed to itsforward()
method, indexed by :param in_keys:.The main difference from
torch.nn.LayerNorm
is that there is no normalized_shape parameter. Instead, the standard deviation and mean (if applicable) are calculated over all dimensions except the samples (first) dimension of eachTensorBlock
.The extra parameter :param mean: controls whether or not the mean over these dimensions is subtracted from the input tensor in the transformation.
Refer to the :py:class`torch.nn.LayerNorm` documentation for a more detailed description of the other parameters.
Each parameter is passed as a single value of its expected type, which is used as the parameter for all blocks.
- Parameters:
in_keys (Labels) –
Labels
, the keys that are assumed to be in the input tensor map in theforward()
method.in_features (List[int]) – list of int, the number of features in the input tensor for each block indexed by the keys in :param in_keys:. If passed as a single value, the same number of features is assumed for all blocks.
out_properties (List[Labels] | None) – list of :py:class`Labels` (optional), the properties labels of the output. By default (if none) the output properties are relabeled using Labels.range.
eps (float)
elementwise_affine (bool)
bias (bool)
mean (bool)
device (device | None)
dtype (dtype | None)
- Mean bool:
whether or not to subtract the mean over all dimensions except the samples (first) dimension of each block of the input passed to
forward()
.
Initialize internal Module state, shared by both nn.Module and ScriptModule.
- class metatensor.learn.nn.InvariantLayerNorm(in_keys: Labels, in_features: List[int], out_properties: List[Labels] | None = None, invariant_keys: Labels | None = None, *, eps: float = 1e-05, elementwise_affine: bool = True, bias: bool = True, mean: bool = True, device: device | None = None, dtype: dtype | None = None)[source]¶
Module similar to
torch.nn.LayerNorm
that works withmetatensor.torch.TensorMap
objects, applying the transformation only to the invariant blocks.Applies a layer normalization to each invariant block of a
TensorMap
passed toforward()
method. These are indexed by the keys in :param in_keys: that correspond to the selection passed in :param invariant_keys:.The main difference from
torch.nn.LayerNorm
is that there is no normalized_shape parameter. Instead, the standard deviation and mean (if applicable) are calculated over all dimensions except the samples (first) dimension of eachTensorBlock
.The extra parameter :param mean: controls whether or not the mean over these dimensions is subtracted from the input tensor in the transformation.
Refer to the :py:class`torch.nn.LayerNorm` documentation for a more detailed description of the other parameters.
Each parameter is passed as a single value of its expected type, which is used as the parameter for all blocks.
- Parameters:
in_keys (Labels) –
Labels
, the keys that are assumed to be in the input tensor map in theforward()
method.in_features (List[int]) – list of int, the number of features in the input tensor for each block indexed by the keys in :param in_keys:. If passed as a single value, the same number of features is assumed for all blocks.
out_properties (List[Labels] | None) – list of :py:class`Labels` (optional), the properties labels of the output. By default (if none) the output properties are relabeled using Labels.range.
invariant_keys (Labels | None) – a
Labels
object that is used to select the invariant keys fromin_keys
. If not provided, the invariant keys are assumed to be those where key dimensions["o3_lambda", "o3_sigma"]
are equal to[0, 1]
.eps (float)
elementwise_affine (bool)
bias (bool)
mean (bool)
device (device | None)
dtype (dtype | None)
- Mean bool:
whether or not to subtract the mean over all dimensions except the samples (first) dimension of each block of the input passed to
forward()
.
Initialize internal Module state, shared by both nn.Module and ScriptModule.
- class metatensor.learn.nn.EquivariantTransformation(modules: List[Module], in_keys: Labels, in_features: int | List[int], out_features: List[int] | int | None = None, out_properties: List[Labels] | None = None, invariant_keys: Labels | None = None)[source]¶
A custom
torch.nn.Module
that applies an arbitrary shape- and equivariance-preserving transformation to an inputTensorMap
.For invariant blocks (specified with
invariant_keys
), the respective transformation contained in :param modules: is applied as is. For covariant blocks, an invariant multiplier is created, applying the transformation to the norm of the block over the component dimensions.- Parameters:
modules (List[Module]) – a
list
oftorch.nn.Module
containing the transformations to be applied to each block indexed by :param in_keys:. Transformations for invariant and covariant blocks differ. See above.in_keys (Labels) –
Labels
, the keys that are assumed to be in the inputTensorMap
in theforward()
method.in_features (int | List[int]) –
list
ofint
, the number of features in the input tensor for each block indexed by the keys in :param in_keys:. If passed as a single value, the same number of features is assumed for all blocks.out_properties (List[Labels] | None) –
list
of :py:class`Labels` (optional), the properties labels of the output. By default the output properties are relabeled using Labels.range.invariant_keys (Labels | None) –
a
Labels
object that is used to select the invariant keys fromin_keys
. If not provided, the invariant keys are assumed to be those where key dimensions["o3_lambda", "o3_sigma"]
are equal to[0, 1]
.>>> import torch >>> import numpy as np >>> from metatensor import Labels, TensorBlock, TensorMap >>> from metatensor.learn.nn import EquivariantTransformation
Define a dummy invariant TensorBlock
>>> block_1 = TensorBlock( ... values=torch.randn(2, 1, 3), ... samples=Labels( ... ["system", "atom"], ... np.array( ... [ ... [0, 0], ... [0, 1], ... ] ... ), ... ), ... components=[Labels(["o3_mu"], np.array([[0]]))], ... properties=Labels(["properties"], np.array([[0], [1], [2]])), ... )
Define a dummy covariant TensorBlock
>>> block_2 = TensorBlock( ... values=torch.randn(2, 3, 3), ... samples=Labels( ... ["system", "atom"], ... np.array( ... [ ... [0, 0], ... [0, 1], ... ] ... ), ... ), ... components=[Labels(["o3_mu"], np.array([[-1], [0], [1]]))], ... properties=Labels(["properties"], np.array([[3], [4], [5]])), ... )
Create a TensorMap containing the dummy TensorBlocks
>>> keys = Labels(names=["o3_lambda"], values=np.array([[0], [1]])) >>> tensor = TensorMap(keys, [block_1, block_2])
Define the transformation to apply to the TensorMap
>>> modules = [torch.nn.Tanh(), torch.nn.Tanh()] >>> in_features = [len(tensor.block(key).properties) for key in tensor.keys]
Define the EquivariantTransformation module
>>> transformation = EquivariantTransformation( ... modules, ... tensor.keys, ... in_features, ... out_properties=[tensor.block(key).properties for key in tensor.keys], ... invariant_keys=Labels( ... ["o3_lambda"], np.array([0], dtype=np.int64).reshape(-1, 1) ... ), ... )
The output metadata are the same as the input
>>> transformation(tensor) TensorMap with 2 blocks keys: o3_lambda 0 1 >>> transformation(tensor)[0] TensorBlock samples (2): ['system', 'atom'] components (1): ['o3_mu'] properties (3): ['properties'] gradients: None
Initialize internal Module state, shared by both nn.Module and ScriptModule.